Abstract
African yam bean, AYB (Sphenostylisstenocarpa), is an underutilized legume of tropical Africa. AYB can boost food and nutritional security in sub-Saharan Africa through its nutrient-rich seeds and tubers. However, inadequate information on germplasm with desirable agro-morphological traits, including insufficient data at the genomic level, has prevented the full exploitation of its food and breeding potentials. Notably, assessing the genetic diversity and population structure in a species is a prerequisite for improvement and eventual successful exploitation. The present study evaluated the population structure and genetic diversity of 169 accessions from the International Institute of Tropical Agriculture (IITA) collection using 26 phenotypic characters and 1789 single nucleotide polymorphism (SNP) markers. The phenotypic traits and SNP markers revealed their usefulness in uniquely distinguishing each AYB accession. The hierarchical cluster of phenotypes grouped accessions into three sub-populations; SNPs analysis also clustered the accessions into three sub-populations. The genetic differentiation (FST) among the three sub-populations was sufficiently high (0.14–0.39) and significant at P = 0.001. The combined analysis revealed three sub-populations; accessions in sub-population 1 were high yielding, members in sub-population 2 showed high polymorphic loci and heterozygosity. This study provides essential information for the breeding and genetic improvement of AYB.
Highlights
PC2 accounted for 13.63% of the total variation of which two quantitative traits; dry seed matter, seed moisture content, and four qualitative traits; mainstem pigmentation (MASPIG), branch pigmentation (BRAPIG), petiole pigmentation (PETPIG), and seed color, contributed most to the observed variation
Phenotypic and molecular methods are widely explored for genetic study in plant s pecies[18,37], neither of the methods is superior to the o ther[29]
Previous characterization studies in AYB likewise reported the relevance of phenotypic traits in understanding genetic diversity in the crop[17,32]
Summary
Characterization at the phenotypic and genotypic levels is reportedly the most widely used in accessing variations in plant s tudies[15,16]. The science of plant breeding centers on identifying and utilizing genetic variation[21], tracking potential DNA markers and regions associated with traits of interest[27,28]. As no single characterization approach is superior to the other[29] and no method has been identified to be sufficient for evaluating every aspect of a species[30], characterization based on phenotypic traits and genotypic data can be used both independently or to complement one a nother[31]. A preliminary study using the DArTseq approach in identifying a few SNPs in AYB was recently reported[36]. No report is available on high throughput sequencing data for genetic diversity and population structure analysis in the crop
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