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

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

Weie Wen et al. Front Plant Sci.

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.

Keywords: SNP assay; Spearman rank correlation coefficient; Triticum aestivum; linkage map construction; map integration.

Figures

FIGURE 1
FIGURE 1
A four-way Venn diagram demonstrates all sets of common SNP markers among the four mapping populations.
FIGURE 2
FIGURE 2
Relationship between the wheat consensus map and the physical map. Based on blastn search of flanking sequences of SNP markers, the consensus maps were aligned to the IWGSC1+popseq database (ftp://ftp.ensemblgenomes.org/pub/plants/release-31/fasta/triticum_aestivum/dna/) (Choulet et al., 2014; International Wheat Genome Sequencing Consortium, 2014; Chapman et al., 2015). The x-axis indicates the position on the consensus map in cM and the y-axis indicates the position on physical map in Mb.
FIGURE 3
FIGURE 3
Distribution of the pair-wise SNP loci genotyped by the multi-locus SNP. A total of 942 pairs of loci including 909 pair-wise loci (e.g., 1A-1B) produced by SNPs mapped to two positions and 33 pair-wise loci (e.g., 1A-1B, 1A-1D, and 1B-1D) produced by SNPs mapped to three positions. The yellow block indicates the pairs between genomes A and B, while the green and gray blocks indicate the pairs between genomes A and D and between B and D, respectively. The red font indicates the pair-wise loci among the homoeologous chromosomes.

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