Analysis workflow for genome-wide variations in TASUKE+ for RAP-DB (version 2.0)


Genome-wide variations were detected using publicly available genome resequencing data for various rice varieties and provided in the multiple genome browser TASUKE+. Here we provide the analysis workflow for the detection of variations.

History

Reference data

  • Genome sequences [FASTA]
    • IRGSP-1.0 genome (including organella and unanchored contig sequences)
  • Gene annotation for snpEff [Annotation GTF] [Protein FASTA]
    • RAP-DB (both representative and predicted genes as of 11 Nov 2021)
    • MSU (all genes in RGAP 7)
  • Illumina adapter sequences attached with the Trimmomatic program (TruSeq2 PE + TruSeq3 PE)
  • Chromosome information (chromosome_list.csv) for TASUKE+
  • $ cat chromosome_list.csv
    chr01,43270923,16610866,17243770
    chr02,35937250,13541821,13872411
    chr03,36413819,19431743,19745569
    chr04,35502694,9744480,9973218
    chr05,29958434,12390387,12627019
    chr06,31248787,15332004,15555636
    chr07,29697621,11887856,12272916
    chr08,28443022,12847483,13061068
    chr09,23012720,2749793,3043847
    chr10,23207287,8082722,8309866
    chr11,29021106,12039480,12482616
    chr12,27531856,11761737,12103486
    
  • Interval file (IRGSP-1.0_12chrom.intervals) for GATK
  • chr01
    chr02
    chr03
    chr04
    chr05
    chr06
    chr07
    chr08
    chr09
    chr10
    chr11
    chr12
    
  • Sample map file (sample.map) for GATK. Sample ID and path to GVCF are separeted by a TAB
  • SAMD00009825    variants_SAMD00009825.g.vcf.gz
    SAMD00010635    variants_SAMD00010635.g.vcf.gz
    SAMD00010636    variants_SAMD00010636.g.vcf.gz
    ...
    ...
    
  • Sample ID list (include_sample.args) for GATK.
  • SAMD00009825
    SAMD00010635
    SAMD00010636
    ...
    ...
    

Analysis tools

  • Java (JDK 1.8.0_191)
  • FastQC v0.11.8
  • BWA (bwa v0.7.17)
  • SamTools (v1.9)
  • BamTools (as of 4 Dec 2018)
  • GATK (v4.0.11.0)/GATK (v4.2.4.0)
  • Trimmomatic (v0.38)
  • Picard (v2.18.17)
  • SnpEff (v5.0e)
  • TASUKE+ (version 20210831)

Commands and parameters used in the workflow

  1. Preprocessing of Illumina paired-end reads
  2. $ java -jar trimmomatic-0.38.jar PE \
        -phred33 read.r1.fastq.gz read.r2.fastq.gz \
        read.pe.r1.fastq.gz read.se.r1.fastq.gz read.pe.r2.fastq.gz read.se.r2.fastq.gz \
        ILLUMINACLIP:adapters.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:10:20 MINLEN:30
    
  3. Making index of the genome
  4. $ bwa index genome.fa
    $ samtools faidx genome.fa
    $ java -jar picard.jar CreateSequenceDictionary \
        REFERENCE=genome.fa \
        OUTPUT=genome.dict
    
  5. Alignment of Illumina reads to the reference genome
  6. $ bwa mem -M genome.fa read.pe.r1.fastq.gz read.pe.r2.fastq.gz \
        | samtools sort -o alignment.sort.bam -
    $ samtools index alignment.sort.bam
    
  7. Make clean BAM
  8. $ java -jar picard.jar FastqToSam \
        FASTQ=read.pe.r1.fastq.gz \
        FASTQ2=read.pe.r2.fastq.gz \
        OUTPUT=uBAM.bam \
        READ_GROUP_NAME=${SAMPLE_ID} \
        SAMPLE_NAME=${SAMPLE_ID} \
        LIBRARY_NAME=${SAMPLE_ID} \
    
    $ java -jar picard.jar MergeBamAlignment \
        ALIGNED=alignment.sort.bam \
        UNMAPPED=uBAM.bam \
        OUTPUT=alignment.merge.bam \
        REFERENCE_SEQUENCE=genome.fa
    

    *User can specify any sample ID in the variable “${SAMPLE_ID}”.

  9. Remove PCR duplicates
  10. $ java -jar picard.jar MarkDuplicates \
        INPUT=alignment.merge.bam \
        OUTPUT=alignment.rmdup.bam \
        METRICS_FILE=rmdup.matrix \
        REMOVE_DUPLICATES=true \
        MAX_RECORDS_IN_RAM=1000000 \
        TMP_DIR=./tmp
    
    $ samtools index alignment.rmdup.bam
    
  11. Variant detection by GATK HaplotypeCaller
  12. $ gatk HaplotypeCaller \
        --input alignment.rmdup.bam \
        --output variants.g.vcf.gz \
        --reference genome.fa \
        -max-alternate-alleles 2 \
        --emit-ref-confidence GVCF
    

    *Step1-6 were performed for each sample before Step7.

  13. import GVCFs into GenomicsDB
  14. $ gatk GenomicsDBImport \
      --genomicsdb-workspace-path gvcfs_db \
      --sample-name-map sample.map \
      --intervals IRGSP-1.0_12chrom.intervals
    
  15. Genotyping and filtering variants by GATK
  16. gatk GenotypeGVCFs \
      --reference genome.fa \
      --variant gendb://gvcfs_db \
      --output variants.genotype.vcf.gz
    

    * Before VariantFiltration, average and standard deviation of depth of coverage was calculated for specifying $DP_AVG_PLUS_5SD.

    gatk VariantFiltration \
      --reference genome.fa \
      --variant variants.genotype.vcf.gz
      --output variants.genotype.filtered_SNP.vcf.gz \
      --filter-expression "DP > $DP_AVG_PLUS_5SD*" --filter-name "DP" \
      --filter-expression "QD < 2.0" --filter-name "QD" \
      --filter-expression "MQ < 40.0" --filter-name "MQ" \
      --filter-expression "FS > 60.0" --filter-name "FS" \
      --filter-expression "SOR > 3.0" --filter-name "SOR" \
      --filter-expression "MQRankSum < -12.5" --filter-name "MQRS" \
      --filter-expression "ReadPosRankSum < -8.0" --filter-name "RPRS"
    
    gatk VariantFiltration \
      --reference genome.fa \
      --variant variants.genotype.vcf.gz \
      --output variants.genotype.filtered_InDel.vcf.gz \
      --filter-expression "DP > $DP_AVG_PLUS_5SD" --filter-name "DP" \
      --filter-expression "QD < 2.0" --filter-name "QD" \
      --filter-expression "FS > 200.0" --filter-name "FS" \
      --filter-expression "SOR > 10.0" --filter-name "SOR" \
      --filter-expression "ReadPosRankSum < -20.0" --filter-name "RPRS"
    
    gatk SelectVariants \
      --reference genome.fa \
      --variant variants.genotype.vcf.gz \
      --output variants.genotype.selected_SNP.vcf.gz \
      --exclude-filtered \
      --select-type-to-include SNP \
      --select-type-to-include MNP \
      --sample-name include_sample.args
    
    gatk SelectVariants \
      --reference genome.fa \
      --variant variants.genotype.vcf.gz \
      --output variants.genotype.selected_InDel.vcf.gz \
       --exclude-filtered \
       --select-type-to-include INDEL \
       --select-type-to-include MIXED \
       --sample-name include_sample.args
    
    java -jar picard.jar MergeVcfs \
      --INPUT variants.genotype.selected_SNP.vcf.gz \
      --INPUT variants.genotype.selected_InDel.vcf.gz \
      --OUTPUT variants.varonly.vcf.gz 
    
  17. Run SnpEff
  18. $ java -jar snpEff.jar build -gtf22 -v RAP_MSU_on_IRGSP-1.0
    
    $ java -jar snpEff.jar \
        -ud 1000 \
        -v RAP_MSU_on_IRGSP-1.0 variants.varonly.vcf.gz | gzip -c > variants.snpEff.varonly.vcf.gz
    

    *Reference genome sequence (FASTA), gene annotation data (GTF) and protein sequences of all genes (FASTA) should be placed in appropriate directories before running SnpEff.

  19. Make depth data for TASUKE+
  20. $ perl tasuke_bamtodepth.pl \
        -s samtools -c chromosome_list.csv -i alignment.rmdup.bam \
        -o alignment_depth.tsv
    
  21. Upload variation and depth data to TASUKE+

The following two output files are uploaded to the TASUKE+ database

  • variants.snpEff.varonly.vcf.gz
  • alignment_depth.tsv

Information of rice varieties and sequence data provided in TASUKE+

Filter:
ID (BioSample) Name Sub variety Type Origin Reference Avg. depth of coverage Other names
SAMD00009825 Omachi TEJ Landrace Japan (Okayama) Arai-Kichise Y et al. 2011 Plant Cell Physiol. 48.5589 JRC32
SAMD00010635 Gohyakumangoku TEJ Elite Japan Arai-Kichise Y et al. 2014 PLoS One 51.1333 -
SAMD00010636 Kameji TEJ Landrace Japan (Shimane) Arai-Kichise Y et al. 2014 PLoS One 44.2013 JRC31
SAMD00010632 Koshihikari TEJ Elite Japan Arai-Kichise Y et al. 2014 PLoS One 51.0671 -
SAMD00010631 Moroberekan TRJ Landrace Guinea Arai-Kichise Y et al. 2014 PLoS One 38.7156 -
SAMD00010634 Norin8 TEJ Elite Japan Arai-Kichise Y et al. 2014 PLoS One 63.6267 -
SAMD00010633 Yamadanishiki TEJ Elite Japan Arai-Kichise Y et al. 2014 PLoS One 38.7664 -
SAMN07767782 Bengal TRJ Elite United States Chai C et al. 2018 Sci. Rep. 26.1568 -
SAMN07767800 Nona Bokra IND Landrace India Chai C et al. 2018 Sci. Rep. 15.8360 -
SAMN07767773 PSRR-1 WEEDY Weedy United States Chai C et al. 2018 Sci. Rep. 33.9277 -
SAMN02179223 IR8 IND Elite Philippines Duitama J et al. 2015 PLoS One 23.2432 -
SAMN02821272 Zafiro TEJ Elite Chile Duitama J et al. 2015 PLoS One 7.1875 -
SAMN02821271 Pionero2010FL IND Elite Venezuela Duitama J et al. 2015 PLoS One 20.8284 -
SAMN02821270 Parao TRJ Elite Uruguay Duitama J et al. 2015 PLoS One 30.0206 -
SAMN02821269 Oryzica Llanos 5 IND Elite - Duitama J et al. 2015 PLoS One 11.6736 -
SAMN02821268 Oryzica 3 IND Elite - Duitama J et al. 2015 PLoS One 12.2288 -
SAMN02821267 L2825-CA TRJ Elite Uruguay Duitama J et al. 2015 PLoS One 12.4445 -
SAMN02821266 IRGA427 IND Elite Brazil Duitama J et al. 2015 PLoS One 26.4875 -
SAMN02821265 IRGA424 IND Elite Brazil Duitama J et al. 2015 PLoS One 11.2004 -
SAMN02821264 IR64 IND Elite Philippines Duitama J et al. 2015 PLoS One 16.2973 -
SAMN02821263 Fedearroz50 IND Elite Latin America Duitama J et al. 2015 PLoS One 10.8657 -
SAMN02821262 Fedearroz2000 IND Elite Latin America Duitama J et al. 2015 PLoS One 11.3621 -
SAMN02821261 Fedearroz174 IND Elite Latin America Duitama J et al. 2015 PLoS One 8.7865 -
SAMN02821260 Fanny TEJ Elite Philippines Duitama J et al. 2015 PLoS One 23.0826 -
SAMN02821259 Esperanza TRJ Elite Philippines Duitama J et al. 2015 PLoS One 7.6551 -
SAMN02821258 Curinga TRJ Elite Philippines Duitama J et al. 2015 PLoS One 12.5996 -
SAMN02821257 CT21375-F4-43-1 IND Elite Colombia Duitama J et al. 2015 PLoS One 24.6233 -
SAMN02821256 CT19021-3-4-1V1-1 IND Elite Colombia Duitama J et al. 2015 PLoS One 24.8150 -
SAMN02821255 CT18685 IND Elite Colombia Duitama J et al. 2015 PLoS One 10.0616 -
SAMN02821254 Camponi IND Elite Colombia Duitama J et al. 2015 PLoS One 11.4020 -
SAMN02821253 175-1-127 IND Elite Philippines Duitama J et al. 2015 PLoS One 25.0442 -
SAMN02821252 Wells TRJ Elite United States Duitama J et al. 2015 PLoS One 4.3020 -
SAMN02821251 TeQing IND Elite China Duitama J et al. 2015 PLoS One 4.6001 -
SAMN02821250 ShuFeng IND Elite China Duitama J et al. 2015 PLoS One 3.4611 -
SAMN02821249 Saber TRJ Elite - Duitama J et al. 2015 PLoS One 36.1230 -
SAMN02821248 Mermentau TRJ Elite - Duitama J et al. 2015 PLoS One 10.5885 -
SAMN02821247 MCR010277 ADMIX Elite United States Duitama J et al. 2015 PLoS One 3.7100 -
SAMN02821246 LM-1 TRJ Elite United States Duitama J et al. 2015 PLoS One 3.7354 -
SAMN02821245 Lemont TRJ Elite United States Duitama J et al. 2015 PLoS One 4.4782 -
SAMN02821244 Lagrue3 TRJ Elite United States Duitama J et al. 2015 PLoS One 5.0532 -
SAMN02821243 LA2177 TRJ Elite - Duitama J et al. 2015 PLoS One 10.6562 -
SAMN02821242 L201 TRJ Elite United States Duitama J et al. 2015 PLoS One 3.8145 -
SAMN02821241 Jupiter TEJ Elite - Duitama J et al. 2015 PLoS One 9.2133 -
SAMN02821240 Jazzman2 TRJ Elite - Duitama J et al. 2015 PLoS One 9.3428 -
SAMN02821239 Jazzman TRJ Elite - Duitama J et al. 2015 PLoS One 8.2021 -
SAMN02821238 Jasmine85 IND Elite Philippines Duitama J et al. 2015 PLoS One 3.9722 -
SAMN02821237 IAC600 TEJ Elite - Duitama J et al. 2015 PLoS One 21.8406 -
SAMN02821236 Hidalgo TRJ Elite United States Duitama J et al. 2015 PLoS One 35.8358 -
SAMN02821235 Francis TRJ Elite United States Duitama J et al. 2015 PLoS One 3.7172 -
SAMN02821234 Dixiebelle TRJ Elite - Duitama J et al. 2015 PLoS One 34.8106 -
SAMN02821233 Della2 TRJ Elite - Duitama J et al. 2015 PLoS One 13.9952 -
SAMN02821232 Cypress2 TRJ Elite United States Duitama J et al. 2015 PLoS One 6.4364 -
SAMN02821231 Cocodrie TRJ Elite United States Duitama J et al. 2015 PLoS One 10.2111 -
SAMN02821230 CMS08B IND Elite - Duitama J et al. 2015 PLoS One 9.3957 -
SAMN02821229 CMS08A IND Elite - Duitama J et al. 2015 PLoS One 11.7241 -
SAMN02821228 CL261 TEJ Elite United States Duitama J et al. 2015 PLoS One 10.7862 -
SAMN02821227 CL152 TRJ Elite United States Duitama J et al. 2015 PLoS One 12.6729 -
SAMN02821226 CL131 TRJ Elite United States Duitama J et al. 2015 PLoS One 15.4790 -
SAMN02821225 CL111 TRJ Elite United States Duitama J et al. 2015 PLoS One 11.2771 -
SAMN02821224 Catahoula TRJ Elite United States Duitama J et al. 2015 PLoS One 14.0305 -
SAMN02821223 CarolinaGoldSelect TRJ Elite United States Duitama J et al. 2015 PLoS One 37.4468 -
SAMN02821222 CarolinaGold TRJ Elite United States Duitama J et al. 2015 PLoS One 23.1022 -
SAMN02821221 Bowman TRJ Elite United States Duitama J et al. 2015 PLoS One 6.0599 -
SAMN02821220 Bengal TEJ Elite United States Duitama J et al. 2015 PLoS One 3.1203 -
SAMN02375091 Badari Dhan IND Landrace Nepal Fawcett J et al. 2013 PLoS One 16.7887 WRC39
SAMN02375099 Deejiaohualuo IND - China Fawcett J et al. 2013 PLoS One 15.0107 WRC98
SAMN02375107 Dunghan Shali JP - Hungary Fawcett J et al. 2013 PLoS One 5.3647 -
SAMN02375104 Hitomebore TEJ Elite Japan Fawcett J et al. 2013 PLoS One 27.6151 -
SAMN02375100 Hong Cheuh Zai IND - China Fawcett J et al. 2013 PLoS One 13.1845 WRC99
SAMN02375106 Iwatekko TEJ Elite Japan Fawcett J et al. 2013 PLoS One 21.2408 -
SAMN02375108 Jaguary TRJ - Brazil Fawcett J et al. 2013 PLoS One 13.7624 WRC47
SAMN02375098 Jena 035 IND Landrace Nepal Fawcett J et al. 2013 PLoS One 11.5162 WRC4
SAMN02375092 Kaluheenati IND Landrace Sri Lanka Fawcett J et al. 2013 PLoS One 13.7260 WRC41
SAMN02375093 Kasalath AUS Landrace India Fawcett J et al. 2013 PLoS One 10.7658 WRC2
SAMN02375101 Keiboba IND Landrace China Fawcett J et al. 2013 PLoS One 11.0198 WRC17
SAMN02375112 NERICA1 JP/GLA Elite Africa Fawcett J et al. 2013 PLoS One 12.0853 -
SAMN02375103 Nipponbare TEJ Elite Japan Fawcett J et al. 2013 PLoS One 19.5170 WRC01
SAMN02375087 W0120 RUF Wild India Fawcett J et al. 2013 PLoS One 21.9471 W0120
SAMN02375083 W1807 RUF Wild Sri Lanka Fawcett J et al. 2013 PLoS One 18.9626 W1807
SAMN02375089 W1886 RUF Wild Thailand Fawcett J et al. 2013 PLoS One 20.3654 W1886
SAMN02375090 W1965 RUF Wild China Fawcett J et al. 2013 PLoS One 24.3307 W1965
SAMN02375085 W1976 RUF Wild Indonesia Fawcett J et al. 2013 PLoS One 22.0253 W1976
SAMN02375084 W2003 RUF Wild India Fawcett J et al. 2013 PLoS One 19.7543 W2003
SAMN02375086 W2057 RUF Wild Bangladesh Fawcett J et al. 2013 PLoS One 24.7482 W2057
SAMN02375081 W593 RUF Wild Malaysia Fawcett J et al. 2013 PLoS One 32.7118 W593
SAMN02375088 W630 RUF Wild Myammar Fawcett J et al. 2013 PLoS One 32.2383 W630
SAMN02375094 Ratul IND Landrace India Fawcett J et al. 2013 PLoS One 16.0517 WRC36
SAMN02375110 Rexmont TRJ Elite United States Fawcett J et al. 2013 PLoS One 14.9360 WRC50
SAMN02375105 Sasanishiki TEJ Elite Japan Fawcett J et al. 2013 PLoS One 15.1857 -
SAMN02375095 Shoni IND Landrace Bangladesh Fawcett J et al. 2013 PLoS One 13.0846 WRC31
SAMN02375096 Surjamukhi IND Elite India Fawcett J et al. 2013 PLoS One 16.4472 WRC33
SAMN02375102 Takanari IND Elite Japan Fawcett J et al. 2013 PLoS One 9.3008 -
SAMN02375111 Tupa729 TRJ Landrace Bangladesh Fawcett J et al. 2013 PLoS One 14.6274 WRC55
SAMN02375097 Tupa121-3 IND Landrace Bangladesh Fawcett J et al. 2013 PLoS One 12.8430 WRC32
SAMN02375109 Urasan1 TRJ Elite Japan Fawcett J et al. 2013 PLoS One 14.4075 WRC51
SAMD00016906 Kitaake TEJ Elite Japan Fujino K et al. 2015 Theor. Appl. Genet. 32.8657 -
SAMN02231725 Nov-93 IND Elite China Gao Z-U et al. 2013 PNAS 42.5526 -
SAMN02207968 Peiai 64s ADMIX Elite China Gao Z-U et al. 2013 PNAS 50.1032 -
SAMN03273435 CDR22 IND Elite China Huang J et al. 2018 PNAS 23.4591 -
SAMN03273436 Chenghui047 IND Elite China Huang J et al. 2018 PNAS 23.3218 -
SAMN03273446 Chuannong422 IND Elite China Huang J et al. 2018 PNAS 20.2367 -
SAMN03273427 Dee geo woo gen IND Elite China Huang J et al. 2018 PNAS 23.2175 -
SAMN03273437 Fuhui838 IND Elite China Huang J et al. 2018 PNAS 20.6486 -
SAMN03273447 Guangchang13 IND Elite China Huang J et al. 2018 PNAS 21.9990 -
SAMN03273433 GUI630 IND Elite China Huang J et al. 2018 PNAS 22.5329 -
SAMN03273438 Hanghui570 IND Elite China Huang J et al. 2018 PNAS 21.9856 -
SAMN03273443 IR1544 IND Elite Philippines Huang J et al. 2018 PNAS 22.3910 -
SAMN03273430 IR20 IND Elite Philippines Huang J et al. 2018 PNAS 22.8904 -
SAMN03273429 IR24 IND Elite Philippines Huang J et al. 2018 PNAS 22.7311 -
SAMN03273431 IR26 IND Elite Philippines Huang J et al. 2018 PNAS 24.0550 -
SAMN03273432 IR30 IND Elite Philippines Huang J et al. 2018 PNAS 21.8960 -
SAMN03273445 IR36 IND Elite Philippines Huang J et al. 2018 PNAS 24.4439 -
SAMN03273428 IR8 IND Elite Philippines Huang J et al. 2018 PNAS 22.2619 -
SAMN03273448 Luchang-3 IND Elite China Huang J et al. 2018 PNAS 20.8180 -
SAMN03273440 Mianhui725 IND Elite China Huang J et al. 2018 PNAS 23.8063 -
SAMN03273434 Minghui63 IND Elite China Huang J et al. 2018 PNAS 21.7331 -
SAMN03273439 Minghui70 IND Elite China Huang J et al. 2018 PNAS 21.1535 -
SAMN03273441 Minghui86 IND Elite China Huang J et al. 2018 PNAS 22.6888 -
SAMN03273449 Nante IND Elite China Huang J et al. 2018 PNAS 21.1887 -
SAMN03273454 W1543 RUF Wild - Huang J et al. 2018 PNAS 22.8741 -
SAMN03273426 Pitai IND Elite Indonesia Huang J et al. 2018 PNAS 22.1235 -
SAMN03273450 Shenglixian IND Elite China Huang J et al. 2018 PNAS 22.4179 -
SAMN03273444 Shuhui527 IND Elite China Huang J et al. 2018 PNAS 20.0411 -
SAMN03273451 Tetep IND Elite China Huang J et al. 2018 PNAS 23.5824 -
SAMN03273442 Wanhui88 IND Elite China Huang J et al. 2018 PNAS 22.2789 -
SAMN03273452 Wanlixian IND Elite China Huang J et al. 2018 PNAS 22.3096 -
SAMN03273453 Zhongnong-4 IND Elite China Huang J et al. 2018 PNAS 22.0484 -
SAMEA966194 Guangluai4 IND Elite China Huang X et al. 2010 Nat. Genet. 17.0946 -
SAMEA871359 Nongken58 TEJ Elite Japan Huang X et al. 2010 Nat. Genet. 11.5697 -
SAMN00027406 Ai-Chiao-Hong IND Landrace China Xu et al. 2011 Nat. Biotech. 15.9009 IRGC51250
SAMN00027400 Arias TRJ Landrace Indonesia (West Java) Xu et al. 2011 Nat. Biotech. 14.5566 IRGC43325
SAMN00027396 Azucena TRJ Landrace Philippines Xu et al. 2011 Nat. Biotech. 15.3492 IRGC328
SAMN00027411 BADAL 89 ADMIX Landrace Bangladesh Xu et al. 2011 Nat. Biotech. 15.3295 IRGC6513
SAMN00027398 Bico Branco ARO Elite Brazil Xu et al. 2011 Nat. Biotech. 15.8042 IRGC38994
SAMN00027390 Binulawan TRJ Landrace Philippines Xu et al. 2011 Nat. Biotech. 15.7614 IRGC26872
SAMN00027418 CA 97-053 NIV Wild Cambodia (Sopoir Tep) Xu et al. 2011 Nat. Biotech. 14.4031 IRGC89215
SAMN00027405 Canella De Ferro TRJ Elite Brazil Xu et al. 2011 Nat. Biotech. 17.1261 IRGC50448
SAMN00027408 Chodongji TEJ Landrace South Korea Xu et al. 2011 Nat. Biotech. 15.9961 IRGC55471
SAMN00027391 Darmali TEJ Landrace Nepal Xu et al. 2011 Nat. Biotech. 11.0102 IRGC27630
SAMN00027416 Davao TRJ Landrace Philippines Xu et al. 2011 Nat. Biotech. 13.1508 IRGC8244
SAMN00027417 DZ78 AUS Landrace Bangladesh Xu et al. 2011 Nat. Biotech. 16.7028 IRGC8555
SAMN00027425 Firooz ARO Landrace Iran Xu et al. 2011 Nat. Biotech. 16.4926 RA4952
SAMN00027415 Gie57 IND Landrace Vietnam Xu et al. 2011 Nat. Biotech. 15.8617 IRGC8231
SAMN00027401 Gotak Gatik TRJ Landrace Indonesia (C.Java) Xu et al. 2011 Nat. Biotech. 12.7603 IRGC43397
SAMN00027407 Guan-Yin-Tsan IND Landrace China Xu et al. 2011 Nat. Biotech. 15.7751 IRGC51300
SAMN00027388 Haginomae Mochi TEJ Elite Japan Xu et al. 2011 Nat. Biotech. 17.0233 IRGC2540
SAMN00027409 HAISHA CAMAN ADMIX Landrace Bangladesh Xu et al. 2011 Nat. Biotech. 13.8375 IRGC60542
SAMN00027413 HK 47 NIV Wild India (Madhya Pradesh) Xu et al. 2011 Nat. Biotech. 13.9759 IRGC80470
SAMN00027393 IR36 IND Elite Philippines Xu et al. 2011 Nat. Biotech. 16.7316 IRGC30416
SAMN00027387 Jambu TRJ Landrace Indonesia Xu et al. 2011 Nat. Biotech. 12.4589 IRGC17757
SAMN00027419 JC101 ARO Elite India Xu et al. 2011 Nat. Biotech. 14.0721 IRGC9060
SAMN00027420 JC111 ARO Elite India Xu et al. 2011 Nat. Biotech. 15.3325 IRGC9062
SAMN00027422 JC91 IND Elite India Xu et al. 2011 Nat. Biotech. 16.1642 IRGC9177
SAMN00027410 Jhona 349 AUS Landrace India Xu et al. 2011 Nat. Biotech. 12.9112 IRGC6307
SAMN00027404 Kalamkati AUS Landrace India Xu et al. 2011 Nat. Biotech. 16.0264 IRGC45975
SAMN00027385 Kitrana 508 ARO Elite Madagascar Xu et al. 2011 Nat. Biotech. 16.7195 IRGC12793
SAMN00027394 KUI SALI ARO Landrace Bangladesh Xu et al. 2011 Nat. Biotech. 14.7886 IRGC31856
SAMN00027382 L 89-12 NIV Wild Laos (Vientiane) Xu et al. 2011 Nat. Biotech. 15.4873 IRGC106154
SAMN00027412 Lemont TRJ Elite United States (TX) Xu et al. 2011 Nat. Biotech. 13.2666 IRGC66756
SAMN00027392 Leung Pratew IND Landrace Thailand Xu et al. 2011 Nat. Biotech. 14.6440 IRGC27762
SAMN00027383 Maintmolotsy TRJ Elite Madagascar Xu et al. 2011 Nat. Biotech. 12.5632 IRGC11010
SAMN00027414 Mansaku TEJ Landrace Japan Xu et al. 2011 Nat. Biotech. 15.6631 JRC22;IRGC8191
SAMN00027386 Mehr AUS Landrace Iran Xu et al. 2011 Nat. Biotech. 15.7186 -
SAMN00027389 Miriti IND Landrace Bangladesh Xu et al. 2011 Nat. Biotech. 12.6810 IRGC25901
SAMN00027381 MV 89-80 NIV Wild India (Medinipur) Xu et al. 2011 Nat. Biotech. 15.3152 IRGC106105
SAMN00027423 Nipponbare TEJ Elite Japan Xu et al. 2011 Nat. Biotech. 11.3721 WRC01
SAMN00027399 Norin20 TEJ Landrace Japan Xu et al. 2011 Nat. Biotech. 14.8839 IRGC418
SAMN00027397 NPE 844 TRJ Landrace Pakistan Xu et al. 2011 Nat. Biotech. 16.8329 IRGC38698
SAMN00027378 042/87/34 NIV Wild India (Dhoni) Xu et al. 2011 Nat. Biotech. 15.3772 IRGC105327
SAMN00027380 DAL DHAN RUF Wild Bangladesh (Chakaria) Xu et al. 2011 Nat. Biotech. 15.6345 IRGC105960
SAMN00027424 P46 RUF Wild China (Hainan) Xu et al. 2011 Nat. Biotech. 13.0530 -
SAMN00027379 PADI PADIAN RUF Wild Indonesia (Kromat Watu) Xu et al. 2011 Nat. Biotech. 15.4170 IRGC105958
SAMN00027426 VOC4 RUF Wild Nepal Xu et al. 2011 Nat. Biotech. 14.7179 -
SAMN00027395 Phudugey TEJ Landrace Bhutan Xu et al. 2011 Nat. Biotech. 15.2611 IRGC32399
SAMN00027402 Popot 165 IND Landrace Indonesia (E.Kalimantan) Xu et al. 2011 Nat. Biotech. 14.9928 IRGC43545
SAMN00027384 Ta Hung Ku TEJ Landrace China Xu et al. 2011 Nat. Biotech. 12.4053 IRGC1107
SAMN00027421 TD2 IND Elite Thailand Xu et al. 2011 Nat. Biotech. 11.1542 IRGC9148
SAMN00027403 Trembese TRJ Landrace Indonesia (East Java) Xu et al. 2011 Nat. Biotech. 12.7607 IRGC43675
SAMN00027427 Yuan 3-9 RUF Wild China (Yunnan) Xu et al. 2011 Nat. Biotech. 11.7131 -
SAMD00078858 Hayamasari TEJ Elite Japan Itoh H et al. 2018 Plant J. 52.0683 -
SAMD00078855 LAC23 TRJ Elite Liberia Itoh H et al. 2018 Plant J. 42.9985 -
SAMD00078853 Bei Khe IND Landrace Cambodia Itoh H et al. 2018 Plant J. 42.0912 WRC03
SAMD00078857 Khao Nam Jen TRJ Landrace Laos Itoh H et al. 2018 Plant J. 48.3483 WRC68
SAMD00078856 Khau Mac Kho TRJ Landrace Vietnam Itoh H et al. 2018 Plant J. 58.5655 WRC48
SAMD00078854 Nona Bokra IND Landrace India Itoh H et al. 2018 Plant J. 37.6017 IRGC022710
SAMD00078852 Tupa 121-3 IND Landrace Bangladesh Itoh H et al. 2018 Plant J. 39.7171 WRC32
SAMD00080339 Kasalath IND Landrace India Tanaka N et al. 2020 Plant Cell Physiol. 21.2901 WRC02
SAMD00080340 Muha AUS - India Tanaka N et al. 2020 Plant Cell Physiol. 39.2000 WRC25
SAMD00080342 Naba IND Landrace India Tanaka N et al. 2020 Plant Cell Physiol. 52.9000 WRC05
SAMD00080343 Basilanon TRJ Landrace Philippines Tanaka N et al. 2020 Plant Cell Physiol. 44.4000 WRC44
SAMD00080344 Deng Pao Zhai IND Elite China Tanaka N et al. 2020 Plant Cell Physiol. 40.3000 WRC19
SAMD00080346 Bleiyo IND Landrace Thailand Tanaka N et al. 2020 Plant Cell Physiol. 37.9000 WRC63
SAMD00080348 Davao 1 IND Landrace Philippines Tanaka N et al. 2020 Plant Cell Physiol. 51.1000 WRC07
SAMD00080349 Vandaran IND Landrace Sri Lanka Tanaka N et al. 2020 Plant Cell Physiol. 39.9000 WRC100
SAMD00080350 Kemasin IND Landrace Malaysia Tanaka N et al. 2020 Plant Cell Physiol. 55.4000 WRC62
SAMD00080351 Badari Dhan IND Landrace Nepal Tanaka N et al. 2020 Plant Cell Physiol. 60.0000 WRC39
SAMD00080352 Anjana Dhan IND Landrace Nepal Tanaka N et al. 2020 Plant Cell Physiol. 31.7000 WRC30
SAMD00080356 Neang Phtong IND Landrace Cambodia Tanaka N et al. 2020 Plant Cell Physiol. 33.3000 WRC59
SAMD00080357 Hakphaynhay IND Landrace Laos Tanaka N et al. 2020 Plant Cell Physiol. 27.5000 WRC60
SAMD00080358 Tima TRJ Landrace Bhutan Tanaka N et al. 2020 Plant Cell Physiol. 56.5000 WRC53
SAMD00080359 Padi Perak TRJ Landrace Indonesia Tanaka N et al. 2020 Plant Cell Physiol. 54.1000 WRC49
SAMD00080361 Ma sho TRJ Landrace Myanmar Tanaka N et al. 2020 Plant Cell Physiol. 55.7000 WRC45
SAMD00080366 Dianyu 1 TEJ Elite China Tanaka N et al. 2020 Plant Cell Physiol. 56.4000 WRC43
SAMD00080368 Nipponbare TEJ Elite Japan Tanaka N et al. 2020 Plant Cell Physiol. 66.7000 WRC01
SAMD00167011 Jena 035 IND Landrace Nepal Tanaka N et al. 2020 Plant Cell Physiol. 24.2900 WRC04
SAMD00167012 Puluik Arang IND Landrace Indonesia Tanaka N et al. 2020 Plant Cell Physiol. 52.9400 WRC06
SAMD00167013 Ryou Suisan Koumai IND Landrace China Tanaka N et al. 2020 Plant Cell Physiol. 34.2400 WRC09
SAMD00080345 Qiu Zao Zhong (Shuusoushu) IND Landrace China Tanaka N et al. 2020 Plant Cell Physiol. 39.8600 WRC10
SAMD00167014 Jinguoyin IND Landrace China Tanaka N et al. 2020 Plant Cell Physiol. 29.6900 WRC11
SAMD00167015 Dahonggu IND Landrace China Tanaka N et al. 2020 Plant Cell Physiol. 30.9400 WRC12
SAMD00167016 Asu IND Landrace Bhutan Tanaka N et al. 2020 Plant Cell Physiol. 26.7400 WRC13
SAMD00167017 IR58 IND Elite Philippines Tanaka N et al. 2020 Plant Cell Physiol. 20.4300 WRC14
SAMD00167018 Co 13 IND Landrace India Tanaka N et al. 2020 Plant Cell Physiol. 50.6200 WRC15
SAMD00167019 Vary Futsi IND Landrace Madagascar Tanaka N et al. 2020 Plant Cell Physiol. 34.2400 WRC16
SAMD00167020 Keiboba IND Landrace China Tanaka N et al. 2020 Plant Cell Physiol. 25.1600 WRC17
SAMD00167021 Qingyu (Seiyu) IND Landrace Taiwan Tanaka N et al. 2020 Plant Cell Physiol. 39.2800 WRC18
SAMD00167022 Tadukan IND Landrace Philippines Tanaka N et al. 2020 Plant Cell Physiol. 28.9000 WRC20
SAMD00167024 Calotoc IND Landrace Philippines Tanaka N et al. 2020 Plant Cell Physiol. 34.5500 WRC22
SAMD00167025 Lebed JP Landrace Philippines Tanaka N et al. 2020 Plant Cell Physiol. 26.1900 WRC23
SAMD00167026 Pinulupot 1 IND Landrace Philippines Tanaka N et al. 2020 Plant Cell Physiol. 34.4900 WRC24
SAMD00167027 Jhona 2 AUS Landrace India Tanaka N et al. 2020 Plant Cell Physiol. 33.2300 WRC26
SAMD00167028 Nepal 8 AUS Landrace Nepal Tanaka N et al. 2020 Plant Cell Physiol. 35.3300 WRC27
SAMD00167029 Jarjan AUS Landrace Nepal Tanaka N et al. 2020 Plant Cell Physiol. 27.2400 WRC28
SAMD00167030 Kalo Dhan AUS Landrace Nepal Tanaka N et al. 2020 Plant Cell Physiol. 29.0000 WRC29
SAMD00167031 Shoni IND Landrace Bangladesh Tanaka N et al. 2020 Plant Cell Physiol. 29.4000 WRC31
SAMD00167032 Surjamukhi AUS Elite India Tanaka N et al. 2020 Plant Cell Physiol. 26.8000 WRC33
SAMD00167033 ARC 7291 AUS Landrace India Tanaka N et al. 2020 Plant Cell Physiol. 35.1000 WRC34
SAMD00167034 ARC 5955 AUS Landrace India Tanaka N et al. 2020 Plant Cell Physiol. 33.5000 WRC35
SAMD00167035 Ratul IND Landrace India Tanaka N et al. 2020 Plant Cell Physiol. 24.5000 WRC36
SAMD00167036 ARC 7047 AUS Landrace India Tanaka N et al. 2020 Plant Cell Physiol. 35.0000 WRC37
SAMD00167037 ARC 11094 AUS Landrace India Tanaka N et al. 2020 Plant Cell Physiol. 36.1000 WRC38
SAMD00167038 Nepal 555 AUS - India Tanaka N et al. 2020 Plant Cell Physiol. 34.9000 WRC40
SAMD00167039 Kaluheenati IND Landrace Sri Lanka Tanaka N et al. 2020 Plant Cell Physiol. 25.6000 WRC41
SAMD00167040 Local Basmati AUS Landrace India Tanaka N et al. 2020 Plant Cell Physiol. 36.4000 WRC42
SAMD00167041 Khao Nok TRJ Landrace Laos Tanaka N et al. 2020 Plant Cell Physiol. 24.6000 WRC46
