A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array

Abstract

A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding.

Genome-Wide Linkage Mapping of Quantitative Trait Loci for Late-Season Physiological and Agronomic Traits in Spring Wheat under Irrigated Conditions

“…Using 9687 polymorphic SNPs, 9330 previously mapped [31] and 357 newly mapped, we constructed a genetic map of 43 LGs that represented all the 21 chromosomes of bread wheat (Table S2) and had a total length of 3633.19 cm and an average marker density of 0.37 cm (Table S2). Our linkage map had a better marker distribution and a higher density compared with those reported in previous studies [11,23,[50][51][52][53][54][55]. However, some gaps were observed in Chr.…”

High throughput SNP discovery and genotyping in hexaploid wheat

“…[ 61 ] and Wen et al . [ 62 ] used a Zhou 8425B × Chinese Spring population to map 5,636 and 14,955 markers, respectively. For these reasons, our map has been selected by the IWGSC as the reference genetic map to anchor and order the wheat genome reference sequence (unpublished data).…”

Mapping quantitative trait loci associated with leaf rust resistance in five spring wheat populations using single nucleotide polymorphism markers

“…The inclusion of both SSR markers along with SNP markers in our consensus map facilitated the comparisons made between the QTL identified in the present study and previous mapping reports. Other published consensus maps [42,43] were generated based on SNP markers only.…”