ArticleBreeding science2015
Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar 'Koshihikari'.
Article in Breeding science, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 29 citations in OpenAlex.
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- Substitution Mapping of a Locus Responsible for Hybrid Breakdown in Populations Derived From Interspecific Introgression Line.Frontiers in plant science · 2021Article
- Genome- wide structural and functional variant discovery of rice landraces using genotyping by sequencing.Molecular biology reports · 2020Article
- Identification and characterization of the stunted sterile (ss) mutant in rice.Genes & genomics · 2020Article
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- Detection of dominant QTLs for stigma exsertion ratio in rice derived fromBreeding science · 2019Article
- Rapid DNA-genotyping system targeting ten loci for resistance to blast disease in rice.Breeding science · 2019Article
- Genetic analysis of male sterility obtained from a rice cultivar Lebed backcrossed with Taichung 65.Rice (New York, N.Y.) · 2018Article
- Haplotype-based allele mining in the Japan-MAGIC rice population.Scientific reports · 2018Article
- Genome-Wide Analysis of Genetic Variations and the Detection of Rich Variants of NBS-LRR Encoding Genes in Common Wild Rice Lines.Plant molecular biology reporter · 2018Article
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- Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.).International journal of molecular sciences · 2016Article
- Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice.Scientific reports · 2016Article
- Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar 'Koshihikari' was performed to extract regions containing large indels (10-51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between 'Koshihikari' and other diverse cultivars, we subtracted the indel regions detected in 'Koshihikari' from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including 'Khao Nam Jen' as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.
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