Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium)

Authors: Larson, Steven; DEHAAN, LEE - The Land Institute; KANTARSKI, TRACI - Kansas State University; ZHANG, XIAOFEI - University Of Minnesota; DORN, KEVIN - Kansas State University; CRAIN, JARED - Kansas State University; POLAND, JESSE - Kansas State University; ANDERSON, JAMES - University Of Minnesota; Robbins, Matthew; Jensen, Kevin; SCHMUTZ, JEREMY - Joint Genome Institute; GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology; JENKINS, JERRY - Hudsonalpha Institute For Biotechnology; GAO, LIANGLIANG - Kansas State University; MASCHER, MARTIN - Leibniz Institute

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/30/2019
Publication Date: 6/6/2019
Citation: Larson, S.R., DeHaan, L., Kantarski, T., Zhang, X., Dorn, K., Crain, J., Poland, J., Anderson, J., Robbins, M.D., Jensen, K.B., Schmutz, J., Grimwood, J., Jenkins, J., Gao, L., Mascher, M. 2019. Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium). Journal of Theoretical and Applied Genetics. 132:2325-2351. https://doi.org/10.1007/s00122-019-03357-6.
DOI: https://doi.org/10.1007/s00122-019-03357-6

Interpretive Summary: Intermediate wheatgrass is a cross pollinated perennial grass closely related to wheat. Genetic maps and a draft genome sequence of intermediate wheatgrass have been developed to identify useful genes and accelerate its domestication as a multipurpose forage and grain crop. In this study, we identified chromosome regions controlling grain production traits in a family of 266 progeny derived from two genetically unique parents. Replicated propagules of each plant were evaluated over three years in Kansas and Utah for 17 traits. Wide variability, exceeding that of the parents, was observed for seed-size, seed-shattering, seed-threshing, inflorescence capacity, fertility, stem, and flowering traits. A total of 111 significant genetic factors were detected in 36 different regions of the 21 chromosome pairs of intermediate wheatgrass. The 25 most significant seed-size effects mapped to 14 different chromosome regions including 12 that correspond to chromosome regions that have been implicated in previous studies of other populations. Two DNA markers were associated with seed size in multiple studies and directly located within gene models that have functions related to lipid metabolism and the biosynthesis of structural carbohydrates. Chromosomes associated with traits of interest include 93 relevant gene models including the Q domesticaton gene, which is responsible for naked seeds of common wheat. A cluster of seed-size and fertility factors were located on a chromosome containing the Z self-incompatibility gene, which could have detrimental effects on pollination and seed size if there is insufficient genetic variability. These findings elucidate pathways and possible hurdles in the domestication of a perennial grain crop.

Technical Abstract: Intermediate wheatgrass (Thinopyrum intermedium), abbreviated IWG, is an outcrossing perennial Triticeae grass closely related to wheat. Genetic and physical maps of allohexaploid IWG (2n=6x=42) have been developed to identify useful genes and accelerate its domestication as a forage and grain crop. Here, we identify quantitative trait loci (QTLs) controlling IWG grain production traits in a family of 266 full-sib progenies derived from two heterozygous parents, M26 and M35. Replicated propagules of each genet were evaluated over three years and two locations for 17 traits with transgressive segregation for seed size, shattering, threshing, inflorescence capacity, fertility, stem, and flowering traits. A total of 111 QTLs were detected in 36 different regions using 3,826 genotype-by-sequence (GBS) markers in 21 linkage groups. The 25 M26 x M35 seed-size QTLs mapped to 14 different regions including 12 that correspond to QTLs or association-mapping (AM) markers identified in previous studies of other populations. Two seed-size markers, significant in QTL and association mapping tests, were directly associated with GDSL lipase and xylogalacturonan xylosyltransferase gene models from the annotated genome sequence of IWG. In total, IWG QTLs aligned to 93 of 142 relevant gene models for 44 domestication orthogenes, including the wheat Q gene. A cluster of seed-size and fertility QTLs on LG06 of homoeologous group 2 showed possible alignment to a Z self-incompatibility gene, which could have detrimental effects if there is insufficient genetic variability. These findings elucidate pathways and possible hurdles in the domestication of a perennial grain crop.