The genetic basis for panicle trait variation in switchgrass (Panicum virgatum)

Zhang, Li; MacQueen, Alice; Weng, Xiaoyu; Behrman, Kathrine D.; Bonnette, Jason; Reilley, John L.; Rouquette, Jr., Francis M.; Fay, Philip A.; Wu, Yanqi; Fritschi, Felix B.; Mitchell, Robert B.; Lowry, David B.; Boe, Arvid R.; Juenger, Thomas E.

doi:10.1007/s00122-022-04096-x

Title: The genetic basis for panicle trait variation in switchgrass (Panicum virgatum)

Journal Article · 01 July 2022 · Theoretical and Applied Genetics

DOI: https://doi.org/10.1007/s00122-022-04096-x · OSTI ID:1893936

^[1]; MacQueen, Alice ^[2]; Weng, Xiaoyu ^[2]; Behrman, Kathrine D. ^[2]; Bonnette, Jason ^[2]; Reilley, John L. ^[3]; Rouquette, Jr., Francis M. ^[4]; Fay, Philip A. ^[5]; Wu, Yanqi ^[6]; Fritschi, Felix B. ^[7]; Mitchell, Robert B. ^[8]; Lowry, David B. ^[9]; Boe, Arvid R. ^[10];

^[2]

Univ. of Texas, Austin, TX (United States); University of Texas at Austin Department of Integrative Biology
Univ. of Texas, Austin, TX (United States)
US Department of Agriculture, Kingsville, TX (United States)
Texas A & M Univ., Overton, TX (United States)
US Dept. of Agriculture, Temple, TX (United States)
Oklahoma State Univ., Stillwater, OK (United States)
Univ. of Missouri, Columbia, MO (United States)
Univ. of Nebraska, Lincoln, NE (United States)
Michigan State Univ., East Lansing, MI (United States)
South Dakota State Univ., Brookings, SD (United States)

Grass species exhibit large diversity in panicle architecture influenced by genes, the environment, and their interaction. The genetic study of panicle architecture in perennial grasses is limited. In this study, we evaluate the genetic basis of panicle architecture including panicle length, primary branching number, and secondary branching number in an outcrossed switchgrass QTL population grown across ten field sites in the central USA through multi-environment mixed QTL analysis. We also evaluate genetic effects in a diversity panel of switchgrass grown at three of the ten field sites using genome-wide association (GWAS) and multivariate adaptive shrinkage. Furthermore, we search for candidate genes underlying panicle traits in both of these independent mapping populations. Overall, 18 QTL were detected in the QTL mapping population for the three panicle traits, and 146 unlinked genomic regions in the diversity panel affected one or more panicle trait. Twelve of the QTL exhibited consistent effects (i.e., no QTL by environment interactions or no QTL × E), and most (four of six) of the effects with QTL × E exhibited site-specific effects. Most (59.3%) significant partially linked diversity panel SNPs had significant effects in all panicle traits and all field sites and showed pervasive pleiotropy and limited environment interactions. Panicle QTL co-localized with significant SNPs found using GWAS, providing additional power to distinguish between true and false associations in the diversity panel.

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Research Organization:: Great Lakes Bioenergy Research Center, Madison, WI (United States); Univ. of Texas, Austin, TX (United States)

Sponsoring Organization:: National Science Foundation Plant Genome Research Program; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: FC02-07ER64494; SC0014156; SC0018409

OSTI ID:: 1893936

Journal Information:: Theoretical and Applied Genetics, Journal Name: Theoretical and Applied Genetics Journal Issue: 8 Vol. 135; ISSN 0040-5752

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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