Agronomic and molecular characterisation of cowpea (Vigna unguiculata) populations from the Northern Thailand

Abstract

Cowpea (Vigna unguiculata [L.] Walp.) is a globally significant annual herbaceous legume, cultivated for its seed grains, vegetable leaves, animal fodder, cover crop and green fertilizer. Despite its hardiness and adaptability to various conditions, including drought and low soil pH, cowpea’s genetic base is narrow due to a bottleneck event during domestication. This self-pollinating plant causes low genetic heterozygosity and high inbreeding. Breeders can create new cowpea varieties by integrating genes from wild cowpea, making the conservation of cowpea’s genetic constitution vital for future breeding programs. Molecular characterisation markers, such as Start Codon Targeted (SCoT), offer more effective genetic characterisation than traditional methods, unaffected by environmental influences or plant growth phases. These genetic resources form the basis of food security and sustainable agricultural development, providing options for developing resistant, productive crops. Therefore, we would like to see the morphologies and agronomical characteristics within and between populations of cowpea, at the same time analyses the seed quality content and the genetic diversity in molecular level using SCoT markers. This research was carried out using twenty-one cowpea accessions sampled from provinces of Northern Thailand, particularly from Chiang Mai, Nan, Phrae, and Tak. One commercial variety of cowpea was added and used as a control. Three experiments were set up to characterize the plants, evaluate the quality of the seeds, and analyse the genetic structure of the collected cowpea accessions to understand the diversity within and among the populations. The research began by identifying the morphologies and the agronomical characteristics of the cowpea accessions. These were done by growing all twenty-one of the cowpea accessions with one commercial cowpea variety as a control in an open field. The evaluations were done using 31 parameters where 17 were qualitative characteristics and 14 quantitative characteristics. Most of the characteristics; seed eye pattern, seed eye colour, growth vigor, growth habit, twinning, terminal leaflet shape, leaflet colour, leaflet texture, flower colour, raceme position, fresh pod colour, dry pod color, were monomorphic within populations of the cowpea accessions. However, polymorphism within the populations was present, particularly in the seeds which are seed shape, seed colour, seed texture, and seed pattern distribution. Diversity among the populations in the plant characteristics can be observed by comparison between provinces. Diversity was discovered highest in Tak (6.035) and lowest in Phrae (0.7931). Chiang Mai and Nan have almost the same diversities, 4.548 and 4.360 respectively. The agronomical characteristics: plant canopy height, plant canopy width, terminal leaflet length, leaflet width, stem girth, number of branches, days to 50% flowering, number of racemes, pod length and pod width, seed dimensions (length x width x thickness), hundred seed weight among the populations were all significantly different statistically. The principal component analysis captures 44.64% of the agronomic characters which are mainly driven by seed length, hundred seed weight, seed thickness, terminal leaflet width, terminal leaflet length, and pod width. The yield of the harvested cowpea seeds was analysed to determine the seed’s major nutritional content. The seed moisture and the seed fat content were not significant. Nonetheless, the seed fiber, seed ash, seed protein, seed carbohydrate, seed iron, and the energy content were significant between the accessions. The young leaf of the cowpea’ DNA was extracted for genetic analysis using the SCoT marker. Three accessions were randomly selected from each province and from the selected accessions, five samples were used to represent them. Ten primers of SCoT were chosen to be performed in the PCR reactions. The AMOVA analysis found that 70% of variation was within populations and the remaining 30% of variation was among the population. The genetic variation, GST value was higher (0.41) and the gene flow, Nm value of 0.72 that proves indicate the existence of divergence and gene flow within the population. The PCoA had separated the population into two major groups between populations of Tak with the rest of the accessions (Chiang Mai, Nan, Phrae). These many variations in morphologies and agronomy shown across the cowpea accessions would benefit many. There is great potential to integrate these variations into the breeding lines, which could aid in developing a superior cowpea variety that is more adapted to the local conditions and simultaneously fulfils market demand. With this approach, extensive information can be yielded which may benefit many sectors.