Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata[L.] Walp)

Abstract

Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 367 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

Phenotypic diversity for phenological and agronomic traits in the UC‐Riverside cowpea (Vigna unguiculata L. Walp) mini‐core collection

“…The presence of large genetic variation provides options for breeding and selection of cowpea for useful traits (Gerrano et al., 2015). The high H 2 estimates for DTF suggest that the expression of this trait is mostly controlled by genetic factors (Manggoel, 2012; Veeckman et al., 2016), making it an amenable trait for quantitative trait loci and genome‐wide association studies to map candidate genes controlling this trait (Paudel et al., 2021). The H 2 estimate obtained for DTF was within the range of the values found in previous studies of cowpea (.50 < H 2 < .96; Omoigui et al., 2006; Shimelis & Shiringani, 2010; Manggoel, 2012; Gerrano et al., 2015).…”

“…Cowpea improvement for multipurpose use requires accurate phenotyping for several morphological, physiological, and agronomic traits, such as plant height, days to flowering, days to pod maturity, pods per plant, seeds per pod, dry biomass yield, and grain yield. In addition, harvest index (HI = grain biomass/total shoot biomass) is a key trait in dual‐purpose cultivars (Omokanye et al., 2003; Anele, 2011; Ayan & Mut, 2012; Ali & Dov, 2017). The estimation of variance components and genetic parameters (i.e., heritability, genotypic values, correlation among traits, genotype × environment interactions, etc.)…”

“…This information benefits plant breeders when selecting plant introductions with useful traits for introduction into breeding programs and for designing genetic improvement for specific traits. Previous research showed that broad‐sense heritability ( H 2 ) estimated for days to flowering ranged from .53 to .95 (Omoigui et al., 2006; Shimelis & Shiringani, 2010; Gerrano et al., 2015; Aliyu & Makinde, 2016; Paudel et al., 2021). Similarly, H 2 for days to pod maturity ranged from .66 to .84 (Omoigui et al., 2006; Shimelis & Shiringani, 2010; Yu et al., 2016) and H 2 for HI ranged from .09 to .60 (Moalafi et al., 2010; Gerrano et al., 2015).…”

Morpho-physiological and biochemical characterization of African spider plant (Gynandropsis gynandra (L.) Briq.) genotypes under drought and non-drought conditions

“…Drought, in particular, reduces a plant's life cycle and duration of flowering. The flowering period shortens under drought conditions due to increased leaf senescence, reduced photosynthetic activity, and sink limitation (Fang and Xiong, 2015;Shavrukov et al, 2017;Paudel et al, 2021). Moreover, the relatively short flowering period has a direct impact on leaf number and leaf size, which accounts for a large portion of the decrease in African spider plant yield.…”