Exploring the tertiary gene pool of bread wheat: sequence assembly and analysis of chromosome 5Mg of Aegilops geniculata |
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Authors: | Vijay K. Tiwari Shichen Wang Tatiana Danilova Dal Hoe Koo Jan Vrána Marie Kubaláková Eva Hribova Nidhi Rawat Bhanu Kalia Narinder Singh Bernd Friebe Jaroslav Doležel Eduard Akhunov Jesse Poland Jamal S. M. Sabir Bikram S. Gill |
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Affiliation: | 1. Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, USA;2. Department of Plant Pathology, Kansas State University, Manhattan, KS, USA;3. Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic;4. Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia |
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Abstract: | Next‐generation sequencing (NGS) provides a powerful tool for the discovery of important genes and alleles in crop plants and their wild relatives. Despite great advances in NGS technologies, whole‐genome shotgun sequencing is cost‐prohibitive for species with complex genomes. An attractive option is to reduce genome complexity to a single chromosome prior to sequencing. This work describes a strategy for studying the genomes of distant wild relatives of wheat by isolating single chromosomes from addition or substitution lines, followed by chromosome sorting using flow cytometry and sequencing of chromosomal DNA by NGS technology. We flow‐sorted chromosome 5Mg from a wheat/Aegilops geniculata disomic substitution line [DS5Mg (5D)] and sequenced it using an Illumina HiSeq 2000 system at approximately 50 × coverage. Paired‐end sequences were assembled and used for structural and functional annotation. A total of 4236 genes were annotated on 5Mg, in close agreement with the predicted number of genes on wheat chromosome 5D (4286). Single‐gene FISH indicated no major chromosomal rearrangements between chromosomes 5Mg and 5D. Comparing chromosome 5Mg with model grass genomes identified synteny blocks in Brachypodium distachyon, rice (Oryza sativa), sorghum (Sorghum bicolor) and barley (Hordeum vulgare). Chromosome 5Mg‐specific SNPs and cytogenetic probe‐based resources were developed and validated. Deletion bin‐mapped and ordered 5Mg SNP markers will be useful to track 5M‐specific introgressions and translocations. This study provides a detailed sequence‐based analysis of the composition of a chromosome from a distant wild relative of bread wheat, and opens up opportunities to develop genomic resources for wild germplasm to facilitate crop improvement. |
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Keywords: | flow sorting SNPs next generation sequencing single gene FISH GenomeZipper synteny |
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