QTL Mapping And BSR-Seq Analysis For Agronomic Traits In Wheat RIL Population Yanda1817×Beinong6

Wheat (Triticum aestivum L.,2n=42, AABBDD genome) is one of the main staple crops in the world and provides 20% of daily protein and calories. Mapping and cloning gene/QTL are one of the most effective approaches to improve the yield, quality biotic and abiotic stress resistance via molecular marker assisted selection (MAS) in wheat breeding program. In this study, a recombinant inbred line (RIL) population derived from the famous stress tolerance wheat landrace Yanda1817 and high-yielding wheat line Beinong6 was employed for QTL mapping agronomic traits. RNA-Seq (RNA sequencing) analysis was used first to find SNPs betweem Yanda1817 and Beinong6 and to develop D genome specific polymorphic markers to enhance the genetic linkage map density. Quantitative trait loci (QTL) mapping for wheat seedling salt-tolerance, root architechture in germinating stage and pre-harvest sprouting resistance were conducted. And BSR-Seq approach was firstly applied for mapping QTL of multiple agronomic traits in wheat. The main results are as follows:The Yanda1817/Beinong6 SNP genetic linkage map contains fewer markers in D genome, limited it’s potential for mapping QTL in the D genome. By applying RNA-Seq approach, a total of 1702 high confident D genome specific SNPs between Yanda1817 and Beinong6 were obtained. Twenty-seven D genome specific SNP markers were developed and successful integrated into the high-density SNP genetic linkage map, suggesting RNA-Seq is an effective tool to develop genome specific ploymorphic marker in wheat.QTL mapping for 14 seedling traits under salt stress treatment and control (CK) in hydroponics condition were conducted using a set of 230 RILs derived from cross Yanda1817 and Beinong6 and the enhanced high-density genetic linkage map. A total of 114 putative QTLs were detected on 20 chromosomes (except for 1A) for all of the investigated traits by inclusive composite interval mapping (ICIM) (LOD≥2.5) with 2.7%-21.7% of the phenotypic variations explained by single QTL. Threeteen QTL could be detected in three or more than three environments. Of which,73 QTL showed positive additive effects originated from Yanda1817, whereas 41 QTLs showed positive additive effects originated from Beinong6, indicating Yanda1817 is an important genetic resource of salt tolerance in wheat.Agar-filled Perspex chambers experiments was conducted to identify QTL for both seminal root architecture (a measurement of the root number and root angle) and gravitropic response (the degree of bending of the growing seminal root when subjected to a 90°rotation) in wheat. A total of 16 additive-effect QTL associated with the target traits were mapped on chromosomes 1A, 1B, 1D,3D, 4A,4B,5A,5B,6B and 7B with additive effects ranged from-3.75 to 2.57. The phenotypic variation explained by individual additive-effect QTL varied from 3.50% to 7.92%. In addiation, comparative genomic analysis was applied to map the major QTL QPhs.cau.3A.2 assosited with pre-harvest sprouting resistance. Precise comparative genetic and QTL mapping revealed TaVp-1A is the candidate of QPhs.cau.3A.2 conferred pre-harvest sprouting resistance in wheat population Yanda1817×Beinong6. These results would be beneficial to understand the genetic basis of complex QTL tratis and maker-assisted selection of salt-tolerance, seminal root traits and pre-harvest sprouting resistance in wheat breeding.BSR-Seq has been proposed to be a powerful tool for fast mapping genes and developing closely linked molecular markers. In this study, BSR-Seq was firstly applied for QTL mapping in complex wheat genome, and two different BSR-Seq pooling strategies were tested. BSR-Seq analyses based on the RIL phonotypes were conducted for stem solidness, plant hight, and seminal root number. A total of 102 candidate SNPs for stem solidness were obtained, and 90 (88%) of them were enriched in the terminal of 3BL chromosome arm, suggesting the stem solidness was controlled by a single gene in the terminal of 3BL at this population. After gene function annotation in candidate 3B chromosome genomic region,7 candidate genes realted to biosynthesis of lignin and cellulose were identified. Most of the candidate SNPs for plant hight was located on chromosome 2A that may be related to QTL QPh.cau.2A.2. The candidate SNPs for root number at germinating stage also were enriched in the chromosome arms containing the major QTL obtained from genetic mapping analysis. BSR-Seq analyses based on the RIL genotypes of target major QTL and RILs phonotypes were proposed for fine mapping QTL of grain and flag leaf size. Altogether,138 and 223 candidate SNPs were identified for the genomic regions of grain size QTL QTgw.cau-5A.2 and QTgw.cau-6B.1, and 71 and 320 candidate SNPs were found for the genomic regions of flag leaf width QTL QFlw.cau-3A and QFlw.cau-5A.1, providing important information for developing polymorphic markers and fine mapping the target QTL. These results suggested that BSR-Seq approach is also appropriated for QTL mapping in complex wheat genome.