Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

Abstract

BackgroundTo create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP) data is required to permit discrimination of chromosome segments among modern cultivars, which are genetically related. Here, we used a high-throughput sequencer to conduct whole-genome sequencing of an elite Japanese rice cultivar, Koshihikari, which is closely related to Nipponbare, whose genome sequencing has been completed. Then we designed a high-throughput typing array based on the SNP information by comparison of the two sequences. Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition.ResultsThe total 5.89-Gb sequence for Koshihikari, equivalent to 15.7× the entire rice genome, was mapped using the Pseudomolecules 4.0 database for Nipponbare. The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67 051 SNPs. A high-throughput typing array consisting of 1917 SNP sites distributed throughout the genome was designed to genotype 151 representative Japanese cultivars that have been grown during the past 150 years. We could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome and 18 consensus haplotype blocks which are inherited from traditional landraces to current improved varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversityConclusionsDetection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties. With the aid of their pedigree information, we clarified the dynamics of chromosome recombination during the historical rice breeding process. We also found several genomic regions decreasing genetic diversity which might be caused by a recent human selection in rice breeding. The definition of pedigree haplotypes by means of genome-wide SNPs will facilitate next-generation breeding of rice and other crops.

Q-TARO: QTL Annotation Rice Online Database

“…The success of this approach implies that the use of a wide range of cross combinations might increase the opportunity to detect unique QTLs. Genome-wide SNP discovery can be performed using closely related cultivars (Yamamoto et al 2010) as well as diverse germplasm accessions (McNally et al 2009). This situation should allow us to perform QTL mapping using almost any cross combination.…”

Integration of Genomics into Rice Breeding

“…Although the application of GWA may be relied on the use of appropriate population and reliable trait evaluation, this study demonstrated a potential power of the connection between haplotype definition and selection in breeding program. In rice, whole-genome genotyping of rice based on SNPs between closely related elite japonica cultivars enabled the definition of 18 consensus haplotype blocks that have been inherited from ancestral landraces, and indicated that haplotype diversity has decreased during the history of rice breeding (Yamamoto et al 2010). The accumulated haplotype information will help us to plan breeding programs and to monitor recombination events between haplotype blocks.…”

Development and application of a 20K SNP array in potato

“…Such a SNP array requires a SNP discovery study, which is facilitated by next-generation sequencing. Different approaches for SNP discovery are used such as (1) whole genome resequencing (Yamamoto et al 2010), (2) transcriptome sequencing (Barbazuk et al 2007;Hamilton et al 2011Trick et al 2009) and (3) reduced representation sequencing based on restriction enzymes (Baird et al 2008). These studies do not need any prior knowledge of a reference genome.…”

“…The study of Uitdewilligen et al (2013) used the potato reference genome (PGSC 2011) to perform a targeted resequencing of a subset of 800 genes (2.1 Mb) from the potato genome. Many of these SNP discovery studies are based on a few genotypes, for example the parents of an important mapping population (Bundock et al 2009), one rice variety compared to the reference genome (Yamamoto et al 2010), six potato varieties (Hamilton et al 2011) or four tomato varieties combined with two wild relatives (Sim et al 2012). Even the most commonly used array in Arabidopsis was based on the sequence of only 19 accessions ).…”