Journal Article

Molecular genetic diversity and linkage disequilibrium structure of the Egyptian faba bean using Single Primer Enrichment Technology (SPET)

Eltaher, Shamaseldeen, Boerner, Andreas, Amro, Ahmed, Sallam, Ahmed, Mourad, Amira M. I., Rafeek, Abdallah

2024

Overview

Faba bean is an important legume crop. The genetic diversity among faba bean genotypes is very important for the genetic improvement of target traits. A set of 128 fab bean genotypes that are originally from Egypt were used in this study to investigate the genetic diversity and population structure. The 128 genotypes were genotyped using the Single Primer Enrichment Technology (SPET) by which a set of 6759 SNP markers were generated after filtration. The SNP markers were distributed on all chromosomes with a range extending from 822 (Chr. 6) to 1872 (Chr.1). The SNP markers had wide ranges of polymorphic information content (PIC), gene diversity (GD), and minor allele frequency. The analysis of population structure divided the Egyptian faba bean population into five subpopulations. Considerable genetic distance was found among all genotypes, ranging from 0.1 to 0.4. The highly divergent genotype was highlighted in this study and the genetic distance among genotypes ranged from 0.1 and 0.6. Moreover, the structure of linkage disequilibrium was studied, and the analysis revealed a low level of LD in the Egyptian faba bean population. A slow LD decay at the genomic and chromosomal levels was observed. Interestingly, the distribution of haplotype blocks was presented in each chromosome and the number of haplotype block ranged from 65 (Chr. 4) to 156 (Chr. 1). Migration and genetic drift are the main reasons for the low LD in the Egyptian faba bean population. The results of this study shed light on the possibility of the genetic improvement of faba bean crop in Egypt and conducting genetic association analyses to identify candidate genes associated with target traits (e.g. protein content, grain yield, etc.) in this panel.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Agricultural research / Animal Genetics and Genomics / Beans / Biomedical and Life Sciences / Broad beans / Chromosomes / Chromosomes, Plant - genetics / Collaboration / Crop yield / Egypt / Gene frequency / Gene loci / Genetic analysis / Genetic distance / Genetic diversity / Genetic diversity indices / Genetic drift / Genetic improvement / Genetic Variation / Genomes / Genomic analysis / Genotype / Genotype & phenotype / Genotypes / Germplasm / Haplotypes / Kinship / LD decay / Legumes / Life Sciences / Linkage analysis / Linkage Disequilibrium / Microarrays / Microbial Genetics and Genomics / Molecular structure / Plant Genetics and Genomics / Polymorphism / Polymorphism, Single Nucleotide / Population genetics / Population structure / Population studies / Proteomics / Research centers / Single-nucleotide polymorphism / SNP marker / Software / STRUCTURE / Subpopulations / Target recognition / Vicia faba - genetics / Vicia faba L