Analysis workflow for detection of genome-wide variations in TASUKE+ of RAP-DB


Genome-wide variation data among >500 accessions was provided in the multiple genome browser TASUKE+ of RAP-DB. Here we provide the analysis workflow for detection of the genome-wide variations (SNPs/InDels).

Reference data

  • Genome sequences
    • IRGSP-1.0 genome (including organella and unanchored contig sequences)
  • Gene annotation
    • RAP-DB (both representative and predicted genes as of 26 Nov 2018)
    • MSU (all genes in RGAP 7)
  • Illumina adapter sequences attached to the Trimmomatic program
  • 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
    

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)
  • Trimmomatic (v0.38)
  • Picard (v2.18.17)
  • SnpEff (v4.3t)
  • TASUKE+ (version 20190826)

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 and filtering by GATK
  12. $ gatk HaplotypeCaller \
        --input alignment.rmdup.bam \
        --output variants.g.vcf.gz \
        --reference genome.fa \
        -max-alternate-alleles 2 \
        --emit-ref-confidence GVCF
    $ gatk GenotypeGVCFs \
        --variant variants.g.vcf.gz \
        --output variants.genotype.vcf.gz \
        --reference genome.fa
    
    $ gatk VariantFiltration \
        --reference genome.fa \
        --variant variants.genotype.vcf.gz \
        --output variants.filter.genotype.vcf.gz \
        --filter-expression "QD < 5.0 || FS > 50.0 || SOR > 3.0 || MQ < 50.0 || MQRankSum < -2.5 || ReadPosRankSum < -1.0 || ReadPosRankSum > 3.5" \
        --filter-name "FILTER"
    
    $ gatk SelectVariants \
        --reference genome.fa \
        --variant variants.filter.genotype.vcf.gz \
        --output variants.varonly.vcf.gz \
        --exclude-filtered \
        --select-type-to-include SNP \
        --select-type-to-include INDEL
    
  13. Run SnpEff
  14. $ java -jar snpEff.jar build -gtf22 -v RAP_MSU_on_IRGSP-1.0
    
    $ java -jar snpEff.jar \
        -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.

  15. Make depth data for TASUKE+
  16. $ perl tasuke_bamtodepth.pl \
        -s samtools -c chromosome_list.csv -i alignment.rmdup.bam \
        -o alignment_depth.tsv
    
  17. 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 accessions and sequence data provided in TASUKE+ of RAP-DB

Filter:
ID (BioSample) Name Sub variety Type Origin Reference DOI Avr. depth of coverage
SAMN02231725 93-11 IND Elite China Gao Z-U et al. 2013 DOI: 10.1073/pnas.1306579110 42.55
SAMN02821253 175-1-127 IND Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 25.04
SAMN00027406 Ai-Chiao-Hong IND Landrace China Xu et al. 2011 DOI: 10.1038/nbt.2050 15.90
SAMD00045866 Aichi Asahi 1 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.66
SAMD00045867 Aichi Asahi 2 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.55
SAMEA104469242 Aigansazhima IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 108.37
SAMD00045868 Aikoku TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.52
SAMD00045869 Aiyama TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.06
SAMD00045870 Akage TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.96
SAMD00045871 Akamai 2 TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.91
SAMD00045872 Akebono TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.11
SAMD00080139 Akidawara TEJ Elite Japan Ogawa D et al. 2018 DOI: 10.1038/s41598-018-22657-3 33.74
SAMD00045874 Akitakomachi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.15
SAMD00045875 Akitsuho TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.58
SAMN00027400 Arias TRJ Landrace Indonesia (West Java) Xu et al. 2011 DOI: 10.1038/nbt.2050 14.56
SAMEA3927580 Arroz da Terra JP Elite Portugal Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 13.28
SAMD00045876 Asahi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.24
SAMD00045877 Asahi Mochi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.52
SAMD00045878 Asominori TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.72
SAMN00027396 AZUCENA TRJ Landrace Philippines Xu et al. 2011 DOI: 10.1038/nbt.2050 15.35
SAMN00027411 BADAL 89 JP/IND Landrace Bangladesh Xu et al. 2011 DOI: 10.1038/nbt.2050 15.33
SAMN02375091 Badari Dhan IND Landrace Nepal Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 16.79
SAMEA3927582 Bahia JP Elite Spain Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 12.73
SAMEA104469235 Bairizao-4 IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 21.39
SAMEA104467892 Bangbanggu IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 30.42
SAMEA104467888 Basmati Surkh 89-15 ARO Elite Pakistan Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 171.00
SAMD00078853 Bei Khe IND Landrace Cambodia Itoh H et al. 2018 DOI: 10.1111/tpj.13906 42.09
SAMD00080140 Bekogonomi TEJ Elite Japan Ogawa D et al. 2018 DOI: 10.1038/s41598-018-22657-3 22.98
SAMN07767782 Bengal TRJ Elite USA Chai C et al. 2018 DOI: 10.1038/s41598-018-32513-z 26.16
SAMN02821220 Bengal TEJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 3.12
SAMD00045879 Benkei TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.33
SAMN00027398 Bico Branco ARO Elite Brazil Xu et al. 2011 DOI: 10.1038/nbt.2050 15.80
SAMN00027390 Binulawan TRJ Landrace Philippines Xu et al. 2011 DOI: 10.1038/nbt.2050 15.76
SAMEA104469231 Binxianludao TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 50.49
SAMEA2017052 BLB JP Anther culture line Korea Jeong I-S et al. 2013 DOI: 10.1186/1939-8433-6-6 45.14
SAMEA3927586 Bomba JP Landrace Spain Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 13.23
SAMN02821221 Bowman TRJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 6.06
SAMD00066624 C9285 IND Landrace Bangladesh Nagoya University None 16.48
SAMN00027418 CA 97-053 NIV Wild Cambodia (Sopoir Tep) Xu et al. 2011 DOI: 10.1038/nbt.2050 14.40
SAMN02821254 Camponi IND Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 11.40
SAMN00027405 Canella DeFerro TRJ Elite Brazil Xu et al. 2011 DOI: 10.1038/nbt.2050 17.13
SAMN02821222 CarolinaGold TRJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 23.10
SAMN02821223 CarolinaGoldSelect TRJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 37.45
SAMN02821224 Catahoula TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 14.03
SAMN03273435 CDR22 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 23.46
