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

Abstract

Background: To 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.

Results: The total 5.89-Gb sequence for Koshihikari, equivalent to 15.7 x 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 diversity

Conclusions: Detection 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.

Figure 1

Frequency distribution of contig lengths among the Koshihikari reads. The contig lengths represent consensus sequences of the Koshihikari reads mapped to the Nipponbare genome.

Figure 2

Distribution of SNPs between Koshihikari and Nipponbare in the 12 rice chromosomes. The number of SNPs in each chromosome is shown in brackets. The x-axis represents the physical distance along each chromosome, split into 500-kb windows. The orange lines represent regions in which no SNPs were detected. The y-axis indicates the common logarithm of the number of SNPs.

Figure 3

Patterns of the pedigree haplotype blocks of Koshihikari and its related cultivars. Only haplotype blocks longer than 500-kb of Koshihikari (No. 61 in additional file 3) and consensus haplotype blocks among three progeny cultivars, Hitomebore (117), Akitakomachi (100), and Hinohikari (113) are shown. The black bars at the top indicate the range of the blocks in the 12 rice chromosomes. Vertical gray lines represent the borders between chromosomes. The numbers at the right indicate the proportion of the Koshihikari genome accounted for by the haplotype blocks. (A) Patterns of haplotype blocks in 12 parental cultivars in the pedigree chart of Koshihikari. Five warm colors (the red component of the 24-bit RGB color equaled 255 for all colors) indicate that the haplotype blocks were derived from the paternal parent, Norin1 (No. 39). Seven cool colors (the red component of the 24-bit RGB color equaled 0 for all colors) indicate that the haplotype blocks were derived from the maternal parent, Norin22 (47). Gray indicates unidentified haplotype blocks that may have been derived from either parent. The three yellow arrows indicate pedigree haplotypes that inherited more than 2 Mb of their length with a density of more than 1 SNP/100 kb. (B) The haplotype blocks of Koshihikari in three progeny cultivars, Hitomebore (117), Akitakomachi (100), and Hinohikari (113). (C) Consensus haplotype blocks between Koshihikari and the three progeny cultivars. Only blocks derived from the six ancestral cultivars of Koshihikari (purple and red names) are indicated. Red horizontal bars represent consensus haplotype blocks longer than 1 Mb and the names of the ancestral landraces.

Figure 4

Haplotype diversity index values for the 12 rice chromosomes in Japanese landraces and modern cultivars. The diversity index was calculated on the basis of a 10-SNP window (see Methods for details). The number of haplotype windows (n) is indicated in parentheses. The x-axis shows the position between the start and end of the haplotype window. The y-axis shows the haplotype diversity index, which is calculated as the number of haplotypes divided by the number of cultivars in each group. The details of Groups 1, 2, and 3 are described in the Results and in additional file 3.