Genome-wide association analyses for revealing QTN, QTN-by-environment and QTN-by-QTN interactions in soybean phenology.

CONTEXT

Phenology plays an important role in determining the yield and environmental adaptation of soybean, but easily affected by quantitative trait nucleotides (QTN)-by-environment interactions (QEI) and QTN-by-QTN interactions (QQIs). Detailed understanding of the genetic basis and the interactions between genome and environments is critical for the development of cultivars with geographical-appropriate phenology.

METHODS

A compressed variance component mixed model (3VmrMLM) was used to detect QTNs, QEIs and QQIs for four key phenological traits of 345 soybean accessions. These traits include days from emergence to first flower (R1), pod beginning (R3), seed formation (R5) and maturity initiation (R7). Meanwhile, QTNs, QEIs and QQIs were identified in at least ten environments and Best Linear Unbiased Prediction (BLUP) value.

RESULTS

(i) A total of 110-193 QTNs, 10-31 QEIs and 4-8 QQIs were identified for each trait. (ii) Sixty-six genes involved in regulation of flower to maturity were identified by functional annotations of GO. (iii) Further haplotype analysis assigned soybean phenology-associated genes into 34 haplotype blocks with 136 haplotypes. (iv) Fifty-nine genes contained within 31 haplotype blocks can be considered as candidate genes for regulating soybean phenology, because changes in these haplotypes led to significant variations in the corresponding phenological traits.

CONCLUSIONS

Extensive genetic analysis of the QEIs and QQIs was conducted on key phenological stages in soybean. The candidate genes predicted provide valuable information for functional validation to elucidate the molecular mechanism underlying the soybean phenology.