Genome-wide Detection of DNA Polymorphisms Between Two Korean Japonica Rice Varieties

Abstract

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Plant Breed. Biotech. 2015 (September) 3(3):208~215 http://dx.ABSTRACT 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.

QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing

“…Despite the detection in the relatively high PHS resistance and seed dormancy among japonica rice varieties, genetic analyses including QTL mapping have been limited in japonica rice varieties because of their low frequencies of polymorphisms in traditional markers, such as restriction-fragment length polymorphism (RFLP) and simple sequence repeats (Zhang et al 1996 ; Mackill 1995 ). Recently, next-generation sequencing (NGS) technology has enabled the large-scale detection of sequence variations among japonica rice varieties (Hori et al 2017 ; Jeong et al 2015 ; Cheon et al 2018 ) and has facilitated the development of high-throughput single nucleotide polymorphism (SNP) marker and QTL mapping in japonica varieties and populations. Among the high-throughput SNP markers, the kompetitive allele-specific PCR (KASP) marker system has the advantages of improved cost efficiency and time-effectiveness (Semagn et al 2014 ; Yuan et al 2014 ).…”

Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties

“…Next-generation sequencing (NGS) technologies have enabled the discovery of numerous sequence variants between closely related genomes, and it became possible to develop enough polymorphic markers for genotyping in populations derived from crosses between closely related varieties [ 8 , 9 , 10 , 11 ]. Single nucleotide polymorphisms (SNPs) can be identified rapidly using whole genome sequencing.…”