Genetic diversity and grouping of pigeonpea [Cajanus cajan Millspaugh] Germplasm using SNP markers and agronomic traits

Abstract

Knowledge of genetic interrelationships and grouping among pigeonpea germplasm collections is fundamental to selecting breeding parents with unique genetic constitutions. The objectives of this study were to assess the genetic diversity and genetic grouping present among 81 pigeonpea genotypes collected from Malawi, Tanzania and Kenya using 4122 single nucleotide polymorphism (SNP) markers and complementary morphological traits. The SNP markers and phenotypic traits revealed significant genetic variation among the assessed genotypes. The test genotypes were resolved into three distinct clusters based on both marker systems. The mean gene diversity and the polymorphic information content (PIC) were 0.14 and 0.11, suggesting moderate genetic differentiation among the genotypes. The analysis of molecular variance revealed that differences among populations accounted for only 2.7% of the variation, while within the population (among individuals) accounted for 97.3% of the variation. The results based on the DArT SNP genotyping complemented the phenotypic data and led to the selection of unique pigeonpea genotypes for effective breeding programs in Malawi and related agroecologies. This suggested that unique breeding populations could be created by identifying and selecting divergent individuals as parental lines. There is a need to create a new genetic variation or introgress genes from genetically unrelated parents to increase the genetic base of the current pigeonpea breeding populations.

Genetic diversity analysis and core germplasm bank construction in cold resistant germplasm of rubber trees (Hevea brasiliensis)

“…Long Qingyi used UPGMA to cluster 289 rubber tree Weikehan germplasm and divided them into three major groups. On other crops, Yukio Nagano and others used Rad-Seq SNP to mark 95 loquat germplasm data, and roughly divided loquat into three categories 26 .Esnart and other genetic structure results based on phylogenetic tree, and 81 cajanus cajanus were divided into three groups 23 .To sum up, there are few clustering results in this experimental group. The main source of this experiment material is that the germplasm screened out by field cold resistance evaluation is cold resistance germplasm, which leads to the lack of differences among genotypes and the lack of clustering results.…”

“…Secondly, the limited source of species, mainly the Weikehan variety, possibly contributed to the decrease in genetic diversity 22 . Thirdly, it may be due to the double allele www.nature.com/scientificreports/ nature of SNP 23 . In the future, we should select more cold-resistant germplasm and use wild germplasm resources for hybridization and improvement to expand the genetic diversity of cold-resistant germplasm of rubber trees.…”

“…Long Qingyi used UPGMA to cluster 289 rubber tree Weikehan germplasm and divided them into three major groups. On other crops, Yukio Nagano and others used Rad-Seq SNP to mark 95 loquat germplasm data, and roughly divided www.nature.com/scientificreports/ loquat into three categories 26 .Esnart and other genetic structure results based on phylogenetic tree, and 81 cajanus cajanus were divided into three groups 23 .To sum up, there are few clustering results in this experimental group.…”

Genetic differentiation of a southern Africa tepary bean (Phaseolus acutifolius A Gray) germplasm collection using high-density DArTseq SNP markers

“…It allows the simultaneous identification of numerous SNPs across a genome at an affordable cost [30]. DArTseq SNP markers have been used for quantitative trait loci (QTL) mapping, genome-wide association studies, the development of linkage maps, genetic diversity, and population structure analyses in several legume crops, including pigeonpea, chickpea, soybean, and common bean [30][31][32][33][34]. Genetic diversity and population structures were examined in Interspecific Mesoamerican X Wild Tepary (IMAWT) population using GBS with high-density SNP markers aligned to the common bean reference genome [5].…”