SAMN02869663 CHANDINA JP Unknown Sri lanka Wang M et al. 2014 DOI: 10.1038/ng.3044 15.74
SAMEA104469244 Changlijingzhan TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 47.91
SAMEA104460755 Changmadao-3 TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 20.07
SAMN03273436 Chenghui047 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 23.32
SAMN00027408 Chodongji TEJ Landrace South Korea Xu et al. 2011 DOI: 10.1038/nbt.2050 16.00
SAMN03273446 Chuannong422 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 20.24
SAMD00045880 Chukyo Asahi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.03
SAMN02821225 CL111 TRJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 11.28
SAMN02821226 CL131 TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 15.48
SAMN02821227 CL152 TEJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 12.67
SAMN02821228 CL261 TEJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 10.79
SAMN02821229 CMS08A IND Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 11.72
SAMN02821230 CMS08B IND Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 9.40
SAMN04275173 CO 39 IND Elite India Mahesh H. B. et al. 2016 DOI: 10.1186/s12864-016-2523-7 142.89
SAMN02821231 Cocodrie TRJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 10.21
SAMN02821255 CT18685 IND Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 10.06
SAMN02821256 CT19021-3-4-1V1-1 IND Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 24.82
SAMN02821257 CT21375-F4-43-1 IND Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 24.62
SAMN02821258 Curinga TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 12.60
SAMN02821232 Cypress2 TRJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 6.44
SAMEA104469238 Dabainuo TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 38.42
SAMD00045882 Dango TEJ Unknown Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.24
SAMEA104467886 Daohuaxiang 2 TEJ Elite China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 94.50
SAMN00027391 Darmali TEJ Landrace Nepal Xu et al. 2011 DOI: 10.1038/nbt.2050 11.01
SAMN00027416 Davao TRJ Landrace Philippines Xu et al. 2011 DOI: 10.1038/nbt.2050 13.15
SAMN03273427 Dee geo woo gen IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 23.22
SAMN02375099 Deejiaohualuo IND Unknown China Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 15.01
SAMN02821233 Della2 TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 14.00
SAMN06620501 Digu IND Unknown China Li W et al. 2017 DOI: 10.1016/j.cell.2017.06.008 22.24
SAMEA104460759 Dishuigu IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 63.57
SAMN02821234 Dixiebelle TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 34.81
SAMN01125970 DJ123 AUS Elite Bangladesh Schatz MC et al. 2014 DOI: 10.1186/s13059-014-0506-z 143.90
SAMEA104469216 DNJ 126 AUS Landrace Bengal Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 64.74
SAMN02869652 Dom Sufid IND Unknown Iran Wang M et al. 2014 DOI: 10.1038/ng.3044 108.87
SAMEA2015633 Dongjin JP Elite Korea Jeong I-S et al. 2013 DOI: 10.1186/1939-8433-6-6 45.36
SAMEA104469240 Dongying-8 TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 44.36
SAMD00045884 Dontokoi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.98
SAMN02375107 Dunghan Shali JP Unknown Hungary Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 5.36
SAMN00027417 DZ78 AUS Landrace Bangladesh Xu et al. 2011 DOI: 10.1038/nbt.2050 16.70
SAMN02821259 Esperanza TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 7.66
SAMN02821260 Fanny TEJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 23.08
SAMN02821261 Fedearroz174 IND Elite Latin America Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 8.79
SAMN02821262 Fedearroz2000 IND Elite Latin America Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 11.36
SAMN02821263 Fedearroz50 IND Elite Latin America Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 10.87
SAMEA104467891 Fengrunhandaozi TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 76.19
SAMN00027425 Firooz ARO Landrace Iran Xu et al. 2011 DOI: 10.1038/nbt.2050 16.49
SAMN02821235 Francis TRJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 3.72
SAMN03273437 Fuhui838 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 20.65
SAMD00045885 Fujisaka 5 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.18
SAMD00045886 Fukoku TEJ Elite Japan (Hokkaido) Yano K et al. 2016 DOI: 10.1038/ng.3596 4.29
SAMD00045887 Fukuhikari TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.22
SAMD00045888 Fukunohana TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.14
SAMD00045889 Funaki Omachi TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.40
SAMD00045890 Futaba TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.62
SAMD00077985 Genkitsukushi TEJ Elite Japan NICS None 58.29
SAMN00027415 Gie 57 IND Landrace Vietnam Xu et al. 2011 DOI: 10.1038/nbt.2050 15.86
SAMEA3927592 Gigante Vercelli JP Elite Italy Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 11.33
SAMD00045891 Gin No Sei TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.70
SAMD00045892 Gin No Yume TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.01
SAMD00045893 Gin Oumi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.16
SAMD00045894 Ginbouzu TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.66
SAMD00045895 Ginbouzu7572 TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.26
SAMD00045896 Ginginga TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.51
SAMEA3927587 Gleva JP Elite Spain Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 12.94
SAMD00010635 Gohyakumangoku TEJ Elite Japan Arai-Kichise Y et al. 2014 DOI: 10.1371/journal.pone.0086312 51.13
SAMD00045897 Gohyakumangoku TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.01
SAMD00045898 Goriki TEJ Landrace Japan (Tottori) Yano K et al. 2016 DOI: 10.1038/ng.3596 4.98
SAMN00027401 Gotak Gatik TRJ Landrace Indonesia (C.Java) Xu et al. 2011 DOI: 10.1038/nbt.2050 12.76
SAMN00027407 Guan-Yin-Tsan IND Landrace China Xu et al. 2011 DOI: 10.1038/nbt.2050 15.78
SAMN03273447 Guangchang13 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.00
SAMEA104467887 Guangluai 4 IND Elite China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 149.84
SAMEA966194 Guangluai-4 IND Elite China Huang X et al. 2010 DOI: 10.1038/ng.695 17.09
