Genetic Diversity And Screening Of Cowpea (Vigna unguiculata L. Walp.) Genotypes For Drought Tolerance In South Africa

Abstract

A survey was carried out to assess the farmers’ production constraints, traits and preferred cowpea varieties. A semi-structured questionnaire was used in a survey in Buhera District, Zimbabwe, in March and April of 2018. Women farmers dominated the survey as they were 52% of the surveyed population, while men occupied 48% of the total population. All participants concurred that cowpeas were used for domestic consumption. Eighty-three percent of the farmers cited shortage, unavailability, and cost of fertiliser, 16% of the farmers acknowledged that they do not have access to quality seed, and 1% cited labour as the major constraints in cowpea production. Farmers ranked heat (86%), drought (10%), and soil fertility (4%) as the most important abiotic factors. Ninety-one percent of the farmers’ ranked rust as the major disease, while 2% ranked storage rot, 1% ranked anthracnose, and 1% ranked downy mildew. Eighty-one percent of the farmers ranked aphids as the main pests, while 3% ranked thrips, 3% ranked legume borers, and 2% ranked pod borers. Fifty-two percent of the farmers preferred varieties that are resistant to diseases such as rust, whereas 48% were not concerned about diseases. For qualitative traits, 50% of the farmers had no specific colour preference, 32% preferred white colour, 14% brown colour, 3% red colour, and 1% tan colour. Ninety-four percent of interviewed farmers were not concerned about the pod shape, 3% preferred the kidney shape, 2% preferred the spherical shape and 1% preferred the globular shape. Ninety-nine percent of farmers agreed that they needed high yielding varieties per unit area and only 1% were unsure. For quantitative traits such as grain size, pod size, plant height, and head size, the preferences of farmers varied. Forty-four percent of the farmer respondents preferred larger cowpea grains, while 56% were not concerned about the size of the grain. A paltry 2% of the farmers were interested in pod size, while 98% did not regard it as important. Thirteen percent of the farmers were interested in climbing varieties, while 87% considered high grain yield as of the utmost importance. The top ranked accessions were CBC1, IT 18, and “Chibundi Chitsvuku”, respectively, while the least ranked was “Kangorongondo”. The survey showed that there is a need to breed for both biotic and abiotic factors, such as drought and moisture stress, as well as against pests and diseases. In order to assess the genetic diversity and population structure among cowpea accessions, diversity arrays technology (DArTSeq) genotype by sequencing technique was used. A total of 85 cowpea accessions (45 from the International Institute of Tropical Agriculture [IITA], 25 from South Africa, and 15 from Zimbabwe) were investigated in this study using 284 single-nucleotide polymorphisms (SNPs). Fifty-one percent of SNPs were polymorphic across the 85 accessions and fulfilled the selection criteria. The genetic distance, estimated based on Nei’s index among genotypes, ranged from 0.14 to 0.44, with a mean value of 0.35. The polymorphic information content value ranged from 0.024 to 0.50, with a mean value of 0.25. Twenty-six percent of the genotypes had genetic diversity values greater than 0.40, suggesting that the genotypes were moderately genetically diversified. A high gene flow (Nm) of 4.89 was observed between Zimbabwean and South African accessions indicating the high germplasm exchange among the neighbouring countries. The analysis of molecular variance revealed highly significant variation among individual accession and low variation within individuals. The accessions showed significant (p<0.001) but low levels of differentiation among the geographic regions. Cluster analysis of the 85 accessions generated by the unweighted pair group method with arithmetic mean (UPGMA) procedure clustered the accessions into three distinct groups. The clustering patterns showed that accessions collected from the same geographic regions tend to cluster in the same groups. SNP data analysis indicated the existence of high levels of genetic diversity among cowpea accessions collected from southern Africa and Nigeria. However, the low genetic variation within individuals suggested the need to further widen the genetic base of the crop. Molecular data should be backed by morphological data to link the SNP markers that are associated with desirable agronomic attributes, such as high tolerances to biotic and abiotic stress factors. Sixty cowpea genotypes were screened for seedling drought tolerance in screen houses. Of these, 33 accessions were from the IITA in Nigeria, 19 accessions were from the Agricultural Research Council – Grain Crops in South Africa, and eight accessions were from smallholder farmers in Buhera District, Zimbabwe. Bartlett’s test of sphericity was significant at p<0.05, while the Kaiser-Meyer-Olkin measure of sampling adequacy was 77, indicating sufficient items for each factor. A principal component analysis (PC) showed that number of pods (NP), seeds per pod (SP), survival count (SC), pod weight (PWT), and stem wilting in week one (WWK1) had the most significant contributions to genetic variability in cowpea accessions to drought tolerance, as well as yield after stress imposition. Based on the PC, accessions IT 07-292-10, RV 343, and IT 95K-2017-15 had the maximum variability for NP, SP, SC, PWT, and WWK1 after drought imposition. There were significant differences among most drought-related traits at the seedling stage with the exception of environment × genotype on days to emergence (DTE), stem greenness at week 1 (SGWK1) after the imposition of water stress and also among replicates in terms of DTE. A total of 37 cowpea accessions from both screen houses were found to be tolerant to drought, while 23 were susceptible. From the results, it was observed that the accessions had similar responses to drought. The findings of the study provided a useful tool for screening and determining the accessions that are drought tolerant and susceptible at the seedling stage. Finally, it was necessary to conduct association mapping for drought tolerance at the seedling stage and yield-related traits of cowpeas. The cowpea accessions were analysed for their possible population structure using STRUCTURE 2.3.4, and the peak of delta K in the greenhouse showed the existence of seven sub- populations, whereas the peak of delta K in the glasshouse indicated the presence of six sub-populations. One SNP marker, 14083649|F|0-9 was associated with number of pods (NP) with a p value <0.001.Fifty SNP markers were associated with pod weight (PWT) at p<0.001. Four SNP markers, 14074781|F|0-16, 100047392|F|0-36, 14083801|F|0-28 and 100051488|F|0-49 were associated with ASPD at p<0.001. SNP markers, 14074781|F|0-16, 14083801|F|0-28 and 100051488|F|0-49 were associated with PL at p <0.001. Five SNP markers, 100047392|F|0-36, 14083801|F|0-28, 100072738|F|0-34, 14076881|F|0-49 and 14076881|F|0-49 were associated with PWDTH at p <0.001. The major difference that was observed in association mapping in the two environments was due to temperature variations. The 67 SNP markers identified can be used in cowpea molecular breeding to select for AVSPD, NP, PL, PWDTH, PWT, and RR through marker assisted selection (MAS).