Welcome to Acta Agronomica Sinica,

Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (10): 2036-2044.doi: 10.3724/SP.J.1006.2021.02082

• RESEARCH NOTES • Previous Articles     Next Articles

Combining QTL-seq and linkage analysis to identify the QTL of mesocotyl elongation in rice (Oryza sativa L.)

LIU Chang1(), MENG Yun1, LIU Jin-Dong1, WANG Ya-Mei1,*(), Guoyou Ye1,2   

  1. 1Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, Guangdong, China
    2International Rice Research Institute, Metro Manila DAPO Box 7777, Philippines
  • Received:2020-11-30 Accepted:2021-03-23 Online:2021-10-12 Published:2021-04-07
  • Contact: WANG Ya-Mei E-mail:woshiyonghwa@163.com;wangyamei@caas.cn
  • Supported by:
    China Postdoctoral Science Foundation(2020M68299);Agricultural Science and Technology Innovation Program Cooperation and Innovation Mission of the Chinese Academy of Agricultural Sciences(CAAS-XTCX2016001)

Abstract:

Mesocotyl length is an important trait, which affects seedling establishment and early seedling vigor after dry direct seeding. Identifying the loci related to mesocotyl elongation, analyzing the genetic mechanism and selecting varieties with long mesocotyl is the most economic and effective way to promote the popularization of dry direct seeding technology. In this study, an F2 population constructed with ‘Changai’ (an extremely long mesocotyl variety) and ‘IR 145’ (an extremely short mesocotyl variety) was used to construct long and short DNA pool, which were re-sequenced at 50×level. Two methods, ΔSNP-index and G-value, were used to identify the quantitative trait loci (QTL) for mesocotyl elongation. A QTL named as qML3, located in the region of 29.56-33.28 Mb on chromosome 3 were detected. After linkage analysis of 184 F2 lines with the newly developed KASP markers based on this locus, the region was narrowed down to 28.89-31.03 Mb. Combining the results of gene annotation, linkage analysis, and gene expression analysis, LOC_Os03g52450, LOC_Os03g56060, LOC_Os03g58290, LOC_Os03g58300, LOC_Os03g58320, LOC_Os03g56050, and LOC_Os03g57640 were speculated to be candidate genes in this region. These genes were involved in the regulation of plant hormones as well as the mechanism of cell division. This study uncovers a locus related to rice mesocotyl elongation and is helpful for the breeding of long mesocotyl varieties.

Key words: mesocotyl, bulked segregant analysis, Δ(SNP-index), linkage analysis, candidate gene

Table S1

Details for KASP markers used for linkage analysis"