SAMN03273433 GUI630 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.53
SAMEA104469239 Guihuanuo IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 49.23
SAMN02869654 GURULEY IND Unknown Bhutan Wang M et al. 2014 DOI: 10.1038/ng.3044 114.31
SAMN03879968 Habun 1 IND Landrace Taiwan Wei FJ et al. 2016 DOI: 10.1016/j.plantsci.2015.09.005 14.68
SAMN00027388 Haginomae Mochi TEJ Elite Japan Xu et al. 2011 DOI: 10.1038/nbt.2050 17.02
SAMN00027409 HAISHA CAMAN JP/IND Landrace Bangladesh Xu et al. 2011 DOI: 10.1038/nbt.2050 13.84
SAMD00045899 Hanafubuki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.23
SAMN03273438 Hanghui570 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 21.99
SAMD00045900 Hatsu Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 6.28
SAMD00045905 Hatsugozen TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.48
SAMD00045901 Hattan 35 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.61
SAMD00045902 Hattan Nishiki 1 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.14
SAMD00045903 Hattan Nishiki 2 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.79
SAMD00045904 Hattansou TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 8.08
SAMD00078858 Hayamasari TEJ Elite Japan Itoh H et al. 2018 DOI: 10.1111/tpj.13906 52.07
SAMD00045906 Hayaoozeki 1 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.52
SAMN02821236 Hidalgo TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 35.84
SAMD00045907 Himenomochi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.26
SAMD00077984 Hinohikari TEJ Elite Japan NICS None 53.03
SAMD00045908 Hinohikari TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.21
SAMD00045909 Hinomaru TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.19
SAMD00045910 Hitachi Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.89
SAMN02375104 Hitomebore TEJ Elite Japan Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 27.62
SAMD00077981 Hitomebore TEJ Elite Japan NICS None 55.27
SAMD00013510 Hitomebore TEJ Elite Japan Takagi H et al. 2015 DOI: 10.1038/nbt.3188 34.79
SAMD00045911 Hitomebore TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.83
SAMD00045912 Hiyadachitou TEJ Landrace Japan (Yamagatai) Yano K et al. 2016 DOI: 10.1038/ng.3596 5.38
SAMN00027413 HK 47 NIV Wild India (Madhya Pradesh) Xu et al. 2011 DOI: 10.1038/nbt.2050 13.98
SAMD00045913 Hokuriku 12 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.66
SAMD00045914 Hokuriku 20 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.31
SAMD00045915 Hokuriku 52 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.80
SAMD00003730 Hokuriku193 IND Elite Japan Yonemaru J et al. 2014 DOI: 10.1186/1471-2164-15-346 37.92
SAMD00045916 Hokushin 1 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.43
SAMN02375100 Hong Cheuh Zai IND Unknown China Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 13.18
SAMEA104469243 Honggu-1 TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 73.77
SAMEA104460747 Honghandao TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 34.83
SAMEA104469245 Hongmangnuo TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 25.15
SAMD00077980 Hoshinoyume TEJ Elite Japan NICS None 55.29
SAMD00045917 Hosogara TEJ Landrace Japan (Aomori) Yano K et al. 2016 DOI: 10.1038/ng.3596 3.12
SAMD00045919 Houmanshinden Ine TEJ Landrace Japan (Kagoshimai) Yano K et al. 2016 DOI: 10.1038/ng.3596 5.05
SAMN02401119 HR-12 IND Elite India Mahesh H. B. et al. 2016 DOI: 10.1186/s12864-016-2523-7 81.15
SAMEA104469232 Huakemangnuo IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 112.51
SAMEA2017528 Hwayeong JP Elite Korea Jeong I-S et al. 2013 DOI: 10.1186/1939-8433-6-6 45.79
SAMEA2016954 HY-04 JP Anther culture line Korea Jeong I-S et al. 2013 DOI: 10.1186/1939-8433-6-6 47.63
SAMEA2017592 HY-08 JP Anther culture line Korea Jeong I-S et al. 2013 DOI: 10.1186/1939-8433-6-6 47.16
SAMD00045920 Hyogo Kita Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.36
SAMD00045921 Hyogo Omachi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.40
SAMD00045922 Hyogo Yumenishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.11
SAMD00045923 Hyokei Sake 18 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.62
SAMD00045924 Hyoukei Ka 56 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.10
SAMD00045925 Hyoukei Ka 62 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 6.02
SAMEA104469219 IAC 25 TRJ Elite Brazil Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 69.10
SAMN02821237 IAC600 TEJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 21.84
SAMD00045926 Ipponjime TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.74
SAMEA104469217 IR 2797-115-3 IND Elite Philippines Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 77.54
SAMN00027393 IR 36 IND Improve Brazil Xu et al. 2011 DOI: 10.1038/nbt.2050 16.73
SAMEA104469229 IR 9209-26-2 IND Elite Philippines Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 79.03
SAMN03273443 IR1544 IND Elite Philippines Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.39
SAMN03273430 IR20 IND Elite Philippines Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.89
SAMN03273429 IR24 IND Elite Philippines Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.73
SAMN03273431 IR26 IND Elite Philippines Huang J et al. 2018 DOI:10.1073/pnas.1806110115 24.06
SAMN03273432 IR30 IND Elite Philippines Huang J et al. 2018 DOI:10.1073/pnas.1806110115 21.90
SAMN03273445 IR36 IND Elite Philippines Huang J et al. 2018 DOI:10.1073/pnas.1806110115 24.44
SAMN02821264 IR64 IND Elite Philippines Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 16.30
SAMN01121943 IR64 IND Elite Philippines Schatz MC et al. 2014 DOI: 10.1186/s13059-014-0506-z 174.56
SAMN02179223 IR8 IND Elite Philippines Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 23.24
SAMN03273428 IR8 IND Elite Philippines Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.26
SAMN02209968 IR8 IND Elite Philippines Kim B et al. 2014 DOI: 10.1186/s12284-014-0022-5 34.94
SAMN02821265 IRGA424 IND Elite Brazil Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 11.20
SAMN02821266 IRGA427 IND Elite Brazil Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 26.49
SAMN02869653 IRGC13793 IND Unknown Brunel Wang M et al. 2014 DOI: 10.1038/ng.3044 13.11
SAMN02869661 IRGC28275 JP Unknown pakistan Wang M et al. 2014 DOI: 10.1038/ng.3044 8.45
