Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9–1

Journal Article · · Rice
ORCiD logo [1];  [2];  [3];  [3];  [3];  [4];  [4];  [5];  [3];  [6];  [6];  [3]
  1. Xiamen Univ., Xiamen (People’s Republic of China); Univ. of California, Davis, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Univ. of California, Davis, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Huazhong Agricultural Univ., Hubei (China)
  3. Univ. of California, Davis, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. Huazhong Agricultural Univ., Hubei (China)
  6. Xiamen Univ., Xiamen (People's Republic of China)
+ Show Author Affiliations

Breeding for genes controlling key agronomic traits is an important goal of rice genetic improvement. To gain insight into genes controlling grain morphology, we screened M3 plants derived from 1,000 whole-genome sequenced (WGS) M2 Kitaake mutants to identify lines with altered grain size. RESULTS:In this study, we isolated a mutant, named fast-neutron (FN) 60-4, which exhibits a significant reduction in grain size. We crossed FN60-4 with the parental line Kitaake and analyzed the resulting backcross population. Segregation analysis of 113 lines from the BC2F2 population revealed that the mutant phenotype is controlled by a single semi-dominant locus. Mutant FN60-4 is reduced 20% in plant height and 8.8% in 1000-grain weight compared with Kitaake. FN60-4 also exhibits an 8% reduction in cell number and a 9% reduction in cell length along the vertical axis of the glume. We carried out whole-genome sequencing of DNA pools extracted from segregants with long grains or short grains, and revealed that one gene, LOC_Os09g02650, cosegregated with the grain size phenotype in the BC1F2 and BC2F2 populations. This mutant allele was named grain shape 9-1 (gs9-1). gs9-1 carries a 3-bp deletion that affects two amino acids. This locus is a new allele of the BC12/GDD1/MTD1 gene that encodes a kinesin-like protein involved in cell-cycle progression, cellulose microfibril deposition and gibberellic acid (GA) biosynthesis. The GA biosynthesis-related gene KO2 is down-regulated in gs9-1. The dwarf phenotype of gs9-1 can be rescued by adding exogenous GA3. In contrast to the phenotypes for the other alleles, the gs9-1 is less severe, consistent with the nature of the mutation, which does not disrupt the open reading frame as observed for the other alleles. In this study, we isolated a mutant, which exhibits altered grain shape and identified the mutated gene, gs9-1. Our study reveals that gs9-1 is a semi-dominant gene that carries a two-amino acid mutation. gs9-1 is allelic to the BC12/GDD1/MTD1 gene involved in GA biosynthesis. These results demonstrate the efficiency and convenience of cloning genes from the whole-genome sequenced Kitaake mutant population to advance investigations into genes controlling key agronomic traits in rice.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1545157
Journal Information:
Rice, Journal Name: Rice Journal Issue: 1 Vol. 12; ISSN 1939-8425
Publisher:
Springer NatureCopyright Statement
Country of Publication:
United States
Language:
English

References (63)

Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley journal July 2006
The million mutation project: A new approach to genetics in Caenorhabditis elegans journal June 2013
‘Green revolution’ genes encode mutant gibberellin response modulators journal July 1999
EMS- and relation-induced mutation frequencies at individual loci in Arabidopsis thaliana (L.) Heynh journal March 1982
A Kinesin-Like Protein Is Essential for Oriented Deposition of Cellulose Microfibrils and Cell Wall Strength journal December 2002
Caenorhabditis elegans mutant allele identification by whole-genome sequencing journal August 2008
EMS- and relation-induced mutation frequencies at individual loci in Arabidopsis thaliana (L.) Heynh journal March 1982
GRAIN SIZE AND NUMBER1 Negatively Regulates the OsMKKK10-OsMKK4-OsMPK6 Cascade to Coordinate the Trade-off between Grain Number per Panicle and Grain Size in Rice journal March 2018
The origin of the naked grains of maize journal August 2005
GL3.3, a Novel QTL Encoding a GSK3/SHAGGY-like Kinase, Epistatically Interacts with GS3 to Produce Extra-long Grains in Rice journal May 2018
A Novel and Pleiotropic Factor SLENDER GRAIN3 Is Involved in Regulating Grain Size in Rice journal May 2018
OsSPL13 controls grain size in cultivated rice journal March 2016
The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies journal June 2017
The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies journal June 2017
Deletion in a gene associated with grain size increased yields during rice domestication journal July 2008
A fast neutron deletion mutagenesis-based reverse genetics system for plants: Fast neutron deletion mutagenesis-based reverse genetics journal August 2001
Brittle Culm 12, a dual-targeting kinesin-4 protein, controls cell-cycle progression and wall properties in rice: BC12 affects cell cycle and wall modification journal April 2010
Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification journal September 2018
Caenorhabditis elegans mutant allele identification by whole-genome sequencing journal August 2008
Mutation of Rice BC12/GDD1 , Which Encodes a Kinesin-Like Protein That Binds to a GA Biosynthesis Gene Promoter, Leads to Dwarfism with Impaired Cell Elongation journal February 2011
Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana journal April 2012
Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid journal October 2000
MULTI-TILLERING DWARF1, a new allele of BRITTLE CULM 12, affects plant height and tiller in rice journal December 2016
The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality journal July 2015
Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome journal January 2008
GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality journal March 2018
The million mutation project: A new approach to genetics in Caenorhabditis elegans journal June 2013
High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies journal August 2008
Genetic bases of rice grain shape: so many genes, so little known journal April 2013
MULTI-TILLERING DWARF1, a new allele of BRITTLE CULM 12, affects plant height and tiller in rice journal December 2016
Map-based cloning of a gene controlling omega-3 fatty acid desaturation in Arabidopsis journal November 1992
Analysis of the early-flowering mechanisms and generation of T-DNA tagging lines in Kitaake, a model rice cultivar journal August 2013
‘Green revolution’ genes encode mutant gibberellin response modulators journal July 1999
GRAIN SIZE AND NUMBER1 Negatively Regulates the OsMKKK10-OsMKK4-OsMPK6 Cascade to Coordinate the Trade-off between Grain Number per Panicle and Grain Size in Rice journal March 2018
Overexpression of the Endoplasmic Reticulum Chaperone BiP3 Regulates XA21-Mediated Innate Immunity in Rice journal February 2010
Exploiting a fast neutron mutant genetic resource in Pisum sativum (pea) for functional genomics journal January 2013
Analysis of the early-flowering mechanisms and generation of T-DNA tagging lines in Kitaake, a model rice cultivar journal August 2013
Overexpression of the Endoplasmic Reticulum Chaperone BiP3 Regulates XA21-Mediated Innate Immunity in Rice journal February 2010
A Receptor Kinase-Like Protein Encoded by the Rice Disease Resistance Gene, Xa21 journal December 1995
GL3.3, a Novel QTL Encoding a GSK3/SHAGGY-like Kinase, Epistatically Interacts with GS3 to Produce Extra-long Grains in Rice journal May 2018
Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification [Supplemental Data] collection September 2018
Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome journal January 2008
Mutation of Rice BC12/GDD1 , Which Encodes a Kinesin-Like Protein That Binds to a GA Biosynthesis Gene Promoter, Leads to Dwarfism with Impaired Cell Elongation journal February 2011
Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation journal July 2016
Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation journal July 2016
Genetic bases of rice grain shape: so many genes, so little known journal April 2013
Genome Resilience and Prevalence of Segmental Duplications Following Fast Neutron Irradiation of Soybean journal September 2014
Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid journal October 2000
Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana journal April 2012
Exploiting a fast neutron mutant genetic resource in Pisum sativum (pea) for functional genomics journal January 2013
Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing journal May 2009
Map-based cloning of a gene controlling omega-3 fatty acid desaturation in Arabidopsis journal November 1992
Brittle Culm 12, a dual-targeting kinesin-4 protein, controls cell-cycle progression and wall properties in rice: BC12 affects cell cycle and wall modification journal April 2010
The origin of the naked grains of maize journal August 2005
Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley journal July 2006
Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis journal January 2011
Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing journal May 2009
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes journal December 2011
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes journal December 2011
A Kinesin-Like Protein Is Essential for Oriented Deposition of Cellulose Microfibrils and Cell Wall Strength journal December 2002
GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality journal March 2018
A Receptor Kinase-Like Protein Encoded by the Rice Disease Resistance Gene, Xa21 journal December 1995
High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies journal August 2008

Cited By (1)

MINI SEED 2 (MIS2) Encodes a Receptor-like Kinase that Controls Grain Size and Shape in Rice journal January 2020

Linked Research (6)

Similar Records

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Oryza sativaL.
Whole-genome sequencing
Grain shape
Fast-neutron-induced mutant population
Kitaake mutant database