Identification of Candidate Genes Controlling Black Seed Coat and Pod Tip Color in Cowpea (Vigna unguiculata[L.] Walp)

Abstract

Seed coat color is an important part of consumer preferences for cowpea (Vigna unguiculata [L.] Walp). Color has been studied in numerous crop species and has often been linked to loci controlling the anthocyanin biosynthesis pathway. This study makes use of available resources, including mapping populations, a reference genome, and a high-density single nucleotide polymorphism genotyping platform, to map the black seed coat and purple pod tip color traits, with the gene symbol Bl, in cowpea. Several gene models encoding MYB domain protein 113 were identified as candidate genes. MYB domain proteins have been shown in other species to control expression of genes encoding enzymes for the final steps in the anthocyanin biosynthesis pathway. PCR analysis indicated that a presence/absence variation of one or more MYB113 genes may control the presence or absence of black pigment. A PCR marker has been developed for the MYB113 gene Vigun05g039500, a candidate gene for black seed coat color in cowpea.

Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers

“…cooking time) and farmers deliberately select white seed types, which have shorter cooking time [33]. The inheritance of seed coat colour is governed by few major genes that will enhance selection progress during cultivar development [34]. In this study, the genotypes Bubebe and Msandile, with predominantly light-green leaves exhibited determinate growth habit in comparison with BBXSC13 and Chimponongo that had dark green leaves and creeping growth habit.…”

Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.)

“…According to this analysis, Sanzi proceeds through to complete all five stages of seed coat development, indicating that the speckling pattern is controlled separately. A biparental RIL population, consisting of lines derived from a cross between Sanzi and Vita 7, which has a brown colored seed with a Full Coat, which was used for mapping the black seed coat color, showed a perfect correlation between black seed coat color and the speckling pattern (Herniter et al 2018). This indicates that the speckling pattern is colocalized with black seed coat color and is likely an allele at the B locus.…”

“…In the biparental RIL populations the R packages "qtl" (Broman et al 2003) and "snow" (Tierney et al 2015) were used as in Herniter et al (2018). In short, probability values were assigned to each SNP using a Haley-Knott regression, tested for significance with 1000 permutations, and marker effects were determined using a hidden Markov model.…”

“…A genotyping array for 51,128 single nucleotide polymorphisms (SNP) was recently developed for cowpea (Muñoz-Amatriaín et al 2017), which offers opportunities to improve the precision of genetic mapping of traits. Numerous biparental populations have been used to map major quantitative trait loci (QTL) for various traits, including heat tolerance (Lucas et al 2013), leaf shape (Pottorff et al 2012), and black seed coat color (Herniter et al 2018) and to develop consensus genetic maps of cowpea (Lucas, Diop, and Wanamaker 2011;Muchero et al 2009;Muñoz-Amatriaín et al 2017). In addition, new populations have been developed for higherresolution mapping including a minicore containing 367 diverse accessions (Muñoz-Amatriaín, unpublished) and an 8-Parent Multi-parent Advanced Generation InterCross (MAGIC) population containing 305 lines .…”

Modernising breeding for orphan crops: tools, methodologies, and beyond

“…The African Orphan Crops Consortium (AOCC, http://afric anorp hancr ops.org/), for instance, is working on sequencing 101 traditional African food crops, adding to the list of more than 700 plant species that have already been sequenced according to the US National Center for Biotechnology Information (NCBI, https ://www.ncbi.nlm.nih.gov/genom e/). The increasing number of diversity panels of orphan crops that have been genotyped using next-generation sequencing (NGS) or highdensity SNP arrays opens new perspectives on unlocking these challenging breeding traits through genome-wide association studies (Upadhyaya 2015;Xu et al 2017;Zhang et al 2018) or high resolution mapping in multi-parent advanced generation intercross (MAGIC) populations (Herniter et al 2018;Ongom and Ejeta 2018).…”