SAMN02869662 IRGC32298 JP Unknown Iran Wang M et al. 2014 DOI: 10.1038/ng.3044 29.83
SAMN02869664 IRGC3860 JP Unknown philippines Wang M et al. 2014 DOI: 10.1038/ng.3044 11.80
SAMN02869650 IRGC50409 IND Unknown Brazil Wang M et al. 2014 DOI: 10.1038/ng.3044 93.12
SAMN02869665 IRGC56350 JP Unknown Senegal Wang M et al. 2014 DOI: 10.1038/ng.3044 27.02
SAMN02869655 IRGC58267 IND Unknown Afghanistan Wang M et al. 2014 DOI: 10.1038/ng.3044 27.46
SAMN02869666 IRGC58398 JP Unknown Brunel Wang M et al. 2014 DOI: 10.1038/ng.3044 108.53
SAMN02869667 IRGC58716 JP Unknown Bangladesh Wang M et al. 2014 DOI: 10.1038/ng.3044 107.22
SAMN02869651 IRGC69559 IND Unknown Egypt Wang M et al. 2014 DOI: 10.1038/ng.3044 82.94
SAMN02869656 IRGC9505 IND Unknown Iraq Wang M et al. 2014 DOI: 10.1038/ng.3044 93.57
SAMD00045927 Ishijiro TEJ Landrace Japan (Toyama) Yano K et al. 2016 DOI: 10.1038/ng.3596 4.02
SAMEA3927601 Italica Livorno JP Elite Italy Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 12.03
SAMD00045928 Iwai TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 6.15
SAMN02375106 Iwatekko TEJ Elite Japan Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 21.24
SAMN02375108 Jaguary TRJ Unknown Brazil Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 13.76
SAMN00027387 Jambu TRJ Landrace Indonesia Xu et al. 2011 DOI: 10.1038/nbt.2050 12.46
SAMN02821238 Jasmine85 IND Elite Philippines Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 3.97
SAMN02821239 Jazzman TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 8.20
SAMN02821240 Jazzman2 TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 9.34
SAMN00027419 JC101 ARO Elite India Xu et al. 2011 DOI: 10.1038/nbt.2050 14.07
SAMN00027420 JC111 ARO Elite India Xu et al. 2011 DOI: 10.1038/nbt.2050 15.33
SAMN00027422 JC91 IND Elite India Xu et al. 2011 DOI: 10.1038/nbt.2050 16.16
SAMN02375098 Jena 035 IND Landrace Nepal Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 11.52
SAMN00027410 Jhona 349 AUS Landrace India Xu et al. 2011 DOI: 10.1038/nbt.2050 12.91
SAMEA104469246 Jinzhan IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 44.90
SAMD00045929 Joushuu TEJ Landrace Japan (Yamagatai) Yano K et al. 2016 DOI: 10.1038/ng.3596 2.78
SAMN02821241 Jupiter TEJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 9.21
SAMD00045930 Kabashiko TEJ Landrace Japan (Miyazaki) Yano K et al. 2016 DOI: 10.1038/ng.3596 4.88
SAMD00019084 Kaijin TEJ Elite Japan Takagi H et al. 2015 DOI: 10.1038/nbt.3188 24.86
SAMD00045931 Kairyo Hattannagare TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.53
SAMD00045932 Kairyo Omachi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.55
SAMD00045933 Kairyo Shinkou TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.55
SAMN00027404 Kalamkati AUS Landrace India Xu et al. 2011 DOI: 10.1038/nbt.2050 16.03
SAMEA3927594 Kalao JP Elite France Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 12.45
SAMN02375092 Kaluheenati IND Landrace Sri Lanka Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 13.73
SAMD00010636 Kameji TEJ Landrace Japan (Shimane) Arai-Kichise Y et al. 2014 DOI: 10.1371/journal.pone.0086312 44.20
SAMN03464928 Kameji TEJ Landrace Japan (Shimane) Wei FJ et al. 2016 DOI: 10.1016/j.plantsci.2015.09.005 14.92
SAMD00045934 Kameji TEJ Landrace Japan (Shimane) Yano K et al. 2016 DOI: 10.1038/ng.3596 3.45
SAMD00045935 Kamenoo TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.00
SAMD00045936 Kamenoo 4 TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.94
SAMD00045937 Kannomai TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.79
SAMN02375093 Kasalath IND Landrace India Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 10.77
SAMD00077988 Kasalath AUS Landrace India NICS None 57.79
SAMD00016340 Kasalath AUS Landrace India Sakai et al. 2014 DOI: 10.1093/dnares/dsu006 24.42
SAMD00004056 Kasalath AUS Landrace India Sakai et al. 2014 DOI: 10.1093/dnares/dsu006 91.44
SAMEA104460752 Kasalath AUS Landrace India Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 182.85
SAMEA104469222 Kbarai Ganja AUS Landrace Pakistan Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 47.37
SAMN02375101 Keiboba IND Landrace China Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 11.02
SAMD00078857 Khao Nam Jen TRJ Landrace Laos Itoh H et al. 2018 DOI: 10.1111/tpj.13906 48.35
SAMD00078856 Khau Mac Kho TRJ Landrace Vietnam Itoh H et al. 2018 DOI: 10.1111/tpj.13906 58.57
SAMD00045938 Kikusui 1 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.79
SAMD00045939 Kinai Omachi TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.57
SAMD00045940 Kinchaku TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.71
SAMD00045941 Kinki 33 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.41
SAMD00045942 Kinmaze TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 19.41
SAMD00045943 Kinmon Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.40
SAMD00016906 Kitaake TEJ Elite Japan Fujino K et al. 2015 DOI: 10.1007/s00122-015-2543-8 32.87
SAMN00027385 Kitrana 508 ARO Elite Madagascar Xu et al. 2011 DOI: 10.1038/nbt.2050 16.72
SAMD00045944 Koiomachi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.26
SAMD00045945 Kojyou Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.34
SAMD00045946 Kokuryomiyako TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.67
SAMEA104459806 Kongyu 131 TEJ Elite China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 106.33
SAMD00010632 Koshihikari TEJ Elite Japan Arai-Kichise Y et al. 2014 DOI: 10.1371/journal.pone.0086312 51.07
SAMD00077979 Koshihikari TEJ Elite Japan NICS None 54.49
SAMD00045947 Koshihikari TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 95.50
SAMEA104460751 Koshihikari TEJ Elite Japan Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 108.81
SAMD00077986 Koshihikari SBL1 TEJ Elite Japan NICS None 56.45
SAMN00027394 KUI SALI ARO Landrace Bangladesh Xu et al. 2011 DOI: 10.1038/nbt.2050 14.79
SAMD00045950 Kuranohana TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.38
SAMD00045951 Kyoto Asahi TEJ Landrace Japan (Kyoto) Yano K et al. 2016 DOI: 10.1038/ng.3596 4.34
SAMD00045952 Kyoutoasahi TEJ Landrace Japan (Kyoto) Yano K et al. 2016 DOI: 10.1038/ng.3596 3.73
SAMN00027382 L 89-12 NIV Wild Laos (Vientiane) Xu et al. 2011 DOI: 10.1038/nbt.2050 15.49
