Additional file 3 of The effects and interaction of soybean maturity gene alleles controlling flowering time, maturity, and adaptation in tropical environments

Additional file 3. ANOVA tables for DTF, DTM, and yield for all RILS. Three ANOVA for agronomic traits of interest

Additional file 1 of The effects and interaction of soybean maturity gene alleles controlling flowering time, maturity, and adaptation in tropical environments

Additional file 1. Recombinant inbred line population development. A generation by generation plan of plants for all five RIL populations used in this study

Additional file 2 of The effects and interaction of soybean maturity gene alleles controlling flowering time, maturity, and adaptation in tropical environments

Additional file 2 Data for RILS in all populations. Data for RILs including population name, experimental name, 2 yr mean DTF and DTM, genotype for E1, E2, E3, Dt1, J

S1 File -

The ability of soybean [Glycine max (L.) Merr.] to adapt to different latitudes is attributed to genetic variation in major E genes and quantitative trait loci (QTLs) determining flowering time (R1), maturity (R8), and reproductive length (RL). Fully revealing the genetic basis of R1, R8, and RL in soybeans is necessary to enhance genetic gains in soybean yield improvement. Here, we performed a genome-wide association analysis (GWA) with 31,689 single nucleotide polymorphisms (SNPs) to detect novel loci for R1, R8, and RL using a soybean panel of 329 accessions with the same genotype for three major E genes (e1-as/E2/E3). The studied accessions were grown in nine environments and observed for R1, R8 and RL in all environments. This study identified two stable peaks on Chr 4, simultaneously controlling R8 and RL. In addition, we identified a third peak on Chr 10 controlling R1. Association peaks overlap with previously reported QTLs for R1, R8, and RL. Considering the alternative alleles, significant SNPs caused RL to be two days shorter, R1 two days later and R8 two days earlier, respectively. We identified association peaks acting independently over R1 and R8, suggesting that trait-specific minor effect loci are also involved in controlling R1 and R8. From the 111 genes highly associated with the three peaks detected in this study, we selected six candidate genes as the most likely cause of R1, R8, and RL variation. High correspondence was observed between a modifying variant SNP at position 04:39294836 in GmFulb and an association peak on Chr 4. Further studies using map-based cloning and fine mapping are necessary to elucidate the role of the candidates we identified for soybean maturity and adaptation to different latitudes and to be effectively used in the marker-assisted breeding of cultivars with optimal yield-related traits.</div

Manhattan plots of GWAS for flowering time (R1), maturity time (R8), and reproductive length (RL) in three hundred twenty-nine <i>G</i>. <i>max</i> accessions.

GWAS results correspond to the analysis across the nine environments. The horizontal dashed lines indicate the statistically significant cut-off of–log (p-value) = 4.16. Significant SNPs IDs correspond to the Wm82.a1.</p

Additional file 4 of The effects and interaction of soybean maturity gene alleles controlling flowering time, maturity, and adaptation in tropical environments

Additional file 4 Histograms of agronomic traits from five RIL populations. Number of RILs is on the y-axis and days is shown on the x-axis. Data for parents of each population are shown with an arrow with the first letter of the parent name to the right. a: Days to Flower of Jake-15 b: Days to Flower of Jake-Pa c: Days to Maturity of Jake-15 d: Days to Maturity Jake-Pa. a-d: Both populations were selected for the long juvenile trait. e: Days to Flower of X97–15 f: Days to Flower of X97-Jen g: Days to Maturity of X97–15 h: Days to Maturity of X97-Jen e-h: Both populations were segregating for E1/e1-as and different alleles of J/j. i: Days to Flower of 534-Can j: Days to Maturity of 534-Can. i-j: This population was segregating to E1/e1-as, E2/e2, E3,e3 or J/j-x

Summary of single-nucleotide polymorphisms (SNPs) significantly associated with flowering time (R1), maturity time (R8), and reproductive length (RL) in three hundred twenty-nine <i>G</i>. <i>max</i> accessions across environments and years.

Summary of single-nucleotide polymorphisms (SNPs) significantly associated with flowering time (R1), maturity time (R8), and reproductive length (RL) in three hundred twenty-nine G. max accessions across environments and years.</p

Planting dates of experimental environments.

The ability of soybean [Glycine max (L.) Merr.] to adapt to different latitudes is attributed to genetic variation in major E genes and quantitative trait loci (QTLs) determining flowering time (R1), maturity (R8), and reproductive length (RL). Fully revealing the genetic basis of R1, R8, and RL in soybeans is necessary to enhance genetic gains in soybean yield improvement. Here, we performed a genome-wide association analysis (GWA) with 31,689 single nucleotide polymorphisms (SNPs) to detect novel loci for R1, R8, and RL using a soybean panel of 329 accessions with the same genotype for three major E genes (e1-as/E2/E3). The studied accessions were grown in nine environments and observed for R1, R8 and RL in all environments. This study identified two stable peaks on Chr 4, simultaneously controlling R8 and RL. In addition, we identified a third peak on Chr 10 controlling R1. Association peaks overlap with previously reported QTLs for R1, R8, and RL. Considering the alternative alleles, significant SNPs caused RL to be two days shorter, R1 two days later and R8 two days earlier, respectively. We identified association peaks acting independently over R1 and R8, suggesting that trait-specific minor effect loci are also involved in controlling R1 and R8. From the 111 genes highly associated with the three peaks detected in this study, we selected six candidate genes as the most likely cause of R1, R8, and RL variation. High correspondence was observed between a modifying variant SNP at position 04:39294836 in GmFulb and an association peak on Chr 4. Further studies using map-based cloning and fine mapping are necessary to elucidate the role of the candidates we identified for soybean maturity and adaptation to different latitudes and to be effectively used in the marker-assisted breeding of cultivars with optimal yield-related traits.</div

Descriptive statistics of phenotypic variation, genotypic variance (G) and broad-sense heritability (H²) of days to flowering (R1), days to maturity (R8), and reproductive length for 329 <i>G</i>. max USDA accessions evaluated at nine environments.

Descriptive statistics of phenotypic variation, genotypic variance (G) and broad-sense heritability (H2) of days to flowering (R1), days to maturity (R8), and reproductive length for 329 G. max USDA accessions evaluated at nine environments.</p

List of potential candidate genes by tagging SNPs with average accuracy and descriptions for flowering time (R1), maturity time (R8), and reproductive length (RL).

List of potential candidate genes by tagging SNPs with average accuracy and descriptions for flowering time (R1), maturity time (R8), and reproductive length (RL).</p