Genetic diversity and population structure of Ethiopian Capsicum germplasms

Abstract

We established a collection of 142 Capsicum genotypes from different geographical areas of Ethiopia with the aim of capturing genetic diversity. Morphological traits and high-resolution melting analysis distinguished one Capsicum baccatum , nine Capsicum frutescens and 132 Capsicum annuum accessions in the collection. Measurement of plant growth parameters revealed variation between germplasms in parameters including plant height, stem thickness, internode length, number of side branches, fruit width, and fruit length. Broad-sense heritability was maximum for fruit weight, followed by length and width of leaves. We used genotyping by sequencing (GBS) to identify single-nucleotide polymorphisms (SNPs) in the panel of 142 Capsicum germplasms and found 2,831,791 genome-wide SNP markers. Among these, we selected 53,284 high-quality SNPs and used them to estimate the level of genetic diversity, population structure, and phylogenetic relationships. From model-based ancestry analysis, the phylogenetic tree and principal-coordinate analysis (PCoA), we identified two distinct genetic populations: one comprising 132 C . annuum accessions and the other comprising the nine C . frutescens accessions. GWAS analysis detected 509 SNP markers that were significantly associated with fruit-, stem- and leaf-related traits. This is the first comprehensive report of the analysis of genetic variation in Ethiopian Capsicum species involving a large number of accessions. The results will help breeders utilize the germplasm collection to improve existing commercial cultivars.

Uncovering Candidate Genes Controlling Major Fruit-Related Traits in Pepper via Genotype-by-Sequencing Based QTL Mapping and Genome-Wide Association Study

“…Genomic DNA was extracted from the samples using the CTAB method ( Lee et al., 2017 ; Siddique et al., 2019 ; Solomon et al., 2019 ) and diluted to 80 ng/µl in distilled water. GBS libraries were constructed via double digestion with two sets of restriction enzymes ( Pst I/ Mse I and EcoR I/ Mse I) as previously described ( Han et al., 2018 ; Siddique et al., 2019 ; Solomon et al., 2019 ). The digested DNA was ligated to adapters and amplified with ‘TA’ primers.…”

Single Nucleotide Polymorphisms Reveal Genetic Diversity in New Mexican Chile Peppers (Capsicum Spp.) 

“…Evaluation of diversity is relevant for broadening the genetic base for identi cation of bene cial alleles for improvement of current germplasm [24]. A GBS approach was used for SNP marker discovery and to examine genetic diversity, population structure, and linkage disequilibrium among a diverse New Mexican Capsicum population.…”

“…Genetic diversity, which represents the magnitude of genetic variability within a population, is an important source of biodiversity [23] and is relevant for association studies, genomic selection, and individual identi cation, and is crucial to the overall success of plant breeding programs [24,25]. Diversity in plant genetic resources provides avenues for plant breeders to develop novel varieties with improved characteristics such as yield potential, pest and disease resistance, and productivity [26,27].…”

Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties

“…Phylogenetic analysis based on molecular markers, pan-genome sequencing, and GBS confirmed that C. chinense and C. frutescens are more closely related to each other than to C. annuum [29, 61, 64]. Several studies attempted to characterize the population relatedness of cultivated C. annuum in restricted geographical areas [29, 36, 40–42, 65]. They revealed that the population structures of the C. annuum accessions were mainly associated to distinct cultivar types with respect to the plant and fruit descriptors, and thus mostly result from human selection for cultivar types in agreement with consumption modes and adaptation to the highly diversified agro-climatic conditions.…”