SAMN02821242 L-201 TRJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 3.81
SAMEA3927598 L202 JP Elite USA Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 13.02
SAMN02821267 L2825-CA TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 12.44
SAMN02821243 LA2177 TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 10.66
SAMD00078855 LAC 23 TRJ Unknown Nigeria Itoh H et al. 2018 DOI: 10.1111/tpj.13906 43.00
SAMN02821244 Lagrue3 TRJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 5.05
SAMN02821245 Lemont TRJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 4.48
SAMN00027412 Lemont TRJ Elite USA (TX) Xu et al. 2011 DOI: 10.1038/nbt.2050 13.27
SAMEA104469236 Lengshuizhan TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 25.73
SAMN00027392 Leung Pratew IND Landrace Thailand Xu et al. 2011 DOI: 10.1038/nbt.2050 14.64
SAMN02821246 LM-1 TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 3.74
SAMEA104460749 Longgeng 31 TEJ Elite China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 96.74
SAMEA3927602 Loto JP Elite Italy Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 11.83
SAMEA3927607 LTH JP Elite China Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 12.71
SAMN03273448 Luchang-3 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 20.82
SAMEA104469249 Luyu132-1 TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 24.85
SAMEA3927608 M202 JP Elite USA Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 11.50
SAMEA104469237 Maguhongmi IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 61.30
SAMN00027383 Maintmolotsy TRJ Elite Madagascar Xu et al. 2011 DOI: 10.1038/nbt.2050 12.56
SAMD00045953 Mangoku TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.71
SAMN00027414 Mansaku TEJ Landrace Japan Xu et al. 2011 DOI: 10.1038/nbt.2050 15.66
SAMD00045954 Mansaku TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.45
SAMN02821247 MCR010277 ADMIX Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 3.71
SAMN00027386 Mehr AUS Landrace Iran Xu et al. 2011 DOI: 10.1038/nbt.2050 15.72
SAMN02821248 Mermentau TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 10.59
SAMN03273440 Mianhui725 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 23.81
SAMEA104469228 Milyang84 TEJ Elite North Korea Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 56.00
SAMEA104469221 Minanok (glut) TRJ Elite Philippines Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 60.79
SAMN03273434 Minghui63 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 21.73
SAMN03273439 Minghui70 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 21.15
SAMN03273441 Minghui86 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.69
SAMN00027389 Miriti IND Landrace Bangladesh Xu et al. 2011 DOI: 10.1038/nbt.2050 12.68
SAMD00045955 Misato Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.57
SAMD00045956 Miyama Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.63
SAMD00003727 Mizuhochikara JP/IND Elite Japan Yonemaru J et al. 2014 DOI: 10.1186/1471-2164-15-346 35.54
SAMD00045957 Morita Wase TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.54
SAMD00010631 Moroberekan TRJ Landrace Guinea Arai-Kichise Y et al. 2014 DOI: 10.1371/journal.pone.0086312 38.72
SAMN03879965 Muteka TEJ Landrace Taiwan Wei FJ et al. 2016 DOI: 10.1016/j.plantsci.2015.09.005 13.86
SAMEA104467889 Mutiara TRJ Elite Indonesia Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 92.26
SAMD00045958 Mutsuhomare TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.19
SAMN00027381 MV 89-80 NIV Wild India (Medinipur) Xu et al. 2011 DOI: 10.1038/nbt.2050 15.32
SAMD00045959 Nada Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.44
SAMD00045960 Nadahikari TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.21
SAMD00045961 Nagoya Shiro TEJ Landrace Japan (Akita) Yano K et al. 2016 DOI: 10.1038/ng.3596 5.89
SAMN03879967 Nakabo TEJ Landrace Taiwan Wei FJ et al. 2016 DOI: 10.1016/j.plantsci.2015.09.005 13.12
SAMD00045962 Nakate Shinriki TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.08
SAMD00045963 Nakate Shinsenbon TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.67
SAMN03273449 Nante IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 21.19
SAMN02375112 NERICA 1 JP/GLA Elite Africa Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 12.09
SAMD00116538 NERICA 3 TRJ/GLA Elite Africa Yamamoto N et al. 2018 DOI: 10.1186/s12284-018-0224-3 41.10
SAMD00116539 NERICA 4 TRJ/GLA Elite Africa Yamamoto N et al. 2018 DOI: 10.1186/s12284-018-0224-3 55.42
SAMD00116540 NERICA 5 TRJ/GLA Elite Africa Yamamoto N et al. 2018 DOI: 10.1186/s12284-018-0224-3 64.00
SAMD00116541 NERICA 7 TRJ/GLA Elite Africa Yamamoto N et al. 2018 DOI: 10.1186/s12284-018-0224-3 47.05
SAMD00045964 Nihonmasari TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.73
SAMN02375103 Nipponbare TEJ Elite Japan Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 19.52
SAMD00077987 Nipponbare TEJ Elite Japan NICS None 51.41
SAMN00139534 Nipponbare TEJ Elite Japan Schatz MC et al. 2014 DOI: 10.1186/s13059-014-0506-z 114.38
SAMN00027423 Nipponbare TEJ Elite Japan Xu et al. 2011 DOI: 10.1038/nbt.2050 11.37
SAMD00045965 Nipponbare TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 91.68
SAMEA104469250 Nipponbare TEJ Elite Japan Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 69.47
SAMD00045966 Nojyouho TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.04
SAMN07767800 Nona Bokra IND Landrace India Chai C et al. 2018 DOI: 10.1038/s41598-018-32513-z 15.84
SAMD00078854 Nona Bokra IND Landrace India Itoh H et al. 2018 DOI: 10.1111/tpj.13906 37.60
SAMEA871359 Nongken-58 TEJ Elite Japan Huang X et al. 2010 DOI: 10.1038/ng.695 11.57
SAMEA104469223 Nonglinnuo-144 TEJ Elite Japan Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 45.33
SAMD00045967 Norin 1 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.39
SAMD00045968 Norin 17 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.69
SAMN00027399 Norin 20 TEJ Landrace Japan Xu et al. 2011 DOI: 10.1038/nbt.2050 14.88
SAMD00045969 Norin 21 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.87
SAMD00045970 Norin 22 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.47
SAMD00045971 Norin 41 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.13
SAMD00045972 Norin 8 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.65
