Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9–1
Abstract
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 genemore »
- Authors:
-
[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)
- Univ. of California, Davis, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Huazhong Agricultural Univ., Hubei (China)
- Univ. of California, Davis, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Huazhong Agricultural Univ., Hubei (China)
- Xiamen Univ., Xiamen (People's Republic of China)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1545157
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Rice
- Additional Journal Information:
- Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1939-8425
- Publisher:
- Springer Nature
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Oryza sativaL.; Whole-genome sequencing; Grain shape; Fast-neutron-induced mutant population; Kitaake mutant database
Citation Formats
Jiang, Liangrong, Li, Guotian, Chern, Mawsheng, Jain, Rashmi, Pham, Nhan T., Martin, Joel A., Schackwitz, Wendy S., Zhao, Juan, Ruan, Deling, Huang, Rongyu, Zheng, Jingsheng, and Ronald, Pamela C. Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9–1. United States: N. p., 2019.
Web. doi:10.1186/s12284-019-0308-8.
Jiang, Liangrong, Li, Guotian, Chern, Mawsheng, Jain, Rashmi, Pham, Nhan T., Martin, Joel A., Schackwitz, Wendy S., Zhao, Juan, Ruan, Deling, Huang, Rongyu, Zheng, Jingsheng, & Ronald, Pamela C. Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9–1. United States. https://doi.org/10.1186/s12284-019-0308-8
Jiang, Liangrong, Li, Guotian, Chern, Mawsheng, Jain, Rashmi, Pham, Nhan T., Martin, Joel A., Schackwitz, Wendy S., Zhao, Juan, Ruan, Deling, Huang, Rongyu, Zheng, Jingsheng, and Ronald, Pamela C. Thu .
"Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9–1". United States. https://doi.org/10.1186/s12284-019-0308-8. https://www.osti.gov/servlets/purl/1545157.
@article{osti_1545157,
title = {Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9–1},
author = {Jiang, Liangrong and Li, Guotian and Chern, Mawsheng and Jain, Rashmi and Pham, Nhan T. and Martin, Joel A. and Schackwitz, Wendy S. and Zhao, Juan and Ruan, Deling and Huang, Rongyu and Zheng, Jingsheng and Ronald, Pamela C.},
abstractNote = {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.},
doi = {10.1186/s12284-019-0308-8},
journal = {Rice},
number = 1,
volume = 12,
place = {United States},
year = {2019},
month = {7}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 3 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid
journal, October 2000
- Tan, Y. F.; Xing, Y. Z.; Li, J. X.
- Theoretical and Applied Genetics, Vol. 101, Issue 5-6
A Novel and Pleiotropic Factor SLENDER GRAIN3 Is Involved in Regulating Grain Size in Rice
journal, May 2018
- Zhongkang, Wang; Dongdong, Zeng; Ran, Qin
- Rice Science, Vol. 25, Issue 3
A Kinesin-Like Protein Is Essential for Oriented Deposition of Cellulose Microfibrils and Cell Wall Strength
journal, December 2002
- Zhong, Ruiqin; Burk, David H.; Morrison, W. Herbert
- The Plant Cell, Vol. 14, Issue 12
Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis
journal, January 2011
- Ashelford, Kevin; Eriksson, Maria E.; Allen, Christopher M.
- Genome Biology, Vol. 12, Issue 3
Genome Resilience and Prevalence of Segmental Duplications Following Fast Neutron Irradiation of Soybean
journal, September 2014
- Bolon, Yung-Tsi; Stec, Adrian O.; Michno, Jean-Michel
- Genetics, Vol. 198, Issue 3
Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome
journal, January 2008
- Ríos, Gabino; Naranjo, Miguel A.; Iglesias, Domingo J.
- BMC Genomics, Vol. 9, Issue 1
The million mutation project: A new approach to genetics in Caenorhabditis elegans
journal, June 2013
- Thompson, O.; Edgley, M.; Strasbourger, P.
- Genome Research, Vol. 23, Issue 10
Map-based cloning of a gene controlling omega-3 fatty acid desaturation in Arabidopsis
journal, November 1992
- Arondel, V.; Lemieux, B.; Hwang, I.
- Science, Vol. 258, Issue 5086
Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana
journal, April 2012
- Belfield, E. J.; Gan, X.; Mithani, A.
- Genome Research, Vol. 22, Issue 7
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
- Xia, Duo; Zhou, Hao; Liu, Rongjia
- Molecular Plant, Vol. 11, Issue 5
A Receptor Kinase-Like Protein Encoded by the Rice Disease Resistance Gene, Xa21
journal, December 1995
- Song, W. -Y.; Wang, G. -L.; Chen, L. -L.
- Science, Vol. 270, Issue 5243
Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation
journal, July 2016
- Li, Guotian; Chern, Mawsheng; Jain, Rashmi
- Molecular Plant, Vol. 9, Issue 7
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
journal, December 2011
- Xu, Xun; Liu, Xin; Ge, Song
- Nature Biotechnology, Vol. 30, Issue 1
The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality
journal, July 2015
- Wang, Shaokui; Li, Shan; Liu, Qian
- Nature Genetics, Vol. 47, Issue 8
‘Green revolution’ genes encode mutant gibberellin response modulators
journal, July 1999
- Peng, Jinrong; Richards, Donald E.; Hartley, Nigel M.
- Nature, Vol. 400, Issue 6741
MULTI-TILLERING DWARF1, a new allele of BRITTLE CULM 12, affects plant height and tiller in rice
journal, December 2016
- Yu, Haiping; Ren, Deyong; Zhu, Yangzhou
- Science Bulletin, Vol. 61, Issue 23
High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies
journal, August 2008
- Srivatsan, Anjana; Han, Yi; Peng, Jianlan
- PLoS Genetics, Vol. 4, Issue 8
OsSPL13 controls grain size in cultivated rice
journal, March 2016
- Si, Lizhen; Chen, Jiaying; Huang, Xuehui
- Nature Genetics, Vol. 48, Issue 4
The origin of the naked grains of maize
journal, August 2005
- Wang, Huai; Nussbaum-Wagler, Tina; Li, Bailin
- Nature, Vol. 436, Issue 7051
Overexpression of the Endoplasmic Reticulum Chaperone BiP3 Regulates XA21-Mediated Innate Immunity in Rice
journal, February 2010
- Park, Chang-Jin; Bart, Rebecca; Chern, Mawsheng
- PLoS ONE, Vol. 5, Issue 2
Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing
journal, May 2009
- Irvine, D. V.; Goto, D. B.; Vaughn, M. W.
- Genome Research, Vol. 19, Issue 6
EMS- and relation-induced mutation frequencies at individual loci in Arabidopsis thaliana (L.) Heynh
journal, March 1982
- Koornneeff, M.; Dellaert, L. W. M.; van der Veen, J. H.
- Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 93, Issue 1
Deletion in a gene associated with grain size increased yields during rice domestication
journal, July 2008
- Shomura, Ayahiko; Izawa, Takeshi; Ebana, Kaworu
- Nature Genetics, Vol. 40, Issue 8
Caenorhabditis elegans mutant allele identification by whole-genome sequencing
journal, August 2008
- Sarin, Sumeet; Prabhu, Snehit; O'Meara, M. Maggie
- Nature Methods, Vol. 5, Issue 10
GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality
journal, March 2018
- Zhao, Dong-Sheng; Li, Qian-Feng; Zhang, Chang-Quan
- Nature Communications, Vol. 9, Issue 1
Analysis of the early-flowering mechanisms and generation of T-DNA tagging lines in Kitaake, a model rice cultivar
journal, August 2013
- Kim, Song Lim; Choi, Minkyung; Jung, Ki-Hong
- Journal of Experimental Botany, Vol. 64, Issue 14
Genetic bases of rice grain shape: so many genes, so little known
journal, April 2013
- Huang, Rongyu; Jiang, Liangrong; Zheng, Jingsheng
- Trends in Plant Science, Vol. 18, Issue 4
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
- Li, Juan; Jiang, Jiafu; Qian, Qian
- The Plant Cell, Vol. 23, Issue 2
A fast neutron deletion mutagenesis-based reverse genetics system for plants: Fast neutron deletion mutagenesis-based reverse genetics
journal, August 2001
- Li, Xin; Song, Yujuan; Century, Karen
- The Plant Journal, Vol. 27, Issue 3
Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification
journal, September 2018
- Li, Guotian; Jones, Kyle C.; Eudes, Aymerick
- BMC Biotechnology, Vol. 18, Issue 1
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
- Guo, Tao; Chen, Ke; Dong, Nai-Qian
- The Plant Cell, Vol. 30, Issue 4
Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley
journal, July 2006
- Zhang, L.; Fetch, T.; Nirmala, J.
- Theoretical and Applied Genetics, Vol. 113, Issue 5
The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies
journal, June 2017
- Li, Guotian; Jain, Rashmi; Chern, Mawsheng
- The Plant Cell, Vol. 29, Issue 6
Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley
journal, July 2006
- Zhang, L.; Fetch, T.; Nirmala, J.
- Theoretical and Applied Genetics, Vol. 113, Issue 5
Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid
journal, October 2000
- Tan, Y. F.; Xing, Y. Z.; Li, J. X.
- Theoretical and Applied Genetics, Vol. 101, Issue 5-6
MULTI-TILLERING DWARF1, a new allele of BRITTLE CULM 12, affects plant height and tiller in rice
journal, December 2016
- Yu, Haiping; Ren, Deyong; Zhu, Yangzhou
- Science Bulletin, Vol. 61, Issue 23
EMS- and relation-induced mutation frequencies at individual loci in Arabidopsis thaliana (L.) Heynh
journal, March 1982
- Koornneeff, M.; Dellaert, L. W. M.; van der Veen, J. H.
- Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 93, Issue 1
Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation
journal, July 2016
- Li, Guotian; Chern, Mawsheng; Jain, Rashmi
- Molecular Plant, Vol. 9, Issue 7
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
- Xia, Duo; Zhou, Hao; Liu, Rongjia
- Molecular Plant, Vol. 11, Issue 5
Genetic bases of rice grain shape: so many genes, so little known
journal, April 2013
- Huang, Rongyu; Jiang, Liangrong; Zheng, Jingsheng
- Trends in Plant Science, Vol. 18, Issue 4
‘Green revolution’ genes encode mutant gibberellin response modulators
journal, July 1999
- Peng, Jinrong; Richards, Donald E.; Hartley, Nigel M.
- Nature, Vol. 400, Issue 6741
The origin of the naked grains of maize
journal, August 2005
- Wang, Huai; Nussbaum-Wagler, Tina; Li, Bailin
- Nature, Vol. 436, Issue 7051
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
journal, December 2011
- Xu, Xun; Liu, Xin; Ge, Song
- Nature Biotechnology, Vol. 30, Issue 1
Caenorhabditis elegans mutant allele identification by whole-genome sequencing
journal, August 2008
- Sarin, Sumeet; Prabhu, Snehit; O'Meara, M. Maggie
- Nature Methods, Vol. 5, Issue 10
GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality
journal, March 2018
- Zhao, Dong-Sheng; Li, Qian-Feng; Zhang, Chang-Quan
- Nature Communications, Vol. 9, Issue 1
Exploiting a fast neutron mutant genetic resource in Pisum sativum (pea) for functional genomics
journal, January 2013
- Domoney, Claire; Knox, Maggie; Moreau, Carol
- Functional Plant Biology, Vol. 40, Issue 12
Analysis of the early-flowering mechanisms and generation of T-DNA tagging lines in Kitaake, a model rice cultivar
journal, August 2013
- Kim, Song Lim; Choi, Minkyung; Jung, Ki-Hong
- Journal of Experimental Botany, Vol. 64, Issue 14
Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing
journal, May 2009
- Irvine, D. V.; Goto, D. B.; Vaughn, M. W.
- Genome Research, Vol. 19, Issue 6
Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana
journal, April 2012
- Belfield, E. J.; Gan, X.; Mithani, A.
- Genome Research, Vol. 22, Issue 7
The million mutation project: A new approach to genetics in Caenorhabditis elegans
journal, June 2013
- Thompson, O.; Edgley, M.; Strasbourger, P.
- Genome Research, Vol. 23, Issue 10
A Kinesin-Like Protein Is Essential for Oriented Deposition of Cellulose Microfibrils and Cell Wall Strength
journal, December 2002
- Zhong, Ruiqin; Burk, David H.; Morrison, W. Herbert
- The Plant Cell, Vol. 14, Issue 12
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
- Li, Juan; Jiang, Jiafu; Qian, Qian
- The Plant Cell, Vol. 23, Issue 2
The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies
journal, June 2017
- Li, Guotian; Jain, Rashmi; Chern, Mawsheng
- The Plant Cell, Vol. 29, Issue 6
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
- Guo, Tao; Chen, Ke; Dong, Nai-Qian
- The Plant Cell, Vol. 30, Issue 4
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
- Zhang, Mu; Zhang, Baocai; Qian, Qian
- The Plant Journal, Vol. 63, Issue 2
Map-based cloning of a gene controlling omega-3 fatty acid desaturation in Arabidopsis
journal, November 1992
- Arondel, V.; Lemieux, B.; Hwang, I.
- Science, Vol. 258, Issue 5086
A Receptor Kinase-Like Protein Encoded by the Rice Disease Resistance Gene, Xa21
journal, December 1995
- Song, W. -Y.; Wang, G. -L.; Chen, L. -L.
- Science, Vol. 270, Issue 5243
Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome
journal, January 2008
- Ríos, Gabino; Naranjo, Miguel A.; Iglesias, Domingo J.
- BMC Genomics, Vol. 9, Issue 1
High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies
journal, August 2008
- Srivatsan, Anjana; Han, Yi; Peng, Jianlan
- PLoS Genetics, Vol. 4, Issue 8
Overexpression of the Endoplasmic Reticulum Chaperone BiP3 Regulates XA21-Mediated Innate Immunity in Rice
journal, February 2010
- Park, Chang-Jin; Bart, Rebecca; Chern, Mawsheng
- PLoS ONE, Vol. 5, Issue 2
Works referencing / citing this record:
MINI SEED 2 (MIS2) Encodes a Receptor-like Kinase that Controls Grain Size and Shape in Rice
journal, January 2020
- Chun, Yan; Fang, Jingjing; Zafar, Syed Adeel
- Rice, Vol. 13, Issue 1