A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

Abstract

The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions. (2), and 90% of its genome was estimated to be repetitive DNA (3). The Ae. tauschii genome and the D genome of hexaploid wheat are closely related due to the recent origin of hexaploid wheat (4). Ae. tauschii is therefore an important resource for wheat breeding, and its genome is an invaluable reference for wheat genomics, as illustrated by the utility of its sequences in the analysis of the wheat gene space (5). The utility of Ae. tauschii for wheat genetics and genomics would be further enhanced by a high-quality draft sequence of its genome. With current technology, the only approach to produce a high-quality de novo draft sequence for a genome of this size and complexity is the orderedclone sequencing approach, which requires a physical map.Physical map construction necessitates fingerprinting multiple genome equivalents of bacterial artificial chromosome (BAC) clones, assembling them into contigs, and anchoring the contigs on a genetic map (6-8). Great strides have been made in BAC fingerprinting techniques (7, 9-12) and software for fingerprint editing and contig assembly (13-16). It is now possible with these technological advances to fingerprint and assemble contigs from hundreds of thousands of BAC clones (7,8,(17)(18)(19). In contrast, contig anchoring remains a weakness in physical mapping of large plant genomes because of their low gene density, extensive gene duplication, and abundance of repetitive DNA. BAC end sequences (BESs) are an effective means of contig anchoring in small genomes (11). In large genomes, however, hundreds of thousands of BESs are needed. DNA hybridization and PCRbased anchoring (6,7,20,21)...

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

“…To generate a pseudomolecule, the extended sequences of 1,326 chromosome 2D-specific SNPs mapped to the Ae. tauschii AL8/78 genetic map 20 were used to perform a BLAST search against the 10,344 'CH Campala Lr22a' scaffolds using an in-house script.…”

“…Recombination frequencies were derived from combining the genetic mapping data from Ae. tauschii 20 and the physical sizes of the 80 'CH Campala Lr22a' scaffolds that were anchored to the genetic map (Supplementary Table 3). Local recombination frequencies (in Mb/cM) along chromosome 2D were calculated in a sliding window averaging ratios of physical to genetic distance over 50 genetic markers.…”

“…tauschii that includes 1,326 chromosome 2D-specific single nucleotide polymorphism (SNP) markers 20 . To do this, we performed a BLAST search 21 with the extended sequences of the Ae.…”

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

“…Because hybridization of tetraploid wheat and Ae. tauschii occurred very few times the D genome in common wheat has much lower genetic diversity, a consequence of which is less molecular marker polymorphism in the D genome of common wheat Luo et al 2013a;Dubcovsky and Dvorak 2007;Salamini et al 2002). Keeping in view that many QTL for yield and physiological traits are located in the D genome, consideration should be given to increasing the number and density of markers in the D genome through technologies such as next generation sequencing.…”

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

“…The Triticeae species, such as wheat (Triticum aestivum, 2n = 6x = 42) and barley (Hordeum vulgare, 2n = 2x = 14), which account for >30% of cereal production worldwide, are essential food and forage resources (faostat.fao.org). International efforts have been launched to decipher their genomes, and dramatic breakthroughs have been achieved on the reference genome of chromosome 3B (1), whole-genome sequencing (2,3), and in-depth phylogenetic and transcriptome analyses (4,5) of hexaploid wheat, as well as generations of draft genome sequences (6,7) and construction of a physical map of its diploid A-genome (Triticum urartu, 2n = 2x = 14) and D-genome (Aegilops tauschii, 2n = 2x = 14) progenitors (6)(7)(8).…”