SAMD00010634 Norin8 TEJ Elite Japan Arai-Kichise Y et al. 2014 DOI: 10.1371/journal.pone.0086312 63.63
SAMN00027397 NPE 844 TRJ Landrace Pakistan Xu et al. 2011 DOI: 10.1038/nbt.2050 16.83
SAMN03263070 O. barthii (IRGC101252) BAR Wild Burkina Faso Zhang Q-J et al. 2014 DOI: 10.1073/pnas.1418307111 37.02
SAMN02941239 O. barthii (IRGC105608) BAR Wild Africa Stein JC et al. 2018 DOI:10.1038/s41588-018-0040-0 109.37
SAMD00116543 O. glaberrima (CG14) GLA Elite Africa Yamamoto N et al. 2018 DOI: 10.1186/s12284-018-0224-3 51.05
SAMN03263068 O. glaberrima (IRGC103486) GLA Landrace Ivory Coast Zhang Q-J et al. 2014 DOI: 10.1073/pnas.1418307111 50.13
SAMN02941241 O. glumaepatula (GEN1233) GLU Wild USA Stein JC et al. 2018 DOI:10.1038/s41588-018-0040-0 73.86
SAMN03263071 O. glumaepatula (IRGC88793) GLU Wild Brazil Zhang Q-J et al. 2014 DOI: 10.1073/pnas.1418307111 71.17
SAMD00003589 O. longistaminata (W1413) LON Wild Sierra Leone Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 10.51
SAMD00003590 O. longistaminata (W1508) LON Wild Madagascar Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 6.74
SAMN03263073 O. meridionalis (IRGC105298) MER Wild Australia Zhang Q-J et al. 2014 DOI: 10.1073/pnas.1418307111 39.29
SAMN02870169 O. meridionalis (OR44/W2112) MER Wild Australia Stein JC et al. 2018 DOI:10.1038/s41588-018-0040-0 92.27
SAMN00027378 O. nivara (042/87/34) NIV Wild India (Dhoni) Xu et al. 2011 DOI: 10.1038/nbt.2050 15.38
SAMN02941243 O. nivara (IRGC100897) NIV Wild India Stein JC et al. 2018 DOI:10.1038/s41588-018-0040-0 85.94
SAMN03263067 O. nivara (IRGC88812) NIV Wild Laos Zhang Q-J et al. 2014 DOI: 10.1073/pnas.1418307111 6.75
SAMN02941238 O. punctata (IRGC105690) PUN Wild Africa Stein JC et al. 2018 DOI:10.1038/s41588-018-0040-0 75.30
SAMN00027380 O. rufipogon (DAL DHAN) RUF Wild Bangladesh (Chakaria) Xu et al. 2011 DOI: 10.1038/nbt.2050 15.63
SAMN00027424 O. rufipogon (P46) RUF Wild China (Hainan) Xu et al. 2011 DOI: 10.1038/nbt.2050 13.05
SAMN00027379 O. rufipogon (PADI PADIAN) RUF Wild Indonesia (Kromat Watu) Xu et al. 2011 DOI: 10.1038/nbt.2050 15.42
SAMN00027426 O. rufipogon (VOC4) RUF Wild Nepal Xu et al. 2011 DOI: 10.1038/nbt.2050 14.72
SAMD00016753 O. rufipogon (W0106) RUF Wild (Or-I) India Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 9.63
SAMN02375087 O. rufipogon (W0120) RUF Wild India Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 21.95
SAMD00004173 O. rufipogon (W0120) RUF Wild (Or-II) India Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 29.06
SAMEA104459802 O. rufipogon (W0123-1) RUF Wild India Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 41.54
SAMEA104469252 O. rufipogon (W0141) RUF Wild India Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 69.88
SAMEA104469253 O. rufipogon (W0170) RUF Wild Thailand Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 70.86
SAMD00004178 O. rufipogon (W0180) RUF Wild (Or-II) Thailand Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 25.97
SAMD00004175 O. rufipogon (W0593) RUF Wild (Or-III) Malaya Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 29.69
SAMD00004172 O. rufipogon (W0630) RUF Wild (Or-I) Burma Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 33.62
SAMD00004177 O. rufipogon (W1230) RUF Wild (Or-I) Dutch New Guinea Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 28.93
SAMD00004176 O. rufipogon (W1236) RUF Wild (Or-II) Australian New Guinea Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 29.96
SAMN03273454 O. rufipogon (W1543) RUF Wild Unknown Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.87
SAMEA104469254 O. rufipogon (W1687) RUF Wild India Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 57.75
SAMEA104469255 O. rufipogon (W1698) RUF Wild Thailand Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 56.41
SAMD00004174 O. rufipogon (W1715) RUF Wild (Or-II) China Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 23.48
SAMEA104469256 O. rufipogon (W1739) RUF Wild India Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 91.69
SAMEA104469257 O. rufipogon (W1754) RUF Wild India Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 93.74
SAMEA104469258 O. rufipogon (W1777) RUF Wild India Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 81.49
SAMN02375083 O. rufipogon (W1807) RUF Wild Sri Lanka Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 18.96
SAMN02375089 O. rufipogon (W1886) RUF Wild Thailand Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 20.37
SAMD00016754 O. rufipogon (W1921) RUF Wild (Or-I) Thailand Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 8.89
SAMEA1523624 O. rufipogon (W1943) RUF Wild (Or-III) China Stein JC et al. 2018 DOI:10.1038/s41588-018-0040-0 15.60
SAMEA104469259 O. rufipogon (W1943) RUF Wild China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 152.52
SAMN02375090 O. rufipogon (W1965) RUF Wild China Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 24.33
SAMN02375085 O. rufipogon (W1976) RUF Wild Indonesia Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 22.03
SAMEA104469260 O. rufipogon (W1979) RUF Wild Indonesia Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 62.08
SAMD00004179 O. rufipogon (W1981) RUF Wild (Or-II) Indonesia Ohyanagi et al. 2016 DOI: 10.1093/pcp/pcv171 28.89
SAMN02375084 O. rufipogon (W2003) RUF Wild India Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 19.75
SAMEA104469261 O. rufipogon (W2012) RUF Wild India Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 108.27
SAMN02375086 O. rufipogon (W2057) RUF Wild Bangladesh Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 24.75
SAMEA104459805 O. rufipogon (W3078-2) RUF Wild China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 89.83
SAMEA104459804 O. rufipogon (W3095-2) RUF Wild China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 85.60
SAMN02375081 O. rufipogon (W593) RUF Wild Malaysia Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 32.71
SAMN02375088 O. rufipogon (W630) RUF Wild Myammar Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 32.24
SAMD00045974 Okayama Yakusake 48 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.66
SAMD00009825 Omachi TEJ Landrace Japan (Okayama) Arai-Kichise Y et al. 2011 DOI: 10.1093/pcp/pcr003 48.56
SAMD00045978 Omachi_1 TEJ Landrace Japan (Okayama) Yano K et al. 2016 DOI: 10.1038/ng.3596 8.45
SAMD00045977 Omachi_2 TEJ Landrace Japan (Okayama) Yano K et al. 2016 DOI: 10.1038/ng.3596 3.22
SAMN02821268 Oryzica 3 IND Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 12.23
SAMN02821269 Oryzica Llanos 5 IND Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 11.67
SAMD00045979 Oseto TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.17
SAMD00045975 Ouu 2 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.10
SAMD00045980 Ouu 237 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.89
SAMD00045981 Ouu 239 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.55
SAMD00045982 Oyama Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.45
SAMEA104469224 Pama TEJ Elite Philippines Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 71.66
SAMN02821270 Parao TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 30.02
SAMEA3927613 Pavlovsky JP Elite Russia Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 10.88
SAMN00027395 Phudugey TEJ Landrace Bhutan Xu et al. 2011 DOI: 10.1038/nbt.2050 15.26
SAMN02821271 Pionero2010FL IND Elite Venezuela Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 20.83
SAMN03273426 Pitai IND Elite Indonesia Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.12
SAMN00027402 Popot 165 IND Landrace Indonesia (E.Kalimantan) Xu et al. 2011 DOI: 10.1038/nbt.2050 14.99
SAMN07767773 PSRR-1 WEEDY Weedy USA Chai C et al. 2018 DOI: 10.1038/s41598-018-32513-z 33.93
SAMEA3927615 Puntal JP Elite Spain Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 13.41
SAMN04442258 Purple puttu IND Landrace India Lachagari V. B. R et al. 2019 DOI: 10.3389/fpls.2019.00513 96.16
SAMEA104469233 Qiananshuinuo TEJ Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 86.23
SAMD00045983 Raiden TEJ Landrace Japan (Kanto Higashiyama) Yano K et al. 2016 DOI: 10.1038/ng.3596 6.43
SAMN02375094 Ratul IND Landrace India Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 16.05
SAMD00045984 Reihou TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.18
SAMD00045985 Reimei TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.00
SAMN02375110 Rexmont TRJ Elite United States Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 14.94
SAMD00045987 Rikutou Rikuu 2 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.07
SAMD00045986 Rikuu 132 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.77
SAMD00045988 Rokko Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.26
SAMN03751782 RP Bio-226 IND Elite India Reddy M M et al. 2015 DOI: 10.3389/fpls.2015.00896 24.13
SAMEA104469234 Ruanzhanjiugu IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 26.66
SAMD00080141 Ruriaoba IND Elite Japan Ogawa D et al. 2018 DOI: 10.1038/s41598-018-22657-3 38.50
SAMN02821249 Saber TRJ Elite Unknown Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 36.12
SAMD00045948 Sachidama 1 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.73
SAMD00045949 Sachidama 2 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.57
SAMD00045989 Sachikaze TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.96
SAMD00045990 Saga No Hana TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.80
SAMD00045991 Saikai 134 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.56
SAMD00045992 Sake Pikari TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.04
SAMN11233562 Samgwang TEJ Elite Korea Kang D-Y et al. 2019 DOI: 10.3390/ijms20102598 68.39
SAMD00045994 Sasanishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.99
SAMN02375105 Sasanishiki TEJ Elite Japan Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 15.19
SAMD00045995 Sasashigure TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.29
SAMN05200854 Seeragasamba IND Landrace India Bindusree G et al. 2017 DOI: 10.1371/journal.pone.0188920 7.20
SAMD00045996 Sekikei 56 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.35
SAMD00045997 Sekiyama TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.39
SAMD00045998 Senbon Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.26
SAMEA3927619 Senia JP Elite Spain Reig-Valiente JL et al. 2016 DOI: 10.1186/s12284-016-0130-5 13.22
SAMN03273450 Shenglixian IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.42
SAMD00046000 Shichimenchou Mochi TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.26
SAMD00046001 Shiga Wataribune 2 TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.95
SAMD00046002 Shin Igou TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.74
SAMD00046003 Shin Yamabuki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 2.74
SAMD00046005 Shinjyu TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.08
SAMN03464929 Shinriki TEJ Landrace Japan (Hyogo) Wei FJ et al. 2016 DOI: 10.1016/j.plantsci.2015.09.005 17.56
SAMD00046006 Shinriki TEJ Landrace Japan (Hyogo) Yano K et al. 2016 DOI: 10.1038/ng.3596 6.73
SAMD00046007 Shinriki Mochi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.35
SAMD00046008 Shinshuu TEJ Landrace Japan (Nagano) Yano K et al. 2016 DOI: 10.1038/ng.3596 3.57
SAMD00046004 Shinyamadaho 1 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.86
SAMD00046009 Shinyamadaho 2 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.05
SAMD00046010 Shiragiku TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.36
SAMD00046011 Shirakaba Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.32
SAMD00046012 Shirayukihime TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.81
SAMD00046013 Shiroine TEJ Landrace Japan (Tokushima) Yano K et al. 2016 DOI: 10.1038/ng.3596 4.06
SAMD00046014 Shirosenbon TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.06
SAMD00046015 Shirotae Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.19
SAMN02375095 Shoni IND Landrace Bangladesh Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 13.08
SAMN02821250 ShuFeng IND Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 3.46
SAMD00046017 Shuhou TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 2.56
SAMN03273444 Shuhui527 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 20.04
SAMEA104469247 Shuihegu IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 40.67
SAMD00046016 Siranui TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.98
SAMEA104469241 Sizhan IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 50.00
SAMN07426270 Suijing18 JP Elite China Nie S et al. 2017 DOI:10.1038/sdata.2017.195 52.81
SAMN02375096 Surjmukhi IND Elite India Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 16.45
SAMD00003728 Suweon258 IND Elite Korea Yonemaru J et al. 2014 DOI: 10.1186/1471-2164-15-346 37.24
SAMEA104469220 T 480-34 IND Elite Cuba Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 74.72
SAMN00027384 Ta HungKu TEJ Landrace China Xu et al. 2011 DOI: 10.1038/nbt.2050 12.41
SAMD00003726 Tachiaoba TEJ Elite Japan Yonemaru J et al. 2014 DOI: 10.1186/1471-2164-15-346 39.45
SAMD00003729 Tachisugata IND Elite Japan Yonemaru J et al. 2014 DOI: 10.1186/1471-2164-15-346 34.04
SAMN04275184 Tadukan IND Landrace Philippines Mahesh H. B. et al. 2016 DOI: 10.1186/s12864-016-2523-7 93.46
SAMN03463201 Taichung 65 TEJ Elite Taiwan Wei FJ et al. 2016 DOI: 10.1016/j.plantsci.2015.09.005 5.70
SAMN02209969 Taichung Native 1 IND Elite Taiwan Kim B et al. 2014 DOI: 10.1186/s12284-014-0022-5 34.44
SAMD00046018 Tajima Goriki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 2.69
SAMN02375102 Takanari IND Elite Japan Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 9.30
SAMD00003725 Takanari IND Elite Japan Yonemaru J et al. 2014 DOI: 10.1186/1471-2164-15-346 34.33
SAMD00046019 Takane Nishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.12
SAMD00046020 Takenari 8043 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.81
SAMD00046021 Tasensho TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.39
SAMN00027421 TD2 IND Elite Thailand Xu et al. 2011 DOI: 10.1038/nbt.2050 11.15
SAMEA104469226 Tebonnet TRJ Elite USA Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 99.18
SAMEA104469227 Teng-870 TEJ Elite Japan Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 56.52
SAMD00077983 Tenkomori TEJ Elite Japan NICS None 54.57
SAMD00077982 Tentakaku TEJ Elite Japan NICS None 55.25
SAMN02821251 TeQing IND Elite China Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 4.60
SAMN03273451 Tetep IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 23.58
SAMN04275185 Tetep IND Landrace Vietnam Mahesh H. B. et al. 2016 DOI: 10.1186/s12864-016-2523-7 45.79
SAMD00046022 Todorokiwase TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.23
SAMD00045881 Togoh 1 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.47
SAMD00045918 Togoh 2 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.76
SAMD00045973 Togoh 3 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 2.97
SAMD00045976 Togoh 4 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.86
SAMD00045873 Togoh 5 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.06
SAMD00045999 Togoh 6 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.43
SAMD00045883 Togoh 7 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.16
SAMEA104460753 Tohoku IL9 TEJ Elite Japan Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 87.96
SAMN02209972 Tongil JP/IND Elite Korean Kim B et al. 2014 DOI: 10.1186/s12284-014-0022-5 45.81
SAMD00046026 Tono 1 TEJ Unknown Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.11
SAMD00046027 Tosanishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.10
SAMD00046023 Toujinohana TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.36
SAMD00046024 Toujinoyume TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.48
SAMD00046025 Toukai Asahi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.50
SAMD00046028 Toyonishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 7.90
SAMN00027403 Trembese TRJ Landrace Indonesia (East Java) Xu et al. 2011 DOI: 10.1038/nbt.2050 12.76
SAMD00046029 Tsuyubakaze TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 2.24
SAMD00078852 Tupa 121-3 IND Landrace Bangladesh Itoh H et al. 2018 DOI: 10.1111/tpj.13906 39.72
SAMN02375111 Tupa 729 TRJ Landrace Bangladesh Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 14.63
SAMN02375097 Tupa121-3 IND Landrace Bangladesh Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 12.84
SAMN02375109 Urasan 1 TRJ Elite Japan Fawcett J et al. 2013 DOI:10.1371/journal.pone.0083720 14.41
SAMEA104469251 W0128 IND Wild India Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 71.04
SAMEA104459803 W3105-1 AUS Wild India Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 145.70
SAMD00116542 WAB 56-104 TRJ Elite Africa Yamamoto N et al. 2018 DOI: 10.1186/s12284-018-0224-3 49.40
SAMD00046030 Wakaba TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.05
SAMD00046031 Wakamizu TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.37
SAMN03273442 Wanhui88 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.28
SAMN03273452 Wanlixian IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.31
SAMD00046032 Wase Asahi TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 5.32
SAMD00046033 Wase Shinriki TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.52
SAMD00046034 Wataribune 1681 TEJ Landrace Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 2.67
SAMN02821252 Wells TRJ Elite USA Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 4.30
SAMEA104459807 Wuyungeng 7 TEJ Elite China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 62.44
SAMEA104467890 Xiangnan-1 IND Elite North Korea Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 72.60
SAMD00046035 Yamabiko TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.76
SAMD00046036 Yamadaho 132 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 7.45
SAMD00010633 Yamadanishiki TEJ Elite Japan Arai-Kichise Y et al. 2014 DOI: 10.1371/journal.pone.0086312 38.77
SAMD00046037 Yamadanishiki TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.47
SAMD00045993 Yamasakae TEJ Unknown Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.53
SAMEA104469248 Yanzhan IND Landrace China Zhao Q et al. 2018 DOI: 10.1038/s41588-018-0041-z 48.15
SAMN00027427 Yuan3-9 RUF Wild China (Yunnan) Xu et al. 2011 DOI: 10.1038/nbt.2050 11.71
SAMN02209992 Yukara JP Elite Japan Kim B et al. 2014 DOI: 10.1186/s12284-014-0022-5 37.96
SAMD00046038 Yukigeshou TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.63
SAMD00046039 Yumesansui TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 3.68
SAMN02821272 Zafiro TEJ Elite Chile Duitama J et al. 2015 DOI: 10.1371/journal.pone.0124617 7.19
SAMD00046040 Zengokuwase TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 8.18
SAMD00046041 Zensyo 26 TEJ Elite Japan Yano K et al. 2016 DOI: 10.1038/ng.3596 4.50
SAMN03273453 Zhongnong-4 IND Elite China Huang J et al. 2018 DOI:10.1073/pnas.1806110115 22.05