Genetic dissection of and genomic selection for seed weight, pod length, and pod width in soybean
Yijie Chen,
Yajun Xiong,
Huilong Hong,
Gang Li,
Jie Gao,
Qingyuan Guo,
Rujian Sun,
Honglei Ren,
Fan Zhang,
Jun Wang,
Jian Song,
Lijuan Qiu
Affiliations
Yijie Chen
College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China; Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434025, Hubei, China
Yajun Xiong
College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
Huilong Hong
National Key Facility for Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Gang Li
College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
Jie Gao
College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
Qingyuan Guo
College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
Rujian Sun
Hulunbuir Institute of Agriculture and Animal Husbandry, Hulunbuir 021000, Inner Mongolia, China
Honglei Ren
Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, Heilongjiang, China
Fan Zhang
College of Life Sciences, Yangtze University, Jingzhou 434025, Hubei, China
Jun Wang
College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China; Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434025, Hubei, China; Corresponding authors.
Jian Song
College of Life Sciences, Yangtze University, Jingzhou 434025, Hubei, China; Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434025, Hubei, China; Corresponding authors.
Lijuan Qiu
College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China; National Key Facility for Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Corresponding authors.
A biparental soybean population of 364 recombinant inbred lines (RILs) derived from Zhongdou 41 × ZYD 02.878 was used to identify quantitative trait loci (QTL) associated with hundred-seed weight (100-SW), pod length (PL), and pod width (PW). 100-SW, PL, and PW showed moderate correlations among one another, and 100-SW was correlated most strongly with PW (0.64–0.74). Respectively 74, 70, 75 and 19 QTL accounting for 38.7%–78.8% of total phenotypic variance were identified by inclusive composite interval mapping, restricted two-stage multi-locus genome-wide association analysis, 3 variance-component multi-locus random-SNP-effect mixed linear model analysis, and conditional genome-wide association analysis. Of these QTL, 189 were novel, and 24 were detected by multiple methods. Six loci were associated with 100-SW, PL, and PW and may be pleiotropic loci. A total of 284 candidate genes were identified in colocalizing QTL regions, including the verified gene Seed thickness 1 (ST1). Eleven genes with functions involved in pectin biosynthesis, phytohormone, ubiquitin-protein, and photosynthesis pathways were prioritized by examining single nucleotide polymorphism (SNP) variation, calculating genetic differentiation index, and inquiring gene expression. The prediction accuracies of genomic selection (GS) for 100-SW, PL, and PW based on single trait-associated markers reached 0.82, 0.76, and 0.86 respectively, but selection index (SI)-assisted GS strategy did not increase GS efficiency and inclusion of trait-associated markers as fixed effects reduced prediction accuracy. These results shed light on the genetic basis of 100-SW, PL, and PW and provide GS models for these traits with potential application in breeding programs.
