Ebook Plant biology and biotechnology (Volume II: Plant genomics and biotechnology): Part 2

Continued part 1, part 2 of ebook Plant biology and biotechnology (Volume II: Plant genomics and biotechnology) provide readers with content about: applications of triploids in agriculture; improving secondary metabolite production in tissue cultures; somaclonal variation in micropropagated plants; in vitro conservation of plant germplasm;... Please refer to the part 2 of ebook for details!

Applications of Triploids in Agriculture 19 Ashwani Kumar and Nidhi Gupta Abstract Triploid hybrids have one of the most important traits, seedlessness, which is the characteristic for the fresh-fruit market Triploid embryos are found in small seeds that not germinate Hybridization-based extensive breeding programmes require very efficient methodologies for embryo rescue and evaluation of ploidy Biotechnology provides powerful tools for plant breeding Triploid plants raised from endosperm are generally sterile Endosperm-ploidy levels and its applications in plant breeding have been discussed here Endosperm-raised triploid plants are of commercial value, e.g timber-yielding plants, edible fruit plants or ornamentals propagated vegetatively and multiplied mainly through micropropagation Illustration cases of many successful endosperm cultures are described here Keywords Triploids • Embryo rescue • Plant tissue culture • Biotechnology • Polyploidy breeding 19.1 Introduction In a fertilization process, the egg fuses with one of the male gametes to form a zygote, which A Kumar Department of Botany, University of Rajasthan, Jaipur, Rajasthan 302004, India N Gupta (*) Department of Biotechnology, C.C.S University, Meerut, Uttar Pradesh 250004, India e-mail: nidhi.05.gupta@gmail.com afterward forms the embryo The other male gamete fuses with the central cell containing two haploid nuclei This second fusion is actually a double fertilization and triple fusion which often results in a triploid structure, the endosperm, and found to be present in all angiosperm families except Orchidaceae, Trapaceae and Podostemaceae Such endosperm-raised triploid plants are generally sterile, but this seedlessness does not affect commercial utility of such plants, e.g edible fruit plants, timber-yielding plants or ornamentals which are multiplied mainly through micropropagation or propagated vegetatively The growth of triploids is generally higher than Bir Bahadur et al (eds.), Plant Biology and Biotechnology: Volume II: Plant Genomics and Biotechnology, DOI 10.1007/978-81-322-2283-5_19, © Springer India 2015 385 A Kumar and N Gupta 386 respective diploids (Thomas and Chaturvedi 2008) Also, triploids are more vigorous than diploids (Morinaga and Fukushima 1935) Rather than the typical pair of chromosomes, a cell having three complete sets of chromosomes is called triploid To produce viable offspring, chromosomes need to occur in pairs But due to chromosomal number three, the triploid plants are sterile as the odd numbers of chromosomes are unable to pair up properly Such plants flowering and bear fruits, but flowers cannot be fertilized and fruit is sterile Some of the examples of triploid crops are: • Seedless watermelons (Citrullus vulgaris) produced due to cross between tetraploid females and diploid males These are commercially cultivated in Japan • Triploid sugar beets (Beta vulgaris) produce larger roots with more sugar content • TV29 of tea produced by Tea Research Association of India is cultivated in North India It produces larger shoots and leaves and is tolerant to drought • Cultivated banana (Musa paradisiacal) produces larger and seedless fruits 19.2 Endosperm and Origin of Triploids Endosperm is a natural and unique triploid tissue in its origin, ploidy level and nature of growth It is the triploid stage of the flowering plant which is produced by fusion of three haploid nuclei; two from the female gametophyte and one from the male gametophyte (Thomas et al 2000) It lacks histological differentiation Lampe and Mills’ (1933) first report on endosperm culture was on maize, whereas La Rue (1949) first reported the establishment of tissue cultures in maize from immature endosperm Since then, mature and immature endosperm of various species has been shown to form continuously growing calli (Bhojwani and Razdan 1996) Johri and Bhojwani (1965) demonstrated totipotency of endosperm for the first time They also demonstrated direct shoot formation from cultured mature endosperm of cherry ballart (Exocarpos cupressiformis) By the time, embryo/shoot/plantlet regeneration Haploid (N) Diploid (2N) Triploid (3N) Tetraploid (4N) Fig 19.1 Haploid (single), diploid (double), triploid (triple) and tetraploid (quadruple) sets of chromosomes from endosperm has been reached to dozen of species (Bhojwani and Razdan 1996) In tissue culture, endosperm tissues provide natural material for regenerating plants with triploid chromosome number, and thus, regeneration of plants from this tissue offers a direct method to produce triploids A number of successful regeneration reports of organogenesis and somatic embryogenesis are available Endosperm culture (Johri and Bhojawani 1977), reviews on endosperm (Cheema and Mehra 1982; Bhatnagar and Sawhney 1981), micropropagation (Driver and Kuniyuki 1984), walnut tissue culture (Mc Granahan et al 1987), embryo rescue (Mc Granahan et al 1986), somatic embryogenesis (Tulecke and McGranahan 1985), triploids in woody perennials (Lakshmi Sita 1987), Hordeum vulgare (Sehgal 1974; Sun and Chu 1981), Triticum aestivum (Sehgal 1974) and Oryza sativa (Bajaj et al 1980; Nakano et al 1975) are already in records (Fig 19.1) 19.3 Production of Triploids Triploids can be produced by crossing an induced tetraploid plant with normal diploid plant Tetraploids can be produced by treating the terminal buds of diploid plants with chemicals such 19 Applications of Triploids in Agriculture 387 b a Triploid Parent creates Diploid Sperm together produce Triploid Offspring Triploid Parent creates Triploid Ovule produces Triploid Offspring Diploid Parent creates Haploid Ovule Fig 19.2 (a) Asexual triploid reproduction via parthenogenesis (b) Triploid-diploid sexual reproduction as colchicine, oryzalin, pronamide, amiprophos methyl and trifluralin (Wan et al 1991) However, such crosses are not always fortunate as it results in reduced seed setting compared to cross between two diploids (Sikdar and Jolly 1995) Moreover, seedling survival and seed germination are also very low Still, triploids play an important role in biomass and soil conservation and thus represent a significant importance in shrubs and trees They help in preserving vast amounts of photosynthetic energy and thus promote vegetative growth Similarly, seedlessness is used to increase the quality of several fruits, like banana, papaya, grapes, apple, etc In some plants, like Miscanthus sinensis, seed-sterile triploids have been grown to prevent seed dispersal in the environment (Petersen et al 2002) (Fig 19.2) 19.4 Examples of Triploid Plants Triploid seedless trait has been described in many crops, especially in fruits Artificially, triploid fruits are produced by first developing tetraploids using above-mentioned chemicals, which are then crossed with respective diploids Such fruits are then commercially used 19.4.1 Watermelon (Citrullus vulgaris) When tetraploid females are crossed with diploid males, seedless watermelons (Citrullus vulgaris) are produced Native African vine Citrullus lanatus (syn C vulgaris) derived modern varieties of the watermelon that are unable to produce viable gametes during meiosis, and thus, their ripened melons are seedless Wild populations of C lanatus var citroides are common in Central Africa and give rise to domesticated watermelons var lanatus (Robinson and Decker-Walters 1997) Wild, ancestral watermelons (var citroides) have a spherical, striped fruit and white, slightly bitter or bland flesh and are commonly known as the citron or citron melon (Fig 19.3) Japan commercially grows seedless watermelons which are produced by crossing tetraploid female with diploid male lines Reciprocal cross was also tried but was not successful Seeds produced by triploid plants are not true seeds; they are small in size having white rudimentary structures like that of cucumber (Cucumis sativus) seeds However, a few normal sized seeds may occur, but they are generally empty It is also to be noted that all cultivated triploid watermelons not have red pulpy flesh They may have seedless yellow, sweet flesh (Fig 19.4) 19.4.2 Little Gourd (Coccinia grandis) Babu and Rajan (2001) developed a triploid variety of Coccinia grandis, fruit of which is used as a vegetable It was also produced by crossing a normal diploid parent with colchicine-induced tetraploid 2.4 % of seeds per fruit were observed Morphologically, the triploid plants were somewhat resembled to the diploid, but the substantial A Kumar and N Gupta 388 Fig 19.4 Triploid watermelon having red flesh Fig 19.3 Citron melon features were its vigorous growth, increased fruit size, lower astringency and higher yield However, these triploid fruits were tastier with good amount of vitamin A, vitamin C and iron and had less polyphenols; hence, they could be used as a salad crop This plant also has many medicinal properties against diabetics, skin infections and bronchitis (Table 19.1 and Fig 19.5) 19.4.3 Citrus Citrus