<i>Aegilops tauschii</i> single nucleotide polymorphisms shed light on the origins of wheat D‐genome genetic diversity and pinpoint the geographic origin of hexaploid wheat

Wang, Jirui; Luo, Ming‐Cheng; Chen, Zhongxu; You, Frank M.; Wei, Yuming; Zheng, Yu; Dvořák, Jan

doi:10.1111/nph.12164

Cited by 233 publications

(289 citation statements)

References 46 publications

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“…Neutral SNP and restriction fragment length polymorphism (RFLP) were shown to have a greater rate of loss in low-recombination regions of Ae. tauschii chromosomes than in high-recombination regions (33,34), presumably due to the effects of selection sweeps and background selection. Polymorphic noncollinear genes must be affected by the same processes as other neutral polymorphism and hence have a greater rate of loss in low-recombination regions compared with high-recombination regions.…”

Section: Discussionmentioning

confidence: 99%

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

Luo

You

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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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)...

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Section: Discussionmentioning

confidence: 99%

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

Luo

You

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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195

259

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“…tauschii populations used as the direct D-genome donors for common wheat are considered to be distributed in a narrow range relative to the entire species range (Feldman, 2001), suggesting that the huge genetic diversity of Ae. tauschii is not necessarily represented in common wheat and that the early-flowering lines of wheat synthetics should include early-flowering D-genome alleles that have not been introduced into the D-genome of Japanese common wheat cultivars (Matsuoka et al, 2013;Wang et al, 2013). Here, we conducted QTL analyses for floweringrelated traits using two F 2 populations derived from crosses between Japanese common wheat cultivars and two selected lines of the early-flowering wheat synthetics to examine whether the D-genome QTLs from Ae.…”

Section: Introductionmentioning

confidence: 99%

Quantitative trait locus analysis for flowering-related traits using two F<sub>2</sub> populations derived from crosses between Japanese common wheat cultivars and synthetic hexaploids

et al. 2015

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Flowering time is an important trait for Japanese wheat breeding. Aegilops tauschii, the D-genome donor of hexaploid wheat, is a useful resource to enlarge the D-genome diversity of common wheat. Previously, we identified floweringrelated QTLs in F 2 populations of synthetic hexaploid wheat lines between the tetraploid wheat cultivar Langdon and Ae. tauschii accessions. Here, to evaluate the usefulness of the early-flowering alleles from Ae. tauschii for Japanese wheat breeding, QTL analyses were conducted in two F 2 populations derived from crosses between Japanese wheat cultivars and early-flowering lines of synthetic hexaploid wheat. Only two chromosomal regions controlling flowering-related traits were identified, on chromosomes 2DS and 5AL in the mapping populations, and no previously identified QTLs were found in the synthetic hexaploid lines. The strong effect of the 2DS QTL, putatively corresponding to Ppd-D1, was considered to hide any significant expression of other QTLs with small effects on flowering-related traits. When F 2 individuals carrying Ae. tauschii-homozygous alleles around the 2DS QTL region were selected, the Ae. tauschii-derived alleles of the previously identified flowering QTLs partly showed an early-flowering phenotype compared with the Japanese wheat-derived alleles. Thus, some early-flowering alleles from Ae. tauschii may be useful for production of early-flowering Japanese wheat cultivars.

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“…meyeri. We selected from this population accession CIae23 35 for the construction of the second Ae. tauschii BNG map.…”

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Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

Luo

Puiu

et al. 2017

Nature

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Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat 1 (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat [2][3][4] . The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence 5 .Here we use an array of advanced technologies, including orderedclone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a referencequality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes.

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Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D‐genome genetic diversity and pinpoint the geographic origin of hexaploid wheat

Cited by 233 publications

References 46 publications

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

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

Quantitative trait locus analysis for flowering-related traits using two F<sub>2</sub> populations derived from crosses between Japanese common wheat cultivars and synthetic hexaploids

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

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