PMID- 31740504
OWN - NLM
STAT- MEDLINE
DCOM- 20210203
LR  - 20210203
IS  - 1532-2548 (Electronic)
IS  - 0032-0889 (Print)
IS  - 0032-0889 (Linking)
VI  - 182
IP  - 2
DP  - 2020 Feb
TI  - Shared Genetic Control of Root System Architecture between Zea mays and Sorghum 
      bicolor.
PG  - 977-991
LID - 10.1104/pp.19.00752 [doi]
AB  - 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.
CI  - (c) 2020 American Society of Plant Biologists. All Rights Reserved.
FAU - Zheng, Zihao
AU  - Zheng Z
AUID- ORCID: 0000-0003-0598-462X
AD  - Department of Agronomy, Iowa State University, Ames, Iowa 50011.
AD  - Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, 
      Ames, Iowa 50011.
FAU - Hey, Stefan
AU  - Hey S
AD  - Department of Agronomy, Iowa State University, Ames, Iowa 50011.
AD  - INRES, Institute of Crop Science and Resource Conservation, Crop Functional 
      Genomics, University of Bonn, Bonn 53113, Germany.
FAU - Jubery, Talukder
AU  - Jubery T
AD  - Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011.
FAU - Liu, Huyu
AU  - Liu H
AD  - Department of Agronomy, Iowa State University, Ames, Iowa 50011.
AD  - Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, 
      Ames, Iowa 50011.
AD  - Department of Plant Genetics & Breeding, China Agricultural University, Beijing 
      100193, China.
FAU - Yang, Yu
AU  - Yang Y
AD  - Department of Agronomy, Iowa State University, Ames, Iowa 50011.
AD  - Department of Plant Genetics & Breeding, China Agricultural University, Beijing 
      100193, China.
FAU - Coffey, Lisa
AU  - Coffey L
AD  - Department of Agronomy, Iowa State University, Ames, Iowa 50011.
FAU - Miao, Chenyong
AU  - Miao C
AUID- ORCID: 0000-0002-0904-3707
AD  - Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 
      Nebraska 68583.
FAU - Sigmon, Brandi
AU  - Sigmon B
AUID- ORCID: 0000-0003-3914-6894
AD  - Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska 
      68583.
FAU - Schnable, James C
AU  - Schnable JC
AUID- ORCID: 0000-0001-6739-5527
AD  - Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 
      Nebraska 68583 schnable@iastate.edu.
FAU - Hochholdinger, Frank
AU  - Hochholdinger F
AUID- ORCID: 0000-0002-5155-0884
AD  - INRES, Institute of Crop Science and Resource Conservation, Crop Functional 
      Genomics, University of Bonn, Bonn 53113, Germany.
FAU - Ganapathysubramanian, Baskar
AU  - Ganapathysubramanian B
AD  - Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011.
FAU - Schnable, Patrick S
AU  - Schnable PS
AUID- ORCID: 0000-0001-9169-5204
AD  - Department of Agronomy, Iowa State University, Ames, Iowa 50011 
      schnable@iastate.edu.
AD  - Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, 
      Ames, Iowa 50011.
AD  - Department of Plant Genetics & Breeding, China Agricultural University, Beijing 
      100193, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20191118
PL  - United States
TA  - Plant Physiol
JT  - Plant physiology
JID - 0401224
SB  - IM
MH  - Biological Variation, Population/*genetics
MH  - Databases, Genetic
MH  - Gene Regulatory Networks
MH  - Genetic Association Studies
MH  - Genome-Wide Association Study
MH  - Genotype
MH  - Image Processing, Computer-Assisted
MH  - Phenotype
MH  - Plant Roots/*anatomy & histology/*genetics/metabolism
MH  - Polymorphism, Single Nucleotide
MH  - Quantitative Trait Loci
MH  - Software
MH  - Sorghum/anatomy & histology/*genetics/metabolism
MH  - Zea mays/anatomy & histology/*genetics/metabolism
PMC - PMC6997706
EDAT- 2019/11/20 06:00
MHDA- 2021/02/04 06:00
PMCR- 2019/11/18
CRDT- 2019/11/20 06:00
PHST- 2019/06/20 00:00 [received]
PHST- 2019/11/03 00:00 [accepted]
PHST- 2019/11/20 06:00 [pubmed]
PHST- 2021/02/04 06:00 [medline]
PHST- 2019/11/20 06:00 [entrez]
PHST- 2019/11/18 00:00 [pmc-release]
AID - pp.19.00752 [pii]
AID - 201900752R1 [pii]
AID - 10.1104/pp.19.00752 [doi]
PST - ppublish
SO  - Plant Physiol. 2020 Feb;182(2):977-991. doi: 10.1104/pp.19.00752. Epub 2019 Nov 
      18.