A Chromosome Bin Map of 16,000 Expressed Sequence Tag Loci and Distribution of Genes Among the Three Genomes of Polyploid Wheat

TLDR

The common wheat genome is large (17,300 Mb), so sequencing and mapping of expressed genes is a logical first step for gene discovery. The study aims to map 7,104 expressed sequence tag (EST) unigenes onto wheat chromosomes. This mapping was performed by Southern hybridization using wheat aneuploids and deletion stocks. The resulting chromosome bin map identified 7,104 EST loci, with 5,774 in the B genome, 5,173 in A, and 5,146 in D, higher density in the D genome, increasing toward chromosome ends, and clustering of agronomically important genes, making it a valuable resource for SNP analysis, comparative mapping, and wheat genome assembly.

Abstract

Abstract Because of the huge size of the common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) genome of 17,300 Mb, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids and deletion stocks. Each EST detected a mean of 4.8 restriction fragments and 2.8 loci. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general, EST density increased relative to the physical distance from the centromere. The majority of EST-dense regions are in the distal parts of chromosomes. Most of the agronomically important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.