Search for and Analysis of Single Nucleotide Polymorphisms (SNPs) in Rice (Oryza sativa, Oryza rufipogon) and Establishment of SNP Markers

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1 DNA Research 9, (2002) Search for and Analysis of Single Nucleotide Polymorphisms (SNPs) in Rice (Oryza sativa, Oryza rufipogon) and Establishment of SNP Markers Shinobu Nasu, Junko Suzuki, Rieko Ohta, Kana Hasegawa, Rika Yui, Noriyuki Kitazawa, Lisa Monna, and Yuzo Minobe Plant Genome Center, Kannondai, Tsukuba, Ibaraki , Japan (Received 20 July 2002; revised 18 September 2002) Abstract We searched for SNPs in 417 regions distributed throughout the genome of three Oryza sativa ssp. japonica cultivars, two indica cultivars, and a wild rice (O. rufipogon). We found 2800 SNPs in approximately 250,000 aligned bases for an average of one SNP every 89 bp, or one SNP every 232 bp between two randomly selected strains. Graphic representation of the frequency of SNPs along each chromosome showed uneven distribution of polymorphism-rich and -poor regions, but little obvious association with the centromere or telomere. The 94 SNPs that we found between the closely related cultivars Nipponbare and Koshihikari can be converted into molecular markers. Our establishment of 213 co-dominant SNP markers distributed throughout the genome illustrates the immense potential of SNPs as molecular markers not only for genome research, but also for molecular breeding of rice. Key words: rice (Oryza sativa L., Oryza rufipogon); single nucleotide polymorphism (SNP); molecular marker; genome sequence; polymerase chain reaction (PCR) 1. Introduction Single nucleotide polymorphisms (SNPs) are the most abundant variations in the genome. They can contribute directly to a phenotype or can be associated with a phenotype as a result of linkage disequilibrium. 1 Most conventional trait markers and molecular markers, such as restriction fragment length polymorphism (RFLP) and cleaved amplified polymorphic sequence (CAPS) markers, are based on SNPs, i.e., nucleotide substitutions or insertions/deletions. Because of their abundance and codominance, the use of SNPs as a marker system has the potential for providing the highest map resolution. Typing of SNPs has progressed remarkably over the last several years, making genome-wide linkage analysis and molecular breeding rapid and efficient. In rice, about 3000 RFLP markers and more than 300 PCR-based genetic markers distributed throughout the genome distinguish the japonica cultivar Nipponbare from the indica cultivar Kasalath. 2 The frequencies of polymorphisms between japonica cultivars detected by RFLP have been published by the Rice Genome Research Program (RGP) ( However, Communicated by Michio Oishi To whom correspondence should be addressed. Tel , Fax , monna@pgcdna.co.jp the positions of polymorphic sites on genome sequences are unknown. As the entire genome sequence of rice has now been released, the significance of SNPs in various rice cultivars, strains, and mutants is increasing for both genetic research and breeding. Recently, we successfully used SNPs as markers in positional cloning of the rice semidwarf gene sd-1. Wesur- veyed SNPs in the candidate region between the japonica cultivar Sasanishiki and the indica cultivar Habataki and converted them to CAPS, derived-caps (dcaps), or SNP markers. 3 In Arabidopsis, more than 50,000 SNPs have been found between ecotypes Columbia and Landsberg and are being analyzed ( SNP information has been accelerating positional cloning in Arabidopsis. 4 We surveyed the frequency of SNPs on all 12 chromosomes in three japonica cultivars, two indica cultivars, and a wild rice (O. rufipogon). We counted the frequency of SNPs in each pair to examine the correlation between genetic distance and SNP frequencies. We also graphed the frequency of SNPs along each chromosome, finding uneven distribution of polymorphism-rich and -poor regions. Finally, we produced 213 co-dominant SNP markers between G4 (indica) and W1943 (O. rufipogon) to illustrate the usefulness of SNPs as a marker system.

2 164 Rice SNPs and SNP Markers [Vol. 9, 2. Materials and Methods 2.1. Plant materials We used three japonica cultivars (Nipponbare, Koshihikari, and Kitaake), two indica cultivars (Kasalath and Guang-lu-ai 4 [G4]), and O. rufipogon W Detection of SNPs Genomic DNA was extracted by the CTAB method. 5 We designed PCR primers to amplify fragments of 500 to 1000 bp in the putative intergenic regions, using the published genome sequence and the RiceGAAS. 6 RFLP marker probes or expressed sequence tag (EST) sequences were used for regions for which the sequences were not available. 2,7 Primer3 software 8 was used to design the primers. Primers were produced at intervals of 5 to 10 cm so that they would be uniformly distributed over all chromosomes. PCR was performed with AmpliTaq Gold (Applied Biosystems, Tokyo, Japan). After the success of amplification was checked by agarose gel electrophoresis, amplified products were treated with ExoSAP-IT (Amersham Biosciences, Tokyo, Japan) to remove excess primers and dntps. Nucleotide sequences of amplified fragments were determined by using DYEnamic ET Terminator reagent (Amersham Biosciences) in a MegaBACE 1000 DNA Sequencing System (Amersham Biosciences). Sequencing was performed at least two times for each primer/strain combination to distinguish mistakes of amplification or sequencing from actual SNPs. The sequence results of each strain were aligned using the DNASIS Pro software (Hitachi Software Engineering Co., Ltd., Kanagawa, Japan), and SNPs were searched for and certified by eye Producing SNP markers for G4/W1943 We produced SNP markers for the G4/W1943 combination on the basis of SNPs detected in this study. SNP primers whose 3 ends lay immediately upstream of the polymorphic site were designed and synthesized. Then a single-nucleotide extension reaction was performed in an AcycloPrime FP SNP Detection Kit (PerkinElmer Life Sciences, Tokyo, Japan) (Fig. 1). The genotype of the target DNA molecule could be determined by excitation of the fluorescent dye in the reaction and measurement on a Wallac 1420 ARVO SX instrument (PerkinElmer Life Sciences) to determine whether a change in fluorescence polarization was observed. 9 When the result of genotyping by AcycloPrime FP analysis was that expected from the result of sequencing, the SNP primer was established as an SNP marker. Figure 1. The principle of AcycloPrime FP analysis. This figure was modified from Chen et al. 9 It shows an example of a C/T genotype. 3. Results and Discussion 3.1. Detection of SNPs From 607 primer sets covering all chromosomes, we successfully sequenced 417 amplification products. More than 80% of the primers designed from the genome sequence gave successful results, whereas nearly half of the primers produced from partial sequences of ESTs etc. failed in amplification or sequencing (Table 1). Probably the reason for this is that the size of the amplification product was not predictable, because of the absence of introns in EST sequences. The amplification products may have been too long to be amplified. Another possible reason is the multiplicity of homologous genes; some primers gave double or multiple bands on gel electrophoresis. A total of 2800 SNPs (substitutions, deletions, insertions, and single sequence repeats) were detected among the six strains. The details are shown in Table 2. The rate of polymorphisms was calculated on the assumption that the average length of an amplification product was 600 bp. The total number of base pairs sequenced was thus about 250,000 bp (417 amplifications 600 bp). The data indicate that rice has an average of one SNP every 89 bp. This level of diversity is lower than maize, but higher than those of human and Drosophila. 10 When the frequencies of polymorphisms were compared for every combination of strains, the highest frequency was between Kasalath and W1943 (0.75%), and the second highest was between G4 and W1943 (0.71%). On the other hand, the frequencies of polymorphisms between japonica cultivars and W1943 were about 0.33% to 0.34%. On the basis of these data, it seems that W1943 is genetically more closely related to japonica than to

3 No. 5] S. Nasu et al. 165 Table 1. Number of primers produced and analyzed in this study. sequenced regions on chromosomes 1, 2, 6, 7, and 8 were putative intergenic regions, but those on the other chromosomes contain both putative intergenic and transcribed regions (Table 1). All SNP-rich regions detected in chromosomes 1, 4, 5, and 7 fell in putative intergenic regions, but that detected in chromosome 11 was in a transcribed region. We also surveyed the association between the density of polymorphisms and chromosomal regions (Fig. 2). On chromosome 7, an SNP-rich locus was detected close to centromere, but no obvious associations were found on the other chromosomes. Shown as number of primers successful in PCR amplification/total number of primers tested. Genome: primers were designed from intergenic regions predicted by Rice- GAAS gene prediction software from the publicly available Nipponbare genome sequence. EST: primers were designed from publicly available 5 and 3 sequences of rice cdnas. Primers on ESTs were designed only for regions whose genome sequences were not yet available. Table 2. Number of SNPs detected between 2 strains. The number of SNPs includes substitutions, insertions, deletions, and single sequence repeats between 2 varieties. On average, 10% 20% of SNPs were insertions/deletions. For example, among 94 SNPs of Nipponbare/Koshihikari, 11 are insertion/deletion polymorphisms. Numbers in parentheses show percentage of polymorphisms (100 number of polymorphisms/sequenced nucleotides.) indica. Passport data and morphological trait data of W1943 are publicly available on the Wild Rice Database ( The frequencies of polymorphisms between japonica cultivars were 0.03% to 0.05%, and between indica cultivars was 0.49%. All combinations of japonica and indica cultivars showed relatively high rates of polymorphisms (0.68% 0.70%). Fig. 2 shows the distributions of SNPs along each chromosome. These graphs reveal that the SNPs are not evenly distributed. Chromosomes 2, 3, 10 have a relatively low SNP rate (< 20 SNPs per fragment), while SNP-rich regions (about 40 SNPs per fragment) were found in chromosomes 1, 4, 5, 7, and 11. All of the 3.2. SNPs detected between japonica cultivars The frequency of SNPs was 0.03% to 0.05% between japonica cultivars; we found 94 SNPs between Nipponbare and Koshihikari, and 135 between Nipponbare and Kitaake. These results show that DNA marker production is possible even between very closely related cultivars, in which it has been difficult to find polymorphisms by conventional methods such as RFLP. Fig. 3 shows the locations of 64 fragments having SNPs among japonica cultivars on the framework of the Nipponbare Kasalath genetic map. 2 Although 43 fragments had only 1 SNP, the other fragments had multiple SNPs (up to 12) (data not shown). RGP has produced RFLP markers between japonica cultivars. The results ( show that 42 RFLP markers were produced between Nipponbare and Koshihikari by using eight restriction enzymes and 400 probes, screened from a total of 2950 probes. 11 In comparison, we found 94 SNPs (in 50 loci) by using 417 primers. The observed difference reflects the higher efficiency of finding SNPs by direct sequencing. Using data obtained for Nipponbare and Koshihikari, frequencies of SNPs found in putative intergenic regions and in transcribed (EST) regions were compared, but there was no significant difference. Further investigation will be needed to clarify the regional characteristics in polymorphism frequency, focusing on introns, exons, promoters, untranscribed regions (UTRs) and intergenic regions Producing SNP markers for G4/W1943 SNPs between G4 and W1943 were found in 312 fragments. SNP primers for these fragments were designed for SNP-typing by AcycloPrime FP reaction, which is based on the single-nucleotide extension method. Fig. 4 shows a sample fluorescence polarization result. As templates we used genomic DNA of each strain and a mixture of both strains as artificial heterozygotes. Thus, only when three clusters (homozygotes of each parent and heterozygotes) were finely separated was the SNP primer accepted as an SNP marker. Consequently, 213 SNP primers produced successful results, and they were es-

4 166 Rice SNPs and SNP Markers [Vol. 9, Figure 2. Distribution of SNPs among six strains of rice along each chromosome. The horizontal scale indicates the genetic distance from the distal end of the short arm (on the RGP Nipponbare Kasalath genetic map 2 ). The vertical scale indicates the number of SNPs counted at each fragment (locus) among the six strains. The pale box in each figure shows the location of the centromere.

5 No. 5] S. Nasu et al. 167 Figure 3. Distribution of SNPs detected among japonica rice cultivars Nipponbare, Koshihikari, and Kitaake. S0214 (chr. 12) is not shown, because its position is unknown. Figure 4. SNP marker (S0050) measured by AcycloPrime FP analysis. Changes in fluorescence polarization for DNA samples genotyped by AcycloPrime FP analysis are plotted in mp units. (mp expresses the degree of polarization.) A change of 40 mp for a dye terminator is scored as positive. A/A: samples positive for the A allele but negative for the G allele (homozygous A); G/G: samples positive for the G allele but negative for the A allele (homozygous G); G/A: samples positive for both alleles (heterozygous). tablished as SNP markers for G4/W1943 (Table 3). The positions of the SNP markers are shown in Fig. 5 on the framework of the Nipponbare Kasalath genetic map. 2 As shown in Fig. 5, the SNP markers established in this study are distributed over all 12 chromosomes. These markers can be used for linkage analysis to construct genetic maps and graphical genotypes. Some intervals between markers are still too long, however, so additional SNP markers in these intervals may be required for further analyses. Using SNP markers for linkage analysis has three advantages: 1) analysis can be performed in the early growth stage of plants, requiring only a small quantity of DNA; 2) a large number of samples can be processed systematically in 96-well plates from sowing to SNP-typing; and 3) time and labor can be saved, as no electrophoresis is needed. Also, compared with CAPS or dcaps, SNP markers set researchers free from restriction-site hunting (or creating, in dcaps) and from purchasing expensive restriction enzymes. Another advantage of SNPs is that they are convertible to CAPS or dcaps markers for laboratories not equipped for SNP typing. It is likely that the SNP loci found in this study exist in other rice cultivars or strains used in research. Overall, SNPs and SNP markers are applicable to many research and commercial uses, such as studies of genetic diversity, marker-assisted breeding, positional cloning, and cultivar discrimination for quality control of rice in the marketplace. Acknowledgements: The authors thank Dr. Z-X. Wang for critical reading of the manuscript.

