Identification of traits and qtls contributing to salt tolerance in rice (oryza sativa l )

Identification of traits and QTLs contributing to salt tolerance in rice (Oryza sativa L.) Thieu Thi Phong Thu 2019 Identification of traits and QTLs contributing to salt tolerance in rice (Oryza sativa L.) A dissertation submitted to Graduate School of Bioscience and Bioenvironmental Science, Faculty of Agriculture, Kyushu University in partial fulfillment of the requirement for the degree of Doctor of Philosophy by Thieu Thi Phong Thu Laboratory of Plant Nutrition Japan, 2019 Table of contents Acknowledgment i Abbreviation ii iii-vi Summary Chapter General introduction Chapter Effects of salt stress on plant growth characteristics and 1-10 11-34 mineral contents in diverse rice genotypes Chapter Allocation of macronutrients in roots, sheaths, and leaves 35-56 determines salt tolerance in rice Chapter Determination of sampling method to identify salt tolerant 57-75 traits in rice Chapter Identification of QTLs by genome wide association study 76-110 (GWAS) in rice for salt tolerance Chapter General discussion 111-122 Appendix 123-129 References 130-146 Acknowledgment I would like to express my sincerest appreciation and deepest gratitude to the following organizations and individuals in the pursuit of my Doctoral degree: Vietnam Government, Ministry of Agriculture and Rural Development, and Ministry of Education and Training for granting me the scholarship; Vietnam National University of Agriculture, and Department of Cultivation Science for allowing me to leave to go on study and their kind supports; My supervisor Assoc Prof Dr Takeo Yamakawa for his guidance, encouragement with all his heart and invaluable advices throughout my research; Prof Dr Ken Matsuoka, Assoc Prof Dr Akiko Nakashita-Maruyama, Dr Masamichi Kikuchi from Laboratory of Plant Nutrition; and Prof Dr Hideshi Yasui, Dr Yoshiyuki Yamagata from Laboratory of Plant Breeding for their kind helps and invaluable comments and suggestions during my study; All members of Plant Nutrition Laboratory for their kind understanding, their enthusiasm supports and helps during my time in Japan; All my Vietnamese friends and other International friends for their helps and moral supports which made my stay in Japan a pleasant and memorable one; Vietnam international education development (VIED) at Ministry of Education and Training and Mrs Nguyen Thi Thanh Tam, an officer of Students Affairs Division, for their kind understanding, their enthusiasm supports and help me to complete both the necessary proceeds in Viet Nam and Japan Last, but not least to my husband Duong Thanh Huan, my little daughter Duong Hong Ngoc and my parents, my parent’s in-law, my sisters and their family, my husband’s older brother and his family for their love and moral support i Abbreviation 3LM ASW C2S Ca CAS Chr CM CT DW EC GWAS HDRA HS HSD IB JB K KCR L LD LW_R Mg MT N Na P PCI QTLs S Sh ShtL_R ShtW_R SES SNP SOS ST ST/CT T WRC Y-sol = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = Three leaves method Artificial seawater Cutting part of leaf sheath between base and up to cm Calcium Cutting part of leaf sheath between cm from base to collar Chromosome Cutting method Control treatment Dry weight Electrical conductivity Genome wide association study High density rice array High salt susceptible group Honesty significant difference Indica Block Japonica Block Potassium Kyushu university cultivated rice Leaf Linkage disequilibrium Leaf dried weight reduction Magnesium Moderately salt tolerant group Nitrogen Sodium Phosphorous Pearson correlation index Quantitative trait loci Salt susceptible group Sheath Shoot length reduction Sheath dried weight reduction Standard evaluation score Single nucleotide polymorphisms Salt overly sensitive Salt stress treatment Salt stress treatment/Control treatment Salt tolerant group World rice collection Yoshida solution ii Thesis Summary The global population is expected to reach to billion people by 2050, increasing the pressure for agricultural production in marginal saline lands Agriculture will have to increase its crop productivity by 70-110% in 2050 to feed that world Globally, it is estimated that 45 million of the 230 million of irrigated lands (19.5%) have to suffer from salinization problems by various degrees This is a serious problem because irrigated areas are responsible for one-third of world food production Therefore, agriculture production has been faced to not only increase crop yields that have not been seen before but also have to this in a changing climate Development of the salt tolerant varieties has been considered one of the key strategies to increase rice production in the coastal area through breeding by genetic methods The important steps have been pointed out for genetic method of improving salt tolerance in rice such as evaluation of variation of genetic sources for salt tolerance in rice, identification of molecular markers associated with QTLs or genes conferred tolerance to salt stress, discovery of genes regulating salt tolerance and development of cultivars harboring those salt tolerance genes Salinity tolerance in rice is regulated by multiple genes Expression of salinity tolerance is the result of many physiological and biochemical activities in plants Therefore, determining the representative traits for salinity tolerance is a very difficult but extremely important task The objectives of this research are to determine the optimal salinity tolerant traits, the effective sampling method, and finally to find QTLs contributing to improving salt tolerance in rice Thirty-seven rice varieties were screened for salt tolerance using a hydroponic system with ion components similar to seawater in growth chamber Two-week-old seedlings were grown for days on Yoshida hydroponic solution The treatment group then additionally received an artificial seawater solution (electrical conductivity, 12 dS m −1) After a 2-week period of salt stress, standard evaluation scores (SES) of visual salt injuries iii were assessed The K, Na, Mg, and Ca contents were then determined