Genome-wide association study of four yield-related traits at the R6 stage in soybean

Abstract

Background The 100-pod fresh weight (PFW), 100-seed fresh weight (SFW), 100-seed dry weight (SDW) and moisture content of fresh seeds (MCFS) at the R6 stage are crucial factors for vegetable soybean yield. However, the genetic basis of yield at the R6 stage remains largely ambiguous in soybean. Results To better understand the molecular mechanism underlying yield, we investigated four yield-related traits of 133 soybean landraces in two consecutive years and conducted a genome-wide association study (GWAS) using 82,187 single nucleotide polymorphisms (SNPs). The GWAS results revealed a total of 14, 15, 63 and 48 SNPs for PFW, SFW, SDW and MCFS, respectively. Among these markers, 35 SNPs were repeatedly identified in all evaluated environments (2015, 2016, and the average across the two years), and most co-localized with yield-related QTLs identified in previous studies. AX-90496773 and AX-90460290 were large-effect markers for PFW and MCFS, respectively. The two markers were stably identified in all environments and tagged to linkage disequilibrium (LD) blocks. Six potential candidate genes were predicted in LD blocks; five of them showed significantly different expression levels between the extreme materials with large PFW or MCFS variation at the seed development stage. Therefore, the five genes Glyma.16g018200 , Glyma.16g018300 , Glyma.05g243400 , Glyma.05g244100 and Glyma.05g245300 were regarded as candidate genes associated with PFW and MCFS. Conclusion These results provide useful information for the development of functional markers and exploration of candidate genes in vegetable soybean high-yield breeding programs. Electronic supplementary material The online version of this article (10.1186/s12863-019-0737-9) contains supplementary material, which is available to authorized users.

Identification of QTNs and Their Candidate Genes for 100-Seed Weight in Soybean (Glycine max L.) Using Multi-Locus Genome-Wide Association Studies

“…As a result, six candidate genes were obtained in this study. Among the six candidate genes, Glyma05g34120 , Glyma06g10830 ( GmCRY1 ), and Glyma06g16920 ( GmCPK11 ) were found to be associated with soybean 100-SW, respectively, in Li et al [ 7 ], Du et al [ 37 ], and Aghamirzaie et al [ 66 ], and Glyma07g07850 , Glyma10g03440 , and Glyma10g36070 were new in soybean ( Table 5 ). These new 100-SW-related candidate genes are valuable in soybean molecular biology research.…”

“…Among them, eight were detected in one environment by at least three ML-GWAS methods, whereas three QTNs were detected by one ML-GWAS method in at least three environments/BLUP ( Table 3 and Table S8 ). The QTNs found across different environments are reliable, i.e., Zhou et al [ 8 ] repeatedly detected 31 QTNs associated with 100-SW in 185 soybean accessions in multiple environments, while Li et al [ 7 ] identified 35 QTNs associated with soybean yield traits in at least three environments. Likewise, the QTNs identified by multiple methods are also reliable when several multi-locus approaches are used to evaluate the same dataset [ 23 ].…”

“…As a result, forty-three QTNs exhibited significant differences of 100-SW between the two alleles ( Figures S1–S6 ), suggesting the reliability of QTNs identified in this study. More importantly, these SW increasing alleles can be utilized in molecular breeding [ 7 , 8 , 18 , 25 , 61 ].…”

“…After domestication, cultivated soybean exhibit diverse traits from wild soybean, and 100-SW for G. max is almost 6–7 fold greater than Glycine soja [ 4 , 5 , 6 ]. Seed weight (SW) is a quantitatively inherited trait and controlled by multiple genes, with various main and epistatic effects [ 2 , 7 , 8 , 9 ], and significantly influenced by the growing environmental conditions. Due to the quantitative nature, it is difficult to develop superior cultivars by traditional breeding.…”

“…Similarly, Gu et al [ 40 ] identified SoyWRKY15a as a candidate gene for seed size, and its orthologous genes GmWRKY15a ( G. max ) and GsWRKY15a ( G. soja ) were associated with seed weight. Five candidate genes, GmRGI-3 [ 41 ], Glyma06g43880 [ 42 ], Glyma02g41270 [ 43 ], Glyma05g34120 [ 7 ], and Glyma15g05650 [ 44 ] have been identified to be associated with seed development, lower seed yield, 100-SW, small seed, and seed development in soybean, respectively. Recently, gene GsCID1 ( Glysoja.04g010563 ) was identified to be associated with SW and highly expressed during seed developmental stages [ 30 ].…”