Abstract
The time to flowering (DF), pod beginning (DPB), seed formation (DSF), and maturity initiation (DMI) in soybean (Glycine max [L.] Merr) are important characteristics of growth stage traits (GSTs) in Chinese summer-sowing soybean, and are influenced by genetic as well as environmental factors. To better understand the molecular mechanism underlying the initiation times of GSTs, we investigated four GSTs of 309 diverse soybean accessions in six different environments and Best Linear Unbiased Prediction values. Furthermore, the genome-wide association study was conducted by a Fixed and random model Circulating Probability Unification method using over 60,000 single nucleotide polymorphism (SNP) markers to identify the significant quantitative trait nucleotide (QTN) regions with phenotypic data. As a result, 212 SNPs within 102 QTN regions were associated with four GSTs. Of which, eight stable regions were repeatedly detected in least three datasets for one GST. Interestingly, half of the QTN regions overlapped with previously reported quantitative trait loci or well-known soybean growth period genes. The hotspots associated with all GSTs were concentrated on chromosome 10. E2 (Glyma10g36600), a gene with a known function in regulating flowering and maturity in soybean, is also found on this chromosome. Thus, this genomic region may account for the strong correlation among the four GSTs. All the significant SNPs in the remaining 7 QTN regions could cause the significant phenotypic variation with both the major and minor alleles. Two hundred and seventy-five genes in soybean and their homologs in Arabidopsis were screened within ± 500 kb of 7 peak SNPs in the corresponding QTN regions. Most of the genes are involved in flowering, response to auxin stimulus, or regulation of seed germination, among others. The findings reported here provide an insight for genetic improvement which will aid in breeding of soybean cultivars that can be adapted to the various summer sowing areas in China and beyond.
Highlights
Soybean (Glycine max [L.] Merr.) is a versatile crop with numerous nutritional qualities and uses
We evaluated 309 diverse soybean accessions across six different agricultural experimental environments to record four growth stage traits (GSTs) [i.e., days to flowering (DF), pod beginning (DPB), seed formation (DSF), and maturity initiation (DMI)], conducted a Fixed and random model Circulating Probability Unification (FarmCPU) genome-wide association study (GWAS) with individual environment and best linear unbiased prediction (BLUP) values by utilizing 61,174 single nucleotide polymorphism (SNP) markers to identify quantitative trait nucleotide (QTN) regions
We evaluated 309 diverse soybean breeding lines across five different environments for four GSTs (DF, DPB, DSF, and DMI), and applied a FarmCPU GWAS with high-density SNPs (>61 k)
Summary
Soybean (Glycine max [L.] Merr.) is a versatile crop with numerous nutritional qualities and uses. Several loci/genes have been reported to regulate flowering in soybean, prominent among them include the E-series (E1–11) (Bernard, 1971; Buzzell and Voldeng, 1980; Mcblain and Bernard, 1987; Kang and Kim, 1996; Bonato and Vello, 1999; Molnar et al, 2003; Watanabe et al, 2009; Cober et al, 2010; Kong et al, 2014; Samanfar et al, 2017; Wang et al, 2019), J (Ray et al, 1995), Dt1 (Liu et al, 2008), and Dt2 (Zhang D. et al, 2019). The dominant alleles tend to delay flowering time and maturity, but the magnitude of effect of each gene can be different
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