Marker Chromosome position Seq C Seq X Seq Y Allele X Allele Y Changai IR 145 Long pool Short pool Sequence
OS900153_K01 1 11341599 TTTCCCTTTCACTCCAAAGAAACGA GAAGGTGACCAAGTTCATGCTTATTGTGGAAATCGCTTGACCCTCC GAAGGTCGGAGTCAACGGATTTATTGTGGAAATCGCTTGACCCTCT G A GG AA AA GG GGTGATGGCGATGCGCGGGGTCGACGGATCGGCAATGGTGAGGCGCGGGGTCAGCGGAATGACGAGGAGTGGGGGTGGCGATCAACGACGGTGAGGCGGATCCATCAGCCATATACATGTGCACACCATGTGCATGGAATCTACACCAATGTTTTCGATTTTTACTGACCTTTCCCTTTCACTCCAAAGAAACGATCTTC[G/A]GAGGGTCAAGCGATTTCCACAATAGTCTCGGTTCTAATAAGAACCGGGACTAAAGATTGTTTTTAGTCCCGGTTAAAAAAAATTTGATATTTAGTCCTGGTTCGTGATCTTTAGTCCTGATTCATCTCCTGTCAGAAGCCTGCGAGGGGGCCGAGGATCTTTAGTCCCGGTTGATTACCACTTTAGTCCCGGATGGTACT
OS900154_K01 2 8278191 TGGCACAGCCTAACAATATGATGGA GAAGGTGACCAAGTTCATGCTAATTGCTCCAGCTTCTGTGTTGTGC GAAGGTCGGAGTCAACGGATTATTGCTCCAGCTTCTGTGTTGTGA G T GG TT TT GG TAGCAAGTTAATCTGGACAATGCAGGTTAGATCTGAAATCATTTGCTCTACAGTTTCATAATGCATATAGTTCCTTATGGTATAATATCAGCTACCAACCTGCCAATATGTTCTACAATCTCATAATGCATACAATGTCTCACAATATCAGCTGATGGATGGCACAGCCTAACAATATGATGGAAATTGTGTGGTCAGAA[G/T]CACAACACAGAAGCTGGAGCAATTTTCCTTCCACTTCTACCTTGACAGAGAAGTTCTGAAGACTGATTTTCATTCTCTGATTCCACCAGCCACTATGACAGAGCATACCTTGCTTCCACTTTTTTCCTTGATGAGGTTGTAGTGTTCCCTTCCCCATATTTTTTTGTTGTTCAACTTAAGATTCTCGCCGTTAAAAAATT
OS900155_K01 2 11054736 CCAGAAGGTTCGTTACTTCCATGTCC GAAGGTGACCAAGTTCATGCTTGAATCCATTTATGTTAGGTGCCATA GAAGGTCGGAGTCAACGGATTTGAATCCATTTATGTTAGGTGCCATC A C AA CC CC AA ACCCCTTTTTAGTACAATTTAGAGCGCACTCACCACCATGTGTAAGCACATGCATGTCCTCTACATACTCTTGAAATAGAGGCATCGAAATCTTATAGAGTATGGTGGACATGCTAAATCACCTACTGAGTACATAATCATAAAATTGGTGGACACTAGTGCTAGATCTAGAATCTGAATCCATTTATGTTAGGTGCCAT[A/C]TCTTGTCGACCAGCTTCTGAATCTATGCTACAATAATTATTTTTATAAGGGACATGGAAGTAACGAACCTTCTGGAGTTGATTTTGTGAAAAATTTTGAACTCTAGAATTGGGTAAAATTCAGAACGGAGGGAGTATGTAAGAAATACGATAAAAAGTGTTAAAAACAACCAACGAGAATAGAAACAAGTCAGTTCAGAT
OS900156_K01 2 30473912 CGCAGGCACAACCCAGTTTACATA GAAGGTGACCAAGTTCATGCTCACTCCATAAAGGAAACAAAATGACTTGTA GAAGGTCGGAGTCAACGGATTTCCATAAAGGAAACAAAATGACTTGTG T C TT CC CC TT GCCAACATGCTGTCGATCCTGCATGTTAGCGGACAATGCTTACAGCAGTGATTTTATGAATGTGATTATCATGAACACTTTTGATCGTCCCGGTAAGTTTTCAGATACTTGTCCAGTTATCTACATGCAAGAAAATAATTAAGTATGTACTGATTACTCAATGTACATGGGTGTGGCGCAGGCACAACCCAGTTTACATA[T/C]ACAAGTCATTTTGTTTCCTTTATGGAGTGTTTCTACAAAACCATGAACACCAATGTTTACACAAGTACAATCGCCTACTTTCTCTCCGGTCGATGGAACAGAGATAAAAGAGATCCAAAAGCACCGAGCCAAACACCAACAAAACCGAAAAAAAAAAGGAAGAGAAAAACTTTTGAATTGAACAACGTTATACTACTTGA
