A high-density intervarietal map of the wheat genome enriched with markers derived from expressed sequence tags

Abstract

Bread wheat (Triticum aestivum L.) is a hexaploid species with a large and complex genome. A reference genetic marker map, namely the International Triticeae Mapping Initiative (ITMI) map, has been constructed with the recombinant inbred line population derived from a cross involving a synthetic line. But it is not sufficient for a full understanding of the wheat genome under artificial selection without comparing it with intervarietal maps. Using an intervarietal mapping population derived by crossing Nanda2419 and Wangshuibai, we constructed a high-density genetic map of wheat. The total map length was 4,223.1 cM, comprising 887 loci, 345 of which were detected by markers derived from expressed sequence tags (ESTs). Two-thirds of the high marker density blocks were present in interstitial and telomeric regions. The map covered, mostly with the EST-derived markers, approximately 158 cM of telomeric regions absent in the ITMI map. The regions of low marker density were largely conserved among cultivars and between homoeologous subgenomes. The loci showing skewed segregation displayed a clustered distribution along chromosomes and some of the segregation distortion regions (SDR) are conserved in different mapping populations. This map enriched with EST-derived markers is important for structure and function analysis of wheat genome as well as in wheat gene mapping, cloning, and breeding programs.

Mapping QTL for stay-green and agronomic traits in wheat under diverse water regimes

“…It comprised 2575 markers spanning 5008.3 cM, with an average distance of 1.9 cM between adjacent markers. The B genome contained the maximum number of markers, followed by the A and D genomes, in accordance with earlier studies (Hao et al 2003;Xue et al 2008;Wang et al 2014;Wu et al 2015).…”

“…In addition, genotyping of those markers was laborious and time-consuming. Compared to earlier genetic maps based on SSR and AFLP markers (Groos et al 2003;Hao et al 2003;Sun et al 2010;Xue et al 2008;Zanetti et al 2001;Huang et al 2006) the present map contained mainly SNP markers (86%) and was obtained by using an Infinium iSelect 9 K SNP beadchip array. It comprised 2575 markers spanning 5008.3 cM, with an average distance of 1.9 cM between adjacent markers.…”

“…7 Marker maps of chromosome 5A. The left map was constructed using the Nanda2419 9 Wangshuibai population (5A) (Xue et al 2008), in which the VRN-A1 gene on 5AL was mapped. The right map is a partial linkage map of 5A (LG33) from the current research, constructed using data from the (H10 9 Lumai14) population height on 4D and 7A and those for TKW on 3D and 7A.…”

“…One of the 5A maps in Fig. 7 was constructed using a Nanda 2419 9 Wangshuibai population (Xue et al 2008), in which VRN-A1 locus was mapped on 5AL. Four markers, Xwmc410, Xgwm595, Xwmc524 and Xgwm291, were distal to the VRN-A1 locus.…”

Detailed Recombination Studies Along Chromosome 3B Provide New Insights on Crossover Distribution in Wheat (Triticum aestivum L.)

“…However, these maps covered only poorly the whole genome with sometimes chromosomes that were not represented (Cadalen et al 1997). The actual sizes of wheat genetic maps range from 2500 to 4000 cM (Sourdille et al 2003;Quarrie et al 2005;Suenaga et al 2005;Akbari et al 2006;Toradaet al 2006;Xue et al 2008), indicating that some of them exceed the expected value. This may suggest genotyping errors, the use of not well-adapted mapping functions, or differences in CO frequencies between different wheat varieties and provides a note of caution on the quality of the genetic maps of wheat.…”