Linkage Disequilibrium And Association Mapping Of Cowpea (Vigna Unguiculata (L.) Walp) Quantitative Traits

Abstract

A genome-wide association study (GWAS) was conducted using 187 cowpea germplasm to study linkage disequilibrium and association mapping of some cowpea quantitative traits. All the accessions with the exception of two which were obtained from the Department of Plant and Environmental Biology, were assembled from International Institute of Tropical Agriculture Germplasm Resources Information Centre. These accessions comprised 94 cultivated types and 93 wild relatives. Data on morpho-agronomic traits were collected using the Cowpea Descriptor by the International Board for Plant Genetic Resources. A total of 32 morpho-agronomic traits and 46 SNPs markers were assessed. Ethanol extracts of pulverized dried cowpea seeds were used to determine the amino acid concentrations. Data analysis involved descriptive statistics, Pearson’s correlation, principal component analysis (PCA), cluster analysis, Nei’s genetic diversity of subpopulations, likelihood ratio test for Hardy Weinberg equilibrium, F statistics and gene flow, population structure and genetic distance analysis. High variation was observed in the morpho-agronomic traits. A total of one hundred and thirty-six (136) significant pairwise correlations were observed in the quantitative traits. Out of the forty-six (46) SNPs markers, forty-three (43) were polymorphic. Means for the quantitative traits studied were as follows: days to 50% germination was 3.93±0.26 days. Mean days to first leaf stage was 12.40±0.24 days. Mean chlorophyll content was 1.44±0.02 mg/liter. Mean days to 50% flowering was 65.97±1.97 days. Mean number of flowers per plant was 8.95±0.55 flowers. Mean peduncle length per plant was 13.39±0.45 cm. Mean number of pods per peduncle was 1.97±0.01 pods. Mean days to 50% pod maturation was 81.86±1.97 days. Mean number of pod per plant was 7.09±0.54 pods. Mean pod length per plant was 11.53±0.28 cm. Mean average seed per pod was 9.86±0.24 seeds. Mean 20 seed weight was 1.5580±0.07 grams. Mean seed yield per plant was 70.31±5.65 seeds. Mean seed abortion rate per plant was 2.14±0.08 percent. All the 19 amino acids analyzed for the seed quality traits were present in the accessions, except L-Cysteine which was beyond detection. However, some accessions recorded 0.00 for Iso-Leucine and Trans-4-Hydroxyl-Proline. Mean concentrations for the amino acids was generally low in the wild relatives. It ranged between 21623.03±5299.45 x 10-5 ppm (L-Tryptophan) to 17.52±5.36 x 10-5 ppm (L-Methionine) while that for the cultivars varied from 3953909.00±7143.39 x 10-5 ppm (L-Tryptophan) to 18266.33±2524.18 x 10-5 ppm (L-Methionine). Mean Nei’s genetic diversity for the overall population was 0.3001, mean Wright’s Fixation coefficient for inbreeding (FIS) was 0.8935, mean degree of differentiation within population (inbreeding at different level) (FIT)was 0.9143, mean degree of genetic differentiation (FST) was 0.1952, mean gene flow (Nm) was 1.0309, mean observed heterozygosity was 0.0242 and mean frequency of cross pollination (C) was 0.0805. Analysis of population structure grouped the cowpea accessions into two clusters. Proportion of membership for cluster 1 was 0.551 and that for cluster 2 was 0.449. The mean FST value for cluster 1 was 0.064 and that for cluster 2 was 0.048. Intra chromosomal linkage disequilibrium estimate for SNPs loci revealed 12.64% and 15.38% at the threshold level of r2 ≥ 0.1 and r2 ≥ 0.05 respectively. The largest LD block observed was 25.0 bp between SNPs markers 6904_1061 and 9815_2051 at correlation co-efficient measure of variability between two loci (r2) of 0.10 and the difference between the gamete frequencies at two different loci (D’) of 0.89. Partial linkage disequilibrium decay was observed from a graph of r2 values of LD (between 0.0 and 0.75) against map distance ranging from 0.0 to 38.75 cM. Significant marker-trait associations were identified with very high potential for exploitation in marker-assisted breeding for the important traits in cowpea. Number of flowers per plant, mean peduncle length, number of pods per peduncle, number of pods per plant, seed yield per plant and DL-Beta phenyl-Alanine were associated with different SNPs markers at 5 cM map distance while 20 seed weight, D-Proline, Iso-Luecine, L-Histidine and L-Serine were associated with different SNP markers at 0.0 cM map distance.