OS900157_K01 5 3752390 GGCACATTACCAATGCAGGACATTT GAAGGTGACCAAGTTCATGCTACACTTTCTACAGTTGGCCTTCAGC GAAGGTCGGAGTCAACGGATTACACTTTCTACAGTTGGCCTTCAGG G C GG CC CC GG AAATCCCTACGTTTGAAACTGATTCTGCCGACAATATTAGCACCTATAGAACCATGTTCTCAATAGTGTAATATAACAATGTATAGTAGTAAAAAAAAATCAGTTTAGGCACATTACCAATGCAGGACATTTTACATGTTCAGGTGTCATTATTTAAAAAGTATTCATTTTACATATAGTAGTAGTGCTTTCGATGCATC[G/C]CTGAAGGCCAACTGTAGAAAGTGTACACTATCGTTAAAATGCCTGCTCGTGATAGTATAACTTCTAAACCTATAAAGTGATGGGGATTTTGGTGCATTCGCGTTTGGGAGGGGAGGAACCGGGATTTAAATTTGGATTTTGCAGTGAATAAAGATGTACTAATTATTGGACGAGGCATTACCAACGATCCATCCAATCTG
OS900158_K01 5 6521522 GCGTAAACCTCGGTGAATTCCTCAC GAAGGTGACCAAGTTCATGCTGACCAACAACAATATTAGCATAGCACAAAA GAAGGTCGGAGTCAACGGATTGACCAACAACAATATTAGCATAGCACAAAG T C CC TT TT CC TCTCCGCAAGGAAAGAGATACCCTTAGTGGAAGGAGGAGTGCATTTGTGCAACCTCACGAGGATAGGGTTGAAAAAGACCCGGCTCTTTGCGAGCCCCTCAACGGAGACTAGAATCCCCTTAAGGATTTGAACTCCGGGAAATACATCGGCGCGTAAACCTCGGTGAATTCCTCACTCTCTTTACCTTCTTGTTCCATTA[C/T]TTTGTGCTATGCTAATATTGTTGTTGGTCGAGCTCACCTCTTTACTTGTGGATTGAATCTAGAGCTCTTAGGTTGTTCTCTTGTTTATATTGTTGTTGTGCAGGTCAGATAGTCTAATATCAGTTCAGACTATCCGATCACATAGGACTATCCGACCTGATATTAGACAATCTGACCCTGTTTTGTTATAGCTTCCGCAT
OS900159_K01 5 14053490 TGAAATCGTGTTAGCCGACAAGTCA GAAGGTGACCAAGTTCATGCTGCATCTCCCAAAGAGCTAAATCGG GAAGGTCGGAGTCAACGGATTGCATCTCCCAAAGAGCTAAATCGA C T CC TT TT CC GGAGCTGACAGTCGGCAGCAAGACTAACCCTACAACATTTTTTGTCTTCGATGGGAAGGGTTCCTACAGCTTATTGCTTGGAAGGGATTGGATCCATGCCAATTGTTGTATTCCTTCAACCATGCATCAATGCTTGATTCAGTGGCAAGACGACAAGATTGAAATCGTGTTAGCCGACAAGTCAGTCAACGTTGCTAGTG[C/T]CGATTTAGCTCTTTGGGAGATGCCTGGTCTCGATTGCTTATCTGGAAAAGTTTGGGATGGAGATTTTCTAAAAGTGTCCAATTGTGATATACAACCAATTGAAGATGGAGAGCCCAAGCTTTTATTTTGAGGGTGTCGTGGAGGGTTCAAATGTCTACACCAAGGACACAGTAGATGATCTCAATGACAAGCAAGGACAG
OS900160_K01 5 21516100 CCATGGCAGTGGGTGTTGAGATTAT GAAGGTGACCAAGTTCATGCTAATGCGGTCATGCTAGTTTTCATCTA GAAGGTCGGAGTCAACGGATTATGCGGTCATGCTAGTTTTCATCTG T C CC TT TT CC GTCAAAGGAAAATTTGCAGATGCTATTTGCTGTTCGCAAACCGAATGAACGAGAGCGATGAGCTATAAGGCCATGCCCAATGCACCACGGTGGCCAGTGGTCTCAAGCATCCACATCGGAGCTGAGCTTCCATGGCAGTGGGTGTTGAGATTATAGGCATATAATGATTTAATCTATTCCATAAATAAATCATGACATTA[C/T]AGATGAAAACTAGCATGACCGCATTATTAGATCTATACATGTAAACTACACAATATAATATGAACAGATCAAATATACGCAATATATTGAACACGTACCGAGGTGGCGGAAAGACCGGCTGCTCGGTCGAAAATTTTCGCAGGCGTCTACGAAGGCACGCAGCACGCGAGCGAAGAGGAAGATGAACCGTCGCGGACGAA