fruits are the most extensively and primarily produced fruit tree crop in the world (FAO 2009) for the fresh-fruit market, especially in the Mediterranean area Area-wise, Spain is the main producer which covers a surface of 330,000 and produces about 6.3 million tons of citrus Diploids are the available genetic resources for citrus fruit, and their naturally produce seeds include polyploid individuals These natural polyploid plants can give rise to interesting characteristics in citrus fruit; thus, they are very useful for genetic breeding projects CIRAD (French Agricultural Research Centre for International Development) has developed genetic breeding programmes for citrus fruit in the Mediterranean Basin to create triploid varieties of sterile and seedless fruit and tetraploid rootstocks resistant to abiotic constraints, such as water deficiency or salinity, both from predominantly diploid genetic resources that would meet agronomic constraints, market expectations and consumer demand (Fig 19.6) 19.4.4 Mandarin As per increasing consumer demand, seedless citrus fruits are the basic requirement for the fresh market Mandarin triploid hybrids have this seedlessness trait as its one of the most important characteristics The availability of a number of high-quality seedless varieties in mandarins is very low; thus the production and recovery of new seedless triploid hybrids of mandarin varieties have a high priority for many citrus industries worldwide (Fig 19.7) Citrus triploid hybrids can be recovered by 2x × 4x (Esen and Soost 1971b; Oiyama et al 1981; Starrantino and Recupero 1981), 2x × 2x (Cameron and Frost 1968; Esen and Soost 1971a; Geraci et al 1975) and 4x × 2x (Cameron and Burnett 1978; Esen et al 1978; Aleza et al 2009) sexual hybridizations as a consequence of the formation of unreduced gametes at low frequency (Aleza et al 2010) For the first time, Esen and Soost (1971a) indicated that triploid embryos were mainly found in between one third and one sixth smaller seeds than normal seeds that not germinate in conventional greenhouse conditions However, still at relatively low germination percentages, 19 Applications of Triploids in Agriculture 389 Table 19.1 Comparative evaluation of diploid, tetraploid and triploid of Coccinia grandis (Source: Babu and Rajan 2001) Characters Days to flowering Flower size Fruit size Fruit length (cm) Fruit girth (cm) Fruit weight (g) Polyphenol per gram of fruit (fig) Fruit colour Leaf size Leaf thickness Fruit yield/plant/year (kg) Diploid 40 Medium Medium 6.59 7.40 15.20 0.300 Green white strips Medium Medium 10.32 Tetraploid 42 Large Small 4.49 8.20 14.50 0.311 Green with white strips Large Very thick 9.34 Triploid 38 Medium Large 7.50 11.60 44.20 0.090 Green with white Medium Medium 15.25 Fig 19.6 Seedless lemon (Citrus limon) Fig 19.5 Coccinia grandis Fig 19.7 (a) Mandarin plant having flowers and fruits (b) Seedless mandarin A Kumar and N Gupta 390 the in vitro culture of whole seeds with their integuments can improve germination rates (Ollitrault et al 1996) In rare cases, triploid hybrids can be found in conventional greenhouse seedlings, as in ‘A-12’ mandarin (Bono et al 2004) and ‘Winola’ mandarin (Vardi et al 1991) 19.4.5 Neem (Azadirachta indica) Because of the arising use of neem and its products in medicine, agriculture, cosmetics and animal health care, it is an important and economic tree of India Triploid plants of neem were obtained from immature endosperm culture (Chaturvedi et al 2003) Over 66 % of the plants were triploid with chromosome number 36 A characteristic feature of the shoots of endosperm origin is the presence of a large number of multicellular glands The selected triploids, expected to be sexually sterile, can be bulked up by micropropagation (Fig 19.8) 19.4.7 Shanin (Petunia violacea) Gupta (1983) reported the formation of haploid, diploid and triploid plants by direct pollen embryogenesis in Petunia violacea In certain species, especially in Petunia, an almost exclusive production of androgenic triploids has been reported which is useful in ornamental plants for the introduction of vigorous foliage and flowers (Fig 19.10) 19.4.8 Triticale Garg et al (1996) describe somatic embryogenesis and triploid plant regeneration from immature endosperm cultures of Acacia nilotica, an important leguminous tree species suitable for afforestation of arid and marginal lands (Fig 19.9) Triticale, first bred in laboratories during the late nineteenth century, is one of the most successful synthetic allopolyploids produced by crossing tetraploid wheat or hexaploid wheat with rye The grain was originally bred in Sweden and Scotland; however, now it is being grown commercially in many parts of the world, e.g Germany, Canada, France and Poland (the largest area), covering an area of around 2.6 million hectares with an annual production of million tons Triticale high-yielding ability and grain qualities of wheat combined with tolerance ability for adverse environment of rye provide its important and desirable features In more than 15 years, the yielding ability of triticales has been increased to about 90 % However, in Sweden, the raw triticales yielded about 50 % of the standard varieties of wheat Fig 19.8 Neem Fig 19.9 Acacia plant having flower and fruit 19.4.6 Acacia (Acacia nilotica) 19 Applications of Triploids in Agriculture 391 Fig 19.10 Shanin flower Fig 19.11 Triticale India have released three varieties of triticales: TL419, DT46 (amber colour grains) and TL1210 Although TL1210 grain yield is comparable to that of the best wheat varieties, its deep grain colour represents its chief drawback, thus mainly grown as a fodder crop in Punjab To overcome the problem, Indian breeders have developed ambercoloured triticales by using white-seeded rye as one of the parents of the triticales (Fig 19.11) Some other examples of allopolyploids are Raphanobrassica, the triploid (AAC) produced by crossing B campestris (AA) with B napus (AACC), Festuca-Lolium hybrids, allopolyploid clovers and some species hybrids in Rubus and jute (Corchorus sp.) 19.4.9 Sugar Beet (Beta vulgaris L.) The triploid varieties of sugar beet are mixtures of diploid, triploid and other ploidy level plants As compared to diploids, triploid sugar beets produce more sugar and larger roots and 10–15 % higher yields per unit area, while tetraploids produce smaller roots and lower yields Commercially, Japan and Europe produce triploid varieties of sugar beet, but their popularity is declining rapidly As the beet flower is small in size, triploid sugar beet seed production is quite difficult (Fig 19.12) Triploid sugar beet seed may be produced by using any of the following two ways: (1) using 4x plant as male and 2x as female or (2) using 4x plants as female and 2x as male The first cross provides higher seed yield but a lower proportion of triploids, while the second gives lower seed yield but a higher proportion of triploids Commercially, interplanting 4x and 2x lines in the ratio 3:1 is used for producing triploid sugar beet seed, and finally, seeds from both 4x and 2x plants are harvested These harvested seeds consist of about 75 % triploid (3x) seeds 19.4.10 Cassava (Manihot esculenta) Cassava, commonly known as poor man’s crop, is an important root crop to be cultivated in tropical countries and propagated by stem cuttings It has become a subsidiary food in many countries It is also used as cattle feed and its raw material for starch-based industries Cultivated cassava is highly heterozygous and cross-pollinated, having a diploid number of chromosomes (2n = 36) Among artificially produced polyploids, cassava triploids have higher starch potential and a higher yield (Jos et al 1987; Sreekumari and Jos 1996) The first triploid variety of cassava named Sree Harsha was released in 1996 (Sreekumari et al 1999) and was produced by crossing induced tetraploid plants with natural diploid The use of a 2x female plant yielded better results than reciprocal crosses Many features of triploid A Kumar and N Gupta 392 Fig 19.12 Sugar beet: (a) seed, (b) flower, (c) root cassava make it superior than its diploid These include higher harvest index, rapid bulking, higher yield, early harvestability, increased dry matter and starch content in the roots, shade tolerance and tolerance to cassava mosaic virus (Fig 19.13) 19.4.11 Tea (Camellia sinensis) Tea Research Association, India, has recently released a triploid clone of tea (Camellia sinensis var assamica) for its commercial cultivation in northern parts of the country This triploid cultivar, TV29, produces larger shoots and, thereby, biomass yields more cured leaf per unit area and is more tolerant to drought than the available diploid cultivars The quality of the triploid clone is comparable to that of diploid cultivars used for making CTC (curl-tear-cut) tea (Fig 19.14) 19.4.12 Mulberry (Morus alba L.) Being an exclusive source of feed for silkworms, mulberry is an indispensable crop for the sericulture industry Both natural and in-vivo-induced mulberry triploids have been reported (Das et al 1970; Katagiri et al 1982; Dwivedi et al 1989) Many of the triploid lines are superior to its diploids (Thomas et al 2000), in cold and disease resistance (Hamada 1963) and in yield and nutritive qualities of leaves (Seki and Oshikane 1959) The endosperm callus differentiated shoots, which could be rooted, and full triploid plants have