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Title: Development of the first consensus genetic map of intermediate wheatgrass (Thinopyrum intermedium) using genotyping-by-sequencing

item KANTARSKI, TRACI - Kansas State University
item Larson, Steven
item ZHANG, XIAOFEI - University Of Minnesota
item DEHAAN, LEE - The Land Institute
item ANDERSON, JAMES - University Of Minnesota
item POLAND, JESSE - Kansas State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/27/2016
Publication Date: 10/13/2016
Citation: Kantarski, T., Larson, S.R., Zhang, X., Dehaan, L., Anderson, J., Poland, J. 2016. Development of the first consensus genetic map of intermediate wheatgrass (Thinopyrum intermedium) using genotyping-by-sequencing. Theoretical and Applied Genetics. 130:137-150.

Interpretive Summary: Intermediate wheatgrass is a forage grass that has been used as a source of plant disease resistance by wheat breeders and has been identified as a species suitable for domestication and improvement as a perennial grain and biofuel crop. However, genetic research tools are needed to accelerate the process of traditional plant breeding, combat emerging new diseases of wheat, and develop of new grain and biofuel crops. Toward that goal, a high-density genetic map was developed by analyzing DNA from a total of 1259 plants comprising seven experimental breeding poulations that display economically useful characteristics including large seed size, high number of seeds per plant, good retention of ripening seeds in the field, and free-threshing grain. A total of 10,029 genetic DNA markers were identified, flanking genes throughout all 21 chromosomes of intermediate wheatgrass. These markers will enable plant breeders to track the inheritance of useful traits, locate genes controlling these traits, and identify plants with superior breeding value. These genomic research tools accelerate development of high-yielding seed, grain, and forage cultivars of intermediate wheatgrass and facilitate the transfer of unique sources of disease resistance in wheat. Improved cultivars of intermediate wheatgrass will enable intensification of sustainable agricultural systems, conservation of natural resources, and help produce global food supply for a growing world population.

Technical Abstract: Intermediate wheatgrass (Thinopyrum intermedium) has been identified as a candidate for domestication and improvement as a perennial grain, forage, and biofuel crop by several active breeding programs. To accelerate this process using genomics-assisted breeding, efficient genotyping methods and genetic marker reference maps are needed. Toward that goal, we present here the first consensus genetic map for intermediate wheatgrass, which confirms the species' allohexaploid nature with disomic inheritance (2n=6x=42) and homology to Triticeae genomes. As a first step, genotyping-by-sequencing was used to identify markers with expected segregation ratios in seven full-sib families, which were used to construct a genetic map for each population. These maps were then integrated to produce a consensus map with 21 linkage groups containing 10,029 markers, 3,601 of which were present in at least two populations. Each of the 21 linkage groups contained between 237 and 683 markers, cumulatively covering 5,061 cM with an average distance of 0.5 cM between each pair of markers. Through mapping the sequence tags to the diploid (2n=2x=14) barley reference genome, we observed high colinearity and synteny between these genomes, with three homoeologous IWG chromosomes corresponding to each of the seven barley chromosomes, and mapped translocations that are known in the Triticeae. The consenuses map is a valuable tool for concurrent work with mapping loci associated with important agronomic traits and will be beneficial for wheat breeders attempting to locate important disease-resistance genes within intermediate wheatgrass. These genomic tools can help lead to rapid improvemnt of IWG and development of high-yielding cultivars of this perennial grain that would facilitate the sustainable intensification of agricultural systems, conserving natural resources while producing food for a growing global population.