Genome-wide Searching of Single-nucleotide Polymorphisms among Eight Distantly and Closely Related Rice Cultivars (Oryza sativa L.) and a Wild Accession (Oryza rufipogon Griff.)

Abstract

We searched the genomes of eight rice cultivars (Oryza sativa L. ssp. japonica and ssp. indica) and a wild rice accession (Oryza rufipogon Griffith) for nucleotide polymorphisms, and identified 7805 polymorphic loci, including single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels), in predicted intergenic regions. Polymorphisms are useful as DNA markers for genetic analysis or positional cloning with segregating populations of crosses. Pairwise comparison between cultivars and a neighbor-joining tree calculated from SNPs agreed very well with relationships between rice strains predicted from pedigree data or calculated with other DNA markers such as p-SINE1 and simple sequence repeats (SSRs), suggesting that whole-genome SNP information can be used for analysis of evolutionary relationships. Using multiple SNPs to identify alleles, we drew a map to illustrate the alleles shared among the eight cultivars and the accession. The map revealed that most of the genome is mono- or di-allelic among japonica cultivars, whereas alleles well conserved among modern japonica paddy rice cultivars were often shared with indica cultivars or wild rice, suggesting that the genome structure of modern cultivars is composed of chromosomal segments from various genetic backgrounds. Use of allele-sharing analysis and association analysis were also tested and are discussed.

Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.)

“…In general, SNP frequency varied depending on the genomic region sequenced and the cultivar. Generally, intergenic regions had relatively many SNPs; for example, the intergenic regions of the indica cultivars GLA4 and Kasalath had 6.30 and 7.33 SNPs per 1 kb, respectively, compared with the reference Nipponbare japonica cultivar (Monna et al 2006). In contrast, when both intergenic regions and genes were included, the detection rate was relatively low; for example, indica cultivar 93-11 had 1.7 SNPs per 1 kb compared with Nipponbare (Feltus et al 2004).…”

Chromosomal Location of HWA1 and HWA2, Complementary Hybrid Weakness Genes in Rice

“…Most of the new markers were based on the indel between Nipponbare and an indica cultivar 93-11 (Shen et al 2004) or those between Nipponbare and Kasalath or an indica cultivar Guangluai 4 (Monna et al 2006). Markers were named by adding KG to the original indel information ID, R*** (Shen et al 2004) or S**** (Monna et al 2006).…”

“…Markers were named by adding KG to the original indel information ID, R*** (Shen et al 2004) or S**** (Monna et al 2006). In redesigning or developing DNA markers, we made alignments of Nipponbare genome sequence (IRGSP 2005), 93-11 genome sequence (Yu et al 2002) and/or BAC-end sequence of Kasalath (http://rgp.dna.affrc.go.jp/blast/runblast.html, Katagiri et al 2004) using DNAsis Pro (Hitachi Software Engineering Co.).…”

Fluorogenic Ribonuclease Protection (FRIP) Analysis of Single Nucleotide Polymorphisms (SNPs) in Japanese Rice (Oryza sativaL.) DNA for Cultivar Discrimination

“…These markers include random amplified polymorphic DNAs (RAPDs), [5][6][7][8][9] simple sequence repeats (SSRs), [10][11][12] amplified fragment length polymorphisms (AFLP), 13) and single nucleotide polymorphisms (SNPs). 14) Improvements in sequencing technology, combined with the availability of expressed sequence tags (ESTs) has led to a rapid increase in public databases for SNPs, insertions, and deletions (indels).…”