Uncovering the genetic architecture of seed weight and size in intermediate wheatgrass through linkage and association mapping

Authors: ZHANG, XIAOFEI - University Of Minnesota; Larson, Steven; GAO, LIANGLIANG - University Of Minnesota; TEH, SOON - University Of Minnesota; DEHAAN, LEE - The Land Institute; FRASER, MAX - University Of Minnesota; SALLAM, AHMAD - University Of Minnesota; KANTARSKI, TRACI - Kansas State University; FRELS, KATHERINE - University Of Minnesota; POLAND, JESSE - Kansas State University; WYSE, DONALD - University Of Minnesota; ANDERSON, JAMES - University Of Minnesota

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/10/2017
Publication Date: 11/28/2017
Citation: Zhang, X., Larson, S.R., Gao, L., Teh, S., Dehaan, L.R., Fraser, M., Sallam, A., Kantarski, T., Frels, K., Poland, J., Wyse, D., Anderson, J.A. 2017. Uncovering the genetic architecture of seed weight and size in intermediate wheatgrass through linkage and association mapping. The Plant Genome. doi:10.3835/plantgenome2017.03.0022.
DOI: https://doi.org/10.3835/plantgenome2017.03.0022

Interpretive Summary: Intermediate wheatgrass is being developed as a new perennial grain crop that has a large complex genome, comprised of three sets of seven chromosome pairs, similar to that of bread wheat. Breeding for increased seed weight is one of the primary goals for improving grain yield of this new crop. However, the genetic control of seed weight and size has not been characterized and selective breeding in intermediate wheatgrass may be more intricate than wheat because of its self-incompatible mating system and perennial growth habit. In this project, we evaluated seed weight, seed area size, seed width and seed length over multiple years, in a heterogeneous breeding poulation comprised of 1,126 plants and two clonally replicated bi-parental families comprised of 172 and 265 progeny. These plants were also screened using 4,731 genetic markers identified by DNA sequencing through a process known as genotype-by-sequencing (GBS). These 4,731 DNA markers have known map positions across all three sets of seven chromosome pairs, making it possible to identify genes and chromosome regions, known as quantitative trait loci (QTL), associated with seed trait variation in these populations. Thirty-three QTL associated with seed weight and size were identified in the heterogeneous breeding population, of which 23 were verified in the biparental families. About 37.6% of seed weight variation in the breeding population was explained by 15 QTL, 12 of which also contributed to either seed length or seed width. Results also indicated that the frequency of favorable QTL alleles were increased to more than 46% by selective breeding. Results of this study fulfill an important milestone in the breeding and gentic analysis seed and grain traits of a new perennial grain crop, intermediate wheatgrass.

Technical Abstract: Intermediate wheatgrass (IWG); Thinopyrum intermedium) is being developed as a new perennial grain crop that has a large allohexaploid genome similar to that of wheat (Triticum aestivum). Breeding for increased seed weight is one of the primary goals for improving grain yield of IWG. As a new crop, however, the genetic architecture of seed weight and size has not been characterized and selective breeding of IWG may be more intricate than wheat because of its self-incompatible mating system and perennial growth habit. Here, seed weight, seed area size, seed width and seed length were evaluated over multiple years, in a heterogeneous breeding population comprised of 1,126 genets and two clonally replicated bi-parental populations comprised of 172 and 265 genets. Among 10,171 DNA markers discovered using genotyping-by-sequencing (GBS) in the breeding population, 4,731 markers were present in a consensus genetic map previously constructed using seven full-sib populations including the two bi-parental populations evaluated in this study. Thirty-three quantitative trait loci (QTL) associated with seed weight and size were identified using association mapping, of which 23 were verified using linkage mapping in the bi-parental populations. About 37.6% of seed weight variation in the breeding population was explained by 15 QTL, 12 of which also contributed to either seed length or seed width. When performing either phenotypic selection or genomic selection for seed weight, we observed the frequency of favorable QTL alleles were increased to more than 46%. This study provides a broad reference analysis of QTL controlling seed weight and size that have been mapped on the IWG consensus genetic map. By combining association mapping and genomic selection, we should be able to effectively select the favorable QTL alleles for seed weight and size in IWG breeding populations.