[Intellectual contribution]

Definition of the pedigree haplotypes of modern rice cultivars in Japan revealed by genome wide SNPs

Toshio YAMAMOTO, Hideki NAGASAKI, Jun-ichi YONEMARU, Kaworu EBANA, Maiko NAKAJIMA, Taeko SHIBAYA, Masahiro YANO

QTL Genomics Research Center

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   The process of crossing and selection during plant breeding has resulted in the recombination and shuffling of ancestral chromosome blocks (haplotypes) to create new variation. The identification of such haplotypes in developed cultivars provides valuable information to support further improvement of rice and other crops. However, owing to technical limitations, fine-scale definition of pedigree haplotypes based on a large number of DNA markers has not yet been performed. In this context, single-nucleotide polymorphisms (SNPs) identified by means of high-throughput genotyping based on array technology could be a useful tool. Two independent technological innovations, the high-throughput sequencer and hybridization arrays, have provided a new opportunity to determine the historical flow of pedigree haplotypes during the breeding of rice cultivars.
   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. The 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. The Koshihikari consensus genome was composed of 654,543 contigs with an average of 468 bp. We detected a total of 67,051 SNPs between Koshihikari and Nipponbare. The distributions of the SNPs were uneven within a chromosome (Fig. 1).
   A high-throughput typing array consisting of 1,917 SNP sites, which are based on the information obtained by comparison of the two sequences and 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 (Fig. 2). The proportions of the Koshihikari genome present in Hitomebore, Akitakomachi and Hinohikari, which are the second, third, and fourth most-grown cultivars in Japan and were developed by crossing with Koshihikari, were estimated to be 80.8%, 80.0% and 61.3% respectively. Eighteen consensus haplotype blocks longer than 1 Mb are inherited from traditional landraces to these four modern varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity.
   Detection of genome-wide SNPs by both highthroughput 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. The definition of pedigree haplotypes by means of genome-wide SNPs analysis will facilitate nextgeneration breeding of rice and other crops.

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Fig. 1  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.

Fig. 2  Patterns of the pedigree haplotype blocks of Koshihikari and its related cultivars Only haplotype blocks longer than 500-kb of Koshihikari and consensus haplotype blocks among three progeny cultivars, Hitomebore, Akitakomachi , and Hinohikari are shown. The black bars at the top indicate the range of the blocks in the 12 rice 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. 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, Akitakomachi, and Hinohikari. (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.

[Reference]

Yamamoto T, Nagasaki H, Yonemaru JI, Ebana K, Nakajima M, Shibaya T, Yano M (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms, BMC Genomics, 11:267.

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