Abstract
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 (QQI). 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 QTN, QEI and QQI 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, QTN, QEI and QQI were identified in at least ten environments and Best Linear Unbiased Prediction (BLUP) value.
Results: (i). A total of 110-193 QTN, 10-31 QEI and 4-8 QQI were identified for each trait. (ii). 40 regions were then divided based on the linkage disequilibrium distance as 500 kb around the above site. (iii). Further differential expression analysis and functional enrichment analysis were finished in 2339 genes and identified 40 genes involved in biological pathways such as flowering and seed maturation. (iv). Haplotype difference analysis revealed that Glyma.02g152200, Glyma.02g152800 and Glyma.02g155200are possibly associated with phenology around a QQI, and Glyma.17g212700 may be useful around a QEI for flowering time to maturity.
Conclusions: Extensive genetic analysis of the QTN-QTN with QTN-environment interaction 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.