Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean

Authors: CHITERI, KEVIN - Iowa State University; RAIRDIN, ASHLYN - Iowa State University; SANDU, KULBIR - Agriculture And Agri-Food Canada; REDSUN, SVEN - National Center For Genome Resources; FARMER, ANDREW - National Center For Genome Research; O`Rourke, Jamie; Cannon, Steven; SINGH, ARTI - Iowa State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/22/2024
Publication Date: 3/12/2024
Citation: Chiteri, K.O., Rairdin, A., Sandu, K., Redsun, S., Farmer, A., O'Rourke, J.A., Cannon, S.B., Singh, A. 2024. Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean. BMC Genomics. 25. Article 270. https://doi.org/10.1186/s12864-024-10156-x.
DOI: https://doi.org/10.1186/s12864-024-10156-x

Interpretive Summary: Controlling flowering time is crucial to optimize plant growth in crops. Plants that mature (flower) too early or too late exhibit reduced yield. Mung bean (Vigna radiata (L.) Wilczek) is an important crop world-wide and is gaining popularity in the US, but relatively little is known about the genetics of this species. To investigate the genetics underlying flowering time in mung bean, 482 diverse accessions were grown in Boone, Iowa over two years with the onset of flowering noted for each accession. These data, coupled with genetic markers were used to conduct a genome wide association study examining days to flowering. The results of this study identified two markers that account for 25% of the phenotypic variance. Using bioinformatics, the orthologs of genes known to be important in flowering in soybean were identified in mung bean. One, E3, which can delay flowering and maturity, was identified in a region associated with a significant marker, indicating it's likely also important for mung bean flowering time. In the second region, 13 copies of FERONIA, a gene that directly regulates flowering time in Arabidopsis, were identified. Four other genes, including phytochrome A and phytochrome interacting factor 3, that are known to be important in regulating flowering time in Arabidopsis were also identified. This study highlights the utility of comparative genomics to identify important candidate genes in species with limited genetic and experimental resources.

Technical Abstract: Mung bean (Vigna radiata (L.) Wilczek), is an important pulse crop in the global south. Early flowering and maturation are advantageous traits for northern and southern latitudes. This study investigates the genetic basis of the Days-to-Flowering trait (DTF) in mung bean, combining genome-wide association studies (GWAS) in mung bean and comparisons with orthologous genes involved with control of DTF responses in soybean (Glycine max (L) Merr and Arabidopsis (Arabidopsis thaliana). The most significant associations for DTF were on mung bean chromosomes 1, 2, and 4. Only the SNPs on chromosomes 1 and 4 were heavily investigated using downstream analysis. The chromosome 1 DTF association is tightly linked with a cluster of locally duplicated FERONIA (FER) receptor-like protein kinase genes, and the SNP occurs within one of the FERONIA genes. In Arabidopsis, an orthologous FERONIA gene has been reported to regulate the expression of the FLOWERING LOCUS C (FLC). For the chromosome 4 DTF locus, the strongest candidates are Vradi04g00002773 and Vradi04g00002778, orthologous to the Arabidopsis PhyA and PIF3 genes, encoding phytochrome A (a photoreceptor protein sensitive to red to far-red light) and phytochrome-interacting factor 3, respectively. The soybean PhyA orthologs include the classical loci E3 and E4 (genes GmPhyA3 and GmPhyA2). The mung bean PhyA ortholog has been previously reported as a candidate for DTF in studies conducted in South Korea (Ha et al., 2021).The top two identified SNPs accounted for a significant proportion (~65%) of the phenotypic variability in mung bean DTF by the six significant SNPs (39.61%), with a broad-sense heritability of 0.93. The strong associations of DTF with genes that have orthologs with analogous functions in soybean and Arabidopsis provide strong circumstantial evidence that these genes are causal for this trait. The three reported loci and candidate genes provide useful targets for marker-assisted breeding in mung beans.