already been established in soil (Fig 19.15) 19.4.13 Ornamental Excised cultures of endosperm from immature fruits having zygotic embryo have been used at 19 Applications of Triploids in Agriculture 393 Fig 19.13 Cassava: (a) flower and (b) root Fig 19.15 Mulberry plant with fruit Fig 19.14 Tea leaves early dicotyledonous stage to produce triploid annual phlox or Drummond’s phlox (Phlox drummondii Hook.) ornamental plants (Razdan et al 2013) It was reported that over 70 % of annual phlox plants were triploid with a chromosome number of 2n = 3x = 21 The growth of triploids is generally higher than respective diploids (Thomas and Chaturvedi 2008) These triploid plants have greater size of leaves, stem, flowers and/or foliage with higher number of pollen and larger stomata as compared to naturally occurring diploid plants (Miyashita et al 2009) Moreover, triploid plant flowers showed enlarged central eye and bright colour, adding to their ornamental value (Razdan et al 2008) (Fig 19.16) 19.4.14 Pomegranate (Punica granatum L.) Pomegranate is one of the oldest known fruit trees of the tropics and subtropics, cultivated for its delicious edible fruits In addition, the tree is also valued for its pharmaceutical properties A Kumar and N Gupta 394 References Fig 19.16 Phlox drummondii flowers 19.5 Discussion Endosperm is a unique tissue in its origin, ploidy level and nature of growth It is mostly formed by the fusion product of three haploid nuclei, one from the male gametophyte and two from the female gametophyte, and is, therefore, triploid Traditionally, triploids are produced by crossing induced superior tetraploids and diploids This approach is not only tedious and lengthy (especially for tree species), but in many cases, it may not be possible due to high sterility of autotetraploids In contrast, regeneration of plants from endosperm, a naturally occurring triploid tissue, offers a direct, single-step approach to triploid production (Bhojwani and Razdan 1996; Kumar 2010; Kumar and Roy 2006, 2011; Kumar and Shekhawat 2009; Neumann et al 2009) 19.6 Conclusion In conclusion, gametic embryogenesis hold great promise for making a significant, low-cost and sustainable contribution to plant breeding, aimed at increasing farm productivity and food quality, particularly in developing countries and in an environmentally friendly way, helping to reduce the proportion of people suffering from chronic hunger and from diseases due to malnutrition Aleza P, Juárez J, Ollitrault P, Navarro L (2009) Production of tetraploid plants of non-apomictic citrus genotypes Plant Cell Rep 28:1837–1846 Aleza P, Juárez J, Cuenca J, Ollitrault P, Navarro L (2010) Recovery of citrus triploid hybrids by embryo rescue and flow cytometry from 2x 2x sexual hybridisation and its application to extensive breeding programs Plant Cell Rep 29:1023–1034 Babu KVS, Rajan S (2001) A promising triploid of little gourd J Trop Agric 39(2001):162–163 Bajaj YS, Saini SS, Bidani M (1980) Production of triploid plants from the immature 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Abscisic acid (ABA), 256, 272, 320, 321, 323, 381, 426, 431, 434, 474, 564, 580, 583, 587, 590, 593, 594, 596–598, 649, 697 Acacia, 390, 725–736 Accessions, 2, 6, 8–10, 13, 14, 18, 115, 121, 213, 214, 334, 348, 349, 359, 378, 423, 429, 446–448, 450–453, 456–458, 462, 472, 474, 492, 493, 495, 496 Activation tagging, 4, 10 ADC See Arginine decarboxylase (ADC) Adventitious root, 316, 400, 401 Adventitious shoot, 316, 317, 428, 497 AEG See N-(2-aminoethyl)-glycine (AEG) AFLP See Amplified fragment length polymorphism (AFLP) AGO See Argonaute (AGO) Agrobacterium rhizogenes, 398, 399, 402, 498, 518, 521 Agrobacterium tumefaciens, 3, 106, 490, 492, 495, 500, 528, 540, 541, 553, 627, 649, 733 Agroforestry, 339, 454, 457, 480, 735, 748, 749 Albugo candida, 18 Algae, 28–31, 33–43, 145, 147, 150, 161, 163–165, 185, 197, 462, 588, 668, 685–716, 749 Algal biotechnology, 28, 29, 43, 749–750 Alkaloids, 100, 398–400, 402, 403, 518, 521, 591, 631, 686, 691, 693, 694, 699, 702, 703, 708, 709, 711 amiRNA See Artificial micro RNA (amiRNA) Amplified fragment length polymorphism (AFLP), 68–71, 73, 99, 118, 119, 208, 209, 211, 213–215, 342, 377, 380, 409, 413, 453, 490–492, 494, 495, 497, 498, 729 Androgenesis, 91–95, 100, 101 Anther culture, 90–92, 94–96, 98, 100, 102, 115, 320 Anthracyclines, 689, 696 Anthraquinones (AQ), 285, 400, 686, 690, 693, 695 Antifouling, 711–713 Anti-inflammatory, 687, 704, 710 Antimicrobial, 296, 400, 500, 614, 687, 695, 703–704, 713 Anti-neoplastic activity, 687–699 Antioxidants, 31, 33, 256, 273, 437, 520, 521, 564, 589, 687, 704, 710–711, 751 Antiprotozoa, 751 Antisense RNA, 51, 267, 273, 559, 615–616, 626, 654 Antitumour compounds, 521 Apiculture, 751 Apoptosis, 146, 149, 306, 700 AP-PCR See Arbitrarily primed PCR (AP-PCR) Aquaculture, 28, 30–31, 748, 749 Arabidopsis Genome, 3, 6, 7, 13, 16, 168, 224, 248, 303, 595, 640 Arabidopsis multiparent RIL (AMPRIL), Arabidopsis thaliana, 1–19, 52, 57, 59, 116, 196, 224, 225, 248, 255, 258, 270, 282, 581, 616, 626, 628, 640, 644, 667, 682 Arbitrarily primed PCR (AP-PCR), 68, 70, 208 Arboreta, 470 Arginine (Arg), 138, 271, 332, 586, 615 Arginine decarboxylase (ADC), 586, 587, 615 Argonaute (AGO), 145, 272, 624, 641, 646, 649 Argonaute proteins (Ago proteins), 145, 272, 624, 641, 646, 649 Artificial micro RNA (amiRNA), 12, 560, 614, 616, 654–655 Artificial seeds, 20, 499 Aseptic cultures, 331–332, 335–337, 421, 731 Association mapping, 8–9, 18, 75, 77, 119–121 Atropine, 518 Autoimmune diseases, 568, 687, 704 Auxins, 12, 34, 55, 95, 256, 271, 318, 320, 321, 323, 332, 334, 336, 338, 351, 357, 366, 402, 488, 727, 728 Azadirachtin, 398–399 B Bacillus thuringiensis (Bt), 299, 535, 536, 538, 544, 564, 615, 617, 618, 627, 749, 753 cotton, 535, 544, 615, 753 crops, 617, 618 gene, 536 Bir Bahadur et al (eds.), Plant Biology and Biotechnology: Volume II: Plant Genomics and Biotechnology, DOI 10.1007/978-81-322-2283-5, © Springer India 2015 755 Index 756 Backcross breeding, 80, 103, 543 Backcrossing, 72, 78–80, 82, 103, 553 Backcross population (BC), 74, 76, 103, 379, 730 Background selection, 80 Bacterial infection, 649 Bacterial pathogens, 60, 224, 296, 553 Bamboo, 331, 339–340, 471, 518, 519 Banana, 114, 116, 117, 119, 124, 190, 248, 251, 317, 331, 337–339, 344, 364, 366, 367, 376, 386, 387, 408, 410–415, 419, 446, 627 Benzylisoquinoline alkaloids (BIAs), 400 Bioactive metabolites, 686, 716 Bioaugmentation, 665, 681 Biodegradation, 665, 677, 680 Biodiesel, 35, 36, 39, 254, 518, 667, 668, 712, 750 Biodiversity, 115, 191, 280, 298, 299, 450, 462–464, 466, 468–470, 476, 481, 482, 545, 664, 666, 673, 746, 747, 751, 752 Bioenergetics, 180 Bioethanol, 518, 666, 712, 750 Biofertilizers, 34–35, 749 Biofortification, 563 Biofuel, 35–38, 56, 170, 518–519, 522, 552, 553, 564, 667, 668, 687, 712–713, 726, 749, 750 Bioinformatics, 12, 16, 49–60, 121, 125, 197, 212, 224, 225, 227, 228, 249, 251, 257, 259, 279–299, 538, 641, 642 Biological control, 501, 613, 749 Biological nitrogen fixation, 748 Biomagnification, 663–664 Biomass, 28–30, 32, 33, 35–43, 115, 387, 392, 399, 401, 518, 519, 521–523, 557, 563, 567–569, 590, 668, 677, 678, 681, 687, 713, 715, 749, 750 Biopesticides, 398, 399, 749 Bioplastics, 534, 552, 556, 565–567 Bioreactors, 344, 399–401, 436, 501, 558, 715, 734 Bioremediation, 37–38, 40, 665–667, 669, 674, 681, 716, 750 Biosafety, 503, 543, 624, 633, 746, 752 Biosensors, 38, 668, 669 Biostabilization, 665 Biostimulation, 665 Biosurfactants, 666 Biotech crops, 531–534, 545 Biotechnology, 28, 29, 38, 43, 49–60, 116, 280, 281, 298, 299, 311, 318, 319, 322, 325, 358, 376, 415, 420, 448, 500, 501, 503, 504, 518, 539, 541, 552, 553, 558, 559, 564, 568, 633, 656, 663–670, 685–716, 725–736, 743–753 Biotic stress, 12, 13, 15, 18–19, 105, 253, 335, 343, 421, 501, 507, 611–618, 625–626, 656 tolerance, 611–618, 625–633 Biotreatment, 666 Biotrophs, 49 Biparental inheritance, 189, 190 Black pepper, 488–491, 499–504 Botanic gardens, 420, 446, 480 Brassica, 3, 16, 18, 36, 91, 93, 100–102, 105, 106, 162, 213, 254, 349, 353, 355–357, 367, 408, 457, 519, 520, 535, 558, 589, 590, 592, 630, 644, 649, 677 Breeding cycle, 78, 102, 364, 367–368, 377 Bridgecross hybrids, 356 Bt See Bacillus thuringiensis (Bt) Bulbosum method, 97 Bulked segregant analysis (BSA), 72, 105 Butanetriol, 561, 562, 565, 566 C Caenorhabditis elegans, 28, 57, 233, 272, 282, 616, 624, 640 Calliclones, 408 Camptothecin (CPT), 402–403, 521 CaMV 35S See Cauliflower mosaic virus 35S (CaMV 35S) CAPS See Cleaved amplified polymorphic sequences (CAPS) Cardamom, 431, 488, 489, 491, 493, 499–503 Carotenoids, 31, 33, 38, 40, 235, 256, 518–520, 558, 561, 589, 630 Cassava, 120, 238, 255, 273, 379, 381, 391–393, 418, 419, 423, 427, 433, 626, 632 Cauliflower mosaic virus 35S (CaMV 35S), 193, 557, 561, 598, 630, 632 CBF See C-repeat binding factors (CBF) cDNA arrays, 295 CDS See Genomic coding sequences (CDS) CEL1 endonuclease, 10 Cellular networks, 305, 307, 309 Cellular signaling networks, 309–310 Cellulose, 257, 338, 480, 519, 521–523, 558, 712 Centromere, 77, 135, 152, 170, 271 Chalcone synthase (CHS), 235, 624, 630 Cheminformatics, 280 Chimeric genes, 185, 197, 655 ChIP See Chromatin immunoprecipitation (ChIP) Chitinase, 54, 502, 564, 614, 616, 715 Chlamydomonas reinhardtii, 32, 40, 145, 156, 537, 560, 643, 644 Chlorella, 28, 29, 31–33, 35, 37–41, 43, 708 Chloroplast DNA (cpDNA), 186, 188, 189, 193, 195, 199, 207, 496 Chloroplast genome, 118, 180–182, 184–189, 195, 198, 199, 553 Choline oxidase A (CodA), 585 Chromatin immunoprecipitation (ChIP), 53, 146, 229, 231, 342 Chromosome doubling, 90, 91, 96, 98–101 Chromosome elimination, 90, 91, 97–98, 367 Circular DNA, 182, 183, 186, 187 Citrus, 114, 116, 117, 123, 213, 256, 258, 366, 367, 375, 388, 389, 419, 423, 468, 480, 591 Classical breeding, 529–530 Cleaved amplified polymorphic sequences (CAPS), 7, 82, 210, 498 Clonal plants, 100, 319 Clonal repositories, 470, 471 Clustered regularly interspaced short palindromic repeats (CRISPRs), 234–235 Index Coat protein (CP), 206, 491, 535, 536, 557, 614, 625, 655 Co-dominant markers, 69 Co-expression, 4, 12, 58, 194, 730 Cognate mRNA, 145 Colchicine, 94, 96, 98, 100, 101, 387, 492 Cold shock proteins (CSP), 715 Cold stress, 14, 15, 256, 272, 580, 593–595, 598, 652 Community seed banks (CSBs), 449 Comparative genomics, 16, 122, 126, 147, 230, 295 Comparative microarray analysis, 232 Composite interval mapping (CIM), 76 Conservation tillage, 748, 749 Constitutive promoters, 557, 559, 589, 595, 598, 653 Contamination, 34, 37, 42, 214, 330, 337, 343, 348, 374, 422, 424, 425, 429, 432, 439, 450, 451, 477, 488, 502, 569, 614, 664, 665, 668, 669, 674, 676, 679–681 Contigs, 114, 224, 228 Coomassie Brilliant Blue, 251 Co-suppression, 10, 55, 273, 557, 561, 589, 624, 626, 655 Co-transformation, 561, 562 Cotton, 18, 34, 55, 124, 235, 236, 256–258, 273, 322, 343, 366, 367, 381, 424, 446, 457, 530, 531, 534, 535, 537, 544, 567, 590–593, 615, 617, 627, 629, 631, 650, 654, 746, 753 cpDNA See Chloroplast DNA (cpDNA) C-repeat binding factors (CBF), 18, 536, 564, 595, 596, 598 Crop improvement, 10, 19, 67, 74, 84, 89–106, 114, 122, 126, 253, 343, 348, 363–381, 410, 445, 446, 481, 490, 492, 612, 613, 618, 623–633, 654–656, 732 Crossability barriers, 349–350, 352, 355, 356 Cryo-gene bank, 469 Cryopreservation, 324, 351, 381, 418–420, 422–424, 428–430, 432, 435, 440, 448, 454, 455, 472, 476–478, 480, 500, 731 Cucumber, 190, 387, 433, 441, 535, 649 Cultivar improvement, 82–83 Cyanobacteria, 28, 34, 38–40, 135, 165, 180, 185, 333, 563, 567, 686, 689, 697, 698, 701, 710, 712, 713 Cyanophycin, 567 Cytochrome, 184, 191, 299, 627, 632, 682, 702, 703 Cytokines, 583, 704, 710 Cytokinins, 55, 95, 115, 320, 321, 323, 324, 332, 336, 338, 351, 352, 363, 366, 409, 438, 581, 727 Cytological markers, 67 Cytoplasmic inheritance, 189 Cytoplasmic male sterile (CMS) lines, 356–357 Cytoscape, 230, 296, 297 Cytotoxicity, 686, 687, 695, 697, 699, 751 D DAF See DNA amplification fingerprinting (DAF) DAPI See 4ʹ, 6-diamidino-2-phenylindole (DAPI) DArT See Diversity array technology (DArT) 757 Database, 4, 5, 12–15, 57–60, 114, 116, 122–124, 146, 181, 185, 192, 198, 206, 216, 224–226, 228–230, 232, 238, 249, 253, 255, 257–259, 279–286, 288, 289, 291, 293, 294, 296, 297, 307, 308, 310, 429, 446, 469, 482, 535–537, 643 Database search, 280, 283–285, 288, 289, 291 Date palm, 413, 434, 725–736 Datura, 90, 91, 93, 402 Datura inoxia, 91 DCL1 See Dicer-Like (DCL1) Dedifferentiation, 341–342, 430 Deficit irrigation, 748–749 Dehydration-responsive transcription factors (DREB), 18, 564 DGE See Digital gene expression (DGE) DH population, 103–105 4ʹ, 6-diamidino-2-phenylindole (DAPI), 94 Dicer, 145, 170, 234, 624, 640 Dicer-Like (DCL1), 145, 640–642, 645, 646, 655 2,4-Dichlorophenoxyacetic acid (2,4-D), 97, 320–322, 324, 535, 731 Differentiation, 49, 146, 165, 168, 170, 187, 212, 256, 272, 316, 317, 321, 324, 341, 342, 366, 386, 398, 495, 497, 522, 647, 704, 729, 744 Digital gene expression (DGE), 116, 117, 256 Dihaploid line, 115 Diosgenin, 399 Direct gene transfer, 331, 554–555, 561, 568, 733 Disease free, 330, 413, 414, 420, 430, 476, 488, 493, 495, 499, 735, 752 Disease loci, 311 Disease resistance, 12, 16, 18, 30, 54–55, 78, 98, 103, 105, 116, 119, 236, 320, 376, 392, 535, 563, 626, 650, 678, 730 Distant hybridization, 364, 368 Diversity array technology (DArT), 69, 124, 211, 213 DNA amplification fingerprinting (DAF), 68, 70, 208, 214 DNA banks, 448, 449, 469, 480 barcode, 190–191, 298, 299 fingerprinting, 71, 121, 205–216, 412, 413 markers, 67–70, 78, 81, 207, 215, 311, 380, 409, 412, 490, 733 methylation, 13, 142, 144, 163, 166, 168–169, 188–189, 266–271, 273–275, 340–342, 409, 412, 413, 437, 646, 729 microarrays, 211, 226, 229, 231–232, 239, 295, 309 polymorphism, 66, 206–207, 428 rearrangements, 180, 181 repair, 152–155, 168, 188, 194, 237, 561 pathway, 561 sequencing, 120, 155, 209, 212–213, 279, 281 transposons, 196, 206 Domain-rearranged methylases (DRMs), 169, 266 Dominant markers, 69–71, 99, 209 Doubled haploids (DH), 74, 75, 90, 91, 96–106, 562, 565, 705 Double haploid line, 101, 115 Index 758 Double-standard RNA (dsRNA), 51, 55, 137, 145, 234, 272, 615, 616, 624, 626–628, 632, 633, 639, 640, 646 2D-PAGE See Polyacrylamide gel electrophoresis (2D-PAGE) Drought, 8, 12, 13, 18, 106, 117, 252–254, 272, 306, 386, 392, 470, 482, 494, 498, 529, 530, 535, 564, 580, 581, 588–598, 611, 628, 629, 651–652, 654, 656, 726, 748 dsRNA See Double-standard RNA (dsRNA) E E-cell, 296, 297, 304–306 Electrophoresis, 53–54, 68, 207–209, 212, 230, 231, 250, 251, 296, 342, 380 Electroporation, 40, 106, 234, 528, 554, 555 Electrospray ionization mass spectrometry (ESI-MS), 54, 259 Embryo abortion, 353, 354, 364–368 Embryo culture, 98, 323, 331, 354, 364–369, 371, 375–380, 732 Embryo development, 7, 8, 254, 321, 349, 353, 364–366, 368, 371, 381 Embryogenesis, 7, 91–97, 100, 104, 106, 315–325, 332, 338, 342, 358, 364, 365, 374, 381, 386, 390, 394, 421, 423, 488, 489, 491, 493, 497, 583, 648, 729, 731–733, 735, 752 Embryogenic, 92–95, 101, 106, 315, 316, 318–324, 336, 401, 425, 436, 491, 492, 499, 729, 731–733 Embryoids, 322, 323, 489, 497 Embryo rescue, 331, 354–355, 358, 363–381, 386, 422, 732 Embryo-sac, 98, 353, 366, 376 EMS See Ethyl methane sulfonate (EMS) Encapsulation, 133, 171, 324, 424, 427, 499, 500, 628 ENCODE project, 146, 298 Endemic species, 420, 482 Endoreduplication, 100 Endosperm, 91, 96–98, 166, 169, 252, 254, 274, 316, 353, 354, 364–368, 377, 385–386, 390, 392, 394, 520, 563 culture, 386, 390 development, 363, 366, 377 Endosymbiosis, 150 Endosymbiotic theory, 180–181 Enhancers, 7, 8, 10, 143, 158, 164, 298, 539, 540, 641, 646 Enhancer trap, Environmental biotechnology, 663–670 Epigenetic changes, 13, 269, 341–343, 409, 410 Epigenetic inheritance, 188, 274–275 Epigenetics, 5, 12, 13, 77, 119, 144, 169, 170, 188, 265–275, 340–343, 407, 409–411, 430, 555, 583, 646 Epigenetic variation, 13, 274, 275, 340, 341, 343 Epigenome, 5, 13 Epigenomics, 5, 13, 168 ESTs See Expressed sequence tags (ESTs) Ethyl methane sulfonate (EMS), 6, 7, 9, 233 Eucalyptus, 77, 122, 125, 156, 213, 331, 335–337, 431, 677 Exportin, 641 Expressed sequence tags (ESTs), 3, 11, 14, 58–60, 68, 105, 114–119, 121, 123, 124, 209, 210, 213, 224, 226, 228, 255, 307, 400, 404, 494, 643 mining, 58 Ex situ conservation, 419, 445–458, 462, 466, 468–481 F Field gene banks, 418, 419, 422, 428, 429, 454, 455 Field trials, 80, 331, 334–339, 453, 536, 542, 599 Fingerprinting, 68, 70, 71, 120, 121, 205–216, 249, 412, 413, 448, 488, 498 Fishery, 749 Flavonoids, 14, 235, 271, 398, 400, 518, 520–521, 565, 567, 589, 630 Floral biology, 373 Floricultural crops, 376–378 Floriculture, 376, 520, 630 Floristic diversity, 462–463 Flow cytometry, 99, 492 Flower color, 630–631 Food security, 248, 257, 259, 379, 458, 468, 545, 612, 653, 726, 730, 744, 747, 752–753 Foreground selection, 80 Foreign DNA, 168, 195–197, 237, 555, 556, 559 Forward genetic tool, 6–11 Fruit crops, 114–116, 119, 121–123, 318, 323, 343, 368–376, 381, 408, 434, 447 Fruit quality, 118, 119, 125, 256, 373–375, 630 Fruit ripening, 17, 116, 188, 256, 559, 632 Functional genomics, 3–12, 14, 51, 60, 96, 116, 223–240, 310, 400, 559, 628, 656 Functional markers, 71–72 Fungal disease, 50, 369, 498, 564, 626–627 Fungal infection, 49, 55, 58, 117, 650 Fungal interaction, 52, 53 Fungal pathogens, 55, 57–59, 368, 379, 614–615, 625, 650, 703 Fungi, 49, 50, 52–55, 57–60, 163, 166, 234, 272, 367, 410, 422, 462, 501, 503, 504, 536, 537, 547, 588, 612, 613, 615, 626, 632, 648, 667, 677, 686, 687, 699, 703, 705, 706, 709–711, 716 Fungi imperfecti, 50 Fusarium oxysporum, 117, 493, 502, 615, 626, 627 G Gain of function, 10–11, 647 Gametoclonal variation, 96, 408–409 Gametoclones, 408, 409 Gametophytic pathway, 94 Gap penalties, 284 Gas chromatography coupled to mass spectrometry (GC-MS), 256, 566 Index Gene, 2, 39, 50, 66, 91, 114, 135, 180, 206, 224, 248, 266, 280, 303, 318, 331, 348, 365, 391, 398, 414, 418, 445–458, 480, 489, 518, 528, 552, 580, 612, 624, 639, 666, 682, 699, 729, 752 bank, 213, 324, 418, 419, 422, 427–430, 440, 446–448, 450–452, 454–458, 489, 499, 752 cloning, 2, 538–539 design, 539–540 discovery, 11, 116, 118, 448, 538 disruption, 6, 7, 51, 237 editing, 236–238 function, 3, 7, 9, 11–15, 51, 57, 234, 282–283, 304, 306, 563, 627 knockout, 51, 234, 559 mapping, 68, 103 pyramiding, 79 regulation, 13, 140, 146, 157, 158, 230, 233, 272, 304, 341, 615, 626, 645–646 silencing, 10, 12, 51, 55, 168, 194, 234, 266, 267, 269, 272, 273, 521, 554, 555, 557, 559–561, 624–627, 629, 630, 632, 633, 646, 655–656 stacking, 539, 553 tagging, 210 Gene expression mapping, 233 Gene expression omnibus(GEO), 12, 232 Gene specific tags (GSTs), 10 Gene targeted and functional markers (GTFM), 71–72 Genetically modified (GM) algae, 28, 39–41 