Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor
Abstract
Determining the genetic control of root system architecture (RSA) in plants via large-scale genome-wide association study (GWAS) requires high-throughput pipelines for root phenotyping. We developed Core Root Excavation using compressed-air (CREAMD), a high-throughput pipeline for the cleaning of field-grown roots, and Core Root Feature Extraction (COFE), a semiautomated pipeline for the extraction of RSA traits from images. CREAMD-COFE was applied to diversity panels of maize (Zea mays) and sorghum (Sorghum bicolor), which consisted of 369 and 294 genotypes, respectively. Six RSA-traits were extracted from images collected from 3,300 maize roots and 1,470 sorghum roots. Single nucleotide polymorphism (SNP)-based GWAS identified 87 TAS (trait-associated SNPs) in maize, representing 77 genes and 115 TAS in sorghum. An additional 62 RSA-associated maize genes were identified via expression read depth GWAS. Among the 139 maize RSA-associated genes (or their homologs), 22 (16%) are known to affect RSA in maize or other species. In addition, 26 RSA-associated genes are coregulated with genes previously shown to affect RSA and 51 (37% of RSA-associated genes) are themselves transe–quantitative trait locus for another RSA-associated gene. Finally, the finding that RSA-associated genes from maize and sorghum included seven pairs of syntenic genes demonstrates the conservation of regulation of morphologymore »
- Authors:
-
[1];
[7];
[8];
[7];
[9];
[4]
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, Iowa 50011
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn 53113, Germany
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, Iowa 50011, Department of Plant Genetics & Breeding, China Agricultural University, Beijing 100193, China
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, Department of Plant Genetics & Breeding, China Agricultural University, Beijing 100193, China
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68583
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn 53113, Germany
- Publication Date:
- Research Org.:
- Iowa State Univ., Ames, IA (United States)
- Sponsoring Org.:
- USDOE Advanced Research Projects Agency - Energy (ARPA-E)
- OSTI Identifier:
- 1574532
- Alternate Identifier(s):
- OSTI ID: 1614887
- Grant/Contract Number:
- AR0000826
- Resource Type:
- Published Article
- Journal Name:
- Plant Physiology (Bethesda)
- Additional Journal Information:
- Journal Name: Plant Physiology (Bethesda) Journal Volume: 182 Journal Issue: 2; Journal ID: ISSN 0032-0889
- Publisher:
- American Society of Plant Biologists
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; root system architecture; high-throughput phenotyping; syntenic orthologs
Citation Formats
Zheng, Zihao, Hey, Stefan, Jubery, Talukder, Liu, Huyu, Yang, Yu, Coffey, Lisa, Miao, Chenyong, Sigmon, Brandi, Schnable, James C., Hochholdinger, Frank, Ganapathysubramanian, Baskar, and Schnable, Patrick S. Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor. United States: N. p., 2019.
Web. doi:10.1104/pp.19.00752.
Zheng, Zihao, Hey, Stefan, Jubery, Talukder, Liu, Huyu, Yang, Yu, Coffey, Lisa, Miao, Chenyong, Sigmon, Brandi, Schnable, James C., Hochholdinger, Frank, Ganapathysubramanian, Baskar, & Schnable, Patrick S. Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor. United States. https://doi.org/10.1104/pp.19.00752
Zheng, Zihao, Hey, Stefan, Jubery, Talukder, Liu, Huyu, Yang, Yu, Coffey, Lisa, Miao, Chenyong, Sigmon, Brandi, Schnable, James C., Hochholdinger, Frank, Ganapathysubramanian, Baskar, and Schnable, Patrick S. Mon .
"Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor". United States. https://doi.org/10.1104/pp.19.00752.
@article{osti_1574532,
title = {Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor},
author = {Zheng, Zihao and Hey, Stefan and Jubery, Talukder and Liu, Huyu and Yang, Yu and Coffey, Lisa and Miao, Chenyong and Sigmon, Brandi and Schnable, James C. and Hochholdinger, Frank and Ganapathysubramanian, Baskar and Schnable, Patrick S.},
abstractNote = {Determining the genetic control of root system architecture (RSA) in plants via large-scale genome-wide association study (GWAS) requires high-throughput pipelines for root phenotyping. We developed Core Root Excavation using compressed-air (CREAMD), a high-throughput pipeline for the cleaning of field-grown roots, and Core Root Feature Extraction (COFE), a semiautomated pipeline for the extraction of RSA traits from images. CREAMD-COFE was applied to diversity panels of maize (Zea mays) and sorghum (Sorghum bicolor), which consisted of 369 and 294 genotypes, respectively. Six RSA-traits were extracted from images collected from 3,300 maize roots and 1,470 sorghum roots. Single nucleotide polymorphism (SNP)-based GWAS identified 87 TAS (trait-associated SNPs) in maize, representing 77 genes and 115 TAS in sorghum. An additional 62 RSA-associated maize genes were identified via expression read depth GWAS. Among the 139 maize RSA-associated genes (or their homologs), 22 (16%) are known to affect RSA in maize or other species. In addition, 26 RSA-associated genes are coregulated with genes previously shown to affect RSA and 51 (37% of RSA-associated genes) are themselves transe–quantitative trait locus for another RSA-associated gene. Finally, the finding that RSA-associated genes from maize and sorghum included seven pairs of syntenic genes demonstrates the conservation of regulation of morphology across taxa.},
doi = {10.1104/pp.19.00752},
journal = {Plant Physiology (Bethesda)},
number = 2,
volume = 182,
place = {United States},
year = {Mon Nov 18 00:00:00 EST 2019},
month = {Mon Nov 18 00:00:00 EST 2019}
}
https://doi.org/10.1104/pp.19.00752
Search WorldCat to find libraries that may hold this journalWeb of Science