6 168 Rice SNPs and SNP Markers [Vol. 9, Table 3. SNP markers established in this study. Genotype amplified cm marker name Genomic PCR primer sets (5' 3') size (bp) SNP primer (5' 3') Type N a Ko a Ki a Ka a G a W a Chromosome 1 CGG CTG AG ATG CG G G G G G 0.0 S0001 CCC TCT ACT AAC TCA GCC GAA ACC GTA GT 799 AAC CAC ACA CGT TCA ATA CAA TTT G/A A 9.5 S0002 GTA CGA GGG AAA ACG CTC AA GCA AGC CAG AAC GAG AGA AC 802 AGA AGG CAC AAG ATG CAA AGT TTT C/T C C C T T C 10.9 S0417 GGT AGA CAG ATT TTC CTT GCT GAC AGA CTC GAA CAA TAA GCC GTT GTC TGA 211 GAG AAC AAT GTT AAT ATT ATC TTG TGA C/T T T T C C T 19.9 S0003 TCC TCG TGG TTC CAG ATT TC ACA CAG GCG CAG TGT CAA TA 804 GAC AAG TCA TTA CCA AAG AGA AAA GGT C C/T C C C T T C 30.5 S0261 TCG GTC AGT TCG GTT ATT TTG G ACT CCA CCC ACT CCT TTG CT 189 TTC GGT TTT TTT CTG CCC ACC C C/G C C C C C G 41.2 S0245 AAT TCA CGG GAA GTT TCA GA CGA CCA GAT TCG CCG TGA TT 254 ATG ATT TCT AGA AAC AGG CCC AAC T/C T T T C T C 50.8 S0246 AAG CAG CAA CGA CGA ACA CG GTT TGC ATG CAT TGA TCG GG 626 GCC AAG TAA GTT TGT ACC TTC TCC ATT ATT G/A G G G G G A 55.4 S0353 GCC TGG AGC GAG ACA AAT CC TGT GCT AAC CGA CCC ATG CT 913 AGG ACC AGC AAA TTA ATC T T/C C C C T T C 60.6 S0247 CAA TTC CTG GCC TAA GGG GG TTG CGA GCT TCC AAA TTG TCC 768 GAG TAT ACT TCC ACC TGC TTT ATT CAT CG A/C A A A C C A 70.1 S0256 ATC GGA GGA GCA ACG ACC AC TTG GAT TTG CAT CCA ACG GA 851 CGG GTC TAG CTA CCC CAA GC G/A G G G A A G 78.0 S0016 TCG TTT TGA CGT GGT TTT CA CGG CTA CAT CGG TTC TCC TA 798 AAG TCA TTC ATT GCT GCT GTT TGT TC G/A A A A A A G 84.0 S0257 TCC ACC TTG ATG AAC ACA TTG G CAA ATG GCG CAA GTG CAA AT 800 TTA TTG TGA CAC ATG GCC TTG CAT T G/A G G G G A G 96.1 S0015 AAC CAA ATT TCC CTT GTC CT TTC CAA TAT GCC TCG GCT AA 477 TCA TTG AAT TAG TTG TAG AGC TA G/T G G G G T G S0355 GGC CTC ATC ACC CGT CTC TC CTG TGC CGA CAC CCC TTT TT 898 AGT AGG CTG TGT TTA GAT CTA A G/T G G G G G T S0356 AGC AAG GCA CCA TTC CCT CA CAC CTC GCT GTC GAT GGG TA 893 GCA GTC GCC TAC AAC TCA TC A/G A A A A A G S0008 ATT GGC ACC AGG ATA GCA AG GGT GGT TGA TCT GGT CTC GT 800 GAT CCT GCT GTC GAC AAA CTG T C/T C C C T T C S0249 AAC CCG GTA ACT GCA AAG GGA GAC AAC CGT GGA TCA TGA AGG A 888 CAA GCA TAT CTT TCC TGC CAA ATA ATT GCA C/T C C C C C T S0358 CAT GTC TTT CGC AGG CCA AC TAG GAA GCC CCA ATG GTT GC 896 ACC AAA GTG AAA AGT CAC CAT G A/C A A A A C A S0010 AAC GGC TGT ATT TCC GAG TG CTT TTG GCC TGT TTG GTT GT 799 CAT GGG CCG GCC CAT AGA AA T/C T T T T C T S0011 CAC AAC CCT AAC AGC CGA AT GAG TGC CAA TTT GGG CTA GA 802 TCT TAA TAT TTC CGA CTC AAT TAG ATA GCC TTA A/T A A A T T A S0012 GGC AGA GTT AAT GCC ATG CT GCC ATC GAG CAA TGT AAG GT 797 CTG TGT AGT TAC TTT TAT GTT CCT AGC CT C/T T T T T C T S0013 AAA TTC GGA ATG GCT AGC TG ACC TCC GAT GAT TCA ACC AA 798 CCA TTT CTC ACT CAG CTT CGT CTT A/T T T T T A T S0359 CGA TCA AAG TTG GGC GTG AA GCT TTG CTG CTG CCT GCA TA 902 GAC AAA TCC TCG CTG GAA AC G/A A A A A A G S0259 TGA GGG CGT GTC AAG CTA GTG ATG CCG TGG CCA TTT TTG TT 778 TTC AAG TTA CTC CCT TAC CAT CAT ACA TAC A/G A A A A G A S0007 GCA TGG ATG ACC CTG CTA AT TGA TGC CGT TGA CTT TTT GA 802 TAC TCC CTC CGT AAT GTA T G/A G G G A A G Chromosome S0030 ACT CCC TCC ATC CCG ATA AA CCG TTA ACA CAC AAG CCT CA 800 ACT GTC TCA TAG AAG AGT ATC CCG TT C/T C C C C C T 17.6 S0031 CGG TCT GTG TTT TCC GAA GT CAA GCG GAT GGT TTT GAG TT 790 CTA ACG TAG CTA CTC CCT CC G/A G G G G A G 22.0 S0294 ATC ACC CAC AGC TCT CTT GTG C AGG CAG CAC GAC AGG ATC AA 775 AAC TCT ACC CGT ATG TCT TGG AAT TAG GA G/C G G G G C G 25.5 S0262 AGC GTG GGA TGA CGC TAT GA TGG CAA GAG CAA ATT GGT GAA 806 GGT ATG GTC AAT GGT ATT ATA TTC TGT TG A/T A A A T T A 30.2 S0295 CAA AAT GGC AAG GCA AAC CA TGC CCC TTT CTA TCC TTG CAT C 820 CTC TTT TGA GAC CTC ACA GAT TAA CTC ATT T/G T T T T T G 51.1 S0296 TGC ACC GGA TCC TAA TCC CTA TCA TAC GAA CGC GCG ACT CT 803 CTC AAA ACG GCC ATT TTA GTC CAA CA T/C T T T C C T 57.9 S0297 GAT CGA GTG GCC CAC ATG TAA GGT TGT GTC CCG ACG ATG AT 813 GCC CAT CAA GAC CTC TTC ACC TAT C/A C C C C C A 62.2 S0028 CGA CGG AAA CTG CCT TTA TC GGC ACG CTT CTC AAT CTT CT 796 GTA ATA TGC CCA AAC CAA TTA TT T/A T T A A A T 88.2 S0019 ACA ACT TGG GCC ACC AGT AA CTT TGA ACC GCA TAG CAA AA 801 GAG TTT GTT GCT AGG GTA AAT A C/T T T T T T C 93.2 S0298 CCA ACG ATG ATC TGA TTT CCT CTG GAA TCC GAC TCT TAT TCT ACT CCT C 226 TCT ATT TTA TGT ATG CCT TTA TTT TTC TCC G/A G G G A A G 98.2 S0299 TCA TCC CAA CAT GTT TGT CCA G TGT GCA CGT GGA AAA CGA GA 789 CCT GGG ACT CAA TCC ACC AAT T C/A C C C C C A S0300 GCA AAT TGC AAC TGG GAG TGA GGG TAA TGC GGC AAA GAA GG 798 ACA GTC AGA TTA AAA GGT AAA TCA ATT CAA T/C T T T T T C S0023 ATC TGA TCC CCC TAC CAA CC CTC ACT GTC CAT CTG CTC CA 798 TGC ATC TGC ATG CAC CAC TA G/C C C C C G C S0024 TCC CTC CAA CTA AAC GCA TC CTA TCC CCA TTT CCC ATC CT 804 TCT CCT CTC TTG GTT TGC TC G/A G G G A A G S0378 CTT GCG CGG GCA AAA GTT AC AGC CGC CTT CCA ATC ATC AG 765 AAA GGT GAG AAA GCT GGC ATT CAT C G/T T T T G G T S0021 CCT GCA CTG ACG GGA AGT AT TAC TCA TCC AGG CCT TCT GC 782 ATT GTC ATC GGC AAG CAT AGA CT G/A A A A A G A S0302 TCG TGA GCT TTT GGA GAG CA TTT GGG GAA AGT TTG GTG TGA A 797 CAT AGA AAA TCC CCC GGT ATT AAT TGC AT C/G C C C G G C S0379 CTG ACA GTC TGA AAC CAG GGC A TGT CAG GTT GGA TGC TGC AAA 573 CTG TTG GAA ACT TAG ACT AGG GAA G/C G G G G C G S0022 TCA TCT CCT CCT CCG TCC TA ATG ACA TGT GGA CCC CAA CT 800 CTC GGT GAG TCA ATA AAT TGG C C/A C C C C A C S0380 GCT GGA GGA GGG ATA CGC AG CGC GAA TGC CGT CTC TAA TTC 692 CTA CAT ATG TCA AGA ATT ACT GCA ACT C/T T T T T C T Chromosome S0332 TTT GCC AAA CAC TGT CTC AA TCC TTT TCA CCA ATG AGA TTA GC 586 AAA CTT TCC GCT GCA ACG CG C/T T T T T T C 6.8 S0037 ATT GCC TGC GGA TTA CAG AC GCG ATT TGC CAA TTT GTT TT 803 CGT CAG AAT CGA TCT CGT GAA CA C/G G G G G G C 11.5 S0323 GGA TGC ATT CGA TGT TTC TG TTT ATA AGG GCA ACT CGA AGG 480 CCC ATA TGT CAA AGA TCC TCC AAC G C/T C C C T T C 16.8 S0275 GGA TGG AAA ACG ATC GAG AA AAC CAC ATC TTC CGT TTT GC 908 AAA GGA AGA TTG GGT CAC ACA TTT C C/T C C C C T C 20.3 S0040 TCT GCT GCC TCT GCA CAT AC AAA ACG ACA CCA CAT CAG CA 898 ACA TAC CAC CTT TCC TAC CTT C C/T T T T T T C 25.0 S0276 GCG AGG TGG CAA AAA CTT CC GCA CAC CCT TTG TCA CCC AAC 798 ACT GGT TCA ACT CGC AAA ATA C G/C C C C C G C 34.8 S0277 CCC CTG TCC TAC CCC ACC TC GAG AAA GCC ACG GCC CTT TT 808 AAT TAC AAG GCT GAC TTT CAT GAC G/A G G G G A G 40.3 S0325 AAG CGG AGT TGA GGA TGC AG GAC TAA ACC TTT TGG GGA CGG 654 CGA ATC TAG ACT ATT ACT TTG ACT ACT G/T T T T G G T 44.1 S0034 CAT GGC TGA CAC ATT TCT GG TGT CAG GTA GGA CGA TGC TG 902 CTG CAC GCT ATG CAT GGC CA C/T T T T T T C 69.2 S0279 GGG GCG CTC CTT CAA AAC TT GGT TTG GCA CAC CAC AAT GG 795 ACA AAG GTA GTA GTC AGG GAC AC G/A G G G G A G 76.6 S0035 GAT CAT GGT CTG GCT TGG TT TTG ACA GCC AAA ACT TGA CG 794 ATC TTG TGA AAA TTA TGT CGC C A/G G G G A A G 86.0 S0280 TAC GGG CAT TCC TCC ACG AT CCC AAT GTG GGG CAA GTT TT 790 TGT AGC ATT TCA CCC GAG AGT A A/T T T T T T A 90.3 S0333 ACG ACG GAA TCT CAA CAG GT ATC CGG TGA AAA CCA TCA AA 449 AGG TAG ATA TAG ACA TAA AAT ACA TTC ATA C/T C C C C T C 94.9 S0330 GGA GTT GGC ACT CGA GAT CA GGC AAG AGG ATT CCC GAT AC 641 CCA CAT AGA TGC ATA TCA TTG TGC T G/C C C C C C G S0036 AGG CAC ATG GGA ACA ATA GC TCC AAA CTA CCG TGA GAT CCT 223 GCA TGC GGA AGG CAA AGG TTT A A/G G G G A A G S0328 TCT GAT AGC ACT GGC AGC AC CAA AGC ATC CTT GAC GGA AT 255 TCG AGC AGA AAA TGG AAA TAT TCA C C/T C C C C C T S0038 GTG GTT TCC TGC ATC GAG TT TAC ATG GGT GTC CCC ATT CT 908 ATT TTT CTT GAT ACT AAT GAA A/G G G G A A G S0045 TGC AAT GTG CCA TTC CAT AG TAT GAC AAG GTG GGC CCT AA 901 GAA GAA GAT TGG GCC GCT GAC AT A/G G G G A A G S0283 GGC CTC CCT GAT GCA TTT TG AAA AGG CAG GAT TTG CGG TTC 767 CGT ACA AAG CCG TAC AAA TCC A C/A A A A A A C S0046 CAC ATA GGA CGT TAG GGT GGA CCA AAA AGA GCA AGG CAG AC 471 ATG TCG GTG CCA AGC ATG TC A/G G G G G A G Chromosome S0063 GCT TCA GTG CAG TTT AAT CG TGG AAG AAA ACA CAT ACA AAC C 771 CGA ATA AGC CTG CAA CTC ATC G/T T T T G G T 3.1 S0052 CAA GTA AAC GTG TAC AGA ACA AGA C CTT AAT GCT GCA TCG GTC G 149 TCT TAT GAT CAT CAA TAG AGA TAG T G/A A A A A G A 16.7 S0050 GAG GGA AAT CGC GAG ACG AA GCG CGG TTT TCA GCT TGT TC 798 ATT TTT ATG TTC ACA TCG AAT GTT T G/A G G G G A G 20.4 S0048 ATG TGA AAG GCC AGG ATG AG CCA CCA TGC GAC AAA ATA AA 201 CTC CCG GCC ACT CCT TCG G/A G G G A G A 48.3 S0057 TGG CAA CAC TTG GGA CAA GC GCC GGC CAG CAA GTG ATT TA 901 AAG AAT TTT CTC CTT CTT AGT GCT C/T C C C C T C 52.6 S0373 GCG TTC TCC ATG GTC AAG AT TGC CAA AGG TAT CGA CAC AA 901 GAG CCT GGA GAG ATG CGG T G/T G G G T T G 59.5 S0059 GGA TCA CCT GCA AGA AGA ATT TCT G TGA GGC TGT TGC CGT TGA 196 GGG CCT GCA GGT TTC CGC G/A A A A G G A

7 No. 5] S. Nasu et al. 169 Table 3. Continued. Genotype amplified Genomic PCR primer sets (5' cm 3') size (bp) SNP primer (5' 3') Type N a Ko a Ki a Ka a G a W a marker name 62.1 S0054 GAT CGC CTC CTT TTC TTT CC TGT CAA GCA AGC AAC ATT GG 170 ACT TTC TTG GGC TCA ATT ACT CAT A G/A G G G G A G 74.5 S0055 CAG TGC ACT TGA TGC GCT TA GTC ACA GTC ATC GTC GGA AG 195 CCG CAC CAC GGC CAC ATG C/T C C T C T C 76.8 S0056 CAG GAC AAT CCG ATG GCA TAG A TGG GAT GGC CCT ACG ACC TA 900 TTG TTA TGA TAG TGG TAT TGG T G/A G G G A A G 78.2 S0053 GCC CCT ATA AAT ACG CAA CCT TTG GTT TGG TTT CTT AAA GTG AAA 156 CAT CAT AAT ATA GTG TAT TCC TCA C C/T 87.1 S0061 AAC CTG CCC AAA CGA ACA G AAT TTG GAG CTA GTA GTT GGC TA 260 TAC CGC CGT AAA AGT GTG AAA C/T T T T C C T 97.7 S0375 CCA CAA AAC ATG ACC TAT CTA GAC CCC CGA TGT TAG TAG TTC TGT ATA ACC AGC A 187 CTT CAC CTT CCA TCA AAA TGA CCG T G/A A A A A A G S0409 TGG GAT CTC CTC GTT GAT TC TTG GAA AAC TCG TGA AAT TCG GAC AA 344 TTC ACC TCA TAC ATG GTT CGT AGA AAT G C/A C C C C C A S0060 CGA GGT GGC GTA AAG GGA TTC CCC ATC CTC ATG GTC CCT TGT 428 TCT TAA TGC TCT CAC CAG ATT C C/T T T T C C T S0051 ACT GAC CAG GCG CTG AAA GG GTG CGT GTC CGC GAT AAA CA 905 AGT TCA TTT TTA GAG TTG AGT ACA G/A A A A G G A Chromosome S0074 TGA ATT TTG TGG TTA ATT TGC AC TGG TGC TAT TTA GTT GCC TAA TTT T 197 TTC TTC TAG ATT CAT GTA AAA AAC T G/A A A A G G A 12.0 S0068 AGC TCA CGA GCC GCT TGT TT GTG TTG GGC CAG GAG GTC AG 900 TCC ACC CCA AGT GCT TCC C/T T T T C C T 21.1 S0072 TGC GAT CAC CTG TGA ATC CAA T TTT TCG ACG GAT GCA TAA ACG A 183 CGA GTA CGT ATT TTA TAC TCC CTC C G/A A A A A G A 27.7 S0292 AAT CGC ACG ATC ACG CTG AC CCC TTT GTA TCC GGC GTG TT 800 AAC GGA GAA AGT AAG TCT AGC TTG C/T C C C T T C 32.0 S0363 TCC TTC CTG CCT CGC TTT GA TGA ACT GCA ACC CCA CGG TA 846 CAG TGA GTG GAA TTA CGG AA C/G C C C C C G 37.0 S0071 TTC CCT TGC GTT GGA GTC GT TTC CTG ACA AGC ATG GGA ACA A 889 GCA TGA AGT AAC AGC AGA C/T T T T T T C 53.2 S0286 TGG CAT GTG AAA GAG AAC CA TCA CTT GCA CTC CAC CAC ACC 796 ATT TGC CTT CGA CTT TAT CTC TCT CT G/A A A A G G A 63.0 S0287 GGT CTG AGG TGG AGG GGA CA TCT CGG CCT TTG GTT GGA AA 847 CCT GGA GTA AGC ACG TAA TGT AC G/T T T T G G T 67.5 S0365 AGT CAT CGG CCG GTC AAC AT CGA TCG TCA TTT GCG TCT GG 848 GAA CAG ATC AGT AGG TAT TGT TA G/C G G G G G C 71.7 S0079 AGC AAG TCA CGG AGA TGT C ATA GGA GCA CAC AGA TTC CA * AAA TCC GCA GAG GCC TCA G/T T T T G G T 74.1 S0289 ACC AAA ATG CCC TCG CCT CT ACG AGG AGA GGG GCA CAC AC 800 CGC GCA TAC ACA TCA AGA TTT TTC G/T T T T T G T 92.0 S0067 TTA GAA AAA CTG AAC AAA TCA ATG T AGG GTA AAT TGA ATG ATA TGA TGA 198 AAG AGG GAG GAA CCT AC G/A G G G G A G S0069 AGC CAT GGC ATT CCA TTA AA TGA GGC ATG AGA AAG GTT GA 196 AGG AGA AGA CAA TGC TAG GTT T C/A C C C A A C S0073 AGC GAA GCA ATC GCT GAT CC CCA ACA CTG CCT GAA TTC CAT GT 195 CGA GAA AGG AAG GCA GAG A G/A G G G G A G S0291 CCG ATG GAT TTG AGG CTT GC CGC GGG AAC AAT ACC TGA CA 807 GGC CTT GCA CAA CTA TAA TCA CAA T G/A G G G A A G Chromosome S0085 AGG ACG TGT TTC CGT ACC AG GCC TGA ACA GAA CCT GAA GC 799 CCA GGT GGC CGT CTG AA C/T T T T C C T 8.2 S0367 CAG AGA TGA ACC CAT GAG CA TGT GCC GTT TAG GGT ACA CA 897 CCA CCT AAA AGT CAA TGG AAT TTT AT A/G A A A A G A 12.9 S0087 CTC CGC AAC TGT TCT GTC AA GAT CAT GGT GGG TCC AAA TC 800 GAC CCT TTG AGT CCG TTG TAA TT A/G A A A G A G 18.5 S0082 ACC CGG ACA TAT TTT GAC CA CCT CCA AGT TTC ATG CAA GG 797 TCT ACC ATA GGT TCT CTA AGT ATT T G/T G G G G T G 25.2 S0252 CGC CAC AGA ACG GAC AAA AG GAC CAA TCC TTT GCC GAA GC 804 CCA TCG TTA CGC TTC ACG CA G/T G G G G T G 34.3 S0092 AAT TGA TGC GTC CGA TCT TC TGG TAG CAA AGC ATG GTT CA 887 TCG ATC GCA CCG ATG GAA GT A/G G G G A A G 45.2 S0080 AGG TCG TTT GTT CCT TCA CG TCC CCC GTG TTA ATT GGT TA 896 GGG TAA AAT CAG ACA CTC ACA A/G A A A A G A 51.0 S0270 CAA CCA AGT GCG TTC ACA TCC AGA AAT CAG CGG CAG CAA TG 785 ATC ATC CTC GCA TTT TTA ACC ATG TCT T G/A G G G A A G 61.6 S0268 ATG ACG GCT TTC CCG TTT TC GAT GCG CAA TTT AGG CAC CA 770 GAC ACA CAA GGA ACA TCC GGT G C/A C C C C A C 65.8 S0127 GTG GGC ATT GTC TGT CTT GG CCT TGG CCT TAC ATG TGT GC 816 GAA AGA GAA TGT GAC CGA GC C/T C C C T T C 66.8 S0086 TCA GTA GCC TCA CAC GTT GG TGC TCC GGG AGG TAT CTA TG 900 TCT ATG ATT CAT ATC TAT AGT AGC C A/G G G G G A G 72.7 S0090 ATG TGG TTG GCG ACT CTA GG CCC TTT TGC ACA CCA CTC TT 798 AAG AAA ATT GTC CAT TGA TGA GC G/T T T T T T G 83.9 S0091 GTA TCG GTG TTT GCG AGG TT GCA TAC TCC CTC CGT CCA TA 796 GTT GCA GTT GTG CTA CGG CT A/G A A A A G A 87.5 S0370 TGA GCT GTT TCT CGA CCT GA ACC GGC TGC TAA ACA AGC TA 906 AAT GCA GTA CAA GAA TTC CT A/C A A A A C A 91.1 S0097 ATG TGC CTT CTC GGA ATC TG CCA GTA AGG CTG CCA CAG TT 797 TAT ATC GAG CAT AGA AAT ATG TAT C/A A A A C C A 98.9 S0089 TGC GTG TAT TTT GGG TGA GA TGC AAA TAC GTG GTG TGG TT 773 ATC ACT TTC ACC ACA CAA CA C/T T T T C C T S0273 GCG GAA CAC TTT AGG GGG AAA CAA TTG CGA CTC GGT GGA AC 770 GTA CAA CCA GAG GCG GAT CTA GGA C C C C T C C/T S0094 CCT TTG TGC TTG CTT CAG TG CAT CGC ATT CTT CCA TTC CT 796 TAA ATA CTT TGT AAT TAC CAG CA A A A A G A A/G S0157 ACT GAA TGC GTT GAT AGG GGA AG TCA ACA CCA CAA CAT TCC GAC AT 212 TAA CGT ACT AGT AAC GTA GCG ACC A G/C G G G G C G S0084 TGG CAC AAT ACA AGC TGC TC TTG