THÔNG TIN TÀI LIỆU
Journal of Integrative Agriculture 2017, 16(1): 16–26 Available online at www.sciencedirect.com ScienceDirect RESEARCH ARTICLE Validation of qGS10, a quantitative trait locus for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.) WANG Zhen*, CHEN Jun-yu*, ZHU Yu-jun, FAN Ye-yang, ZHUANG Jie-yun State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, P.R.China Abstract Grain size is a major determinant of grain weight and a trait having important impact on grain quality in rice The objective of this study is to detect QTLs for grain size in rice and identify important QTLs that have not been well characterized before The QTL mapping was first performed using three recombinant inbred line populations derived from indica rice crosses Teqing/IRBB lines, Zhenshan 97/Milyang 46, Xieqingzao/Milyang 46 Fourteen QTLs for grain length and 10 QTLs for grain width were detected, including seven shared by two populations and 17 found in one population Three of the seven common QTLs were found to coincide in position with those that have been cloned and the four others remained to be clarified One of them, qGS10 located in the interval RM6100–RM228 on the long arm of chromosome 10, was validated using F2:3 populations and near isogenic lines derived from residual heterozygotes for the interval RM6100–RM228 The QTL was found to have a considerable effect on grain size and grain weight, and a small effect on grain number This region was also previously detected for quality traits in rice in a number of studies, providing a good candidate for functional analysis and breeding utilization Keywords: grain size, quantitative trait locus, residual heterozygote, rice (Oryza sativa L.) in rice is determined by three components, i.e., number of Introduction Rice (Oryza sativa L.) is one of the most important cereal crops, feeding half of the world’s population Grain yield panicles per plant, number of grains per panicle and grain weight Grain size is a major determinant of grain weight, and a trait having important impact on the market value of rice grain Long and slender grains are preferred in the major segment of the international market, whereas short and round grains are favored in northern China, Korea and Japan (Calingacion et al 2014) In addition, slender grains Received 11 January, 2016 Accepted 25 April, 2016 WANG Zhen, Tel: +86-571-63370197, Fax: +86-571-63370364, E-mail: mimi_9124@qq.com; Correspondence ZHUANG Jie-yun, Tel: +86-571-63370369, Fax: +86-571-63370364, E-mail: zhuangjieyun@caas.cn * These authors contributed equally to this study are more likely to have lower grain chalkiness thus a better © 2017, CAAS Published by Elsevier Ltd This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/) doi: 10.1016/S2095-3119(16)61410-7 major negative regulator controlling grain length and weight appearance quality (Wang et al 2005) Over the last two decades, a large number of quantitative trait loci (QTLs) for grain size and grain weight in rice were detected and some of them were cloned since 2006 GS3, a is the first QTL cloned for grain size (Fan et al 2006) Eight more QTLs were cloned up to date, including GL3.1/qGL3 WANG Zhen et al Journal of Integrative Agriculture 2017, 16(1): 16–26 (Qi et al 2012; Zhang et al 2012), TGW6 (Ishimaru et al 2013), GW6a (Song et al 2015), and GW7/GL7 (Wang S K et al 2015; Wang Y X et al 2015) determining grain length and weight, and GW2 (Song et al 2007), qSW5/ GW5 (Shomura et al 2008; Weng et al 2008), GS5 (Li Y et al 2011), and GW8 (Wang et al 2012b) responsible for grain width and weight It has been commonly applied that QTLs exhibiting major and consistent effects in primary mapping populations were first targeted for cloning As a result, QTLs that have been cloned for yield traits in rice, either those for grain size and grain weight described above, or others associated with grain number (Ikeda et al 2013; Yan et al 2013), all showed large effects for the trait under study Because few QTLs of this kind is available, it is not uncommon that different groups separately make great efforts on the same QTL (Shomura et al 2008; Weng et al 2008; Qi et al 2012; Zhang et al 2012; Ikeda et al 2013; Wang S K et al 2015; Wang Y X et al 2015) Diversifying rice crosses in constructing populations for primary QTL mapping may facilitate the detection of new QTLs and alleviate the shortage of candidate QTLs for cloning In the present study, QTL mapping for grain size in rice was performed using three primary populations, followed by the validation of one QTL region Fourteen QTLs for grain length and 10 QTLs for grain width were detected in three recombinant inbred line (RIL) populations derived from the indica rice crosses Zhenshan 97/Milyang 46 (ZM), Xieqingzao/Milyang 46 (XM) and Teqing/IRBB lines (TI) One QTL shared by different populations and located in a region that was away from those that have been cloned was selected for validation Two lines of the TI population were crossed to develop an F2:3 population and three sets of near isogenic lines (NILs) The target QTL, qGS10 located in the interval RM6100–RM228 on the long arm of chromosome 10, was validated to have a considerable effect on grain size and grain weight Materials and methods 2.1 Plant materials The three RIL populations used in this study have been reported by Mei et al (2013) Both the female and male parents of the TI population are indica rice restorer lines, of which the male parent included six IRBB lines (IRBB50, IRBB51, IRBB52, IRBB54, IRBB55, and IRBB59) that are NILs in the genetic background of IR24 (Huang et al 1997a) The numbers of RILs included in the TI population are 122 for Teqing/IRBB52, 77 for Teqing/IRBB59, two for Teqing/IRBB50, and one each for Teqing/IRBB51, Teqing/ 17 IRBB54 and Teqing/IRBB55 The female parents of the ZM and XM populations, Zhenshan 97 and Xieqingzao, are maintainer lines of the commercial