OS900161_K01 5 24914119 AGGGCACTCACACTGCGTCACTAAT GAAGGTGACCAAGTTCATGCTGTCTAGGTGGCAGTTTTGGCTTCTT GAAGGTCGGAGTCAACGGATTGTCTAGGTGGCAGTTTTGGCTTCTC T C CC TT TT CC GAGGGGGAGAGGGGTGCCGGCGGTGGGTGGGAGAGAGAGGGGCACCAGCGGCGCAGTAGAGGAGCGGGAGCGGCGGGGAAAGGGAGAGAGAGAGAGGAGAGAGAGCGGGTGGGACCCACTGTAAGGGAAAAAGTAGACCACATGCATTGTGGAGGTTGTTGCTTACGAAGTTATTAGTCTAGGTGGCAGTTTTGGCTTCT[C/T]AAAAATTAGTGACGCAGTGTGAGTGCCCTGATAAAATCTGGCATACATGACTCAGTTGCAAGCTACTTGAAACAAGAAAATAAGAGTCGATTCTGCCTATACCGATCGTAATGACAAGACAGACAAGTCAAACACCTTGCATATAGAGGTGTACTTAGGATTTATGGTTCTAGAAAATATCATATTATATTCTAGATTAA
OS900162_K01 5 28105720 GAATTCAAATTTTCATGTTTGTGGAG GAAGGTGACCAAGTTCATGCTCATCCCTCGATATCTTCTCGTTTGG GAAGGTCGGAGTCAACGGATTCATCCCTCGATATCTTCTCGTTTGA G A GG AA AA GG TTCAGAGCCTTTTCGCGCACTTGAATGCATATGCATGAGTTAATTTGCACACTGTGGACGCAGGGGAACACAAGAACAATGGCATGCATGCATACGTTTCGTGTAGGGCAGCTGCTGGCTAGCTTCTCCCGTACAGTGTGCTCGTGCGTGTGTGCTGCTAGCTGGGAAAGTGAAATCATCCCTCGATATCTTCTCGTTTG[G/A]TGCATGTCACCTAAATAGTCAAAAAATTATTAAAAAATTATCAACATATATTAATATGAAATATATTACTCCACAAACATGAAAATTTGAATTCAATTTCTACAAGTTGTAACAAAAATAACAAATATAGTCGAATGTGTGATAACTGTTTTCAGTTTAATTTGTTATTATTGTAGCAACTTGTAGAAGTTGAATTTGGC
OS900163_K01 7 12402368 CTCAACCTGCCTACGCAACTCTTTC GAAGGTGACCAAGTTCATGCTGCAGCATGCAAGTCGAAGGTT GAAGGTCGGAGTCAACGGATTGCAGCATGCAAGTCGAAGGTC T C CC TT TT CC ACACCTGATTAGGGCGTTCGTACACATCCAACTGGAGAAGATCCCTGTTGTCTATTCCTAAAGAGGTATACCATGAAAGCAAACAGTGACAAGTGTGATCGTGAGACTGCAGGACCGGATGGGGTGCATGAAAATTACATAACAAACATGATGATGATTGAAGCATTTGGAGTGATGAGGGCAGCATGCAAGTCGAAGGT[C/T]GCATATGAAAGAGCTATGGTTATTTTGAAAGAGTTGCGTAGGCAGGTTGAGGAGGTACCACAAGATATTCAAGTTGTTGTTTGTGTTCTGTCTCTCAACCGCTCAAGACAAGGAAGGACAGTGTCTCGTGGGAATCAGGGGTAAGGGTAAGCCACCGTGCCAAATTTATTTGATTTGAGAGAGAGTACACATATCTTCTT
OS900164_K01 8 28356273 AACAGGCCGAGGCTCTTCACCTACT GAAGGTGACCAAGTTCATGCTACTCCCTAGTTCCCAAACACTCTCA GAAGGTCGGAGTCAACGGATTACTCCCTAGTTCCCAAACACTCTCT A T AA TT TT AA ATATATATATATATATATATATATATATATATATATATATATACATATATATATATATATTTGTTGGATTAATTAGTAGTAGTTGATTTATGGGGTGTTTAGGAGAGAGGGGCTAAACTTAAAAATATAAGTCTCTAGAGTAGGGACTTATATTTTTAAAAAAAGGGCTAAAGTTTACTCCCTAGTTCCCAAACACTCTC[A/T]TAGATTAGCTAGTCGATCGATCGGCTTACTGTCCAGTAGGTGAAGAGCCTCGGCCTGTTGTCCCCATACAGCTCAGGGCTGACCTGACTACAAGGAAGGAAACATGCAAATGCTTCAGATTCAGATTTAGATCCAATTATATATATGCTCAGCTCTGCTCAATACTACTACTAGTATGAATTAATACTCCTAGGAGTATA
OS900165_K01 9 19464447 ACGGGATATGTGGTGGGACCAG GAAGGTGACCAAGTTCATGCTTGTATAAATTGCGAGAATGCTCAACG GAAGGTCGGAGTCAACGGATTTGTATAAATTGCGAGAATGCTCAACT C T CC TT TT CC CGAATACACTAGGTGAAACATTTTTTTATGAAAAAAAACAAACCAAATTTCCTTAATAGATGGTTTCCAAAATATGTAGGTGATTTGTTTTATATGGATAAGTGACAGGTGGGGACACGGGATATGTGGTGGGACCAGGTGGGCACGTGATGGGGGGAGGGGGGAGCGACCGATTTTTTTCCCCTCCCCCGCGCGCCCGA[C/T]GTTGAGCATTCTCGCAATTTATACAAGTTGAATTTTCAACCTGTCTGTCTGTGGAACGCTATATTTCGTATTAATCATCTTATTAATTTTGGTCAACTTACAATAAACGAGTGGATTGTTCATCAATCCCTCTCCGGTGCACATGCTATTTAGATTCCGACGTGGACGGTGCACGTCCAGTCGTCCACCACCACCACCAC