Genetically modified (GM) bacteria, 667 Genetically modified (GM) crops, 528, 530, 531, 534–536, 543–547, 612, 617, 633, 746 Genetically modified (GM) foods, 530, 537–538, 545, 547 Genetically modified (GM) plants, 280, 295, 298, 531, 537, 540, 667 Genetic code, 137–140, 282 Genetic diversity, 66, 73, 118, 119, 348, 447–449, 456–458, 481, 488–490, 492–495, 497, 498, 733, 752–753 Genetic engineering, 39–41, 54–55, 170, 235–237, 268–269, 273, 323, 343, 399, 520, 521, 528–530, 538, 579–599, 611–618, 623, 651, 681, 682, 687, 730, 733, 735, 736 Genetic fidelity, 324, 414, 490, 726, 729–730, 733 Genetic mapping, 73, 78, 105, 161, 162 Genetic markers, 65–84, 118, 119, 121, 124, 148, 210, 414 Genetic networks, 143, 228, 238, 303–306 Genetic resources, 3–5, 9, 13, 120, 375, 388, 420, 429, 430, 445–458, 462, 466, 468–470, 476, 480, 499–500, 503, 731, 753 Genetic stability, 43, 324, 340, 408, 413–414, 419, 420, 422, 423, 428–429, 436, 494, 729 Genetic transformation, 18, 40, 104, 316, 317, 331, 335, 358, 399, 401, 407, 408, 490–495, 498, 518, 528, 543, 627, 729, 731, 733, 735–736 Gene transfer, 147, 181, 193–196, 198, 331, 348, 358, 365, 366, 490, 495, 498, 520, 553–555, 561, 568, 612, 733 759 in plants, 568 Gene traps, Genome, 2, 39, 58, 73, 114, 132, 180, 206, 224, 233, 247–260, 270, 280, 293, 303, 412, 528, 553, 562, 614, 733 collinearity, 161–163 engineering, 237–238, 562–563 evolution, 122, 147, 151, 156, 181, 185, 193, 196 sequencing projects, 3, 60, 114–115, 248 size, 3, 114, 116, 138, 141, 152, 154, 155, 157–162, 181–184, 196, 206, 282, 733 structure evolution, 132 Genome wide association mapping (GWAS), 8, 9, 311 Genome-wide selection (GWS), 81, 82, 84 Genomic coding sequences (CDS), 140, 144, 156, 157, 168, 226, 228 Genomic imprinting, 169, 273–274, 340 Genomics, 3–17, 19, 50–52, 56–60, 70–81, 96, 114–116, 119–126, 131–171, 180–18, 184, 186, 189–191, 193–195, 198, 208–212, 215, 223–240, 248, 254, 257, 267, 268, 270, 273–274, 279–299, 303, 310, 340, 342, 378, 380, 400, 412, 448, 449, 480, 494, 497, 524, 530, 538, 542, 628, 643, 656, 669, 682, 733–735 Genomic selection (GS), 73, 81, 104, 115, 119, 125, 733 Genomic survey sequences (GSS), 114 Genotyping, 8, 71–74, 77, 79, 80, 82, 115, 119, 120, 125, 212–214, 310 by sequencing, 72, 120, 212 platforms, 82 Geographic information system (GIS), 482 Geospatial technology, 481–482 Germplasm, 66, 71, 75, 96–98, 102, 115, 118, 120, 121, 123, 213, 214, 324, 325, 330, 331, 343, 350, 368, 376, 378, 417–440, 445–448, 453, 455, 458, 465, 470, 471, 473, 474, 477, 480, 482, 488, 491, 498–500, 530, 729, 733, 735, 751, 752 conservation, 325, 330, 331, 419, 421, 426, 428, 437, 438, 455, 465, 482, 488, 735 storage, 419, 429, 729 Ginger, 378, 488, 489, 491–494, 499–502, 504 Ginsenoside, 398, 400–402 Ginsenoside saponin, 400 Global alignment, 284 Global positioning system (GPS), 450, 482 Globular embryo, 93, 318, 365, 425 Glucanase, 54, 502, 558, 564, 614 Glucanes, 54, 522 Glycine betaine (GB), 14, 116, 159, 564, 585, 586 Golden rice, 520, 536, 563 Grapes, 114, 116, 120, 123, 163, 214, 238, 317–321, 323–325, 331, 364, 366, 368–373, 380, 387, 401, 536 Growth retardants, 338, 418–420, 424, 426, 435 Guide strand, 641 GWAS See Genome wide association mapping (GWAS) Gynogenesis, 91, 378 760 H Hairy root cultures, 398–401, 403, 521, 628, 631 Haploids, 74, 89–106, 114, 115, 123, 132, 159, 232, 282, 325, 338, 364, 367, 368, 381, 385, 387, 390, 394, 408, 409, 433, 480, 500, 629, 734, 752 Haplotype map, 115, 311 Hasty, 641, 642, 647 Heat-shock proteins (HSPs), 256, 257, 558, 564, 590–591, 653 Heat stress, 252, 558, 581, 588, 591, 596, 651–653 Heavy metals, 37, 38, 235, 268, 523, 581, 588, 590, 593, 628, 664, 668, 674, 675, 678, 682, 711 Helicoverpa armigera, 236, 627 Hemibiotrophs, 49, 52 Hemicellulose, 519, 522 Herbal gardens, 470 Herbal spices, 488, 497–499 Herbicides, 100, 268, 348, 378, 409, 528, 534, 535, 540, 542, 545, 547, 553, 558, 563, 564, 613, 617, 667, 674, 677, 746, 747 Herbicide tolerance, 535, 542, 617, 746 Heterologous DNA sequences, 182 Heterosis, 77, 119, 254, 270–271 Heterotrophic systems, 42–43 HGT See Horizontal gene transfer (HGT) Hidden Markov models (HMM), 226–228 High density marker maps, 114 High-performance liquid chromatography (HPLC), 51, 249, 342 High-throughput genome sequences (HTGs), 114 Histone modification, 144, 169, 266, 271–272, 340–342 Homeobox genes, 163–168 Homologous recombination, 51, 154, 182, 185, 197, 237, 554, 556, 562 Horizontal gene transfer (HGT), 147, 181, 195, 196 Horticultural crops, 17, 114–116, 118, 122, 125, 323, 364, 368, 474 Host-pathogen interaction, 310 HPLC See High-performance liquid chromatography (HPLC) HSPs See Heat-shock proteins (HSPs) HUA ENHANCER (HEN1), 641, 642, 655 Human metabolome database, 296 Hybrid breeding, 103, 270–271 Hybrid embryos, 97, 349, 352–354, 357, 358, 363–381 rescue, 363–381 Hybrid vigour, 379 Hydraulic control, 676, 679 Hyoscyamine, 518 Hypericin, 400, 401 HYPONASTIC LEAVES1 (HYL1), 640, 642, 655 I ICAT See Isotope coded affinity tags (ICAT) Immature embryo, 323, 365, 368, 374, 376, 378, 381 Immunoinformatics, 280 Immunoprecipitation (IP), 11, 12, 53, 229, 231, 342 Index incRNAs See Long intergenic non-coding RNAs (incRNAs) Indian flora, 462–465 Induced mutations, 233–234 Inducible promoters, 10, 231, 556, 558–559, 567, 595, 596 Insect repellents, 520 Insect resistance, 236, 528, 535, 538, 615–617, 746 Insects, 40, 50, 60, 150, 196, 234, 236, 237, 415, 422, 451, 520, 528, 529, 535–538, 542–545, 547, 552, 564, 588, 612, 613, 615–618, 625, 627, 628, 631, 632, 648 Insertional mutagenesis, 7–8, 10, 51, 225, 233, 559–560 Insertion-deletion polymorphisms (IDPs), 119 Insertion mutants, 7, In situ conservation, 418, 421, 428, 462, 466–468, 481 In situ hybridization, 52, 67, 497, 643 In situ RT-PCR, 52 Integrated breeding platform, 82 Integrated crop livestock management, 749 Integrated pest management (IPM), 501, 529, 613, 749, 752 Interactome, 5, 15, 57–60, 168, 224, 517 Interactomics, 15, 56 Intergeneric crosses, 368, 381 Inter-organellar gene transfer, 194, 195 Inter simple sequence repeats (ISSR), 68, 70, 73, 119, 209, 213–215, 342, 380, 409, 412–414, 489–498, 730, 733, 734 Interspecific crosses, 190, 349, 351, 352, 366–368, 375, 377–379 Interspecific hybrids, 98, 152, 159, 214, 358, 376–379, 495 Interspersed repeats, 206 Intertransposon amplified polymorphism (IRAP), 69, 71, 210, 213 Interval mapping, 76, 77 Intra-molecular recombination, 181, 184, 185 Introgression lines (IL), 74 Intron, 75, 122, 135, 136, 140–142, 144, 145, 157, 159, 163, 164, 180, 182, 184, 186, 192, 194–197, 206, 210, 225, 226, 228, 496, 539, 540, 559, 640 Inverted repeats (IR), 69, 105, 161, 182, 186, 187, 195, 206, 269, 631, 645 In vitro clonal propagation, 330 In vitro conservation, 324, 407, 408, 417–440, 454, 455, 476–480, 499 In vitro culture, 97, 100, 103, 316, 317, 330, 332, 337, 357, 364, 390, 401, 411, 419, 425, 426, 429, 430, 432, 435, 454, 455, 476, 529 In vitro fertilization, 353, 358 In vitro gene bank, 324, 418, 427, 430, 489, 499 In vitro pollination, 352–353, 358, 376, 492, 493 In vitro propagation, 368, 421, 472 In vitro regeneration, 322, 342, 496, 541–542, 727, 735 Ionomics, 125, 258 IPM See Integrated pest management (IPM) IRAP See Intertransposon amplified polymorphism (IRAP) Index 761 Isoflavones, 400, 401 Isoprenoids, 519 Isotope coded affinity tags (ICAT), 251, 258 Isozymes, 67, 68, 99, 100, 207, 409, 412, 413, 630 markers, 99 ISSR See Inter simple sequence repeats (ISSR) Long terminal repeats (LTRs), 161, 206, 210, 211 LOPIT See Localization of organelle proteins by isotope tagging (LOPIT) LTRs See Long terminal repeats (LTRs) LUCA See Last universal common ancestor (LUCA) Luciferase (Luc), 8, 540, 669, 715 J Jasmonic acid (JA), 55, 583, 587, 596 Jatropha curcas, 36, 254, 255, 331–335, 344, 591, 677 Jojoba, 725–736 M MAAP See Multiple arbitrary amplicon profiling (MAAP) MAB See Marker-assisted breeding (MAB) MABC See Marker assisted backcrossing (MABC) MAGIC See Multiple advanced generation intercross (MAGIC) Maize, 1, 3, 8, 17–19, 34, 72, 75, 77, 79, 83, 84, 92, 93, 96–97, 105, 115, 116, 119, 126, 141, 152, 158, 159, 161, 162, 182, 187, 188, 193, 195, 196, 206, 209, 231, 234–236, 238, 248–250, 253–254, 257, 270, 323, 353, 367, 386, 446, 456, 457, 491, 492, 521, 530, 531, 535, 536, 557, 560, 562, 563, 567, 569, 591–594, 596, 599, 614, 615, 617, 628, 629, 648, 667, 678, 746, 748, 750 MALDI See Matrix-assisted laser desorption ionization (MALDI) MALDI-TOF See Matrix assisted laser desorption ionisation-time of flight (MALDI-TOF) Male sterile, 104, 235, 348, 356, 629 Mandarin, 114, 123, 256, 388–390 Mango, 118, 119, 122, 213, 214, 319, 323, 364, 366, 373–375, 380 Mannitol, 33, 100, 426, 431–433, 435, 439, 585, 587, 588 Mannitol-1-phosphate-D-(mtl-D), 587 MAP See Microbe-assisted phytoremediation (MAP) Mapping populations, 6, 9, 74–77, 120, 121, 481, 490 MAPS See Marker-assisted pedigree selection (MAPS) Marine algae, 686, 687, 710, 712, 713, 715 Marine bacteria, 686–688, 695, 703, 705, 711–713, 715, 716 Marine biotechnology, 685–716 Marine fungi, 686, 690, 699–701, 703, 708, 710 Marine organisms, 686, 711, 715, 716 Marker assisted backcrossing (MABC), 80, 82–84 Marker-assisted breeding (MAB), 72, 121, 488 Marker-assisted pedigree selection (MAPS), 80 Marker-assisted recurrent selection (MARS), 80–82, 84 Marker assisted selection (MAS), 65–84, 103, 105, 114, 118–119, 121, 126, 488, 503, 530, 539, 730, 752 