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

Abstract

Background Productivity of cowpea [Vigna unguiculata (L.) Walp] in sub-Sahara Africa is curtailed by a lack of farmer-preferred and improved cultivars and modern production technologies. The objectives of the study were to determine the extent of genetic diversity present among a collection of cowpea accessions from Zambia and Malawi using phenotypic traits and single nucleotide polymorphism (SNP) markers and, to select distinct and complementary parental lines for cultivar development. One hundred cowpea genotypes were evaluated for agronomic traits in two selected sites in Zambia, using a 10 × 10 alpha lattice design with two replications. Ninety-four of the test genotypes were profiled with 14,116 SNP markers. Results Number of pods plant− 1 (NPP), pod length (PDL), and number of seeds pod− 1 (NSP), were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes such as CP411, CP421, CP645, CP732, Chimponongo, and MS1–8–1-4 exhibited higher grain yield of > 1200 kg/ha with excellent performance in yield components such as NSP, PDL, HSW and GYD. Grain yield had significant (p < 0.05) associations with NPP (r = 0.50), NSP (r = 0.46) and PDL (r = 0.42) useful for simultaneous selection for yield improvement in cowpea. The SNP markers revealed gene diversity and polymorphic information content of 0.22 and 0.17, respectively, showing that the tested cowpea accessions were genetically diverse. Test genotypes were classified into four genetic groups irrespective of source of collection allowing selection and subsequent crosses to develop breeding populations for cultivar development. Conclusions Genotypes Bubebe, CP411, CP421, CP645, Chimponogo and MS1–8–1-4 were identified to be the most genetically divergent and high yielding making them ideal parental lines for breeding. This study provided a baseline information and identified promising cowpea genetic resources for effective breeding and systematic conservation.

Genetic Diversity and Primary Core Collection Construction of Turnip (Brassica rapa L. ssp. rapifera Matzg) Landraces in Tibet Revealed via Morphological and SSR Markers

“…The clustering maps estimated from 58 morphological traits and 31 SSR markers demonstrated discordance to a certain extent. This was confirmed by the results exhibited by the Mantel test, consistent with earlier studies on other vegetable species [17,45]. Unexpectedly, 31 genetic and 58 morphological markers both showed a moderate-quality clustering, which indicates they were not identifying the varieties well separately.…”

Molecular Fingerprinting and Hybridity Authentication in Cowpea Using Single Nucleotide Polymorphism Based Kompetitive Allele-Specific PCR Assay

“…We continued to assemble SNP fingerprints of parental lines and used them to dissect the genetic relationships among parents and the F 1 progenies to discern which crosses benefited from maximum diversity between the parents. Analysis of genetic relatedness among plant germplasm plays a key role in plant breeding as it allows effective characterization of parental lines for hybridization (Govindaraj et al, 2015;Mafakheri et al, 2017;Khanna, 2018;Nkhoma et al, 2020). In the present study, genetic similarity analysis placed the parental lines into three groups, with a modest amount of variation still detectable within the groups.…”

“…This process is lengthy and costly, yet the eventual creation of the intended variation through hybridization and the ability to further study the genetics of cowpea cultivar development requires validity of the initial cross. First, the parents of a cross should not be genetically similar in order to maximize the diversity for selection and improvement (Mafakheri et al, 2017;Nkhoma et al, 2020). It is therefore advantageous to fingerprint parental lines and assess relatedness prior to hybridization.…”

Genetic variability, heritability and correlation analysis among maturity and yield traits in Cowpea (Vigna unguiculata (L) Walp) in Northern Ghana

“…On the other hand, SARI-2-2-1 and SARI-5-5-5 used 62.56 ± 2.18 and 59.78 ± 4.96 days to reach DNPM, respectively, compared with Songotra (64.67 ± 0.07) ( Table 5 ). Early maturity is precursor for drought escape, thus cultivars with a short flowering period and maturity are mostly preferred by farmers ( Nkhoma et al., 2020 ).…”