A 2600-Locus Chromosome Bin Map of Wheat Homoeologous Group 2 Reveals Interstitial Gene-Rich Islands and Colinearity With Rice

Abstract

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a highdensity EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7.H EXAPLOID common wheat (Triticum aestivum L.) related diploid genomes designated A, B, and D with seven chromosomes each (2n ϭ 6x ϭ 42). Extensive is one of the most important staple crops globally. The hexaploid wheat genome is composed of three genetic and cytogenetic characterization of diploid, tetraploid, and hexaploid wheat relatives has made it a model system for the study of allopolyploid evolution.

A Molecular-Cytogenetic Method for Locating Genes to Pericentromeric Regions Facilitates a Genomewide Comparison of Synteny Between the Centromeric Regions of Wheat and Rice

“…Recurrent origin of pericentromeric inversions: Previously Qi et al (2006) reported that pericentric regions in the Triticeae, especially those of group-4 chromosomes, have undergone rapid and recurrent rearrangements. Pericentromeric inversions close to the centromere regions were detected in wheat chromosomes 2B, 3B, 4A, 4B, 5A, and 6B, as well as in other Triticeae species (Conley et al 2004;Linkiewicz et al 2004, Miftahudin et al 2004Qi et al 2004Qi et al , 2006. Analyzing W7-R8 centromere homology, we observed two independent pericentromeric inversions involving chromosome 7R of rye and 7D of wheat (Figures 1b and 2).…”

“…These ESTs are diagnostic markers detecting pericentric inversions in homologous groups 2, 3, 4, 5, and 6 in the Triticeae and are markers for the pericentromeric regions of wheat chromosomes (Conley et al 2004;Linkiewicz et al 2004;Miftahudin et al 2004;Qi et al 2004Qi et al , 2006. Two cDNA clones, PSR161 and BCD1072, were previously mapped to the centromere of chromosome 1B (Sandhu et al 2001;Francki et al 2002).…”

“…W3-R1 and W6-R2 chromosomes and their centromeres have maintained perfect synteny (Figure 3). The remaining wheat and Triticeae chromosomes are associated with linkage blocks corresponding to two or three rice chromosomes (Ahn et al 1993;Gale and Devos 1998;Sorrells et al 2003;Conley et al 2004;Hossain et al 2004;La Rota and Sorrells 2004;Linkiewicz et al 2004;Miftahudin et al 2004;Peng et al 2004;Randhawa et al 2004;Salse et al 2008). Chromosome W1 arose from the fusion of chromosomes with homology to R5 and R10 but its centromere was derived from R5 ( Figure 3).…”

Divergent functions of orthologous NAC transcription factors in wheat and rice

“…The wheat physical map was adapted from previously published maps (Sourdille et al 2004;Conley et al 2004). The rice physical map was adapted from the Rice Functional Genomics Database website (http://signal.salk.edu/cgi-bin/RiceGE).…”

“…Sourdille et al (2004) mapped gwm374 to the proximal region of chromosome 2BS using wheat deletion lines (C-2BS1-0.53 bin) confirming our previous assignment of GPC-B2 to this centromeric bin. Conley et al (2004) further dissected the C-2BS1-0.53 centromeric bin into 3 consensus bins (designated CS, 1S and 2S from proximal to distal, Fig. 2) and mapped BF291736 and other wheat ESTs to CS, the most proximal bin (Fig.…”