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Illumina-based genetic linkage map for wheat leaf rust.

Joly, D.L., Mulock, B.S., Cuomo, C.A., Saville, B.J., McCallum, B.D., and Bakkeren, G. (2013). "Illumina-based genetic linkage map for wheat leaf rust.", 27th American Genetics Society meeting on Fungal Genetics, Asilomar, CA, USA

Abstract

Few genetic maps have been made for rust fungi; yet they are useful in identifying candidate loci for phenotypic traits or in unravelling chromosomal arrangements. This lack of maps is, in part, due to the obligate biotrophic nature of rusts and the difficulties in manipulating their life cycle in a way that enables controlled crosses. Recently, the genome sequence of a wheat leaf rust (Puccinia triticina) isolate was determined and this prompted the sequencing of additional isolates using next-generation sequencing technologies. This has dramatically increased the amount of sequence information available at a substantially decreased per base cost. Fifty-seven F2 progeny of a wheat leaf rust sexual cross between race 9 (SBDG) and race 161 (FBDJ) were sequenced using Illumina. In order to generate a high-resolution genetic linkage map, genome-wide single-nucleotide polymorphisms (SNPs) were identified. Employing the genome sequence information from the two parents and the F1 isolate, more than 25,000 SNPs were selected and used to generate a genetic linkage map. Although they were obtained from different isolates, the genetic map and the reference genome were integrated, allowing the creation of pseudomolecules. Those represent a strong improvement over the currently fragmented status of the reference genome. Moreover, at least 9 seedling and 2 adult-plant avirulence genes were shown to segregate in this F2 population and candidate genes identified using the genetic map are currently being investigated.

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