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논문 기본 정보
- 자료유형
- 학술저널
- 저자정보
- 발행연도
- 2015.1
- 수록면
- 208 - 215 (8page)
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Closely-related cultivars generally used for crossing in breeding lack sufficient known DNA polymorphisms with already developed DNA markers even though they exhibit remarkable phenotype difference. However, next-generation sequencing (NGS) enables the identification of massive DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes. This study conducted a whole-genome re-sequencing of two Korean japonica rice varieties, Junam and Nampyeong. The sequencing yielded 16.6 × 10 9 bps for Junam, and 15.1 × 10 9 bps for Nampyeong. After quality trimming and read mapping onto the reference genome sequence of Nipponbare, 11.9 × 10 9 bps from Junam and 10.6 × 10 9 bps from Nampyeong were mapped onto the reference sequence. The final effective mapping depth was 31.98x for Junam and 28.41x for Nampyeong. This study found 398,123 DNA polymophisms between Junam and Nampyeong. These were classified into 352,478 SNPs (88.5%) and 45,645 InDels (11.5%) by polymorphism types, 338,485 homozygous (85%) and 59,638 (15%) heterozygous by zygosity, and 331,855 intergenic (83.4%) and 66,268 genic (16.6%) by genomic location. To see the availability of these results in DNA marker development, Cleaved Amplified Polymorphic Sequences (CAPS) markers were developed based on 22 SNPs lying in restriction enzyme sites. Among them, 17 CAPS markers showed polymorphisms between Junam and Nampyeong. It is expected that sufficient DNA markers for mapping genes/QTLs with progeny population from a cross between Junam and Nampyeong can be developed based on the results of the study.
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등록된 정보가 없습니다.
참고문헌 (19)
참고문헌 신청
Abe A / 2012 / Genome sequencing reveals agronomically important loci in rice using MutMap / Nat Biotechnol 30:174~178
Arai-Kichise Y / 2014 / Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups / PLoS One 9:e86312
Arai-Kichise Y / 2011 / Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing / Plant Cell Physiol 52:274~282
Gao ZY / 2013 / Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences / Proc Natl Acad Sci U S A 110:14492~14497
Guo L / 2014 / Application of resequencing to rice genomics, functional genomics and evolutionary analysis / Rice (N Y) 7:4
Arai-Kichise Y / 2014 / Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups / PLoS One 9:e86312
Arai-Kichise Y / 2011 / Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing / Plant Cell Physiol 52:274~282
Gao ZY / 2013 / Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences / Proc Natl Acad Sci U S A 110:14492~14497
Guo L / 2014 / Application of resequencing to rice genomics, functional genomics and evolutionary analysis / Rice (N Y) 7:4
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