MARS See Marker-assisted recurrent selection (MARS) MAS See Marker assisted selection (MAS) Massively parallel signature sequencing (MPSS), 3, 4, 11, 225 Mass spectrometry (MS), 13, 14, 50, 53, 54, 125, 230, 248–252, 254, 256–259, 296, 307, 309, 310, 317, 319, 321–323, 332, 334, 336, 338, 339, 344, 377–379, 566 Mass spectrometry matrix-assisted laser, 249 Maternal inheritance, 188–190 K Kinases, 149, 166, 256, 258, 259, 309, 581, 583, 593–595, 701 Kitchen garden, 752 Knock-down, 10, 51, 559, 627 Knock-out, 6, 10, 51, 234, 237, 297, 307, 559, 585, 594 L Laser microdissection (LM), 53 Last universal common ancestor (LUCA), 137, 140, 141, 145, 147–151, 153, 154, 156 Late embryogenesis abundant (LEA) protein, 583, 590, 591 LC-MS See Liquid chromatography–mass spectrometry (LC-MS) LD See Linkage disequilibrium (LD) Leaf development, 647 LEA protein See Late embryogenesis abundant (LEA) protein let-7, 640 Lignocellulosic biomass, 519, 750 Lilies, 376–377, 520 lin-4, 640 lin-14, 640 lin-41, 640 lincRNAs See Long intronic non-coding RNAs (lincRNAs) LINEs See Long interspersed nuclear elements (LINEs) Linkage disequilibrium (LD), 8, 74, 75, 121 mapping, 75 Linkage maps, 8, 67, 69, 74, 76, 119–123, 126 Linolenic acid, 519, 704 Liquid chromatography–mass spectrometry (LC-MS), 251, 252, 254, 257, 258 Little gourd, 387–388 lncRNAs See Long non-coding RNAs (lncRNAs) Local alignment, 228, 284 Localization of organelle proteins by isotope tagging (LOPIT), 251 Local landraces, 449, 752 Long intergenic non-coding RNAs (lincRNAs), 144 Long interspersed nuclear elements (LINEs), 161, 206 Long intronic non-coding RNAs (lincRNAs), 144 Long non-coding RNAs (lncRNAs), 142, 144, 652 762 Matrix assisted laser desorption ionization–time of flight (MALDI-TOF), 231, 241, 251, 252, 257, 258, 296, 309 Matrix-assisted laser desorption ionization (MALDI), 54 Mature embryo, 323, 365, 366, 368, 374, 376, 378, 381 Mature miRNA, 145, 640, 641, 643, 645, 653, 655 MCS See Multi-cellular structure (MCS) Medical informatics, 280 Medicinal plants, 192, 213, 331, 400, 403, 422, 437, 468, 471, 482, 751–752 Meristem culture, 324, 419, 421, 422, 430, 478, 736 Messenger RNA (mRNA), 12, 51, 52, 135, 140, 142, 144, 145, 151, 188, 196, 228, 232–234, 239, 249, 270, 272, 273, 296, 307, 309, 381, 398, 497, 542, 555, 559–561, 564, 570, 583, 597, 624, 628, 630, 640, 642, 645–651, 653, 655 Metabolic engineering, 104, 238, 398, 517–524, 557, 558, 560–570 Metabolic modeling, 58, 238, 305 Metabolic networks, 14, 56, 58, 146, 224, 238–239, 257, 306–307 Metabolites, 5, 14, 15, 36, 41, 54, 56, 57, 118, 135, 146, 158, 170, 234, 238, 296, 306, 310, 343, 397–403, 422, 428, 488, 500–501, 517–523, 552, 557, 563, 565, 566, 583–585, 598, 614, 616, 631–632, 678, 686–690, 692, 694, 696–698, 700, 701, 705–708, 710, 716, 730 Metabolome, 5, 16, 224, 253, 280, 296, 517 Metabolomics, 5, 14–15, 50, 56, 125, 229, 255, 258, 280, 293, 296, 299, 302, 310, 398, 682 Metagenomics, 687, 714–716 Methylomics, 125 Microalgae, 27–43, 668, 713, 715 Microarray, 4, 11, 12, 53, 59, 77, 116, 123, 166, 206, 208, 211–214, 226, 229, 231–233, 239, 258, 295–297, 303, 307, 309, 310, 650 Microbe-assisted phytoremediation (MAP), 681 Microbes, 58, 59, 502, 700 Micropropagation, 329–344, 358, 385, 386, 390, 394, 407, 408, 410, 412–415, 420–422, 488, 489, 491–493, 495–497, 501, 503, 726–733, 735, 752 Microrhizome, 489, 493, 499 MicroRNA (miRNA), 12, 121, 122, 135, 142, 144, 145, 150, 165, 167, 225, 228, 231, 233, 341, 342, 560, 584, 597, 624, 639–656 biogenesis, 560, 641, 656 genes, 642, 643, 645, 653, 654 interference, 653 MicroRNA induced gene silencing (MIGS), 655–656 Microsatellites, 70, 71, 118, 120, 207–209, 211, 380, 409, 413, 488, 489, 494, 495, 498 Microspore, 90–96, 98–101, 104, 106, 322, 333, 353, 379, 408, 629 Microsporogenesis, 91 Millennium seed bank project (MSBP), 446 miRNA See MicroRNA (miRNA) Mitochondrial DNA (mtDNA), 182, 185, 190, 193–196, 207, 282, 294 Mitochondrial genome, 180–185, 190–199, 299 Index Mitogen-activated protein kinase (MAPK), 57, 309, 581, 583, 593, 594 Model plant, 1–3, 17, 19, 57, 168, 212, 255, 257, 266, 536, 538, 559, 560, 653, 730 Molecular markers, 7, 66, 68, 69, 72, 74, 78, 80, 81, 83, 99, 103–105, 114, 116–119, 207, 324, 334, 380, 410, 412, 413, 428, 488, 490, 494, 497, 498, 539, 729, 733 Molecular pharming, 553, 568 Molecular profiling, 413–414, 491 Molecular scissor, 528 Monoploids, 90, 367 Monosaccharides, 519 Morphogenesis, 12, 59, 96, 256, 274, 323, 381, 497, 630, 652, 727 MPSS See Massively parallel signature sequencing (MPSS) MudPIT See Multidimensional protein identification technology (MudPIT) Mulberry, 122, 392, 393, 435, 440, 590, 592, 750 Multi-cellular structure (MCS), 92, 93, 353 Multidimensional protein identification technology (MudPIT), 54, 251, 258 Multiple advanced generation intercross (MAGIC), 4, 9, 75 Multiple arbitrary amplicon profiling (MAAP), 68, 208–210 Multiple sequence alignment, 280, 284, 286–288, 290, 291 Mushroom cultivation, 751 Mutant selection, 103–104 Mycorrhiza, 53, 410, 501, 503 Mycotoxins, 57, 536, 614 N NAM See Nested association mapping (NAM) N-(2-aminoethyl)-glycine (AEG), 134, 135 Nanomaterials, 38 Nanotechnology, 38, 682 National Centre for Biotechnology Information (NCBI), 60, 116, 117, 119, 181, 185, 281, 285, 286, 291, 294, 295 Natural antisense transcripts (NATs), 144 NCBI See National Centre for Biotechnology Information (NCBI) Near infrared reflectance (NIR), 125 Near isogenic lines (NILs), 72, 74, 730 Necrotrophic, 18, 49 Neem, 390, 398–399, 502 Nematode resistance, 236, 530, 617 Nematodes, 57, 58, 79, 196, 234, 236, 303, 367, 503, 612, 613, 616–617, 624, 625, 628, 632, 643, 648, 651, 656 Nested association mapping (NAM), 8, 75 Next generation sequence (NGS), 7, 11, 54, 66, 71, 72, 77, 84, 114, 116, 118–120, 122, 125, 126, 155, 181, 212, 216, 232, 233, 642, 643, 650 NGS See Next generation sequence (NGS) Index NHEJ See Non-homologous end joining (NHEJ) Nicotine, 399, 535 NILs See Near isogenic lines (NILs) NIR See Near infrared reflectance (NIR) Non-coding RNAs, 133, 144–145, 236, 624 Non-embryogenic, 106, 321, 729 Non-homologous end joining (NHEJ), 237, 562 Non-Mendelian inheritance, 164, 190 Non-orthodox seeds, 455, 474, 476 Non-ribosomal peptide synthetase (NRPS), 133, 697, 714, 715 NOR See Nucleolus-organizing region (NOR) Northern blot analysis, 542 NRPS See Non-ribosomal peptide synthetase (NRPS) Nuclear DNA, 94, 168, 188, 192, 196, 198, 282, 494 Nuclear genome, 141, 159, 180, 184, 189, 191, 193–196, 198, 357, 554–556 Nucleolus-organizing region (NOR), 152 Nutraceuticals, 30, 102, 235, 402, 713–714, 751 Nutritional improvement, 563, 629–630 Nutritional quality, 234, 545, 629 O Oil seed crops, 31, 254–255, 355, 519, 750 Oilseed rape, 235, 254, 268, 519 Oligonucleotide microarrays, 211–212 Oligosaccharides, 519 Olive, 37, 213, 276, 432, 439 Ontogenesis, 317 Open reading frame (ORF), 184, 190, 210, 226–228, 232, 294 Organ development, 7, 8, 166, 168, 648 Organellar genes, 193, 194, 197, 198 Organellar inheritance, 189–190 Organeller genomes, 179–199 Organelle transformation, 189 Organogenesis, 316–318, 324, 332, 334, 341, 342, 386, 488, 493, 497, 731, 735 Origin of codons, 138–140 Orn See Ornithine (Orn) Ornamental crops, 378, 432, 448, 520 Ornithine (Orn), 585, 586 Orthodox seeds, 451, 455, 471–476, 478 Osmolytes, 564, 585, 588 Osmosensors, 581 Ovary culture, 100, 352, 354, 364, 376, 377 Ovule culture, 354, 358, 364, 369, 371, 376, 377, 381 Oxidative stress, 252, 564, 589, 590, 674, 700, 703, 711 P PAHs See Polycyclic aromatic hydrocarbons (PAHs) Paired-end-tag RNA sequencing (RNA-PET), 115 Pair-wise sequence alignment, 291 Pan-genomics, 310–312 Papaya, 114, 116, 119, 123, 214, 256, 364, 366, 375, 387, 457, 472, 531, 535, 614, 625 Parasexual hybridization, 364, 381 763 Parthenogenesis, 91, 96–97, 114, 387 Particle bombardment, 106, 234, 494, 498, 540–541, 554–556, 561, 733 Particle gun, 528, 540 Passenger strand, 641 Pathogen-derived resistance (PDR), 613, 614, 625 Pathogenesis-related (PR) proteins, 14, 54, 55, 188, 253, 564, 614 genes, 54, 564 Pathogen free, 324, 422, 492, 568 PAZ domain, 641 PCBs See Polychlorinated biphenyls (PCBs) PCP See Pentachlorophenol (PCP) PCR See Polymerase chain reaction (PCR) PDB See Protein Data Bank (PDB) PDR See Pathogen-derived resistance (PDR) Pectin methylesterase, Pentachlorophenol (PCP), 667, 675 PEP See Plastid-encoded RNA polymerase (PEP) Peptide nucleic acids (PNAs), 134, 135 Peptides, 50, 54, 57, 132–134, 136–138, 191, 194, 249, 251, 254, 257, 309, 520, 541, 556, 558, 561, 614, 686–689, 697, 699, 701, 703, 706, 713–715 Permafrost running title, 452, 457, 458 Personalized medicine, 310 Pest resistance, 105, 367, 536, 545, 627 Petunia, 2, 17, 235, 273, 390, 520, 521, 535, 617, 624 Pharmaceuticals, 31–34, 40, 41, 43, 56, 102, 118, 279, 280, 292, 298, 299, 311, 393, 398, 399, 490, 500, 518, 522, 523, 552, 553, 556, 558, 564, 568–569, 704, 726 Pharmacoinformatics, 280 PHB See Polyhydroxybutyrate (PHB) Phenolics, 374, 400, 503, 518, 666 Phenome, Phenomics, 296 Phenotyping, 72, 74–78, 82, 105, 120, 122–125 Phlox, 393, 394 Photosynthetic efficiency, 563 Phototrophic systems, 41–42 Phycobiliproteins, 33 Phyconanotechnology, 38–39 Phylogenetic analysis, 190, 280, 291, 298, 489, 492, 493 Phytoalexins, 55, 565 Phytochemicals, 398, 399, 500 Phytodegradation, 676–677, 679 Phytoextraction, 676–678, 681 Phytoremediation, 37, 38, 235, 553, 556, 665, 667, 673–682 