Genetic diversity and structure of Iberian Peninsula cowpeas compared to world-wide cowpea accessions using high density SNP markers

Abstract

BackgroundCowpea (Vigna unguiculata L. Walp) is an important legume crop due to its high protein content, adaptation to heat and drought and capacity to fix nitrogen. Europe has a deficit of cowpea production. Knowledge of genetic diversity among cowpea landraces is important for the preservation of local varieties and is the basis to obtain improved varieties. The aims of this study were to explore diversity and the genetic structure of a set of Iberian Peninsula cowpea accessions in comparison to a worldwide collection and to infer possible dispersion routes of cultivated cowpea.ResultsThe Illumina Cowpea iSelect Consortium Array containing 51,128 SNPs was used to genotype 96 cowpea accessions including 43 landraces and cultivars from the Iberian Peninsula, and 53 landraces collected worldwide. Four subpopulations were identified. Most Iberian Peninsula accessions clustered together with those from other southern European and northern African countries. Only one accession belonged to another subpopulation, while two accessions were ‘admixed’. A lower genetic diversity level was found in the Iberian Peninsula accessions compared to worldwide cowpeas.ConclusionsThe genetic analyses performed in this study brought some insights into worldwide genetic diversity and structure and possible dispersion routes of cultivated cowpea. Also, it provided an in-depth analysis of genetic diversity in Iberian Peninsula cowpeas that will help guide crossing strategies in breeding programs.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4295-0) contains supplementary material, which is available to authorized users.

Evaluating stress responses in cowpea under drought stress

“…Two Portuguese genotypes, a commercial variety (Cp5051) and a Northern landrace (Vg50), as well as two control genotypes with already described drought responses (Bambey 21 and CB46), were selected for this work. The two Portuguese genotypes were previously characterized using morphological and agronomical parameters (Carvalho et al, 2017a) and single nucleotide polymorphism (SNP) analysis through the Illumina Cowpea iSelect Consortium Array (Carvalho et al, 2017b). Both Portuguese genotypes were selected under different climatic conditions, being the Cp5051 selected under a hotter and dryer spring and summer (South Portugal) and Vg50 selected in a more temperate area (Northern Portugal).…”

The genome of cowpea (Vigna unguiculata [L.] Walp.)

“…A highly fragmented draft assembly and BAC sequence assemblies of IT97K‐499‐35 were previously generated (Muñoz‐Amatriaín et al ., ). Although these resources enabled progress on cowpea genetics (Yao et al ., ; Carvalho et al ., ; Misra et al ., ; Huynh et al ., ; Lo et al ., ), they lacked the contiguity and completeness required for accurate genome annotation, detailed investigation of candidate genes or thorough genome comparisons. Here, we re‐estimated the genome size of V. unguiculata and produced a genome assembly using single‐molecule real‐time sequencing combined with optical and genetic mapping.…”

The genome of cowpea (Vigna unguiculata[L.] Walp.)

“…A highly fragmented draft assembly and BAC sequence assemblies of IT97K-499-35 were previously generated . Although these resources enabled progress on cowpea genetics (Yao et al, 2016;Carvalho et al, 2017;Misra et al, 2017;Huynh et al, 2018;Lo et al, 2018), they lacked the contiguity and completeness required for accurate genome annotation, detailed investigation of candidate genes or thorough genome comparisons. Here, we re-estimated the genome size of V. unguiculata and produced a genome assembly using single-molecule real-time sequencing combined with optical and genetic mapping.…”