The genetic basis for panicle trait variation in switchgrass (Panicum virgatum)
Abstract
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 environmentmore »
- Authors:
-
[1];
[1]
- 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)
- Publication Date:
- Research Org.:
- Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States); Univ. of Texas, Austin, TX (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation Plant Genome Research Program
- OSTI Identifier:
- 1893936
- Grant/Contract Number:
- SC0018409; FC02-07ER64494; SC0014156; IOS-1444533
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Theoretical and Applied Genetics
- Additional Journal Information:
- Journal Volume: 135; Journal Issue: 8; Journal ID: ISSN 0040-5752
- Publisher:
- Springer Nature
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
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., and Juenger, Thomas E. The genetic basis for panicle trait variation in switchgrass (Panicum virgatum). United States: N. p., 2022.
Web. doi:10.1007/s00122-022-04096-x.
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. The genetic basis for panicle trait variation in switchgrass (Panicum virgatum). United States. https://doi.org/10.1007/s00122-022-04096-x
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., and Juenger, Thomas E. Sat .
"The genetic basis for panicle trait variation in switchgrass (Panicum virgatum)". United States. https://doi.org/10.1007/s00122-022-04096-x. https://www.osti.gov/servlets/purl/1893936.
@article{osti_1893936,
title = {The genetic basis for panicle trait variation in switchgrass (Panicum virgatum)},
author = {Zhang, Li and MacQueen, Alice and Weng, Xiaoyu and Behrman, Kathrine D. and Bonnette, Jason and Reilley, John L. and Rouquette, Jr., Francis M. and Fay, Philip A. and Wu, Yanqi and Fritschi, Felix B. and Mitchell, Robert B. and Lowry, David B. and Boe, Arvid R. and Juenger, Thomas E.},
abstractNote = {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.},
doi = {10.1007/s00122-022-04096-x},
journal = {Theoretical and Applied Genetics},
number = 8,
volume = 135,
place = {United States},
year = {Sat Jul 02 00:00:00 EDT 2022},
month = {Sat Jul 02 00:00:00 EDT 2022}
}
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