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Genome-wide DNA polymorphism and transcriptome analysis of an early-maturing rice mutant

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Abstract

In order to develop a rice population with improved important traits such as flowering time, we developed 2,911 M2 targeting-induced local lesions in genomes (TILLING) lines by irradiating rice seeds with γ-rays. In all, 15 M3 lines were obtained from 3 different M2 lines that exhibited an early-maturing phenotype: these plants matured approximately 25 days faster than wild-type (WT) plants. To identify genome-wide DNA polymorphisms, we performed whole-genome resequencing of both the plant types, i.e., WT and early-maturing TILLING 1 (EMT1), and obtained mapped reads of 118,488,245 bp (99.53 %) and 128,489,860 bp (99.72 %), respectively; Nipponbare was used as the reference genome. We obtained 63,648 and 147,728 single nucleotide polymorphisms (SNPs) and 33,474 and 31,082 insertions and deletions (InDels) for the WT and EMT1, respectively. Interestingly, there was a higher number of SNPs (2.6-fold) and slightly lower number of InDels (0.9-fold) in EMT1 than in WT. The expression of at least 202 structurally altered genes was changed in EMT1, and functional enrichment analysis of these genes revealed that their molecular functions were related to flower development. These results might provide a critical insight into the regulatory pathways of rice flowering.

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Abbreviations

TILLING:

Targeting-induced local lesions in genomes

EMT:

Early-maturing TILLING

WT:

Wild type

LRR-RLK:

Leucine-rich repeat receptor-like kinase

Hd1 :

Heading date 1

Ehd1 :

Early heading date 1

Ghd7 :

Grain number, plant height, and heading date 7

BAM:

Binary format

SAM:

Sequence alignment map

SNP:

Single nucleotide polymorphism

InDels:

Insertions and deletions

SVs:

Structural variations

GO:

Gene ontology

CTAB:

Cetyltrimethylammonium bromide

AFLP:

Amplified fragment length polymorphism

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Acknowledgments

This work was supported by grants from iPET (Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries), Ministry for Food, Agriculture, Forestry and Fisheries and the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ009084), Rural Development Administration, Republic of Korea and 2013 Research Grant from Kangwon National University (No. 120131456).

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Authors and Affiliations

  1. Plant Genomics Laboratory, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, South Korea

    Sun-Goo Hwang, Jin Gyu Hwang & Cheol Seong Jang

  2. Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk, 580-185, South Korea

    Dong Sub Kim

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  1. Sun-Goo Hwang
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  2. Jin Gyu Hwang
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  3. Dong Sub Kim
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  4. Cheol Seong Jang
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Correspondence to Cheol Seong Jang.

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Hwang, SG., Hwang, J.G., Kim, D.S. et al. Genome-wide DNA polymorphism and transcriptome analysis of an early-maturing rice mutant. Genetica 142, 73–85 (2014). https://doi.org/10.1007/s10709-013-9755-0

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  • DOI: https://doi.org/10.1007/s10709-013-9755-0

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