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Title: 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 » 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.« less

Authors:
ORCiD logo [1];  [2];  [3];  [3];  [3];  [4];  [4];  [5];  [3];  [6];  [6];  [3]
+ Show Author Affiliations
  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)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (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.
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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
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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.
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@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}
}
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    MINI SEED 2 (MIS2) Encodes a Receptor-like Kinase that Controls Grain Size and Shape in Rice
    journal, January 2020

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