Meta-analysis identifies pleiotropic loci controlling phenotypic trade-offs in sorghum

Mural, Ravi V.; Grzybowski, Marcin; Miao, Chenyong; Damke, Alyssa; Sapkota, Sirjan; Boyles, Richard E.; Salas Fernandez, Maria G.; Schnable, Patrick S.; Sigmon, Brandi; Kresovich, Stephen; Schnable, James C.; Juenger, ed., T. E.

doi:10.1093/genetics/iyab087

Title: Meta-analysis identifies pleiotropic loci controlling phenotypic trade-offs in sorghum

Journal Article · Tue Jun 08 00:00:00 EDT 2021 · Genetics (Online)

DOI:https://doi.org/10.1093/genetics/iyab087· OSTI ID:1808016

^[1];

^[1]; Damke, Alyssa ^[2]; Sapkota, Sirjan ^[3];

^[4]; Salas Fernandez, Maria G. ^[5];

^[5]; Sigmon, Brandi ^[2]; Kresovich, Stephen ^[6];

^[1]; Juenger, ed., T. E.

Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA, Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634, USA
Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634, USA, Pee Dee Research and Education Center, Clemson University, Florence, SC 29532, USA
Department of Agronomy, Iowa State University, Ames, IA 50010, USA
Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634, USA, Feed the Future Innovation Lab for Crop Improvement, Cornell University, Ithaca, NY 14850, USA

Abstract Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here, we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome-wide association studies (GWAS) conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35–43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.

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Research Organization:: Univ. of Nebraska, Lincoln, NE (United States)

Sponsoring Organization:: USDOE Advanced Research Projects Agency - Energy (ARPA-E); USDOE Office of Science (SC), Biological and Environmental Research (BER); Foundation for Food and Agriculture Research; National Science Foundation (NSF)

Grant/Contract Number:: SC0020355; 18/CJ000/01/0; OIA-1826781

OSTI ID:: 1808016

Alternate ID(s):: OSTI ID: 1853602

Journal Information:: Genetics (Online), Journal Name: Genetics (Online) Vol. 218 Journal Issue: 3; ISSN 1943-2631

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum Mace, Emma S.; Tai, Shuaishuai; Gilding, Edward K. Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms3320	journal	August 2013
Genetic architecture of photosynthesis in Sorghum bicolor under non-stress and cold stress conditions Ortiz, Diego; Hu, Jieyun; Salas Fernandez, Maria G. Journal of Experimental Botany, Vol. 68, Issue 16 https://doi.org/10.1093/jxb/erx276	journal	July 2017
Sorghum Dw1, an agronomically important gene for lodging resistance, encodes a novel protein involved in cell proliferation Yamaguchi, Miki; Fujimoto, Haruka; Hirano, Ko Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep28366	journal	June 2016
Comparative Genetics of Seed Size Traits in Divergent Cereal Lineages Represented by Sorghum (Panicoidae) and Rice (Oryzoidae) Zhang, D.; Li, J.; Compton, R. O. G3: Genes\|Genomes\|Genetics, Vol. 5, Issue 6 https://doi.org/10.1534/g3.115.017590	journal	March 2015
Genome-Wide Association Study for Nine Plant Architecture Traits in Sorghum Zhao, Jing; Mantilla Perez, Maria B.; Hu, Jieyun The Plant Genome, Vol. 9, Issue 2 https://doi.org/10.3835/plantgenome2015.06.0044	journal	January 2016

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59 BASIC BIOLOGICAL SCIENCES
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