QTN mapping, gene prediction and simulation breeding of four-seed pod numbers of soybean

Ming Yuan¹Xu Sun²Zhiyuan Yu²Haoyue Sun¹Sheng Dong²Jie Zhang²Bo Hu²Wen-Xia Li²Hailong Ning^2*Wencheng Lu³

• ¹Qiqihaer Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihaer, Heilongjiang Province, China
• ²Northeast Agricultural University, Harbin, China
• ³Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, China

The number of four-seed pods (NFSP) in soybean is an important yield trait and a quantitative trait regulated by multiple genes. Mapping quantitative trait nucleotide (QTN), mining major genes and screening excellent breeding schemes for NFSP are of great significance for the breeding highyield soybean varieties. In this study, a germplasm population (GP) containing 455 soybean varieties was planted in 5 environments to investigate NFSP. SNP genotype data were obtained based on Axiom_SoyaSNP 180K chip, and genome-wide association analysis (GWAS) was used to locate QTN which were used to predicting candidate genes and simulating breeding. The results showed that there was genetic variation in NFSP and different gene expression in various environments. The broad sense heritability of NSFP over multiple environments was 72.7%. A total of 89 QTN correlated with the number of four pods were identified on 20 chromosomes, including 34 stable QTN repeatedly detected by multiple methods or in multiple environments and 4 QTN with additive by environment interact effect. In the decay regions of 34 stable QTN, three genes related to NFSP of soybean were screened and verified by haplotype analysis, namely Glyma.13G105400, Glyma.04G063700 and Glyma.04G063100. Multiple regression analysis of 89 QTNS on NFSP was used to establish molecular-assisted selection models for five environments, which could explain 44.82%-55.06% of the phenotypic variation of NFSP. Based on this model, 153 breeding schemes were selected for 5 environments, which could achieve the breeding goals of NFSP over 43, 43, 25, 31 and 40 under 21AC, 21XY, 23WD, 23QQHE and 23AC environments, respective ly. These results laid the foundation for understanding the genetic mechanism of pod formation in soybean and molecular breeding high-yield varieties.