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Title: 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 » across taxa.« less

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [5];  [6]; ORCiD logo [7]; ORCiD logo [8]; ORCiD logo [7]; ORCiD logo [9];  [3]; ORCiD logo [4]
  1. Department of Agronomy, Iowa State University, Ames, Iowa 50011, Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, Iowa 50011
  2. 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
  3. Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011
  4. 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
  5. Department of Agronomy, Iowa State University, Ames, Iowa 50011, Department of Plant Genetics & Breeding, China Agricultural University, Beijing 100193, China
  6. Department of Agronomy, Iowa State University, Ames, Iowa 50011
  7. Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68583
  8. Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583
  9. 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. 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, and Schnable, Patrick S. Mon . "Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor". United States. doi: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 = {2019},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1104/pp.19.00752

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Cited by: 1 work
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