Molecular characterization of QTL-allele system for drought tolerance at seedling stage and optimal genotype design using multi-locus multi-allele genome-wide association analysis in a half-sib population of soybean (Glycine max (L.) Merr.)

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作   者：

Khan, Mueen Alam;  Tong, Fei;  Wang, Wubin;  He, Jianbo;  Zhao, Tuanjie;  Gai, Junyi; 

作者机构：

Nanjing Agr Univ;  Peoples R China;  MARA Key Lab Biol & Genet Improvement Soybean Gen;  Nanjing 210095;  Natl Key Lab Crop Genet & Germplasm Enhancement;  Jiangsu Collaborat Innovat Ctr Modern Crop Prod;  M;  S;  Jiangsu; 

关键词：

QTL-allele matrix;  soybean (Glycine max (L.) Merr.);  gene annotations;  drought tolerance;  optimal cross-design;  genome-wide association analysis; 

期刊名称：

Plant Genetic Resources Characterization and Utilization

i s s n：

1479-2621

年卷期：

2020 年 18 卷 5 期

页   码：

295-306

页   码：

摘   要：

Characterizing the whole genetic architecture of drought tolerance (DT) is a persistent challenge for the breeders. Here we developed a half-sib population comprising of 404 lines of two recombinant inbred line (RIL) populations with M8206 as the joint parent (M8206 x TongShan and ZhengYang x M8206) and tested for its DT under sand culture. The population was sequenced using restriction-site-associated DNA sequencing filtered with minor allele frequency >= 0.01; 55,936 single nucleotide polymorphisms (SNPs) were obtained and assembled into 6137 SNPLDBs (SNP linkage disequilibrium blocks). The restricted two-stage multi-locus genome-wide association analysis characterized with error and false-positive control identified 40 QTLs with 93 alleles on an average of 34.75% of the phenotypic variance (PV) collectively for relative root length (RRL) and relative shoot length (RSL) that served as potential DT indicators. Among these, eight loci corresponded to previously reported QTLs, whereas 32 loci were therefore novel. The identified QTLs with their corresponding alleles for RRL and RSL were organized into QTL-allele matrices, depicting the comprehensive DT genetic architecture of the three parents/half-sib population. From the matrices, we predicted the possible best/optimal genotype with weighted average value (WAV) 1.553 over two indicators, while for the top 10 single crosses among RILs with 95(th) percentile WAV was 1.218-1.257, transgressive over the parents (0.693-0.794) yet much less than 1.553. From the detected QTL-allele system, 65 potential candidate genes collectively for both indicators explaining on an average of 24.41% PV were annotated and chi(2)-tested as a DT candidate gene system involving nine biological processes.