Stability and genetic diversity of cowpea elite lines in Uganda

Abstract

Cowpea yields in farmers’ fields continue to be low because of multiple stresses exacerbated by adverse effects of climate change. Therefore, there is a need to develop new cowpea varieties that have combined resilience to stress as well as good yield to mitigate the challenges of low yields. This study aimed to determine the performance of elite breeding lines across multiple environments and understand the genetic diversity at the molecular level of 129 cowpea advanced breeding lines and 6 checks. These genotypes were evaluated in three locations for two seasons in an Alpha lattice experimental design with 3 replications. In addition, 135 cowpeas were genotyped with 21 SNP markers. Data were collected on yield and yield component traits and diseases. Highly significant (p<0.001) differences were observed among genotypes for traits measured as an indication of presence of genetic variation among the tested lines. There was highly significant (P<0.001) genotype by environment interaction effects for pod per plant, peduncles per plant, pods per peduncle,100 seed weight, seed per pod, seed yield; meaning the performances of the tested genotypes were inconsistent across the testing experimental sites. AMMI analysis of variance confirmed and explained the significant GxE effect on yield. The first two PCs (IPCA1 and IPCA2) in the AMMI model were both highly significant (p<0.001) and both contributed 79% of the total genotype by environment effect. GGE analysis identified four genotypes 49 (MUAL 19 033), 60 (MUAL 19 041), 109 (MUAL 19 095), and 114 (MUAL 19 089) that are stable and high-yielding across the test environments. To estimate the genetic diversity among these 135 cowpea genotypes at the molecular level, phylogenetic analysis and PCoA were used. The SNP markers showed average polymorphic information content (PIC) of 0.39, and average heterozygosity of 0.03 implying that the tested lines had achieved a high level of homozygosity. Genetic diversity ranged from 0.12 to 0.66 with an average of 0.45. The narrow genetic diversity may be attributed to the genetic exchange of parents with similar genetic background among the breeding programs in Africa. Cluster analysis using different methods grouped the genotypes into two major categories. Therefore, the SNP markers used in the study proved to be effective in determining genetic diversity among improved cowpea breeding lines in Uganda thus generating useful information to be utilized by the breeding program. In this study, it can be inferred that the presence of GxE interaction caused a significant effect of environment on yield and yield components among the genotypes. Adequate genetic variation was observed and this diversity can further be exploited for cowpea improvement in Uganda and the whole East Africa region.