Open Access Highly Accessed Research article

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

Toshio Yamamoto, Hideki Nagasaki, Jun-ichi Yonemaru, Kaworu Ebana, Maiko Nakajima, Taeko Shibaya and Masahiro Yano*

Author Affiliations

QTL Genomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan

For all author emails, please log on.

BMC Genomics 2010, 11:267  doi:10.1186/1471-2164-11-267

Published: 27 April 2010

Additional files

Additional file 1:

Sequencing depth of the Koshihikari short reads generated using the Solexa Genome Analyzer with reference to the Nipponbare genome. The x-axis shows the physical distance along the rice reference genome (Nipponbare). Red lines indicate regions in which the Koshihikari short reads could not be mapped at all owing to low reliability of the Nipponbare reference sequence (i.e., regions containing more than 50% unidentified bases, Ns). The y-axis shows the sequencing depth, which represents the mean number of reads mapped in 100-kb windows. The mean total sequencing depth was 15.7× the genome (Table 1).

Format: PPT Size: 243KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 2:

Relationships among the coverage of the rice genome by short read contigs and the number of SNPs detected as a function of the sequencing depth. White bars correspond to the left vertical scale (% coverage of the genome by the assembled short read contigs) and the black line corresponds to the right vertical scale (number of SNPs detected).

Format: PPT Size: 125KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 3:

List of the Oryza sativa ssp. japonica cultivars used in the single-nucleotide polymorphism (SNP) analysis. (Group 1, late 1800s to about 1921; Group 2, 1931 to 1974; Group 3, 1975 to 2005).

Format: XLS Size: 48KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Population structure analysis plots with three K values (K = 2, 3, 4) using STRUCTURE program [54]. The top panel (K = 2) showed that Japanese cultivars were divided by 192 SNP genotypes of Nipponbare (Red arrow) and Koshihikari (Green arrow). This is natural result because all SNPs tested were extracted from the mapping result of Koshihikari short sequences to Nipponbare genome. The other panels show the relatively same population size of Koshihikari SNP group, but with further population subdivision within the Nipponbare SNP group from K = 3. All panels (K = 2, 3, 4) indicate that population structure was not associated with the year each cultivar released.

Format: PPT Size: 211KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 5:

Graphical representation of the genotypes of the 151 Japanese rice landraces and cultivars in additional file3 that have been grown in the past 150 years. To visualize the genome compositions of these cultivars, the SNP type is indicated in blue (Koshihikari type; No. 61 in additional file 3), in yellow (Nipponbare type; 72), in dark green (heterozygous), and in gray (missing data). The cultivar names are ordered from top to bottom by their year of development, as are the three groups (Group 1, late 1800s to about 1921; Group 2, 1931 to 1974; Group 3, 1975 to 2005).

Format: PPT Size: 1.1MB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 6:

Pedigree diagram for Japanese rice cultivars that are ancestors or descendants of Koshihikari. Numbers in parentheses are the serial numbers designated in additional file 3. Black, shaded, and white backgrounds represent the following varietal groups, respectively: Group 1 (landraces developed before 1921), Group 2 (cultivars developed from 1931 to 1974), and Group 3 (cultivars developed from 1975 to 2005). This classification is based on the categorization of R. Yamamoto [55].

Format: PPT Size: 128KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 7:

Median values of the estimate of linkage disequilibrium (D') between SNP pairs within a 5000-kb distance on rice chromosome 1. The median D' was calculated using 200-kb distances. Triangles represent the points for the simulation of the size of sliding window at distances of 0.4, 1, 2, and 3 Mb.

Format: PPT Size: 148KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 8:

Simulation results from the sliding-window haplotype analysis of cultivars in Group 1 on chromosome 1. Changes in the haplotype diversity index are based on 2-, 5-, 10-, and 15-SNP sliding windows on the assumption of a mean distance of 200 kb between adjacent SNP pairs in the rice genome. On this basis, the window sizes of the 2-, 5-, 10-, and 15-SNP sliding windows were 0.4, 1, 2, and 3 Mb respectively.

Format: PPT Size: 415KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 9:

Average number of haplotypes per 10-SNP interval.

Format: XLS Size: 27KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data