Construction of a High-Density Genetic Map and Its Application for QTL Mapping of Leaflet Shapes in Mung Bean (Vigna radiata L.)

Abstract

Mung bean ( Vigna radiata L.) is an important but understudied food legume in Asia and now worldwide. Genetic studies may help to accelerate the exploitation of new genes for breeding in this crop. Here, we used a recombination inbred line population to construct an SNP genetic linkage map by genome sequencing technology. We obtained 21,508 high-quality SNP markers integrated into 1,946 bin markers that were mapped onto 11 linkage groups (LGs) with 99–258 bin markers per LG. The total genetic length of the map was 1060.2 cM (38.76–168.03 cM per LG), with an average distance between markers of 0.54 cM. However, there were 18 gaps >5 cM, distribution on LG1, 3, 5, 7, and 9. Gene mapping for lobed and indented leaflets was conducted using the map. A major quantitative trait locus (QTL) associated with indented leaflets was detected on chromosome 10, with phenotypic variation explained (PVE) values of 39.7% and 45.4% under two different environments. Several QTLs for lobed leaflets were detected and most of them were tightly linked together on Chromosome 3. However, only one major QTL, which explained the largest phenotypic variation (27.7–69.5%), was stably detected under two different environments using both R and Q methods. In the two main stable QTLs regions on chromosomes 3 and 10, candidate genes for regulating the molecular mechanism of different leaflet shapes were detected by functional annotation. The overlap of major QTLs under different environments indicated that the present map would be good enough for precisely mapping genes, and both the QTL analysis and gene prediction were useful for investigating the mechanism of leaf development in mung bean or legumes.

Construction of a high-density genetic linkage map and QTL mapping for bioenergy-related traits in sweet sorghum [Sorghum bicolor (L.) Moench]

“…We discovered 1438 SNP markers dispersed over 10 LGs (Figure 1), perfectly matching the number of chromosomes in S. bicolor (n = 10), demonstrating the power of the method. Despite the average interval distance being sufficient for precise mapping (Wang et al, 2020b), there were a few> 10 cM gaps in our map, especially on LG7 (Figure 1). Such gaps are occasionally observed in linkage maps in cases such as the mapping population being generated from two parents whose genetic backgrounds are similar in some regions, or due to divergence from the reference genome (Wang et al, 2020b).…”

“…Despite the average interval distance being sufficient for precise mapping (Wang et al, 2020b), there were a few> 10 cM gaps in our map, especially on LG7 (Figure 1). Such gaps are occasionally observed in linkage maps in cases such as the mapping population being generated from two parents whose genetic backgrounds are similar in some regions, or due to divergence from the reference genome (Wang et al, 2020b). The 2021), who developed genetic maps for sorghum with GBS, which were similar in length (1368.8 cM) but with greater variance in SNP distribution across the…”

Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era

“…Several genetic maps of mungbean based on SSR markers have been developed ( Bohra et al, 2014 ). Later, a genetic map measuring 1,060.2 cM was developed from an intraspecific mapping population ( Wang et al, 2020 ) and a denser genetic map with 1,291.7 cM and harboring 538 SNPs was developed from an interspecific mapping population derived from Vigna radiata × V. umbellate cross ( Mathivathana et al, 2019 ) ( Table 4 ).…”