A chromosome bin map of 2148 expressed sequence tag loci of wheat homoeologous group 7

Abstract

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat (Triticum aestivum L.), to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes.

Figure 1.—

Physical EST maps of chromosomes of group 7 showing distribution of ESTs mapped in different deletion bins. The deletion bins for each chromosome are marked on the left. The intrabin duplicated loci are represented only once per bin. The number of loci per bin is that presented in Table 1 minus the duplications. Information on the exact locus designation and restriction fragment mapped to each bin can be found at http://wheat.pw.usda.gov/cgi-bin/westsql/map_locus.cgi. The short arm of each chromosome is oriented toward the top while the long arm is toward the bottom. (A) physical map of chromosome 7A; (B) physical map of chromosome 7B; (C) physical map of chromosome 7D.

Figure 1.—

Physical EST maps of chromosomes of group 7 showing distribution of ESTs mapped in different deletion bins. The deletion bins for each chromosome are marked on the left. The intrabin duplicated loci are represented only once per bin. The number of loci per bin is that presented in Table 1 minus the duplications. Information on the exact locus designation and restriction fragment mapped to each bin can be found at http://wheat.pw.usda.gov/cgi-bin/westsql/map_locus.cgi. The short arm of each chromosome is oriented toward the top while the long arm is toward the bottom. (A) physical map of chromosome 7A; (B) physical map of chromosome 7B; (C) physical map of chromosome 7D.

Figure 1.—

Physical EST maps of chromosomes of group 7 showing distribution of ESTs mapped in different deletion bins. The deletion bins for each chromosome are marked on the left. The intrabin duplicated loci are represented only once per bin. The number of loci per bin is that presented in Table 1 minus the duplications. Information on the exact locus designation and restriction fragment mapped to each bin can be found at http://wheat.pw.usda.gov/cgi-bin/westsql/map_locus.cgi. The short arm of each chromosome is oriented toward the top while the long arm is toward the bottom. (A) physical map of chromosome 7A; (B) physical map of chromosome 7B; (C) physical map of chromosome 7D.

Figure 2.—

Consensus map of homoeologous group 7 of wheat including the ancient translocation involving 7BS, 4AL, and 5AL. (A) consensus map of the long arm of group 7; (B) consensus map of 7AS and 7DS (on the left) with landmark probes shared with 7BS (0.00–0.59 interval). Forty-four EST detected loci mapped to 7AS and 7DS (0.59–1.00 interval) and translocated from 7BS to 4AL. A smaller segment of 5 EST detected loci representing an unequal translocation from 5AL to 7BS. Probes in boldface type were ordered on the basis of the corresponding markers mapped on the linkage maps of chromosomes 6 and 8 of rice.

Figure 2.—

Consensus map of homoeologous group 7 of wheat including the ancient translocation involving 7BS, 4AL, and 5AL. (A) consensus map of the long arm of group 7; (B) consensus map of 7AS and 7DS (on the left) with landmark probes shared with 7BS (0.00–0.59 interval). Forty-four EST detected loci mapped to 7AS and 7DS (0.59–1.00 interval) and translocated from 7BS to 4AL. A smaller segment of 5 EST detected loci representing an unequal translocation from 5AL to 7BS. Probes in boldface type were ordered on the basis of the corresponding markers mapped on the linkage maps of chromosomes 6 and 8 of rice.

Figure 3.—

Pattern of distribution of EST loci duplicated along the length of the arms of consensus chromosome 7. The vertical axis is the number of loci. The horizontal axis divides the short and long arms into approximately a proximal one-third and distal two-thirds portions.

Figure 4.—

Comparison of map positions of molecular markers of rice and barley with tentatively ordered EST loci on the consensus map of homoeologous group 7. The linkage map of barley chromosome 7, adapted from Künzel et al. (2000), is depicted on the right. The stepwise increases in the height of the colored diagonal lines were used in wheat group 7 to differentiate among the regions.