Phytostabilization, 676, 678–679, 681 Phytovolatilization, 676, 679 Pigment, 28, 31–34, 257, 273, 323, 624, 630, 631, 687, 713, 715 piRNAs See Piwi-interacting RNAs (piRNAs) PIWI domain, 641 Piwi-interacting RNAs (piRNAs), 145 Placental pollination, 352, 358 PLANEX See Plant co-expression database (PLANEX) 764 Plant breeding, 65–84, 90, 91, 99, 101, 103, 105, 115, 118, 274–275, 348, 349, 358, 364, 366, 376, 377, 394, 407, 408, 410, 438, 445, 453, 458, 471, 524, 543, 613, 681 Plant co-expression database (PLANEX), 4, 12 Plant development, 12, 16, 17, 167, 169, 266, 273, 318, 319, 342, 369, 371, 433, 531, 558, 593, 594, 596, 646, 647, 652, 656 Plant-fungal interaction, 49–60 Plant genetic resources, 445–458, 466, 469, 470, 753 Plant growth regulators, 269, 316–318, 320, 321, 323, 332, 333, 338, 419, 430, 431, 497, 726, 727, 731 Plant propagules, 401, 480 Plant regeneration, 316, 317, 319, 320, 322–324, 334, 341, 378, 390, 421, 488, 489, 491–493, 495–498, 555, 729, 731–733 Plant tissue culture, 319, 330, 343–344, 365, 399, 415, 420, 422, 428, 518, 521, 522 Plastid DNA, 186, 188–189, 191, 193, 195, 198, 282, 293, 299 Plastid-encoded RNA polymerase (PEP), 188 Plastid genome, 181, 184–191, 195–199, 555, 556 Plastid transformation, 555, 556 Platform chemicals, 552, 556, 561, 564–567 PMC See PubMed central (PMC) PNAs See Peptide nucleic acids (PNAs) Pollen bank, 350, 358, 448, 469, 480 Pollen storage, 350–351, 358, 447, 448, 480 Polyacrylamide gel electrophoresis (2D-PAGE), 53, 207, 249, 251, 252, 254–256, 296 Polyamines (PAs), 583, 585–587, 615, 616, 629 Polychlorinated biphenyls (PCBs), 669, 675–677 Polycyclic aromatic hydrocarbons (PAHs), 664, 675–677, 680 Polyembryony, 373, 377 Polyhydroxybutyrate (PHB), 556, 565–567 Polymerase chain reaction (PCR), 10, 51, 52, 65, 68, 70, 73, 82, 120, 207–211, 213, 230, 233, 234, 399, 491, 494, 496, 538, 539, 542, 714, 734, 752 Polymers, 132–135, 137, 138, 254, 519, 522, 523, 552, 553, 565–567, 628, 686 Polyploidization, 114, 158–160, 358, 374 Polyploidy, 58, 100, 151, 159, 160, 364 Polyploidy breeding, 388 Pomegranate, 117, 119–121, 323, 393, 495–497, 499 Post-fertilization barriers, 349, 353–355, 358, 365, 376, 377 Post-transcriptional gene silencing (PTGS), 10, 269, 272, 273, 555, 559 Post-translational modifications, 13, 142, 248, 249, 259, 271, 522, 554, 568, 584, 593, 715 Post-zygotic incompatibility, 379 Prebiotic chemistry, 132, 133 Pre-fertilization barriers, 349, 351–352, 355, 358, 365, 376, 492 Pre-mRNA, 140, 141 Presence-absent variants (PAVs), 119, 668 Primordial replicator, 133–135 Pro-embryonic mass, 321 Index Proline, 138, 564, 585, 697, 699, 715 Promiscuous DNA, 180, 193 Promoters, 7, 8, 10, 13, 17, 69, 75, 104, 142–144, 157, 158, 161, 168, 169, 194, 206, 225, 226, 231, 267–269, 271, 298, 341, 342, 381, 398, 400, 403, 491, 492, 520, 539, 540, 556–559, 561, 562, 565, 567, 570, 583, 589, 595, 596, 598, 625, 629–632, 648, 653, 654, 715 Protected area, 462, 467–469 Proteinase inhibitors, 616 Protein Data Bank (PDB), 281, 282, 291, 292 Protein profiling, 230–231, 255 Proteome, 5, 13, 14, 16, 53–54, 59, 116, 148, 149, 224, 226, 232, 249–255, 257–259, 280, 295, 296, 555, 584, 597 Proteomics, 5, 13–15, 54, 56, 59, 60, 125, 226, 230–231, 247–260, 280, 293, 295–296, 299, 303, 310, 517, 538, 682 Protoclones, 408 Protoderm, 365 Protoplasts, 40, 185, 316, 320, 353, 408, 420, 490–492, 494, 495, 497, 498, 502, 554, 555, 560, 591, 626, 732–733, 735 culture, 40, 408, 420, 490–492, 494, 495, 498 PR proteins See Pathogenesis-related (PR) proteins Pseudogenes, 184, 185, 206 PTGS See Post-transcriptional gene silencing (PTGS) PubMed central (PMC), 283 Putrescine, 586, 615 Q Quantitative inheritance, 104 Quantitative PCR (qPCR) analysis, 116, 232, 542, 669 Quantitative trait loci (QTL), 4, 8, 9, 16, 17, 74–75, 114, 118 R Rainwater harvesting, 748–749 Random amplified microsatellite polymorphism (RAMP), 68, 210, 497 Random amplified polymorphic DNA (RAPD), 68–71, 73, 99, 100, 118, 208–210, 213–215, 324, 342, 378, 380, 409, 412–414, 436, 489–498, 730, 733, 734 RAP-PCR See RNA fingerprinting by arbitrary primed PCR (RAP-PCR) RBIP See Retroposon-based insertion polymorphism (RBIP) RdDM See RNA-directed DNA methylation (RdDM) Reactive oxygen species (ROS), 252, 254, 256, 268, 581, 583, 584, 586–590, 594, 687 Real-time PCR, 51–53 Recombinant inbred lines (RILs), 8, 9, 74, 75 Regenerants, 94, 96, 98, 99, 269, 316, 323, 324, 338, 339, 343, 408, 415 Regeneration, 91, 93, 94, 96, 106, 149, 316–320, 322–325, 330, 334–336, 338, 341, 342, 358, 378, Index 379, 381, 386, 390, 394, 401, 409, 421, 423, 427, 428, 436–438, 449, 450, 453–454, 473, 474, 488–499, 520, 541–542, 555, 556, 727, 729, 731–733, 735, 744 Regulatory proteins, 13, 142, 259, 342, 583, 593, 595, 656 Regulatory sequences, 13, 142–144, 206 REMAP See Retrotransposon-microsatellite amplified polymorphism (REMAP) Remote sensing (RS), 482 Repetitive DNA, 3, 152, 340 Reporter genes, 8, 230, 539, 540, 654, 715 Research Collaboratory for Structural Bioinformatics (RCSB), 291 Resistance genes (R genes), 18, 55, 79, 83, 103, 117, 225, 267, 491, 493, 494, 501, 614 Restoration, 104, 252, 449, 535, 664–666, 681 Restriction endonucleases, 188, 528 Restriction fragment length polymorphism (RFLP), 68–70, 73, 118, 119, 205, 207–210, 215, 409, 491, 730 Resveratrol 1, 402 Re-transformation, 562, 563, 736 Retroposon-based insertion polymorphism (RBIP), 69, 211, 213 Retrotransposon-microsatellite amplified polymorphism (REMAP), 69, 71, 211, 213 Retrotransposons, 145, 158, 161, 170, 196, 206, 269, 643 Reverse breeding, 104 Reverse genetics, 7, 9, 10, 50, 51, 60, 105 Reverse genetic tool, 9, 51 Reverse vaccinology, 310–312 RFLP See Restriction fragment length polymorphism (RFLP) R genes See Resistance genes (R genes) Rhizobacteria, 501 Rhizofiltration, 676, 678, 681 Ribonucleoproteic (RNP), 137 Ribonucleotide acid (RNA), 132 editing, 181, 198, 225, 556 enzyme, 136, 137 ligase, 134, 135 polymerase, 134, 142–144, 161, 170, 186, 188, 398, 556, 642, 646, 714 riboswitches, 133 silencing, 55, 144, 145, 167, 234, 560, 598, 614, 632, 648, 650 Ribosomal RNAs (rRNAs), 133, 141, 144, 147, 161, 184, 186, 228, 233, 494, 497, 669 Ribozymes, 51, 134–138, 614 RILs See Recombinant inbred lines (RILs) RISC See RNA induced silencing complex (RISC) RMSD See Root mean square deviation (RMSD) RNA See Ribonucleotide acid (RNA) RNA-dependent RNA polymerase (RdRP), 170 RNA-directed DNA methylation (RdDM), 169, 170, 266, 341, 646, 657 RNA fingerprinting by arbitrary primed PCR (RAP-PCR), 208 765 RNAi See RNA interference (RNAi) RNA induced silencing complex (RISC), 145, 234, 624, 641, 642, 645 RNA interference (RNAi), 4, 10, 12, 51, 135, 144, 145, 194, 233–236, 266, 267, 272–273, 340, 342, 523, 560, 615–618, 623–633, 652 RNA-PET See Paired-end-tag RNA sequencing (RNA-PET) RNA pol II, 640 RNase III, 145, 234, 624, 640 RNA world, 132, 133, 135–138, 140, 148, 154, 156, 639 hypothesis, 132, 133 RNP See Ribonucleoproteic (RNP) Root cultures, 398–403, 513, 521, 628, 631 Rooting, 148, 330, 331, 333–339, 357, 374, 422, 726–728, 735 Root mean square deviation (RMSD), 201 ROS See Reactive oxygen species (ROS) rRNAs See Ribosomal RNAs (rRNAs) Rural development, 744, 745, 752, 753 Rural poverty, 745–747 S Saccharification, 521, 522 S-adenosylmethionine decarboxylase (SAMDC), 586, 587, 615, 629 SAGE See Serial analysis of gene expression (SAGE) Salicylic acid, 55, 351, 491, 583, 649 Salinity, 13, 14, 253, 272, 348, 388, 494, 529, 550, 564, 580, 581, 588–592, 594, 596, 611, 628, 651–652, 681, 695, 726 SAMDC See S-adenosylmethionine decarboxylase (SAMDC) Saponins, 400, 402 SAR See Systemic acquired resistance (SAR) Satellite DNA, 206–207 SBML See Systems Biology Markup Language (SBML) SBW See Systems Biology Workbench (SBW) SCAR See Sequence characterized amplified region (SCAR) Scopolamine, 518 SCV See Somaclonal variation (SCV) SDA See Subtracted diversity array (SDA) Secondary metabolites, 41, 54, 57, 146, 158, 234, 343, 397–403, 422, 500–501, 504, 518–522, 524, 552, 614, 616, 631–632, 651, 678, 697, 700, 710 Seed bank, 358, 446, 447, 449–454, 457, 462, 752 Seed drying, 446, 451, 454 Seed Information Database (SID), 446 Seedlessness, 364, 385, 387, 388 Seeds community, 449 Seed spices, 488, 497–499, 511 Seed storage, 67, 257, 418, 429, 447, 451, 454, 471–475, 480 Seed viability, 368, 381, 451, 454, 472, 473 Selectable marker genes, 539, 540, 553, 561, 715 SELEX technique See Systematic evolution of ligands by exponential enrichment (SELEX) 766 Semi-quantitative RT-PCR, 52 Sequence characterized amplified region (SCAR), 68, 70, 73, 82, 99, 100, 210, 212, 214, 490, 492, 496, 498 Sequence related amplified polymorphism (SRAP), 68, 69, 71, 210, 490, 498 Sequence specific amplification polymorphism (S-SAP), 69, 211 Sequence tagged microsatellite sites (STMS), 68, 71, 209 Sequence tagged sites (STS), 68, 82, 209, 498 Serial analysis of gene expression (SAGE), 11, 116, 118, 295 Sericulture, 392, 750 Sex determination, 116, 729–730, 733 Shanin, 390, 391 Shoot elongation, 331, 334, 336, 338, 437 Shoot proliferation, 334, 336, 338, 496 Short interspersed elements (SINEs), 161, 206 SID See Seed Information Database (SID) Signaling pathway, 12, 15, 17, 57, 146, 147, 163, 168, 224, 305, 309, 581, 583, 587, 594, 598, 649, 710, 714 Signalling, 248, 252, 256, 258, 522 Signal recognition particle (SRP), 135, 653 Signal transduction pathway, 50, 55, 146, 520, 583, 589, 593–595, 700, 703 Simple