CAA CAT TCA GTG ATT CC 259 GGA ATT TTC ATC GTT CTT GC G/C C C C C C G S0088 CGT ACG TGT GCT CTC ATT TCT G GGG GTG TTA CGG GCT ACC TA 282 GCA TCA AAC TGG AAC ACT ACT AC G/C G G G C C G Chromosome S0303 TGG CTT GCT TGT CAC CTG CT TGT TGG TGG GTC TGT GTG GA 800 CAT TTT ACT ATA GGA CTA GAG GAG GTC AGG G/A G G G A A G 8.8 S0101 TCG TCT GGG TCA ACG GGA AA AGG CCA TTG TCT TCG CAT CG 847 GAC AAA ACC TCC ATG CAG TGA T C/T T T T C C T 24.2 S0100 GCA TGA TGG ATC CGG AGA TG TGT CAT GCA TGG CTC CTC AG 869 ATG GTG ATC ATG GCA TAT TT C/T T T T C C T 31.0 S0099 GGC AAA ACG CAA CCC ATA CA GGA GGC CAA AAA CAC GGT TC 874 CCC CAA ATC TGT CTT AGC AC C/T C C C C T C 35.7 S0109 CCG ATG GCA GCA CAA ATC TT TCA GTT TGG CTT GGG TCT CC 850 CAA CTC ACA ACA GTT ATT ACT ACT G/A A G G A G A 45.5 S0264 TTC GGT GAG GTC TGC ATG GT CTT ATC CGT TCC CGC CTT TC 803 ACT TCA ATG GGG CTG GCA GC T/C T T T C C T 61.9 S0103 ATG CCA TCA CAA CCC ACA AC CGT TTG CAC TGA GAC CAA GG 848 GGA TAA AAG GAG AGA GAA GAG A G/T G G G G T G 69.2 S0104 GGC GCC TGA ATT GAC ATA AA TGC TCC AGC TCC AAG AAT TT 794 AAC TCG TAC CTT TGA AGT GT G/C G G G C C G 76.2 S0113 AAG CGT TAC GGA TTC GAT GA CAC GAA CGG TGG CAG ATT AT 804 GCA TGA TTG TCA GTG GTA GAT ATT A/G A A A ND b G A 77.8 S0307 TTG TAC GAG CCG TGG GAT CA TGG TGC TGT CAT CGT GCA GT 846 TCC TGC AAA TAC TAT TAG TAA GAA ACA ACT G/A G G G G A G 83.3 S0114 ACA ACC GGT CCA AGT TCG AT CAA AGC AAC GGT TTG GCA TA 800 CTA CAC ACT ATC GCA AAG GT C/G C C C C C G 89.9 S0118 GTG GCA AAA GCT TGC TTC CT CAA CAC GGA TGA GCT TGC AT 801 ACA CTA CCC TTT AAT GAC CTA G/T G G G T T G 94.7 S0116 TGT GCA GAT TGA GCG TTG GA ATC GGA ATT TCG TGG CTG GT 815 GCA AAA GGC CAA AAG GTT GGA T/G T T T G G T 99.3 S0120 CGC CCG CAT CTC ATC ATA TT TAC CTC AAG CGA TGC AGC AA 805 CCA TTT AAT TCA ATA AAC GCT TC A/C A A A A A C S0124 CCC ACG GAA ACA GCC AAA AG TGC TGC CAT GCA AAG AAT CG 956 ATT TTG GAA TGG GGG GAG TA C/A C C A A A C S0306 TGG AGC TCG TGA GGA GTT GA CAC CCT GGA AAT TCA GCA CA 812 GTT TGA CCG TTC GTC TTA TTC AAA AAC TTT TG T/A T T T T A T S0121 CCA TGC CCT GCA AAT TCT TT GAA GTG CAG GGC CAG TCT TT 174 ATT GGC CTC TCT CAA CTT GC A/G A A A A A G S0125 TTC CGA GGA GAG TGT ATG TG TCC GCT ATA CGT GAG AGT GA 287 AGA CCA GCA CAA CAT TGG C G/C G G G C C G Chromosome S0133 TGA CGC TAC CAG CCA ACT GA ACC CTC CCC TCA TCG TGA TT 930 GCA CCT AGC TAC TCA CAT CTA GA C/G C C C C G C 8.2 S0334 ATT TTA GGC GTC CTG GGA AT AAC CGC TGC CTG AAT TTT TA 501 CCA GCT ACA GGA GAA CCA GGA A C/T T T T T T C 13.9 S0132 TGA CCG CAA GTC CGC AAC CT CGT TGA CCC AGC TTG CCA CA 853 CTC AGT CAA CAA ATC TAG GGA C/T C C C C C T 16.4 S0131 CTT GCA ACA GCG CTC AAG GA GCA ACC AAG TGC CCA AAA CC 845 AGC GGC CAT TCT TAA TGA GC G/T G G G G G T 20.2 S0308 CGC TAA AAA CCG GTG AAC CA GCA AGA ACC GCA GCT CTG AA 791 TTC GAA TCC CTT CCC AAA TGG TTA A C/T C C C T T C 29.4 S0309 CAT CGA GGT TGC CAC ACA CA GGC CTT GTA GCC AGT GCA AA 789 AAC CTT CCT TGG TTC TAG ACT GC T/A A A A T T A 35.7 S0130 ACG GAC ATG AGG TTC CCT TG GCA GGA GGG GTT TCC TCA TT 850 TGA GGA ATA GCA GTG AAG GCT G/A G G G A A G 40.2 S0310 GAG GGA GTA TGT ATT ACC TCC AAA A ACC AGG CAC AGC TTG GAA TA 455 CTG CAC AGA CAA TCT GGG CC A/T T T T T A T 44.6 S0135 GTG CTG CAA AGG GGA GTA TG CGC CAA CCT CGT AAA TCA AA 852 CGG GAG GCT ACC ATT CAT GA C/T C C C T T C

8 170 Rice SNPs and SNP Markers [Vol. 9, Table 3. Continued. cm marker name amplified size (bp) SNP primer (5' 3') Type N a Ko a Ki a Ka a G a W a 49.5 S0335 GCA AAA ATA TAC GTC AAA AAG GTG GTC CCC AAC TAT CCC CAT TT 405 CCA TGT CAT CAT TCA TGC AAA ATC TAT G/A G G G G G A 53.7 S0136 TGC AAC ACA CGA GCC TTT AGC ACC CTC AGC GCC GGA GTA TT 618 GCT TCG AGA GGT CCG CTT C/A C C C A A C 60.1 S0267 TCC CGG ATT GGT AGA GGG TTA CCT AAT TTG GAT ATC AGA CGT TGT GC 204 CTA GCT AGC AAG CCA TGT ATG TAT CCC C/T C C C C T C 67.3 S0138 CAA CCC TGC GTG TTT GTC AT CGC GCT GCT GAG AGA GTT TA 839 ATT AAG TCG TAT CAC CTC AA G/T T T T T G T 72.2 S0128 TTG TCA CCG CTC CCA CAC AT TGG TTG GGT TTT GGG TCC AC 908 GAG AGT GCC CTC CAT TGA AA G/T G G G G T G 76.7 S0139 GAA GCG AAA ACC CGA CGT GA TGG ATC GCT GCA CTT CCT GA 918 TGT GAA ATG TGC GTG GAG C/A C C C C A C 81.6 S0140 GCA CGC CCA CAT TTC TCT CC TGC AAG CAT GCA CCG TAT TG 411 GAA GCT CAT TTC TGA ACG TG C/T C C C T T C 84.5 S0266 GCT TTG CTG CGG GAT TCA T GGA TGC TTC ACA AGG GGA AAA 800 GCA TTG ACA CAT CAT CTA TAA TAC TCC C T/A T T T A A T 87.6 S0337 TGC ATG CCG ATT TAA CTA TGA GTG GCA CTG ACT GTG AAT G 522 GGT GCC AGC CAG CAA AAT CTC C/G G G G C C G 92.2 S0141 CCT CCC ACA GTC CCA CTA GA CCA GTG CCA CCT TCT AGC TT 233 TGC AGG ATA ATA TGC CAC TTA C C/T C C C T T C 99.6 S0142 ACG