Genotyping-by-Sequencing (GBS) Revealed Molecular Genetic Diversity of Iranian Wheat Landraces and Cultivars

Abstract

Background: Genetic diversity is an essential resource for breeders to improve new cultivars with desirable characteristics. Recently, genotyping-by-sequencing (GBS), a next-generation sequencing (NGS) technology that can simplify complex genomes, has now be used as a high-throughput and cost-effective molecular tool for routine breeding and screening in many crop species, including the species with a large genome.Results: We genotyped a diversity panel of 369 Iranian hexaploid wheat accessions including 270 landraces collected between 1931 and 1968 in different climate zones and 99 cultivars released between 1942 to 2014 using 16,506 GBS-based single nucleotide polymorphism (GBS-SNP) markers. The B genome had the highest number of mapped SNPs while the D genome had the lowest on both the Chinese Spring and W7984 references. Structure and cluster analyses divided the panel into three groups with two landrace groups and one cultivar group, suggesting a high differentiation between landraces and cultivars and between landraces. The cultivar group can be further divided into four subgroups with one subgroup was mostly derived from Iranian ancestor(s). Similarly, landrace groups can be further divided based on years of collection and climate zones where the accessions were collected. Molecular analysis of variance indicated that the genetic variation was larger between groups than within group.Conclusion: Obvious genetic diversity in Iranian wheat was revealed by analysis of GBS-SNPs and thus breeders can select genetically distant parents for crossing in breeding. The diverse Iranian landraces provide rich genetic sources of tolerance to biotic and abiotic stresses, and they can be useful resources for the improvement of wheat production in Iran and other countries.

Genetic diversity analysis of a Flax (Linum usitatissimum L.) global collection

“…We found all markers moderately or low informative as PIC value for all markers was less than 0.5 (35). Other researchers also found similar results in ax (36), winter wheat (37,38), rice (39) and maize (40). Bi-allelic nature of SNP marker and probably low mutation rate (41) restrict the PIC value within 0.5.…”

Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

“…In conclusion, GBS proved to be a valuable tool to study the population genetics and relationships in common bean germplasm, even at local level, as already observed for other crops [67][68][69][70]. In addition, our work is relevant regarding the preservation of local landraces of the common bean from genetic erosion, and could be useful for future studies to tackle the identification of interesting traits relating to plant adaptation for breeding purposes.…”

GWAS revealed a novel resistance locus on chromosome 4D for the quarantine disease Karnal bunt in diverse wheat pre-breeding germplasm

“…www.nature.com/scientificreports www.nature.com/scientificreports/ in wheat contains comparatively fewer polymorphic markers than the A and B genomes due to low recombination attributed to its evolutionary and domestication history. Consistent with previous findings, the B genome contains a greater number of polymorphisms than the A and D genomes, which is attributed to a greater number of effective recombination events in the B genome [24][25][26] . The average number of SNPs per chromosome was 304, and the value ranged from 147 (4B) to 500 (7D) ( Supplementary Fig.…”

“…Chromosome 3B appears to be a hot spot for various disease resistance genes, as it is the location of QTLs for KB resistance 24 and resistance to tan spot 39 , yellow rust 39 , leaf rust 24 and crown rot 26 . Genomic regions inherited as multi-disease resistance loci are not uncommon in wheat 39 .…”