SAMD00167042 Jaguary TRJ - Brasil Tanaka N et al. 2020 Plant Cell Physiol. 24.8000 WRC47
SAMD00167043 Rexmont TRJ Elite United States Tanaka N et al. 2020 Plant Cell Physiol. 25.2000 WRC50
SAMD00167044 Urasan 1 TRJ Landrace Japan Tanaka N et al. 2020 Plant Cell Physiol. 30.6000 WRC51
SAMD00167045 Khau Tan Chiem TRJ Landrace Vietnam Tanaka N et al. 2020 Plant Cell Physiol. 25.9000 WRC52
SAMD00167046 Tupa729 TRJ Landrace Bangladesh Tanaka N et al. 2020 Plant Cell Physiol. 31.4000 WRC55
SAMD00167047 Milyang 23 IND Elite Korea Tanaka N et al. 2020 Plant Cell Physiol. 30.4000 WRC57
SAMD00167048 Neang Menh IND Landrace Cambodia Tanaka N et al. 2020 Plant Cell Physiol. 37.2000 WRC58
SAMD00167049 Radin Goi Sesat IND Landrace Cambodia Tanaka N et al. 2020 Plant Cell Physiol. 35.6000 WRC61
SAMD00167050 Padi Kuning IND Landrace Indonesia Tanaka N et al. 2020 Plant Cell Physiol. 34.2000 WRC64
SAMD00167051 Rambhog IND Landrace Indonesia Tanaka N et al. 2020 Plant Cell Physiol. 35.4000 WRC65
SAMD00167052 Bingala IND Landrace Myanmar Tanaka N et al. 2020 Plant Cell Physiol. 36.5000 WRC66
SAMD00167053 Phulba TRJ Landrace India Tanaka N et al. 2020 Plant Cell Physiol. 35.4000 WRC67
SAMD00167054 Chin Galay IND Landrace Myanmar Tanaka N et al. 2020 Plant Cell Physiol. 35.3000 WRC97
SAMD00167055 Deejiaohualuo IND - China Tanaka N et al. 2020 Plant Cell Physiol. 31.7000 WRC98
SAMD00167056 Hong Cheuh Zai IND - China Tanaka N et al. 2020 Plant Cell Physiol. 27.0000 WRC99
SAMD00167023 Shwe Nang Gyi IND Landrace Myanmar Tanaka N et al. 2020 Plant Cell Physiol. 25.1000 WRC21
SAMD00237861 Gaisen Mochi TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 29.9984 JRC01
SAMD00237862 Hinode TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 22.0778 JRC03
SAMD00237863 Senshou TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 27.0409 JRC04
SAMD00237864 Yamada Bake TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 32.4332 JRC05
SAMD00237865 Kaneko B TRJ Elite Japan Tanaka N et al. 2021 Plant Cell Physiol. 23.0103 JRC06
SAMD00237866 Iruma Nishiki TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 29.2314 JRC07
SAMD00237867 Okka Modoshi TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 32.3903 JRC08
SAMD00237868 Hirayama TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 27.6050 JRC10
SAMD00080360 Kahei TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 34.7443 JRC11
SAMD00237869 Oiran TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 28.0609 JRC12
SAMD00237870 Bouzu Mochi TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 36.5632 JRC13
SAMD00237871 Meguro Mochi TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 28.1926 JRC14
SAMD00080363 Akage TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 37.0053 JRC17
SAMD00237872 Hassokuho TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 28.9450 JRC18
SAMD00237873 Wataribune TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 29.0418 JRC19
SAMD00237874 Hosogara TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 30.9410 JRC20
SAMD00237875 Akamai (Kochi) IND Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 28.6000 JRC21
SAMD00237876 Mansaku TEJ Elite Japan Tanaka N et al. 2021 Plant Cell Physiol. 25.5995 JRC22
SAMD00237877 Ishijiro TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 29.9013 JRC23
SAMD00237878 Joushuu TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 29.0708 JRC24
SAMD00237879 Dango TEJ - Japan Tanaka N et al. 2021 Plant Cell Physiol. 23.2960 JRC25
SAMD00237880 Aikoku TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 28.3321 JRC26
SAMD00237881 Ginbouzu TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 31.0499 JRC27
SAMD00080365 Shinriki Mochi TEJ Elite Japan Tanaka N et al. 2021 Plant Cell Physiol. 34.6197 JRC28
SAMD00237882 Shichimenchou Mochi TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 35.4953 JRC29
SAMD00080364 Morita Wase TEJ Elite Japan Tanaka N et al. 2021 Plant Cell Physiol. 33.2287 JRC30
SAMD00237883 Kameji TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 17.3763 JRC31
SAMD00237884 Omachi TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 25.0257 JRC32
SAMD00237885 Shinriki TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 28.4815 JRC33
SAMD00237886 Kyoutoasahi TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 36.0453 JRC34
SAMD00237887 Kabashiko TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 23.3370 JRC35
SAMD00237888 Sekiyama TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 32.2303 JRC36
SAMD00237889 Shinyamadaho 2 TEJ Elite Japan Tanaka N et al. 2021 Plant Cell Physiol. 27.7439 JRC37
SAMD00237890 Nagoya Shiro TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 27.6835 JRC38
SAMD00237891 Shiroine (Kemomi) TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 39.8976 JRC39
SAMD00237892 Akamai (Nagasaki) TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 26.5000 JRC40
SAMD00237893 Akamai (Tokushima) IND Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 23.6785 JRC41
SAMD00237894 Touboshi IND Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 20.4025 JRC42
SAMD00237895 Akamai (Kanto-tosan) IND Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 29.6658 JRC43
SAMD00237896 Karahoushi IND Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 36.3217 JRC44
SAMD00237897 Hiyadachitou TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 26.1398 JRC45
SAMD00237898 Fukoku TEJ Elite Japan Tanaka N et al. 2021 Plant Cell Physiol. 22.9888 JRC46
SAMD00237899 Okabo TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 26.2761 JRC47
SAMD00237900 Hakamuri (Yokoyama) TRJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 23.6305 JRC48
SAMD00237901 Rikutou Rikuu 2 TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 32.9268 JRC49
SAMD00237902 Himenomochi TEJ Elite Japan Tanaka N et al. 2021 Plant Cell Physiol. 25.0803 JRC50
SAMD00237903 Shinshiuu TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 24.5986 JRC51
SAMD00237904 Aichiasahi TEJ Elite Japan Tanaka N et al. 2021 Plant Cell Physiol. 29.8767 JRC52
SAMD00237905 Raiden TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 28.5143 JRC53
SAMD00237906 Houmanshinden Ine TEJ Landrace Japan Tanaka N et al. 2021 Plant Cell Physiol. 35.3062 JRC54
SAMD00077979 Koshihikari TEJ Elite Japan Fujino K et al. 2021 Breed Sci. 54.4906 -
SAMD00077980 Hoshinoyume TEJ Elite Japan Fujino K et al. 2021 Breed Sci. 55.2865 -
SAMD00077981 Hitomebore TEJ Elite Japan Fujino K et al. 2021 Breed Sci. 55.2704 -
SAMD00077982 Tentakaku TEJ Elite Japan Fujino K et al. 2021 Breed Sci. 55.2501 -
SAMD00077983 Tenkomori TEJ Elite Japan Fujino K et al. 2021 Breed Sci. 54.5682 -
SAMD00077984 Hinohikari TEJ Elite Japan Fujino K et al. 2021 Breed Sci. 53.0279 -
SAMD00077985 Genkitsukushi TEJ Elite Japan Fujino K et al. 2021 Breed Sci. 58.2948 -
SAMD00077986 Koshihikari SBL1 TEJ Elite Japan Fujino K et al. 2021 Breed Sci. 56.4454 -
SAMD00077987 Nipponbare TEJ Elite Japan Fujino K et al. 2021 Breed Sci. 51.4076 WRC01
SAMD00077988 Kasalath AUS Landrace India Fujino K et al. 2021 Breed Sci. 57.7870 WRC02
SAMN01125970 DJ123 AUS Elite Bangladesh Schatz MC et al. 2014 Genome Biol. 143.9010 -
SAMN01121943 IR64 IND Elite Philippines Schatz MC et al. 2014 Genome Biol. 174.5630 -
SAMN00139534 Nipponbare TEJ Elite Japan Schatz MC et al. 2014 Genome Biol. 114.3790 WRC01
SAMN02209968 IR8 IND Elite Philippines Kim B et al. 2014 Rice 34.9394 -
SAMN02209969 Taichung Native 1 IND Elite Taiwan Kim B et al. 2014 Rice 34.4374 -
SAMN02209972 Tongil ADMIX Elite Korean Kim B et al. 2014 Rice 45.8063 -
SAMN02209992 Yukara JP Elite Japan Kim B et al. 2014 Rice 37.9616 -
SAMD00003730 Hokuriku193 IND Elite Japan Yonemaru J et al. 2014 BMC Genomics 37.9196 -
SAMD00003727 Mizuhochikara ADMIX Elite Japan Yonemaru J et al. 2014 BMC Genomics 35.5425 -
SAMD00003728 Suweon258 IND Elite Korea Yonemaru J et al. 2014 BMC Genomics 37.2444 -
SAMD00003726 Tachiaoba TEJ Elite Japan Yonemaru J et al. 2014 BMC Genomics 39.4542 -
SAMD00003729 Tachisugata IND Elite Japan Yonemaru J et al. 2014 BMC Genomics 34.0382 -
SAMD00003725 Takanari IND Elite Japan Yonemaru J et al. 2014 BMC Genomics 34.3349 -
SAMD00116543 CG14 GLA Elite Africa Yamamoto N et al. 2018 51.0451 -
SAMD00116542 WAB 56-104 TRJ Elite Africa Yamamoto N et al. 2018 49.3995 -
SAMD00116541 NERICA 7 TRJ/GLA Elite Africa Yamamoto N et al. 2018 47.0491 -
SAMD00116540 NERICA 5 TRJ/GLA Elite Africa Yamamoto N et al. 2018 64.0022 -
SAMD00116539 NERICA 4 TRJ/GLA Elite Africa Yamamoto N et al. 2018 55.4221 -
SAMD00116538 NERICA 3 TRJ/GLA Elite Africa Yamamoto N et al. 2018 41.1014 -
SAMN03879968 Habun 1 IND Landrace Taiwan Wei FJ et al. 2016 Plant Sci. 14.6830 -
SAMN03464928 Kameji TEJ Landrace Japan (Shimane) Wei FJ et al. 2016 Plant Sci. 14.9155 JRC31
SAMN03879965 Muteka TEJ Landrace Taiwan Wei FJ et al. 2016 Plant Sci. 13.8629 -
SAMN03879967 Nakabo TEJ Landrace Taiwan Wei FJ et al. 2016 Plant Sci. 13.1222 -
SAMN03464929 Shinriki TEJ Landrace Japan (Hyogo) Wei FJ et al. 2016 Plant Sci. 17.5570 JRC33
SAMN03463201 Taichung 65 TEJ Elite Taiwan Wei FJ et al. 2016 Plant Sci. 5.6980 -
SAMD00080141 Ruriaoba IND Elite Japan Ogawa D et al. 2018 Sci Rep. 38.5023 -
SAMD00080140 Bekogonomi TEJ Elite Japan Ogawa D et al. 2018 Sci Rep. 22.9765 -
SAMD00080139 Akidawara TEJ Elite Japan Ogawa D et al. 2018 Sci Rep. 33.7393 -
SAMD00003589 W1413 LON Wild Sierra Leone Ohyanagi et al. 2016 Plant Cell Physiol. 10.5140 -
SAMD00003590 W1508 LON Wild Madagascar Ohyanagi et al. 2016 Plant Cell Physiol. 6.7440 -
SAMD00016753 W0106 RUF Wild India Ohyanagi et al. 2016 Plant Cell Physiol. 9.6325 -
SAMD00004173 W0120 RUF Wild India Ohyanagi et al. 2016 Plant Cell Physiol. 29.0575 -
SAMD00004178 W0180 RUF Wild Thailand Ohyanagi et al. 2016 Plant Cell Physiol. 25.9672 -
SAMD00004175 W0593 RUF Wild Malaya Ohyanagi et al. 2016 Plant Cell Physiol. 29.6920 -
SAMD00004172 W0630 RUF Wild Burma Ohyanagi et al. 2016 Plant Cell Physiol. 33.6172 -
SAMD00004177 W1230 RUF Wild Dutch New Guinea Ohyanagi et al. 2016 Plant Cell Physiol. 28.9251 -
SAMD00004176 W1236 RUF Wild Australian New Guinea Ohyanagi et al. 2016 Plant Cell Physiol. 29.9574 -
SAMD00004174 W1715 RUF Wild China Ohyanagi et al. 2016 Plant Cell Physiol. 23.4751 -
SAMD00016754 W1921 RUF Wild Thailand Ohyanagi et al. 2016 Plant Cell Physiol. 8.8899 -
SAMD00004179 W1981 RUF Wild Indonesia Ohyanagi et al. 2016 Plant Cell Physiol. 28.8946 -