three-line indica rice hybrid Shanyou 10 and Xieyou 46, respectively, and the common male parent Milyang 46 is the restorer line of the two hybrids (Mei et al 2013) In the rice zone of middle-lower reaches of Yangtze River in China, Zhenshan 97 and Xieqingzao are used as early-season rice, and Milyang 46, Teqing and IR24 are grown as middle-season rice Development of secondary populations for the validation of qGS10 were described below and illustrated in Fig Two lines of the TI population, having distinct phenotypes in grain size and different genotypes in the interval RM6100– RM228 on the long arm of rice chromosome 10, were selected and crossed 120 F2 plants were produced and assayed using the four markers in the qGS10 region, i.e., RM6100, RM3773, RM3123, and RM228 Plants that were heterozygous in all the four marker loci were identified as residual heterozygotes (RHs) for qGS10 They were then subjected to genotyping with 122 polymorphic SSR markers located in other regions One plant was selected, remained to be heterozygous in the target region and identified to be heterozygous and homozygous at 19 and 103 marker loci in the background, respectively This plant was selfed to produce a F2-type population and then a F2:3-type population Teqing/IRBB lines Two lines differing in the interval RM6100–RM228 on chromosome 10 Cross F1 Selfing F2 Marker assay A residual heterozygote (RH) for the interval RM6100–RM228 Selfing RH-F2 Marker assay RH-F2:3 Marker assay Three plants that were heterozygous in RM6100–RM228 Selfing New RH-F2 Marker assay Non-recombinant homozygotes Selfing Three sets of NILs Fig Construction of a residual heterozygote (RH)-derived F2:3 population and three sets of near isogenic lines (NILs) 18 WANG Zhen et al Journal of Integrative Agriculture 2017, 16(1): 16–26 The F2:3 population consisting of 307 individuals was used for QTL analysis on grain size and yield traits In the mean time, three F3 plants that were heterozygous at the four marker loci in the target region and at four or five marker loci in the background were selected New RH-F2 populations were developed and assayed with the segregating markers Plants showing no recombination in the target region were identified in each population Selfing seeds of these plants resulted in the development of three sets of NILs, of which each consisted of two homozygous genotypic groups differing in the target region 2.2 Trait measurement All the rice populations were planted in the middle rice growing season in the paddy field of the China National Rice Research Institute located in Hangzhou, Zhejiang, China The three RIL populations were tested for two years, including 2008 and 2009 for TI, 2009 and 2010 for ZM, and 2003 and 2009 for XM The 307 F3 families and the three NIL sets were tested for one year in 2013 and 2015, respectively A randomized complete block design with two replications was used In each replication, one line was grown in a single row of 12 plants, except that six-row plots with 12 plants per row was employed for XM in 2003 The planting density was 16.7 cm between plants and 26.7 cm between rows Field management followed the normal agricultural practice At maturity, five middle plants of each row/plot were harvested in bulk for trait measurement The three RIL populations were only measured for grain length and width, and the F3 families and three NIL sets were measured for seven traits including grain length (GL), grain width (GW), 000-grain weight (TGW), number of panicle per plant (NP), number of grains per panicle (NGP), number of spikelet per panicle (NSP), and grain yield per plant (GY) The grain length and width were estimated by the Rice Product Quality Inspection and Supervision Testing Center of the Ministry of Agriculture of China according to the National Standard GB/T 178911999 (1999) for the three RIL populations, and measured using an automatic instrument (Model SC-G, Wanshen Ltd., Hangzhou, China) for the RH-derived F2:3 population and the three NIL sets 2.3 DNA marker analysis Total DNA was extracted following the conventional method (Lu and Zheng 1992) for plants assayed with 126 markers and using the mini-preparation protocol (Zheng et al 1995) for other plants PCR amplification was performed according to Chen et al (1997) The products of the SSR markers were visualized on 6% non-denaturing polyacrylamide gels using silver staining All the SSR markers were selected from the Gramene database (http://www.gramene.org/) 2.4 Data analysis In each trial, phenotypic values of the two replications were averaged for each line and used for data analysis Basic descriptive statistics, including mean trait value, standard deviation, coefficient of variation, the minimum and maximum trait values, skewness, and kurtosis, were computed for each population in each trial Linkage maps for the three RIL populations used in this study were constructed previously (Mei et al 2013), in which the genetic distance in centiMorgan (cM) was derived using Kosambi function The TI, ZM and XM maps are 197.7, 814.7 and 080.4 cM in length, consisting of 127, 256 and 240 DNA markers, respectively (Appendix A) All the 12 chromosomes are well-covered in the ZM and XM maps, whereas the major segment of chromosomes and are un-covered in the TI map due to parental monomorphism As compared to the ZM, the map distance is generally expanded in XM and compressed in TI For the RH-derived F2 population, Mapmaker/Exp 3.0 (Lander et al 1987) was used for map construction, with the genetic distances in cM also derived using the Kosambi function For the three RIL populations in which the phenotypic data were available for two years, QTL analysis was performed using QTL Network 2.0 (Yang et al 2008) Critical F values for genome-wise type I error were calculated with 000 permutation test and used for claiming a significant event Significant level of P
Ngày đăng: 15/03/2023, 20:39
Xem thêm: