QTL for seed shattering and threshability in intermediate wheatgrass align closely with well-studied orthologs from wheat, barley, and rice

Authors: Altendorf, Kayla; DEHAAN, LEE - The Land Institute; Larson, Steven; ANDERSON, JAMES - University Of Minnesota

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/29/2021
Publication Date: 10/9/2021
Citation: Altendorf, K.R., DeHaan, L.R., Larson, S.R., Anderson, J.A. 2021. QTL for seed shattering and threshability in intermediate wheatgrass align closely with well-studied orthologs from wheat, barley, and rice. The Plant Genome. 14(3). Article e20145. https://doi.org/10.1002/tpg2.20145.
DOI: https://doi.org/10.1002/tpg2.20145

Interpretive Summary: Perennial grain crops have the potential to improve the sustainability of agriculture, however, few existing species produce enough grain yield to be economically viable. Plant breeders are selecting intensely on yield and domestication traits in the forage species, intermediate wheatgrass to develop it as the world’s first perennial grain crop for human consumption. Understanding the genetic control of these important traits may expedite the process. Genetic research into three domestication traits, including: floret and brittle rachis shattering (loss of seeds at maturity, prior to harvest) and threshing-ability revealed that the genetic control of these traits is complex and the results were dependent on families, environments, and analysis method. Regardless, many known genes that confer the same traits in other well-studied annual grass species like barley, wheat, and rice were implicated as important in intermediate wheatgrass. These results will be used to inform more efficient breeding methodologies. The results demonstrate that in the case of intermediate wheatgrass, a century worth of scientific investigation into the domestication history of annual cereal crops may inform in our efforts to domesticate their perennial relatives at unprecedented rates to improve agricultural sustainability.

Technical Abstract: Perennial grain crops have the potential to improve agricultural sustainability, but few existing species produce sufficient grain yield to be economically viable. The outcrossing, allohexaploid, and perennial forage species intermediate wheatgrass (Thinopyrum intermedium; IWG) has shown promise in undergoing direct domestication as a perennial grain crop using phenotypic and genomic selection. However, decades of selection will be required to achieve yields on par with annual small grain crops. Marker aided selection could accelerate progress if important genomic regions associated with domestication were identified. Here we utilize the IWG Nested Association Mapping (NAM) population, with 1,168 F1 progeny across ten families to dissect the genetic control of brittle rachis, floret shattering, and threshability. We used a genome-wide association study (GWAS) with 8,003 SNP markers and linkage mapping, both within-family and combined across families, with a robust phenotypic dataset collected from four unique year by location combinations. A total of 29 QTL in GWAS and in 20 in the combined linkage analysis were detected across 12 chromosomes, and most large effect QTL were in common across the two analysis methods. We reveal that the genetic control of these traits in IWG is complex, with significant QTL for the same trait across multiple chromosomes, sometimes within and across homoeologous groups, and effects that vary depending on the family. In some cases, these QTL align within 216 bp – 31 Mbp of BLAST hits for known domestication genes in related species and may serve as precise targets of selection and directions for further study to advance the domestication of IWG.