SAMEA3927619 Senia JP Elite Spain Reig-Valiente JL et al. 2016 Rice 13.2208 -
SAMEA3927615 Puntal JP Elite Spain Reig-Valiente JL et al. 2016 Rice 13.4068 -
SAMEA3927613 Pavlovsky JP Elite Russia Reig-Valiente JL et al. 2016 Rice 10.8798 -
SAMEA3927608 M202 JP Elite USA Reig-Valiente JL et al. 2016 Rice 11.4981 -
SAMEA3927607 LTH JP Elite China Reig-Valiente JL et al. 2016 Rice 12.7087 -
SAMEA3927602 Loto JP Elite Italy Reig-Valiente JL et al. 2016 Rice 11.8253 -
SAMEA3927601 Italica Livorno JP Elite Italy Reig-Valiente JL et al. 2016 Rice 12.0301 -
SAMEA3927598 L202 JP Elite USA Reig-Valiente JL et al. 2016 Rice 13.0215 -
SAMEA3927594 Kalao JP Elite France Reig-Valiente JL et al. 2016 Rice 12.4522 -
SAMEA3927592 Gigante Vercelli JP Elite Italy Reig-Valiente JL et al. 2016 Rice 11.3304 -
SAMEA3927587 Gleva JP Elite Spain Reig-Valiente JL et al. 2016 Rice 12.9380 -
SAMEA3927586 Bomba JP Landrace Spain Reig-Valiente JL et al. 2016 Rice 13.2332 -
SAMEA3927582 Bahia JP Elite Spain Reig-Valiente JL et al. 2016 Rice 12.7348 -
SAMEA3927580 Arroz da Terra JP Elite Portugal Reig-Valiente JL et al. 2016 Rice 13.2843 -
SAMEA104469261 W2012 RUF Wild India Zhao Q et al. 2018 Nat. Genet. 108.2650 -
SAMEA104469260 W1979 RUF Wild Indonesia Zhao Q et al. 2018 Nat. Genet. 62.0809 -
SAMEA104469259 W1943 RUF Wild China Zhao Q et al. 2018 Nat. Genet. 152.5240 -
SAMEA104469258 W1777 RUF Wild India Zhao Q et al. 2018 Nat. Genet. 81.4856 -
SAMEA104469257 W1754 RUF Wild India Zhao Q et al. 2018 Nat. Genet. 93.7394 -
SAMEA104469256 W1739 RUF Wild India Zhao Q et al. 2018 Nat. Genet. 91.6866 -
SAMEA104469255 W1698 RUF Wild Thailand Zhao Q et al. 2018 Nat. Genet. 56.4120 -
SAMEA104469254 W1687 RUF Wild India Zhao Q et al. 2018 Nat. Genet. 57.7547 -
SAMEA104469253 W0170 RUF Wild Thailand Zhao Q et al. 2018 Nat. Genet. 70.8607 -
SAMEA104469252 W0141 RUF Wild India Zhao Q et al. 2018 Nat. Genet. 69.8758 -
SAMEA104469251 W0128 IND Wild India Zhao Q et al. 2018 Nat. Genet. 71.0352 -
SAMEA104469250 Nipponbare TEJ Elite Japan Zhao Q et al. 2018 Nat. Genet. 69.4697 -
SAMEA104469249 Luyu132-1 TEJ Landrace China Zhao Q et al. 2018 Nat. Genet. 24.8455 -
SAMEA104469248 Yanzhan IND Landrace China Zhao Q et al. 2018 Nat. Genet. 48.1541 -
SAMEA104469247 Shuihegu IND Landrace China Zhao Q et al. 2018 Nat. Genet. 40.6704 -
SAMEA104469246 Jinzhan IND Landrace China Zhao Q et al. 2018 Nat. Genet. 44.9016 -
SAMEA104469245 Hongmangnuo TEJ Landrace China Zhao Q et al. 2018 Nat. Genet. 25.1518 -
SAMEA104469244 Changlijingzhan TEJ Landrace China Zhao Q et al. 2018 Nat. Genet. 47.9052 -
SAMEA104469243 Honggu-1 TEJ Landrace China Zhao Q et al. 2018 Nat. Genet. 73.7683 -
SAMEA104469242 Aigansazhima IND Landrace China Zhao Q et al. 2018 Nat. Genet. 108.3700 -
SAMEA104469241 Sizhan IND Landrace China Zhao Q et al. 2018 Nat. Genet. 50.0038 -
SAMEA104469240 Dongying-8 TEJ Landrace China Zhao Q et al. 2018 Nat. Genet. 44.3556 -
SAMEA104469239 Guihuanuo IND Landrace China Zhao Q et al. 2018 Nat. Genet. 49.2285 -
SAMEA104469238 Dabainuo TEJ Landrace China Zhao Q et al. 2018 Nat. Genet. 38.4193 -
SAMEA104469237 Maguhongmi IND Landrace China Zhao Q et al. 2018 Nat. Genet. 61.3042 -
SAMEA104469236 Lengshuizhan TEJ Landrace China Zhao Q et al. 2018 Nat. Genet. 25.7286 -
SAMEA104469235 Bairizao-4 IND Landrace China Zhao Q et al. 2018 Nat. Genet. 21.3866 -
SAMEA104469234 Ruanzhanjiugu IND Landrace China Zhao Q et al. 2018 Nat. Genet. 26.6613 -
SAMEA104469233 Qiananshuinuo TEJ Landrace China Zhao Q et al. 2018 Nat. Genet. 86.2297 -
SAMEA104469232 Huakemangnuo IND Landrace China Zhao Q et al. 2018 Nat. Genet. 112.5070 -
SAMEA104469231 Binxianludao TEJ Landrace China Zhao Q et al. 2018 Nat. Genet. 50.4862 -
SAMEA104469229 IR 9209-26-2 IND Elite Philippines Zhao Q et al. 2018 Nat. Genet. 79.0333 -
SAMEA104469228 Milyang84 TEJ Elite North Korea Zhao Q et al. 2018 Nat. Genet. 55.9982 -
SAMEA104469227 Teng-870 TEJ Elite Japan Zhao Q et al. 2018 Nat. Genet. 56.5179 -
SAMEA104469226 Tebonnet TRJ Elite USA Zhao Q et al. 2018 Nat. Genet. 99.1763 -
SAMEA104469224 Pama TEJ Elite Philippines Zhao Q et al. 2018 Nat. Genet. 71.6591 -
SAMEA104469223 Nonglinnuo-144 TEJ Elite Japan Zhao Q et al. 2018 Nat. Genet. 45.3321 -
SAMEA104469222 Kbarai Ganja AUS Landrace Pakistan Zhao Q et al. 2018 Nat. Genet. 47.3709 -
SAMEA104469221 Minanok (glut) TRJ Elite Philippines Zhao Q et al. 2018 Nat. Genet. 60.7881 -
SAMEA104469220 T 480-34 IND Elite Cuba Zhao Q et al. 2018 Nat. Genet. 74.7164 -
SAMEA104469219 IAC 25 TRJ Elite Brazil Zhao Q et al. 2018 Nat. Genet. 69.1017 -
SAMEA104469217 IR 2797-115-3 IND Elite Philippines Zhao Q et al. 2018 Nat. Genet. 77.5406 -
SAMEA104469216 DNJ 126 AUS Landrace Bengal Zhao Q et al. 2018 Nat. Genet. 64.7366 -
SAMEA104467892 Bangbanggu IND Landrace China Zhao Q et al. 2018 Nat. Genet. 30.4241 -
SAMEA104467891 Fengrunhandaozi TEJ Landrace China Zhao Q et al. 2018 Nat. Genet. 76.1892 -
SAMEA104467890 Xiangnan-1 IND Elite North Korea Zhao Q et al. 2018 Nat. Genet. 72.6022 -
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SAMN12672924 PR 106 IND - India Zhou Y et al. 2020 Sci. Data 92.4712 IRGC53418-1
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