Genomic regions, cellular components and gene regulatory basis underlying pod length variations in cowpea (V. unguiculata L. Walp)

Abstract

SummaryCowpea (V. unguiculata L. Walp) is a climate resilient legume crop important for food security. Cultivated cowpea (V. unguiculata L) generally comprises the bushy, short‐podded grain cowpea dominant in Africa and the climbing, long‐podded vegetable cowpea popular in Asia. How selection has contributed to the diversification of the two types of cowpea remains largely unknown. In the current study, a novel genotyping assay for over 50 000 SNPs was employed to delineate genomic regions governing pod length. Major, minor and epistatic QTLs were identified through QTL mapping. Seventy‐two SNPs associated with pod length were detected by genome‐wide association studies (GWAS). Population stratification analysis revealed subdivision among a cowpea germplasm collection consisting of 299 accessions, which is consistent with pod length groups. Genomic scan for selective signals suggested that domestication of vegetable cowpea was accompanied by selection of multiple traits including pod length, while the further improvement process was featured by selection of pod length primarily. Pod growth kinetics assay demonstrated that more durable cell proliferation rather than cell elongation or enlargement was the main reason for longer pods. Transcriptomic analysis suggested the involvement of sugar, gibberellin and nutritional signalling in regulation of pod length. This study establishes the basis for map‐based cloning of pod length genes in cowpea and for marker‐assisted selection of this trait in breeding programmes.

Identification of genetic factors controlling domestication-related traits in cowpea (Vigna unguiculataL. Walp)

“…In subsp. sesquipedalis, QTL for DRTs including pod shattering, pod length and flower color have been also reported (Kongjaimun et al 2012;Suanum et al 2016;Xu et al 2011;Xu et al 2017). However, to date no candidate genes underlying domestication traits have been reported in cowpea.…”

SNP marker-based genetic mapping of rust resistance gene in the vegetable cowpea landrace ZN016

“…The genotypes of the 119 RILs were retrieved from Xu et al (2017), where 7,988 high quality SNP data were acquired by using the Cowpea iSelect Consortium Array which represents a publicly accessible resource for screening 51 128 SNPs. The Cowpea iSelect Consortium Array is available from Illumina (Illumina Inc., San Diego, CA, USA; http://www.illu mina.com/areas-of-interest/agrigenomics/ consortia.html).…”

The Genetic Driving Force for the Grain-Vegetable Cowpea Diversification: A Focus on the Pod Length

“…Lush et al also reported that duration of photosynthetic activity has increased after cowpea is domesticated [11]. Transcriptomic analysis suggests that sugar metabolism, gibberellin and nutritional signalling are involved in pod length regulation in cowpea [10].…”

“…QTL co-localization analysis has helped understanding the co-domestication of different traits, either favorable or unfavorable for vegetable use. For example, QTLs controlling pod number per pod and pod length are co-localized but in different directions in terms of effect [10][11][12], explaining the paradox of pod quality and yield that has long been faced by cowpea growers [13][14]. Co-localizations of QTLs governing pod tenderness and pod length were also reported, which well explained why cowpea varieties with longer pods are often more soft [15,16].…”

“…Through a genomic scan of population differentiation index (FST) and nucleotide diversity (π) between the two subgene pools, as well as between the landraces and cultivars/breeding lines of the long-podded subpopulation [10], serious loss of genetic diversity in the vegetable cowpea gene bank was found, leading to the conclusion that the domestication of yard-long bean was accompanied by selection of pod traits and other characters. Pod length then became the only primary trait being selected during further improvement of vegetable cowpea.…”