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

Kayla R Altendorf, Lee R. DeHaan, Steve R. Larson, James A. Anderson

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

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 (IWG) [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey] 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 use the IWG nested association mapping (NAM) population, with 1,168 F1 progeny across 10 families to dissect the genetic control of brittle rachis, floret shattering, and threshability. We used a genome-wide association study (GWAS) with 8,003 single nucleotide polymorphism (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 quantitative trait loci (QTL) using GWAS and 20 using the combined linkage analysis were detected, 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 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 to 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.

Original languageEnglish (US)
Article numbere20145
JournalPlant Genome
Volume14
Issue number3
DOIs
StatePublished - Nov 2021

Bibliographical note

Funding Information:
This work was supported by the Perennial Agriculture Project in conjunction with the Malone Family Land Preservation Foundation and The Land Institute. The authors would like to thank Xiaofei Zhang for obtaining funding for this project and assistance in initiating the population, Garett C. Heineck for assistance on phenotypic data collection and analysis methodology, Prabin Bajgain for guidance in developing genotyping by sequencing libraries, and Jeff Neyhart for extensive instruction in genomic data handling. Furthermore, thank you to Brett Heim and Marty Christians for technical assistance in processing and in the field. Thanks to the numerous University of Minnesota undergraduate students, 2017 & 2018 summer interns at The Land Institute for assistance in data collection Thank you to the Minnesota Agricultural Student Trainee Program (MAST), specifically Andressa Spuri Azarias, Arthur Martins, Oswaldo Birungi, Caroline Elmer, Phoebe Wanjira, and Mario Fagundes for assistance with harvesting and postharvest processing procedures, including the repeated dropping of many, many spikes from 20 cm height.

Funding Information:
This work was supported by the Perennial Agriculture Project in conjunction with the Malone Family Land Preservation Foundation and The Land Institute. The authors would like to thank Xiaofei Zhang for obtaining funding for this project and assistance in initiating the population, Garett C. Heineck for assistance on phenotypic data collection and analysis methodology, Prabin Bajgain for guidance in developing genotyping by sequencing libraries, and Jeff Neyhart for extensive instruction in genomic data handling. Furthermore, thank you to Brett Heim and Marty Christians for technical assistance in processing and in the field. Thanks to the numerous University of Minnesota undergraduate students, 2017 & 2018 summer interns at The Land Institute for assistance in data collection Thank you to the Minnesota Agricultural Student Trainee Program (MAST), specifically Andressa Spuri Azarias, Arthur Martins, Oswaldo Birungi, Caroline Elmer, Phoebe Wanjira, and Mario Fagundes for assistance with harvesting and postharvest processing procedures, including the repeated dropping of many, many spikes from 20 cm height.

Publisher Copyright:
© 2021 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America

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