Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS

Abstract

Background: Physical maps employing libraries of bacterial artificial chromosome (BAC) clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of the hexaploid bread wheat. The diploid ancestor of the D-genome of hexaploid wheat (Triticum aestivum), Aegilops tauschii, is used as a resource for wheat genomics. The barley diploid genome also provides a good model for the Triticeae and T. aestivum since it is only slightly larger than the ancestor wheat D genome. Gene co-linearity between the grasses can be exploited by extrapolating from rice and Brachypodium distachyon to Ae. tauschii or barley, and then to wheat.

Results: We report the use of Ae. tauschii for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of Ae. tauschii with 85 EST on the Ae. tauschii and barley genetic maps. The 24 contigs were aligned to the rice and B. distachyon genomic sequences and a high density SNP genetic map of barley. As expected, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in B. distachyon and chromosome 3H in barley. However, the chromosome scale of the comparative maps presented provides new insights into grass genome organization. The disruptions of the Ae. tauschii-rice and Ae. tauschii-Brachypodium syntenies were identical. We observed chromosomal rearrangements between Ae. tauschii and barley. The comparison of Ae. tauschii physical and genetic maps showed that the recombination rate across the region dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs.

Conclusions: The physical map reported here is the first physical map using fingerprinting of a complete Triticeae genome. This study demonstrates that global fingerprinting of the large plant genomes is a viable strategy for generating physical maps. Physical maps allow the description of the co-linearity between wheat and grass genomes and provide a powerful tool for positional cloning of new genes.

Figure 1

Ae. tauschii physical and genetic maps of chromosome 3DS. Alignment of Ae. tauschii physical map onto Ae. tauschii genetic map of chromosome 3DS. The Ae. tauschii AL8/78 × AS75 F₂ genetic map used EST based markers [11].

Figure 2

Comparative maps of Ae. tauschii 3DS with rice, Brachypodium and barley genome. Physical map of the distal region of Ae. tauschii 3DS compared to the orthologous genomic sequences of B. distachyon Bd2 (8× release) and rice Os2, and to the genetic map of barley 3HS. The underlined ctg names indicate the contigs which were aligned onto the Ae. tauschii AL8/78 × AS75 F₂ genetic map [11]. The names to the right are rice genes as listed in MSU Rice Genome Annotation (Osa1) Release 6.0. The barley Steptoe x Morex genetic map used gene-based SNP [15,16].

Figure 3

Model of chromosomal rearrangements of the Ph2 locus in rice, Brachypodium, Ae. tauschii and barley. 1-5 indicate chromosomal segments, A-D, the putative breakpoints. The breakpoint B would be located within the ctg5 of Ae. tauschii physical map. The names on top are rice genes as listed in MSU Rice Genome Annotation (Osa1) Release 6.0.