Identification of genetic loci and candidate genes related to soybean flowering through genome wide association study

Abstract

Background: As 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.

Results: GWAS 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.

Conclusions: This 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.

Keywords: Candidate genes; Genetic improvement; Genome wide association study; Soybean growth periods.

Fig. 1

Geographical distribution of 278 soybean germplasm resources. The map was made by the completely free software R [31] version 3.6.1 (https://mirrors.tuna.tsinghua.edu.cn/CRAN/)

Fig. 2

Single-nucleotide polymorphism for 278 soybean accessions. a Distribution of the SNP markers across 20 soybean chromosomes. b Minor allele frequency distribution of SNP alleles

Fig. 3

The linkage disequilibrium (LD), principal component and kinship analyses of soybean genetic data. a The estimated average linkage disequilibrium (LD) decay of soybean genome. The dashed line in blue indicated the position where r² was 0.5. b The first three principal components of 34,710 SNPs used in the GWAS indicated little population structure among 278 tested accessions. c The population structure of the soybean germplasm collection reflected by principal components. d The heat map of the kinship matrix of the 278 soybean accessions calculated from the same 34,710 SNPs used in the GWAS, suggesting low levels of relatedness among 278 individuals

Fig. 4

The positions of flowering time-related SNP loci on the chromosomes. The SNP loci associated with soybean flowering time and other growth periods in one or more environments were labeled black or blue, respectively. The soybean flowering candidate genes were then found in the linkage disequilibrium block of four SNP sites associated with soybean flowering found in multiple environments, which were marked red. The left number of each chromosome showed the relative in the genome, 1 = 100 kb

Fig. 5

Manhattan plot and LD block of Gm5_27111367 (Gm5_26143758~28,193,474), Gm11_10629613 (Gm11_9712686~11,611,890), Gm11_10950924 (Gm11_9745828~11,940,522) and Gm19_34768458 (Gm19_33680089~35,785,309). Black arrow indicated target SNPs. The up panel was the Manhattan plots of negative log₁₀-transformed P-values vs. SNPs, the significant (−log₁₀P > 3.75) or extremely significant (−log₁₀P > 4.44) threshold was denoted by the green or red line. The down panel was haplotype block based on pairwise linkage disequilibrium r² values. R1: Flowering time; R2: Full bloom; R3: Beginning pod; R4: Full pod; R5: Beginning seed; R6: Full seed. 2015 H: 2015 Harbin; 2016 H: 2016 Harbin; 2015 C: 2015 Changchun; 2016 C: 2016 Changchun; 2015 S: 2015 Shenyang; 2016 S: 2016 Shenyang

Fig. 6

Phenotypic statistics for soybeans carrying two alleles of four SNPs in six environments. The box plot showed the differences in flowering time of the varieties carrying two alleles of different SNPs, the major and minor alleles of significant loci was marked by green and blue, respectively. R1: Flowering time; R2: Full bloom; R3: Beginning pod; R4: Full pod; R5: Beginning seed; R6: Full seed. 2015 H: 2015 Harbin; 2016 H: 2016 Harbin; 2015 C: 2015 Changchun; 2016 C: 2016 Changchun; 2015 S: 2015 Shenyang; 2016 S: 2016 Shenyang. ^* and ^** indicated that the threshold value -log₁₀P were greater than 3.75 and 4.44, respectively