Genetic Diversity Study of Ethiopian Faba Bean (Vicia faba L.) Varieties Using Phenotypic Traits, ISSR and SNP Markers

Abstract

Faba bean (Vicia faba L.) is one of the earliest food legumes of the world used as source of high protein for human and animal consumption. In Ethiopia, no studies were conducted on faba bean varieties genetic diversity assessment based on molecular markersand this study is designed to fill this gap. The study was designed to reveal the genetic diversity existing among Ethiopian faba bean varieties using phenotypic traits, ISSR and SNP markers. Field experiment was conducted at three locations (Sinana, Agarfa and Selka) for agro-morphological performance, while the molecular part was conducted at Addis Ababa University (ISSR) and UK, LGC genomics (KASP SNP genotyping). A total of 32 faba bean varieties were used for phenotypic and ISSR markers, whereas 16 additional breeding lines were included for SNP markers. A total of 23 phenotypic traits,11 ISSR and 37 SNP primers were used to assess genetic diversity and interrelationship among Ethiopian faba bean varieties. The genomic DNA extraction was made based on modified CTAB method and Oktopure extraction kit method from bulked young leaf sample for ISSR and SNP markers, respectively. The combined analysis of variance over the three locations showed highly significant (p<0.01) variations among the varieties for the majority of traits. Genotype by environment interaction showed highly significant difference (p< 0.01) among traits. UPGMA constructed based on phenotypic traits revealed five major clusters and the first six principal components (PCs) accounted for 85% of the entire diversity among the varieties for all the 23 traits and the first three PCA revealed 66% of the total variation. Eleven ISSR primers amplified 120 bands, of which 107 loci were polymorphic. The highest gene diversity (0.38) and Shannon index (0.56) were recorded by primer 860, while the least gene diversity (0.18) was revealed by primer 848 and 857. UPGMA cluster and PCO analysis grouped the cultivars into three major clusters based on Jaccard’s similarity coefficient ranging from 0.41 to 0.77. Out of the 37 scoreable SNP markers, one was monomorphic across all the 48 genotypes and 36 SNP showed polymorphism with rate of 95.58%. Relatively high average Nei’s genetic diversity (0.41) and PIC (0.32) were revealed by SNP markers. Based on obtained PIC value, 31 SNP primers were found to be reasonably informative. Genetic dissimilarity between different pairs of varieties varied from 0.15 (Dosha and Mesay) to a maximum of 0.80 (Tumsa and Kulumsa local varieties) with an average mean of 0.45. STRUCTURE, UPGMA and PCOA suggested that the varieties were divided into three main genetic groups. Therefore, the observed genetic variation in the study indicated the opportunity of using these materials in future faba bean breeding program via introgression with other germplasm resources for improvement of better genotypes.