Next‐generation sequencing and syntenic integration of flow‐sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content

Abstract

SUMMARYWheat is the third most important crop for human nutrition in the world. The availability of high-resolution genetic and physical maps and ultimately a complete genome sequence holds great promise for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread wheat (Triticum aestivum) genome (approximately 17 Gb/1C) and the triplication of genic sequence resulting from its hexaploid status have impeded genome sequencing of this important crop species. Here we describe the use of mitotic chromosome flow sorting to separately purify and then shotgun-sequence a pair of telocentric chromosomes that together form chromosome 4A (856 Mb/1C) of wheat. The isolation of this much reduced template and the consequent avoidance of the problem of sequence duplication, in conjunction with synteny-based comparisons with other grass genomes, have facilitated construction of an ordered gene map of chromosome 4A, embracing ‡85% of its total gene content, and have enabled precise localization of the various translocation and inversion breakpoints on chromosome 4A that differentiate it from its progenitor chromosome in the A genome diploid donor. The gene map of chromosome 4A, together with the emerging sequences of homoeologous wheat chromosome groups 4, 5 and 7, represent unique resources that will allow us to obtain new insights into the evolutionary dynamics between homoeologous chromosomes and syntenic chromosomal regions.

Draft genome of the wheat A-genome progenitor Triticum urartu

“…In comparison with the 28,000 genes estimated for the A genome of hexaploid wheat 7 , our gene set for T. urartu contained 6,800 more members, indicating a more complete representation of genes in our analysis. However, the different approaches used in this work and in a previous study 7 , and the extensive loss of genes in the hexaploid A genome compared with its diploid progenitor 8 , may also have contributed to this difference.…”

“…6) and 4A (ref. 7). More recently, a whole-genome shotgun sequence analysis of bread wheat and its diploid relatives 8 has allocated more than 60% of the genes to the A, B and D genomes with more than 70% confidence.…”

Flow cytometric chromosome sorting from diploid progenitors of bread wheat, T. urartu, Ae. speltoides and Ae. tauschii

“…The inactivation of major nOrs was also observed after the formation of the allopolyploid Aegilops species (Badaeva et al 2004;Molnár et al 2011a;Feldman et al 2012). The difference in the hybridization pattern of chromosome 4A between T. urartu and bread wheat is due to the pericentric inversion of 4A and translocations involving chromosomes 5A and 7B, which occurred at the polyploid level (Hernandez et al 2012). Smaller differences in the FISH karyotype were detected between Ae.…”

A Review of Genome Sequencing in the Largest Cereal Genome, <i>Triticum aestivum</i> L.

“…The Genome Zipper approach [72] makes use of comparisons of shotgun sequences with reference grass genomes such as Brachypodium, rice and sorghum. Genes identified within the syntenic regions generated by these comparisons are used to construct a genomic build along a scaffold of markers, taking into account the order of the sequence tagged genes within their reference genomes and the order deduced from the scaffold of markers [73]. Vitulo et al (2011) [74] generated a genome zipper for the short and long arms of chromosome 5A of wheat by identifying conserved homologies in Brachypodium, rice and sorghum.…”