Genetic diversity and population structure of cowpea [Vigna unguiculata (L.) Walp.] accessions from Togo using SSR markers

Abstract

Cowpea [Vigna unguiculata (L.) Walp.] is a crop with significant agronomic and nutritional value. In Togo, the crop is very appreciated by local people. It is the third food habit in Togo after maize and rice. However, several accessions of cowpea cultivated in Togo are now prone to extinction, creating a risk of genetic erosion. It is therefore urgent to assess the genetic diversity of accessions in order to set up a good conservation program. To achieve this, genetic diversity and phylogenetic relationships among 70 accessions of cowpea collected in the five (5) administrative regions of Togo were assessed using Simple Sequence Repeat (SSR) molecular markers. The twenty-eight SSR primers used in this study generated a total of 164 alleles with an average of 5.82 alleles per locus. Polymorphic Information Content (PIC) values ranged from 0.20 to 0.89 with an average value of 0.58. Population structure analysis using model-based revealed that the cowpea germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 98% of genetic variation existed among accessions within regions. The fixation index (Fst) value, which was 0.069 was low, indicating relatively low population differentiation. The phylogenetic analysis grouped the 70 accessions into two main groups that can be further divided into four groups independent of their origins. This study provides a foundation for a Togolese cowpea germplasm conservation program and can serve for the selection of parental material for further studies aimed at the genetic improvement of local germplasm.

Dissecting the Genetic Diversity of USDA Cowpea Germplasm Collection Using Kompetitive Allele Specific PCR-Single Nucleotide Polymorphism Markers

“…Analyzing genomes from multiple cowpea subpopulations helps to identify both core (conserved) and non-core (variable) genes potentially important for adaptation and breeding goals [ 8 ]. The diversity of global cowpea accessions has been reported by various researchers using DNA markers, including amplified fragment length polymorphism [ 9 , 10 , 11 ], random amplified polymorphic DNA [ 12 , 13 , 14 ], restriction fragment length polymorphism, simple sequence repeats [ 15 ], and inter-simple sequence repeats [ 16 ]. Lately, single nucleotide polymorphisms (SNP) have become the marker of choice to analyze the population structure in cowpea germplasm [ 17 , 18 ].…”

Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers

“…Liu et al analyzed the genetic diversity of 1481 individuals using SSR markers and SNP haplotypes [21]. In addition, SSR also plays an essential role in the study of the genetic diversity of cowpea [22], barley [23], beans [24,25], maize [26], and other crops. Therefore, it is feasible to screen specific SSR primers for genetic diversity analysis of Shanlan upland rice to explore its geographical origin.…”

Genetic variation, population structure, and marker-trait association of rice (Oryza sativa L.) cultivars using morphological characteristics and molecular markers

“…The most versatile crop rice is grown under various ecological conditions (Nath 2015). Genetic diversity is the degree to which heritable factors differs within accessions as a result of evolution and domestication (Dagnon et al 2022). Each of the individual rice genotypes has necessary traits, that could be subjugated for genetic enhancement; speci cally, wild cultivars may possess advantageous characteristics that have yet to be fully explored.…”