Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population

Abstract

Flowering time and active accumulated temperature (AAT) are two key factors that limit the expanded production especially for soybean across different regions. Wild soybean provides an important germplasm for functional genomics study in cultivar soybean. However, the studies on genetic basis underlying flowering time in response to AAT especially in wild soybean were rarely reported. In this study, we used 294 wild soybean accessions derived from major soybean production region characterized by different AAT in Northeast of China. Based on genome-wide association study (GWAS), we identified 96 SNPs corresponded to 342 candidate genes that significantly associated with flowering time recorded in two-year experiments. Gene Ontology enrichment analysis suggests that the pathways of photosynthesis light reaction and actin filament binding were significantly enriched. We found three lead SNPs with -log10(p-value) > 32 across the two-year experiments, i.e., Chr02:9490318, Chr04:8545910 and Chr09:49553555. Linkage disequilibrium block analysis shows 28 candidate genes within the genomic region centered on the lead SNPs. Among them, expression levels of three genes (aspartic peptidase 1, serine/threonine-protein kinase and protein SCAR2-like) were significantly differed between two subgroups possessing contrasting flowering time distributed at chromosome 2, 4 and 9, respectively. There are 6, 7 and 3 haplotypes classified on the coding regions of the three genes, respectively. Collectively, accessions with late flowering time phenotype are typically derived from AAT zone 1, which is associated with the haplotypic distribution and expression levels of the three genes. This study provides an insight into a potential mechanism responsible for flowering time in response to AAT in wild soybean, which could promote the understanding of genetic basis for other major crops.

The Population Divergence and Genetic Basis of Local Adaptation of Wild Soybean (Glycine soja) in China

“…The broad geographic distribution and resilience to harsh environmental conditions suggest a wealth of adaptive genes within G. soja [ 9 , 11 ]. Numerous beneficial genes or genetic loci have been identified in G. soja resources, including those conferring abiotic resistance [ 18 , 19 , 20 , 21 ], biotic resistance [ 22 ], and adaptation to various environmental conditions [ 9 , 23 , 24 , 25 , 26 ].…”

“…A recent study suggests that the introgression from adapted sympatric wild soybeans facilitated the local adaptation of landraces during the expansion of cultivated soybean [ 17 ]. Numerous beneficial genes or genetic loci have been identified from G. soja resources, including those conferring abiotic resistance [ 18 , 19 , 20 , 21 ], biotic resistance [ 22 ], and adaptation to various environmental conditions [ 23 , 24 , 25 , 26 ]. Consequently, wild soybean represents a valuable gene reservoir for the genetic enhancement of cultivated soybeans, providing them with the capacity to adapt to new environments.…”

Genome-Wide Association Analysis of Active Accumulated Temperature versus Flowering Time in Soybean [Glycine max (L.) Merr.]

“…But there are few studies that focus on the adaptation to temperature changes. Yang et al identified three genes in 294 wild soybean accessions distributed at chromosomes 2, 4, and 9 that are associated with the pathways of photosynthesis light reaction and actin filament binding [11]. Zhu et al located a homolog of the vernalization pathway gene GmFRL1 in soybean [12].…”

Screening of Early Flowering Lotus (Nelumbo nucifera Gaertn.) Cultivars and Effects of Different Cultivars on Flowering Period

“…Chen [12] found that elevated soil temperature would lead to an increase in soil effective accumulated temperature, and the effective accumulated temperature was linearly related to the germination progress of Fraxinus chinensis. Major genetic loci related to flowering under accumulated temperature response were identified in soybean populations [13]. There are few reports studying the flowering period of lotus through accumulated temperature, but systematic studies are still lacking [14].…”