Genome-Wide Association Studies of Photosynthetic Traits Related to Phosphorus Efficiency in Soybean

Abstract

Photosynthesis is the basis of plant growth and development, and is seriously affected by low phosphorus (P) stress. However, few studies have reported for the genetic foundation of photosynthetic response to low P stress in soybean. To address this issue, 219 soybean accessions were genotyped by 292,035 high-quality single nucleotide polymorphisms (SNPs) and phenotyped under normal and low P conditions in 2015 and 2016. These datasets were used to identify quantitative trait nucleotides (QTNs) for photosynthesis-related traits using mrMLM, ISIS EM-BLASSO, pLARmEB, FASTmrMLM, FASTmrEMMA, and pKWmEB methods. As a result, 159 QTNs within 31 genomic regions were found to be associated with four photosynthesis-related traits under different P stress conditions. Among the 31 associated regions, five (q7-2, q8-1, q9, q13-1, and q20-2) were detected commonly under both normal and low P conditions, indicating the insensitivity of these candidate genes to low P stress; five were detected only under normal P condition, indicating the sensitivity of these candidate genes to low P stress; six were detected only under low P condition, indicating the tolerantness of these candidate genes to low P stress; 20 were reported in previous studies. Around the 159 QTNs, 52 candidate genes were mined. These results provide the important information for marker-assisted breeding in soybean and further reveal the basis for the application of P tolerance to photosynthetic capacity.

Keywords: QTNs; candidate gene; mrMLM; multi-locus GWAS; phosphorus efficiency; photosynthesis-related traits; soybean.

Figure 1

Histogram of the frequency distributions for the four photosynthesis-related traits in soybean under L/NP condition in 2015 and 2016.

Figure 2

Soybean chromosomes and QTLs for the studied traits under different P conditions. The outside/inside wheat-colored circle indicates the LOD/ r² value curve for the studied traits across environments. The outermost circle indicates the 20 soybean chromosomes; QTLs for the studied traits under different P conditions.