CCT CAT CAG CCG GTG TA CCG CCG CCG TTG TTT AAT GT 853 CCC TGG ATC AAG TAG TCT GGT A C/T C C C C C T S0338 CCG TGA ATT TTA TGG CCG AAC TTT CTT GCG GCG ATG TGC TA 795 TAG CAT CCC TAG GTG AAA CTA GT G/A G G G A A G S0143 TTC ATT GCC TGT CCC CAT CA TTT CTT GCG GCG ATG TGC TA 843 CCG CCG AGA AAG TCA TTT GAC TA C/G C C C C C G S0144 TGG CTG ACC AAC AAG CCT TC ACG TGG ATG GTG TCG ACG TT 875 GAT TTT GGG CCT CTT CAT GC T/C T T T C C T S0145 CCG CAC TTT GAC CGA TGT CT AGC ATG GGC CTT ACT GCA AA 863 GTC CCA CGA AAA ACC GAT C/T C C C T T C Chromosome S0151 CAT GAT CGG TCT GCA CCA GAA AAA CTG GCC ACC TGC AGA CA 291 TTG TTG AAA GTA GAA ACT GCA GCC T G/C G G G C C G 6.8 S0316 CGA TGC TTC CTG CAC CTC AA CGA ATA GCG TGT GAC GAT GG 817 TGA GAA ACA ATC TTC ATG AAA GTA TAT ATT GTT T/G T T T ND b G T 30.6 S0313 AAG CAA AGC ACG ATC GAC CA TGC GCA AGG AAA GCC TTC TA 233 GCT CTC ACC TGG CTG GCT AGA T/G T T T T T G 36.0 S0152 ACA AGA ACC GCC CAA ATG GT TGC ATT CTC TCA GCT TGC ATT G 283 GCA GCA CAG TTA GCA CGT GC T/C T T T C C T 40.1 S0153 CGG CAG AGT TTG ACC CAA GA CCC AAG ACA ATG GGC AGC TA 358 GTT GTA ATG TGT CAG GCA CTT GAC T G/C G G G G C G 55.9 S0155 TCC CCG AAC ATA TTA TCC TTT CGT CGA CAC CAT CGA CAA CGT CA 364 ACA AAA CCC AAC TCT GAT GGC ACA G T/C T T T C C T 62.4 S0156 GGC ACC GAC TTC AAC ACC AG AAG GAG GAA CCT GGA CAA CGA 241 TCT TTT TCA TCC AAT TGC AGT ACA CGG C/T C C C C C T 72.1 S0160 GGT CCA CAG GTG CGT ACG TGA C TTG GAT GAA TTT TGT AGG ACC AGT G 248 CCA GGT CTC CGT GAG CTC CT C/T C C C C C T 72.1 S0167 TCA CGC CAT CAT ATC GGT CA GCC ATC AAG AAT GGG GTG AA 311 TGA GCG TCT TGC GGT CGA C G/A G G G A A G 76.9 S0314 GGG CAG TTC ACA AGG CAT TC TGT TCC CAG CTT TCG CTC AA 360 GTT GTG CAG GTC TAC CTA CTG CAT C G/T G G G T T G 82.4 S0158 TGC CTG GTA GAA TTC TGG ACT TG AAA AGG AGG TCA GGT CGC TCG AT 390 GGC GAT GGC TCT AAC TCC AAT T A/C A A A C C A 90.4 S0159 CAG CGT AAG ACC TCC CTC CA CGA AGA GAG CGA GGA CAC CA 293 TGC TCC TTG CTA GTG TTC GGA T/C T T T T T C Chromosome S0339 GGT GAA ACA ACG CCC GAT ATA AAC G TCG ATC GGT GGA TCA AGT CG 356 GTT GCA CGA TGT TCC ACC AAG TAT AT C/T T T T C C T 1.1 S0168 GGA TCG ATC AAA CAC CGC TAA CT TTC ACT GGC AAT CTA GGG AGA GG 386 GAT AGC ACC TGC GGT ACT GTA ACC A/G A A A G G A 5.5 S0161 TGC TGG CAG GTG CTG CGT GA TGC GCA ACT AGG GAT TTT CC 340 GGA AGA CAG CTT CTG CTT GTT TGT G/A A A G G G A 9.6 S0340 CCC CTG CCA ATC ATT TAG CC CGT TGA GGC GAA AAA TCG AA 792 TCC AAG TAC TCA CAT ATG TTC ACA CT G/T T T T G G T 15.7 S0162 GCG TAA CTC GGT CCA CCA TAG TA TAC TCG AAT GCT GAA GGA AAT GG 302 GCA TAC TGA CTA GAG CTT GAA CCA AC G/A G G G A A G 26.1 S0163 TCT CAA GAG CTG GGT TGA AGG GCA AGC TTT CCA TGC CTT TG 345 CTA CGT CAC TGC GTT ACT GCA AGA C/T C C C C C T 29.8 S0342 GGG CAA AGC ACC ATT TGT CA TCC CAG CCT TTC AGG GCT AT 842 ATG ATT TTG AAA GAT TTC AAC CCT AGA G G/A A A A G G A 35.1 S0164 CAT TGC CTG GTT TGG TGG AA TTG CGT AGA TGC CAC CTG AAA 310 TCA AAT ACT TTG ATT TGA TAG TGT ATC A/T A A A A A T 35.9 S0165 CCT TGA GGT CAC AGA TTG CTC A AAC AGG TAC CCT GAA GCA AAA A 324 AAC ATT AAA CAG AGA CTA CCA TGC AG A/T A A A A A T 61.7 S0260 CGT GGT GAA GGA TGA TGA GGA TGA ATC GTA TGT TCT ATG GTG CTT G 259 TCA CAC TAT ATT CTA CGA ATT TAC ACC C A/C A A A A C A 68.6 S0411 CGC ACG GTA AAA CCG ACT GA TCC GGA TTT TGT GCA ACC TG 806 CGC ATA AAT CAG ATG AGA GAG ATA GAC G/T T T T T T G 71.4 S0169 TTG CCT TTC TTT CAC TGC TTG G TTG CTC CAC AAT TTA GAA GGC AGT 200 CCG TTC TTC CAT AAG GCC ATT ACA TTA TAT A/G A A A G G A 83.0 S0170 AAA AGG AGG TCA GGT CGC TCG AT TTC CCT GGA AGA CAC CTA GTT CC 351 GGG CGA TGG CTC TAA CTC CAA TT A/C A A A C C A Chromosome S0172 GCA TCA AGC AGC ACA TGG AGG CTT CTT CGT TGT GAT CAG TCT GTG CT 207 CAG CTC CAC TGG CGT CAC C/T T T T C C T 17.0 S0389 CCC ATC ATG AAG TGT GAT GTG GA TAC AGC AGC CAC CGG ACA AA * GCC AAA AGA ATG ATG TTA ACA G/T G G G T G T 27.8 S0186 CTC CAC TCC TGC ATC TGG CAA TGC CAC ATC GTT CTT GAC TCA GTT 157 AGT TCT AGA AAA ACT TGA TTA TGA TAC C/T T T T T C T 35.6 S0346 CGT GCT TGG ATT TTT GTA AGC GCA TCC AGC TGC ACA TTT CC 677 GAT GTA GTG GGC TTT AAC TTT ATA GAA A G/T T G G T T G 45.0 S0173 GGA ATG CGT CGA TGG TGG TTG TTG CCG GAG TGC CCA CGT 149 TTG CAA GTG TGG AGG ACA GT G/A G G G A A G 55.1 S0347 CGG TGT ACT GAA CTA TCA GGT ATG GAC GAT GTT TAG TGT GGT TTC TGG AAA CCA * CCA GCA CGT GGT CAT ATC CCT C/T 74.9 S0179 GCT CAA GAA CCC TCA GCA TTA ACA C TCA TGT ATC CCC CAA AGT TGA GAG G 216 TTC TAA AAC CTT ATG TAA AGT GC C/T C C C T T C 80.5 S0390 AGG TCG AGA GAT GGC GAC AA GGT CCC AAA TAC TAC CCA TCA A * CGG AAA TGG ATC CAG CA C/T T T T T G T 89.0 S0181 CAC GGT TCC AAC CTT CTC GGA GCA GGG TGC ATT CAG TGT TTC AAG 