for the roots, sheaths, and leaves Following the SES results, the 37 varieties were divided into four groups: salttolerant (STGs), moderately salt-tolerant (MSTGs), salt-sensitive (SSGs), and highly saltsensitive (HSSGs) In the control treatment, STGs had the highest sheath K content, whereas HSSGs had the lowest Sheath K content was also highly and negatively correlated with SES This suggests that sheath K may be useful for identifying salt-tolerant varieties under nonsaline conditions Plant growth was significantly affected under salt stress, but STGs had the smallest decrease in dry weight of sheath SES was significantly correlated with sheath and leaf Na, sheath K and Mg contents, and sheath and leaf Na/K and Na/Mg ratios The results suggested that sheath K content, Na/K, and Na/Mg ratios may be useful indicators for genetic analyses of salt-tolerant varieties under salt stress conditions Another set of twenty-nine rice varieties were screened for salt tolerance using a hydroponic system with ion components similar to seawater in a green house Following the SES results, the 29 varieties were divided into three groups: salt tolerant (STG), moderately salt tolerant (MSTG), salt susceptible (SSG) Under the control treatment, salt tolerant varieties exhibited low K content in root Under the salt stress treatment, the salt tolerant varieties exhibited low SES, high N content in leaves and sheaths, low Na content in leaves and sheaths, low Mg contents in leaves and sheaths, and low Ca content in sheaths The salt tolerant varieties also showed high ratio of sheath dry matter in salt stress treatment and sheath dry matter in control treatment, high N content in leaves and sheaths, high K content in sheaths, and low Na/K ratios in leaves and sheaths Therefore, these parameters might be useful to understand salt tolerance in rice Four rice varieties were used in sampling method experiment in phytotron In the control, Yoshida solution was used continuously during the experiment In the salt treatment, seedlings were grown for two weeks in a 12 dS m−1 salt solution Two sampling methods iv were tested including cutting method and three leaves method The results showed that cutting method and three leaves method are useful for experiments related to salt tolerance in rice The mineral contents in salt tolerant cultivars was significantly different in comparison with salt susceptible variety in cutting part of leaf sheath between cm and collar (CAS) and leaf blade The CAS and the leaf blade were useful for identifying salt tolerant related traits Leaving roots and shoots from the base to cm might be possible to continue the growth of seedling and produce seeds which will be used for re-phenotyping of the progeny The first three leaves may not be needed for sampling to determine mineral contents As a result, it is possible to take a sample without the first three leaves and using cutting part of leaf sheath between cm and collar The K content, Na content, Mg content and Na/K ratio in CAS and Na content, Na/K ratio in leaf blade should be used as salt tolerant traits in molecular and genetic analysis A genome wide association study (GWAS) was performed to identify potential QTLs associated with salt stress tolerance in rice by correlating the genotyping data set with the phenotypic expression of 225 diverse rice accessions for 11 biochemical and agronomic traits GWAS was run using a mixed linear model (MLM) and population parameters previously defined (P3D) in Tassel 5.0 and predicts genomic regions associated with traits for Japonica subpopulation and Indica subpopulation To analyze single nucleotide polymorphisms (SNP) calls, a high-density rice array of 700,000 SNPs was used, which derived from the sequencing of wild and domesticated rice The kinship matrix (K) estimated from SNP genotyping data Association signals at the same QTL block were confirmed location on chromosome by analysis of linkage disequilibrium (LD) block using gPlink2.050 and Halotypeview version 4.2 GWAS resulted in detection of numerous SNP markers scattered over the rice genome that were associated with various salt tolerance traits A QTLs region on chromosome was found to contribute to the variation in salt tolerance in Indica v subpopulation and related to two traits of sheath Ca content and sheath Mg content Three QTLs regions on chromosome 2, 4, were found to contribute to the variation in salt tolerance in Japonica subpopulation and related various traits of sheath Na content, sheath Mg content, sheath Na/K ratio, leaf Na content, leaf Na/k ratio GWAS and LD analysis showed several SNP makers highly related to salt tolerant traits The results of this thesis dressed out both the insight in traits and mechanisms related to salt tolerance and sampling method for salt stress experiment in rice The underlying genetics as presented in this thesis is of direct use to breeders and scientists and will significantly contribute to improving the salt tolerance traits in rice vi Chapter General introduction 1.1 The salinization and current worldwide problems The global population is expected to reach to billion people by 2050, increasing the pressure for agricultural production in marginal saline lands (Negrão et al 2011) Global food production will need to increase by approximately 50% by 2050 to match population growth (Flowers 2004; Rengasamy 2006) Tester and Langridge (2010) also reported that crop productivity of agriculture has to increase by 70-110% in 2050 to feed that world However, agricultural production faces increasing challenges from salt intrusion due to global warming, ice melt, and rising sea levels The area and salinity level of salt-affected soil have been increasing in parallel with the increase of world population Globally, it is estimated that saline and sodic soils cover 397 million and 434 million (FAO 2016), respectively, while 45 million of irrigated lands (19.5%) have been affected by salinization This is a serious problem because irrigated areas are responsible for one-third of world food production 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