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.
Highlights
IntroductionBreeding is a long-term process and molecular marker tools open the way for more rapid and efficient breeding strategies (Tester and Langridge, 2010)
Common wheat (Triticum aestivum L.) is an allohexaploid species (2n = 6x = 42, AABBDD) derived from the hybridization of diploid Aegilops tauschii (DD) and tetraploid wild emmer (AABB) 10,000 years ago (Dubcovsky and Dvorak, 2007), with a genome size of about 17 gigabase (Gb) (Choulet et al, 2014); it is one of the most important crops, supplying food for 35% of the world population (International Wheat Genome Sequencing Consortium, 2014)
After filtering the genotypic data based on the criteria mentioned above, 11,012 (Doumai × Shi 4185), 11,979 (Gaocheng 8901 × Zhoumai 16), 10,443 (Linmai 2 × Zhong 892), and 14,955 (Zhou 8425B × Chinese Spring) markers were used to construct the genetic linkage maps
Summary
Breeding is a long-term process and molecular marker tools open the way for more rapid and efficient breeding strategies (Tester and Langridge, 2010). Over the last three decades molecular markers have increasingly served as a tool for genetic analysis of plant species. Decreasing costs of marker assays are making marker-assisted selection (MAS) increasingly used in breeding programs (Soto-Cerda et al, 2015; Vinod et al, 2015; Yaniv et al, 2015; Arruda et al, 2016; Vasistha et al, 2016). Linkage mapping is a major strategy to identify markers tightly linked with quantitative trait loci (QTL) underlying many economically important traits (Zheng et al, 2015; Dong et al, 2016; Su et al, 2016)
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