Abstract
BackgroundAs a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. To examine the genetic architecture of soybean growth periods, we performed a genome-wide association study (GWAS) using a panel of 278 soybean accessions and 34,710 single nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) higher than 0.04 detected by the specific-locus amplified fragment sequencing (SLAF-seq) with a 6.14-fold average sequencing depth. GWAS was conducted by a compressed mixed linear model (CMLM) involving in both relative kinship and population structure.ResultsGWAS revealed that 37 significant SNP peaks associated with soybean flowering time or other growth periods related traits including full bloom, beginning pod, full pod, beginning seed, and full seed in two or more environments at -log10(P) > 3.75 or -log10(P) > 4.44 were distributed on 14 chromosomes, including chromosome 1, 2, 3, 5, 6, 9, 11, 12, 13, 14, 15, 17, 18, 19. Fourteen SNPs were novel loci and 23 SNPs were located within known QTLs or 75 kb near the known SNPs. Five candidate genes (Glyma.05G101800, Glyma.11G140100, Glyma.11G142900, Glyma.19G099700, Glyma.19G100900) in a 90 kb genomic region of each side of four significant SNPs (Gm5_27111367, Gm11_10629613, Gm11_10950924, Gm19_34768458) based on the average LD decay were homologs of Arabidopsis flowering time genes of AT5G48385.1, AT3G46510.1, AT5G59780.3, AT1G28050.1, and AT3G26790.1. These genes encoding FRI (FRIGIDA), PUB13 (plant U-box 13), MYB59, CONSTANS, and FUS3 proteins respectively might play important roles in controlling soybean growth periods.ConclusionsThis study identified putative SNP markers associated with soybean growth period traits, which could be used for the marker-assisted selection of soybean growth period traits. Furthermore, the possible candidate genes involved in the control of soybean flowering time were predicted.
Highlights
As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean
A total of 200 diverse soybean accessions with different resistance to SCN HG Type 2.5.7 were genotyped by SLAF-seq for genome-wide association study (GWAS), and the results revealed 13 Single nucleotide polymorphisms (SNP) associated with resistance to SCN HG Type 2.5.7, and 30 candidate genes underlying SCN resistance were identified [30]
Our studies provided an insight into the genetic architecture of soybean growth periods and the identified candidate markers and genes would be valuable for the marker-assisted selection of soybean
Summary
As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. The complex growth period traits are controlled by both internal and external factors, which make great effects on crop adaptability, biomass and economic yield [2]. J was the dominant functional allele of GmELF3 [17] In addition to these major loci, many minor-effect quantitative traits loci (QTLs) related to soybean flowering time and maturity had been identified. Many other orthologs of Arabidopsis flowering genes such as GmCOLs [18], GmSOC1 [19], and GmCRY [20] had been identified Taken together, these results showed a complex genetic basis of flowering and maturity in soybean
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