sequence repeat polymorphism (SSRP), 209 Simple sequence repeats (SSR), 68, 71, 73, 82, 99, 100, 117, 120–122, 124, 125, 209, 211–215, 342, 413, 491, 497, 498, 733 SINEs See Short interspersed elements (SINEs) Single nucleotide polymorphism (SNP), 4, 7–9, 38, 68, 71, 73, 82, 115–121, 192, 206, 212, 214, 215, 225, 237, 294, 311, 493, 494, 733, 734 Single strand conformation polymorphism (SSCP), 68, 210, 493, 496 siRNAs See Small interfering RNAs (siRNAs) Slow growth, 344, 419, 420, 424, 427, 429–431, 434, 435, 454, 476, 477, 499 Small interfering RNAs (siRNAs), 12, 64, 135, 144, 150, 167, 170, 234, 266, 341, 615, 624–627, 639, 641, 646, 652, 654, 655 Small nuclear ribonucleic particules (snRNPs), 141 Small nuclear RNAs (snRNAs), 135, 141 Small RNA (sRNAs), 4, 11–13, 126, 144, 145, 225, 233, 234, 270, 272, 597, 616, 619, 624, 626, 633, 640, 641, 643, 649, 650, 652, 654–656 SNP See Single nucleotide polymorphism (SNP) snRNAs See Small nuclear RNAs (snRNAs) snRNPs See Small nuclear ribonucleic particules (snRNPs) Somaclonal variants, 117, 214, 337, 408–414, 498 Somaclonal variation (SCV), 269, 316, 340–344, 407–415, 422–424, 427–430, 729–731, 733 Somaclones, 407–410, 488, 491, 492, 494 Somatic embryogenesis, 315–325, 332, 358, 364, 374, 381, 386, 390, 421, 488, 489, 491, 493, 497, 729, 731–733, 735, 752 Index Somatic embryos, 100, 316–324, 330, 334, 338, 371, 420, 421, 427, 435, 436, 441, 477, 499, 500, 554, 729, 731, 732 Somatic hybridization, 358, 490, 492, 752 Southern blot analysis, 542 Soybean, 34, 36, 67, 238, 248–250, 253, 254, 258, 324, 456, 519, 521, 522, 530, 531, 534, 535, 543, 560, 598, 617, 650, 651, 682, 746, 750 Spermidine, 586, 615 Spermine, 586, 615 Spices, 440, 454, 457, 474, 487–504 Spirulina, 28–30, 32, 33, 39, 40, 42, 44, 713 Spliceosome, 140–142, 151 Splicing, 135, 140–142, 181, 184, 186, 188, 194, 233, 236, 266, 272, 583, 628 Sporophytic pathway, 94–96 SRAP See Sequence related amplified polymorphism (SRAP) sRNAs See Small RNA (sRNAs) SRP See Signal recognition particle (SRP) S-SAP See Sequence specific amplification polymorphism (S-SAP) SSCP See Single strand conformation polymorphism (SSCP) SSH See Suppression subtractive hybridization (SSH) SSHA See Suppressive subtractive hybridization array (SSHA) SSR See Simple sequence repeats (SSR) SSRP See Simple sequence repeat polymorphism (SSRP) STMS See Sequence tagged microsatellite sites (STMS) Stress tolerance, 12, 17–18, 83, 253, 257, 535, 556, 558, 564, 579–599, 611–618, 625, 628–629, 651, 652, 667 Structure analysis tasks, 291, 292, 299 STS See Sequence tagged sites (STS) Subtracted diversity array (SDA), 68, 211, 213, 214 Sugar alcohols, 426, 564, 585, 587 Sugar beet, 18, 115, 196, 386, 391, 392, 531, 535, 592, 628 Sugars, 15, 34, 50, 115, 206, 319, 391, 427, 432, 518, 552, 563, 565, 583, 585, 587, 588, 632, 666, 668, 677, 686, 695, 733, 734 Sunflower, 36, 83, 254, 519, 560, 750 Supplemental irrigation, 749 Suppression subtractive hybridization (SSH), 52–53, 117, 211, 490, 491, 493 Suppressive subtractive hybridization array (SSHA), 211, 213 Suspension culture, 317, 319, 321, 323, 342, 353, 398–401, 408, 409, 436, 500, 501, 558, 731 Sustainable agriculture, 449, 503, 746–749, 753 Sustainable solutions, 663–670, 749 Synseed technology, 499 Synthetic biology, 131, 170–171, 518, 570 Synthetic RNA world, 135 Synthetic seeds, 316, 324, 325, 489, 499, 729 Systematic evolution of ligands by exponential enrichment (SELEX), 135–138 Index Systemic acquired resistance (SAR), 7, 15, 18, 54, 55 Systems biology, 5, 15, 55–57, 226, 229, 230, 238–240, 280, 293–299, 301–312, 570, 599 Systems Biology Markup Language (SBML), 296–297 Systems Biology Workbench (SBW), 230, 296, 297 T TAIL-PCR See Thermal asymmetric interfaced-PCR (TAIL-PCR) TALENs See Transcription activator-like effector nucleases (TALENs) Targeted mutagenesis, 10, 57 Target induced local lesions in the genomes (TILLING), 9–10, 51, 105, 752 Target region amplification polymorphism (TRAP), 69, 71, 210, 213, 498 T-DNA, 7, 8, 10, 66–68, 231, 233, 237, 402, 533, 540, 554, 559, 594, 646, 733 mutagenesis, 9, 10, 51 Tea, 386, 392, 396 Terpenoid indole alkaloids (TIAs), 398–400, 403, 521 Terpenoids, 50, 146, 273, 398, 518–521, 631, 686, 687 TGS See Transcriptional gene silencing (TGS) Thaumatin, 614 Thermal asymmetric interfaced-PCR v(TAIL-PCR), 9, 10 Threose nucleic acid (TNA), 133, 135 TIAs See Terpenoid indole alkaloids (TIAs) TILLING See Target induced local lesions in the genomes (TILLING) Tilling array (TA), 11–13, 116 Ti-plasmid, 553, 554 Tissue culture, 40, 269, 316, 319, 322, 324, 330, 334, 335, 337–340, 342, 364, 365, 386, 397–399, 401, 407–415, 418–422, 424, 428–430, 438, 440, 477, 478, 492, 493, 498, 500, 518, 521, 522, 547, 726, 727, 730, 731, 734, 735, 738, 752 Tissue hardening, 331 TNA See Threose nucleic acid (TNA) Tocopherols, 522, 704 Totipotency, 96, 386, 420, 430, 729 TPS See Trehalose phosphate synthase (TPS) Transcript analysis with aid of affinity capture (TRAC analysis), 52 Transcription activator-like effector nucleases (TALENs), 562 Transcriptional gene silencing (TGS), 266, 269, 272, 273, 624 Transcriptional networks, 307–309 Transcription factors, 13–15, 18, 21, 115, 140, 142–144, 146, 147, 163, 166, 167, 169, 224, 226, 230, 231, 342, 398, 519, 536, 558, 564, 583, 595–597, 627, 630, 647–649, 651–653, 656, 700, 704 Transcription regulation, 583 Transcriptome, 4, 12–14, 54, 57, 84, 115–118, 125, 126, 155, 172, 212, 224, 226, 228, 232, 233, 249, 253, 270, 280, 295, 309, 560, 583, 584, 588, 596, 597, 660 767 Transcriptomics, 11, 15, 50, 56, 118, 125, 258, 280, 293, 295, 296, 299, 310 Transfer RNAs (tRNAs), 133, 135–137, 144, 161, 184, 190, 195, 196, 198, 228 Transformation, 3, 7, 10, 18, 37, 40, 104, 106, 133, 233, 234, 269, 316, 317, 322, 323, 331, 335, 358, 399, 401, 408, 490, 491, 494, 495, 498, 500, 518–520, 528, 540, 541, 543, 553–556, 559–562, 568, 588, 616, 617, 627, 630–632, 639, 653, 668, 676, 677, 679, 681, 682, 729–731, 733, 735–736, 744, 747 Transgene, 55, 106, 168, 170, 266–269, 273, 274, 490, 519, 528, 542, 543, 555–563, 598, 617, 618, 624, 626, 632 expression, 269, 556–558, 562 flow, 555, 617 silencing, 267, 269, 274 Transgenic crops, 344, 534, 538, 612, 613, 615–618, 624, 632, 652 Transgenic organism, 528 Transgenic plants, 54, 106, 269, 274, 448, 519, 542–543, 554, 557, 561, 563–565, 567, 570, 585, 586, 588, 589, 591, 592, 594–598, 613–618, 627–629, 631, 632, 648, 651–653, 655, 656, 667, 681–682, 733 Transgenics, 17, 33, 40, 55, 106, 501, 564, 618, 629, 630, 751 Transgenic technology, 106, 612, 613, 617, 682, 746, 752 Transplastomic, 189, 193, 554–556 Transporters, 18, 306, 399, 583, 591–593 Transposable element (TEs), 7, 8, 69, 196, 267, 269, 342, 409, 560, 640 Transposon display (TD), 211, 213, 214 Transposon mutagenesis, 560 TRAP See Target region amplification polymorphism (TRAP) Trap lines, 7–8 Tree species, 125, 214, 343, 350, 390, 394, 418, 447, 448, 470, 471, 476, 482, 730, 735 Trehalose, 564, 585, 588 Trehalose phosphate synthase (TPS), 588 Triploid hybrids, 377, 388, 390 Triploids, 158, 338, 368, 376–378, 381, 385–394 Triticale, 97, 98, 101, 103, 267, 349, 364, 390–391, 529 tRNAs See Transfer RNAs (tRNAs) Tropane alkaloids, 399, 518 Turmeric, 387, 436, 488, 489, 493–494, 499–502 Two-dimensional gel electrophoresis (2DE), 53, 250, 253, 254, 256–259 U Ubiquitination, 249, 252, 271, 584, 597–598 Uniparental inheritance, 189 3ʹ-Untranslated region (3ʹ-UTR), 559, 640, 646 V Vaccine, 41, 310, 311, 398, 537, 545, 556, 568, 569, 751 Value-added compounds, 564 Index 768 Vanilla, 438, 488, 489, 495, 499–501 Variable number of tandem repeats (VNTRs), 68, 207, 208, 380 Variants, 6, 9, 13, 67, 68, 70, 72, 84, 117, 146, 205, 214, 249, 270, 274, 275, 311, 337, 339, 343, 408–415, 478, 493, 498, 615, 629, 642, 646, 653 Vegetative propagules, 418, 421, 482 VIGS See Virus induced gene silencing (VIGS) Village seed bank, 752 Vinblastine, 399, 403, 521 Vincristine, 399, 403, 521 Viral diseases, 350, 535, 625–626 Virtual cell, 296, 297, 305, 310 Virtual rice project, 296, 297 Viruses, 12, 18, 54, 57, 83, 135, 144, 148, 150, 151, 183, 196, 234, 235, 267, 273, 298, 310, 316, 320, 331, 337, 343, 367, 378, 392, 415, 418, 419, 421, 422, 429, 462, 491, 530, 536, 540, 547, 554, 556, 557, 560, 562, 569, 612–614, 625, 626, 648, 649, 654, 655, 668, 708, 749 elimination, 331, 442 Virus induced gene silencing (VIGS), 12, 234, 560, 626 VNTRs See Variable number of tandem repeats (VNTRs) W Watermelon, 182, 386–388, 535 Weeds, 1–3, 16, 449, 450, 473, 534, 547, 552, 611–613, 617, 748 Western blot analysis, 53, 542 WGA See Whole genome arrays (WGA) Whole genome arrays (WGA), 11, 13 Wide hybridization, 90, 91, 97–98, 348, 349, 358, 364, 365, 378, 381 Wide hybrids, 348, 349, 352–359 Y Yeast two-hybrids (Y2H), 230, 231 Z Zinc finger nucleases (ZFN), 235–237, 562 ... (Kong et al 20 04, 20 13, 20 14) Bir Bahadur et al (eds.), Plant Biology and Biotechnology: Volume II: Plant Genomics and Biotechnology, DOI 10.1007/978-81- 322 -22 83-5 _20 , © Springer India 20 15 397... Bahadur et al (eds.), Plant Biology and Biotechnology: Volume II: Plant Genomics and Biotechnology, DOI 10.1007/978-81- 322 -22 83-5 _22 , © Springer India 20 15 417 P.E Rajasekharan and L Sahijram 418... pharmaceuticals and help in the design of new therapies (Bender and Kumar 20 01; Kumar and Roy 20 06, 20 11; Kumar and Sopory 20 08, 20 10; Neumann et al 20 09; Kumar and Shekhawat 20 09; Kumar 20 10; Fernandez