New Genetic Loci Associated with Preharvest Sprouting and Its Evaluation Based on the Model Equation in Rice

doi:10.3389/fpls.2017.01393

. 2017 Aug 8:8:1393.

doi: 10.3389/fpls.2017.01393. eCollection 2017.

New Genetic Loci Associated with Preharvest Sprouting and Its Evaluation Based on the Model Equation in Rice

Gi-An Lee^{1

2}, Young-Ah Jeon¹, Ho-Sun Lee³, Do Yoon Hyun¹, Jung-Ro Lee¹, Myung-Chul Lee¹, Sok-Young Lee¹, Kyung-Ho Ma¹, Hee-Jong Koh²

Affiliations

¹ National Agrobiodiversity Center, National Institute of Agricultural SciencesJeonju, South Korea.
² Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea.
³ International Technology Cooperation CenterJeonju, South Korea.

PMID: 28848592
PMCID: PMC5550670
DOI: 10.3389/fpls.2017.01393

New Genetic Loci Associated with Preharvest Sprouting and Its Evaluation Based on the Model Equation in Rice

Gi-An Lee et al. Front Plant Sci. 2017.

. 2017 Aug 8:8:1393.

doi: 10.3389/fpls.2017.01393. eCollection 2017.

Authors

Gi-An Lee^{1

2}, Young-Ah Jeon¹, Ho-Sun Lee³, Do Yoon Hyun¹, Jung-Ro Lee¹, Myung-Chul Lee¹, Sok-Young Lee¹, Kyung-Ho Ma¹, Hee-Jong Koh²

Affiliations

¹ National Agrobiodiversity Center, National Institute of Agricultural SciencesJeonju, South Korea.
² Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea.
³ International Technology Cooperation CenterJeonju, South Korea.

PMID: 28848592
PMCID: PMC5550670
DOI: 10.3389/fpls.2017.01393

Abstract

Preharvest sprouting (PHS) in rice panicles is an important quantitative trait that causes both yield losses and the deterioration of grain quality under unpredictable moisture conditions at the ripening stage. However, the molecular mechanism underlying PHS has not yet been elucidated. Here, we explored the genetic loci associated with PHS in rice and formulated a model regression equation for rapid screening for use in breeding programs. After re-sequencing 21 representative accessions for PHS and performing enrichment analysis, we found that approximately 20,000 SNPs revealed distinct allelic distributions between PHS resistant and susceptible accessions. Of these, 39 candidate SNP loci were selected, including previously reported QTLs. We analyzed the genotypes of 144 rice accessions to determine the association between PHS and the 39 candidate SNP loci, 10 of which were identified as significantly affecting PHS based on allele type. Based on the allele types of the SNP loci, we constructed a regression equation for evaluating PHS, accounting for an R² value of 0.401 in japonica rice. We validated this equation using additional accessions, which exhibited a significant R² value of 0.430 between the predicted values and actual measurements. The newly detected SNP loci and the model equation could facilitate marker-assisted selection to predict PHS in rice germplasm and breeding lines.

Keywords: dormancy; genetic resources; preharvest sprouting (PHS); regression model; rice.

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Figures

**FIGURE 1**
SNP Density plot of SNPs between PHS resistant and susceptible accessions and the locations of reported QTLs; SNP loci associated with PHS and GI in tested accessions are presented.

**FIGURE 2**
Validation of regression equation model for PHS; 56 *japonica* accessions. ^∗ [PHS predicted value = 33.082 - 12.171(qLTG3.1) - 14.479(V2) - 11.629(V5) - 20.62(S4) + 22.544(S21) + 12.209(S3) + 10.864(S13) + 11.767(Awn)]

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References

1. Bailey P., Mckibbin R., Lenton J., Holdsworth M., Flintham J., Gale M. (1999). Genetic map locations for orthologous Vp1 genes in wheat and rice. Theor. Appl. Genet. 98 281–284. 10.1007/s001220051069 - DOI
1. Basra S., Farooq M., Tabassam R., Ahmad N. (2005). Physiological and biochemical aspects of pre-sowing seed treatments in fine rice (Oryza sativa L.). Seed Sci. Technol. 33 623–628. 10.15258/sst.2005.33.3.09 - DOI
1. Bentsink L., Jowett J., Hanhart C. J., Koornneef M. (2006). Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 103 17042–17047. 10.1073/pnas.0607877103 - DOI - PMC - PubMed
1. Bewley J. D., Black M. (1982). Physiology and Biochemistry of Seeds in Relation to Germination: Viability, Dormancy and Environmental Control Vol. 2. Berlin: Springer-Verlag; 10.1007/978-3-642-68643-6 - DOI
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[1] Bailey P., Mckibbin R., Lenton J., Holdsworth M., Flintham J., Gale M. (1999). Genetic map locations for orthologous Vp1 genes in wheat and rice. Theor. Appl. Genet. 98 281–284. 10.1007/s001220051069 - DOI

[2] Bailey P., Mckibbin R., Lenton J., Holdsworth M., Flintham J., Gale M. (1999). Genetic map locations for orthologous Vp1 genes in wheat and rice. Theor. Appl. Genet. 98 281–284. 10.1007/s001220051069 - DOI

[3] Basra S., Farooq M., Tabassam R., Ahmad N. (2005). Physiological and biochemical aspects of pre-sowing seed treatments in fine rice (Oryza sativa L.). Seed Sci. Technol. 33 623–628. 10.15258/sst.2005.33.3.09 - DOI

[4] Basra S., Farooq M., Tabassam R., Ahmad N. (2005). Physiological and biochemical aspects of pre-sowing seed treatments in fine rice (Oryza sativa L.). Seed Sci. Technol. 33 623–628. 10.15258/sst.2005.33.3.09 - DOI

[5] Bentsink L., Jowett J., Hanhart C. J., Koornneef M. (2006). Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 103 17042–17047. 10.1073/pnas.0607877103 - DOI - PMC - PubMed

[6] Bentsink L., Jowett J., Hanhart C. J., Koornneef M. (2006). Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 103 17042–17047. 10.1073/pnas.0607877103 - DOI - PMC - PubMed

[7] Bewley J. D., Black M. (1982). Physiology and Biochemistry of Seeds in Relation to Germination: Viability, Dormancy and Environmental Control Vol. 2. Berlin: Springer-Verlag; 10.1007/978-3-642-68643-6 - DOI

[8] Bewley J. D., Black M. (1982). Physiology and Biochemistry of Seeds in Relation to Germination: Viability, Dormancy and Environmental Control Vol. 2. Berlin: Springer-Verlag; 10.1007/978-3-642-68643-6 - DOI

[9] Bolger A. M., Lohse M., Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 2114–2120. 10.1093/bioinformatics/btu170 - DOI - PMC - PubMed

[10] Bolger A. M., Lohse M., Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 2114–2120. 10.1093/bioinformatics/btu170 - DOI - PMC - PubMed

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New Genetic Loci Associated with Preharvest Sprouting and Its Evaluation Based on the Model Equation in Rice

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New Genetic Loci Associated with Preharvest Sprouting and Its Evaluation Based on the Model Equation in Rice

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