167 TGT AAT AAG GTT GGC CTT CGT C C/T T T T C C T 97.0 S0175 CCC TTA GCC TTA CGA GCG CA AGC CAG CAT CCA GCG AAG AG * ATA CAG AGG CAG GCA GGC AAT GGT GGT G/C G G G G C G S0187 GTT AAA ATG CCA AAT GCA TGG TCG AT AAT GCT CCG GTA TTG AGA TTT TAC CAG 181 GCA TTA CTG GAT AAG CAT TGG CGA CA G/T G G G T T G S0386 TTC CGG CTG GTT TTC TCC TG TTT GCT GGA TCG GCC TTC TC 842 CTT CCA TCT TCC ATG GCC A/C A A A ND b C A Chromosome 12 Genomic PCR primer sets (5' 3') 5.5 S0188 AAT TTT CTG CTG ATA CTG ACA CTG TTC TGT ACC TAG CAA GTA CTC CAG CAG TTT 321 GTC AAC TGA CTT CTC TAC G/A A A A G G A 6.3 S0213 GTG ATT TCC AAC ACG CGC AC CCT CAT CCA ATG GCT TGC AC 608 AAA CCA TGT TTT ATG AAG AAG AGA G A/T A A A T T A 12.2 S0212 TGC CCT TGT TTA TGG AAG AAG CA CAG TCC ATC CTC CGT CAT GC 760 AAC CTT AAT AGT ACA AGT ATG CC G/C C C C C G C 23.0 S0189 GGA CGG AAT ACA TAA CAT CGC GTA GT TCG CTG ATG ATG TTG GTC GTC TC 170 AGG ATT GCT GTA CTG TGG GC G/A G G G G A G 30.0 S0196 ACT GGG AAA ATC GCT GCC AA ATT GCT GAT GCC TGG GAT GG 675 GCC TCA AAA TCT CAA CCA A C/T T T T C C T 30.0 S0199 GGT TTC GTC CAG TGT TCA AGT AGC A TCG TCA CAA TAT TTT CTT AAC AGC CA 528 CAA ATA CAA ATA CAT GGG CCT AC C/T C C C T T C 39.7 S0211 GCG AGC TTG AGA AGC GTG GT CAT CGT TTC GCT GAT CGT GC 642 ATG AAT CTG TGA AGA GCG TGG G/C G G G G C G 42.7 S0208 CTC CCT CCG CTC CCA GAA AT ATT TTG GTG GAG CGT CCC CT * CTC GAG CTC GAA GAT GGC G/C C G G C C G 61.6 S0207 CTA CGC TGA TGT TTA ACA GAT CTT CCC CGG GCA ACT GAT ACC AGG ACA 198 ATG GAT ATG TCG TCT TCT G C/T 61.6 S0210 ACG TGT CCT CCA TCC CCC TT TGC TCT GTG GTT GCT GGG AG 621 GTT TCG GTT TTT TCG GGT TC G/T G G G G T G 66.6 S0204 TGA AAA TGC TCT AAA TTT CTT GTC TTC CCT CAT GGT TCC CAT CAA AA 192 GTT CTC AGG CTC AAC GGC G/A G G G G A G 88.6 S0311 CAT GCC AGT GGT TTT TGC TA CCA TGA TCT TTG GGT GGT TT 904 GGA CGG TCA AAC GTT GGG CA C/T C C C C T C 92.0 S0192 GAG AGA GAT GGA GAT GTG CAT GGA T GTA TGG ATG GCT CAA ACA GCT AAC G 423 CTG AAA AGG CAC ATC GCT C G/T T T T T T G 95.1 S0206 CAA TAC TTC CAT GAG TAT ACT GCT TCT AAG AGT GCA GGA GCA AAG ACC AA 199 CAC TGG ACC TGC CCG AAC G/A A A A G G A S0195 CCG CAC TAC CTC ACA ATT GAA GAC T AAT TTT CAC TTC AGA CCG TGG ATG A 526 TCC CTC CAC ACC ATC CTC CA G/A G G G G G A *Precise fragment length is unknown. a Abbreviations for name of strain. N: Nipponbare, Ko: Koshihikari, Ki: Kitaake, ka: Kasalath, G: Guang-lu-ai 4 (G4), W: W1943. b No data is available because of dificulty in PCR amplification. Genome PCR and AcycloPrime FP reaction was performed following instructions of AcycloPrime FP SNP Detection Kit (PerkinElmer Life Sciences). Genotype

9 No. 5] S. Nasu et al. 171 Figure 5. Distribution of SNP markers established for G4 and W1943. This figure is based on the RGP s Nipponbare Kasalath linkage map and Current Genome Sequencing Status as at April Markers were distributed on all chromosomes, but some regions had very few markers (for example, an interval of about 30 cm between S0330 and S0036 on chr. 3). References 1. Risch, N. and Merikangas, K. 1996, The future of genetic studies of complex human diseases, Science, 273, Harushima, Y., Yano, M., Shomura, A. et al. 1998, A high-density rice genetic linkage map with 2275 markers using a single F 2 population, Genetics, 148, Monna, L., Kitazawa, N., Yoshino, R. et al. 2002, Positional cloning of rice semidwarfing gene, sd-1: rice green revolution gene encodes a mutant enzyme involved in gibberellin synthesis, DNA Res., 9, Lukowits, W., Gillmor, C. S., and Scheible, W. R. 2000, Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you, Plant Physiol., 123, Murray, M. G. and Thompson W. F. 1980, Rapid isolation of high molecular weight plant DNA, Nucleic Acids Res., 8, Sakata, K., Nagamura, Y., Numa, H. et al. 2002, Rice- GAAS: an automated annotation system and database for rice genome sequence, Nucleic Acids Res., 30, Wu, J., Maehara, T., Shimokawa, T. et al. 2002, A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites, Plant Cell, 14, Rozen, S. and Skaletsky, H. 2000, Primer3 on the WWW for general users and for biologist programmers, Methods Mol Biol, 132, Chen, X., Levine, L., and Kwok, P. Y. 1999, Fluorescence Polarization in Homogeneous Nucleic Acid Analysis, Genome Res., 9, Tenaillon, M. I., Sawkins, M. C., Long, A. D., Gaut, R. L., Doebley, J. F., and Gaut, B. S. 2001, Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.), Proc. Natl. Acad. Sci. USA, 98, Kurata, N., Nagamura, Y., Yamamoto, K. et al. 1994, A 300 kilobase interval genetic map of rice including 883 expressed sequences, Nature Genetics, 8,

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