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ARS Home » Midwest Area » St. Paul, Minnesota » Cereal Disease Lab » Research » Publications at this Location » Publication #334432

Title: Genotyping-by-sequencing facilitates a high resolution consensus linkage map for Aegilops umbellulata, a wild relative of cultivated wheat

item Edae, Erena
item OLIVERA, PABLO - University Of Minnesota
item Jin, Yue
item Rouse, Matthew

Submitted to: Genes, Genomes, and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/20/2017
Publication Date: 3/29/2017
Citation: Edae, E.A., Olivera, P., Jin, Y., Rouse, M.N. 2017. Genotyping-by-sequencing facilitates a high resolution consensus linkage map for Aegilops umbellulata, a wild relative of cultivated wheat. Genes, Genomes, and Genomics. 7:1551-1561.

Interpretive Summary: Stem rust is a devastating fungal disease of wheat. Emerging strains of the wheat stem rust fungus such as Ug99 threaten wheat production because of their broad virulence to currently grown wheat varieties. Several accessions of a wild relative of wheat, Aegilops umbellulata are resistant to Ug99. Identifying wheat stem rust resistance genes from wild wheat relatives such as Aegilops umbellulata is limited by a lack of genomic resources. In this work we used two biparental populations and genotyping-by-sequencing to create a consensus genetic linkage map for Aegilops umbellulata. The consensus map is composed of 5,404 markers and is the first consensus map of the diploid Aegilops umbellulata genome. This consensus map will facilitate the validation of stem rust resistance segregating in both populations and the identification of other traits of interest from Aegilops umbellulata. This work facilitates the use of traits derived from wild wheat relatives, such as Ug99 stem rust resistance, to improve wheat germplasm in order for wheat breeders to develop improved wheat varieties for the United States.

Technical Abstract: High density genetic maps are useful to precisely localize QTL or genes that might be used to improve traits of nutritional and/or economical importance in crops. However, high-density genetic maps are lacking for most wild relatives of crop species including wheat. Aegilops umbelluata is a wild relative of wheat known for its potential as a source of biotic and abiotic stress resistance genes. In this work, we have developed a framework consensus genetic map using two bi-parental populations derived from accessions PI 298905, PI 542369, PI 5422375 and PI 554395. The framework map comprised 3,009 genotype-by-sequence SNPs with a total of map size of 948.72 cM. On average, there were three SNPs per cM interval for each chromosome. Chromosome 1U was the shortest (66.5 cM) with only 81 SNPs whereas the remaining chromosomes consisted between 391 and 591 SNP markers. A total of 2,395 unmapped SNPs were added to the linkage maps through recombination frequency approach and increased the number of SNPs placed on the consensus map to a total of 5,404 markers. It was noticed that segregation distortion was disproportionally high for chromosome 1U for both populations used to construct component linkage maps, and thus segregation distortion could be one of the probable reasons for the exceptionally reduced linkage size for chromosome 1U. The present consensus map may serve as a reference for QTL mapping and validation, and as a scaffold to develop reference genome sequence for Ae. umbellulata.