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.
Highlights
To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices
We applied an array-based single-nucleotide polymorphism (SNP) detection system to 151 representative Japanese japonica rice cultivars, and were able to define haplotype blocks and trace their inheritance during rice breeding in Japan, even though these cultivars were closely related. These results revealed the changes in genetic diversity in particular chromosomal regions during the long history of rice breeding in Japan
The reliability of the pedigree haplotype depends on the number of SNPs in the respective haplotype blocks, we could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome
Summary
To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. We designed a high-throughput typing array based on the SNP information by comparison of the two sequences We applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition. Several types of DNA markers with high levels of polymorphism between indica and japonica cultivars have been reported, but the level of polymorphism within japonica is low [4,5,6,7]. Despite this low level of DNA polymorphism, wide phenotypic diversity is believed to exist [8]. The detection of genome-wide SNPs in eukaryotes using high-throughput resequencing has been reported for the human, nematode, Arabidopsis, and rice genomes [18,19,20,21]
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