OS900166_K01 10 180016 CGATAACCTAGGATGATGCACTGCTG GAAGGTGACCAAGTTCATGCTAAGGCTTGCTCGGCAGTTTTA GAAGGTCGGAGTCAACGGATTGTAAGGCTTGCTCGGCAGTTTTT A T TT AA AA TT CGCCTCATCATCCAATTCTATGTGGCATTTTTAGGGCAACACATCAAGTATCATATAGTACTTTGCCCTTAGTTGCTATCCTATTGGATGTATATGCCAGAGTACCATATCATTATCTTGAAATTGGGATGTCTATAAAAGTAGATGGTGTTTCTCATGTCTGACACCTATTTCCCTGGTAAGGCTTGCTCGGCAGTTTT[T/A]CAGCAGTGCATCATCCTAGGTTATCGAACTGTCGACAATTCTGAAAATAATTGATCAGCTATGGATCATGTGTTTTTCTGTGCGTGCGGTCTTGCGATAGCTTCTTTATACGTTTGATCATAACCTATATAAGATGTTAGAATGAAGGAATTCAGTATGATTAGTGACATTGCAGTTGAATTGTAATAAATAAAGATGCA
OS900167_K01 10 4232779 TCGAGGTTCGACACGTTTATAGCAA GAAGGTGACCAAGTTCATGCTGTTCTCTTCAGGATGCTTGTCGTGT GAAGGTCGGAGTCAACGGATTGTTCTCTTCAGGATGCTTGTCGTGC T C CC TT TT CC ACCCAAGAAGTCAATAAGTGGAGTTCGCCAGTCTTTCATTGTCTTGATGTCAACAATGACATGTTCGACCTCTTGAGCCCCCGAGGAGTTGTCGGTATTGGCCATGGTACCTTCGTCGTGCGACTCTTTTACAGACGGTTTTGTCAGGACATCTAAGAAAGTTCCTAGTTCAAGAGGTTCTCTTCAGGATGCTTGTCGTG[C/T]TAAGTCATCTGGTTCAATGTTATCCTTGCTATAAACGTGTCGAACCTCGATGCCGTCAAACTTCTGCTCTAGCTTCTTGACTTCAAAGAGGTACTTAGCCAACTCAGGATTGGAGCATTTGTAATCCTTATCCACTTGGTTTGCGACTAATTTTGAGTCCCCTCTCACAATCAATCGTTTAACTCCTAGTGCAACGGCTG
OS900168_K01 12 2919839 TCGTTTCGCAATCAGTAGGAGGAAA GAAGGTGACCAAGTTCATGCTGGGTGGTGTCAGATTCACTACTCATT GAAGGTCGGAGTCAACGGATTGGGTGGTGTCAGATTCACTACTCATC T C CC TT TT CC CCACCATACACTTTAAAGCCTAAAAATTAAAATAAAATTATTCTCAATGTAAAATATTCAGGTCATATTATTTGTCATTATTTTTACTTTACTTCAAAAGAAATTGATGGTTCGAGGTTAGGGAAATAACAAAAATCCACTTAACTTTTCGGAGAATCCATATGACAGTGGTGATGGGTGGTGTCAGATTCACTACTCAT[C/T]ACCACTACGTACTATTATAGAAAAGCACTTCAAGTAGTACCTACATTTTTCAAGTTGTAGCTAGATCTTTTTACGAATTTGAACTTTCCTCCTACTGATTGCGAAACGAATTAACCGGCCACCGTACAAACTTTTCATGGTACAGGCATGCATGCTTCTTGATCCTTTGCATTTCAAATCATGGTGTTTATGCCGTGTAC
OS900169_K01 12 7367534 GCTAGCACATATGACTGATGCATTACA GAAGGTGACCAAGTTCATGCTGAGTAGCTGGTGTATTTTTCAGTGATT GAAGGTCGGAGTCAACGGATTGAGTAGCTGGTGTATTTTTCAGTGATA T A TT AA AA TT TTTAATTAAATCTAACATTGAATATATTTAAATAGTATGTTTGTTTCGCATTACAAATATTATTATGTAATTTTTAATCTCGGTCAAACTTAAAAAAATAACTTAGAAAAAAATCAAAGAATTACCATAATTTGGCTAATAATTAGTTTTATTTTAGTATGGTCAAACTATTTAGAGTAGCTGGTGTATTTTTCAGTGAT[T/A]CTCTTGTAGAGTAGGATTGTAATGCATCAGTCATATGTGCTAGCTATACTATTGAATAATTGAATGTGGACCGATGTAGTTTATAGCATTGTAAGGGTTATGGTTTACGTCATATATCACATGAAGGAAATGAAGATGACGCAAACCAAGTTGATGGATTGCGTCTTAGCAAGAACGACCAAACTTATCATGGTCCATCC
OS900170_K01 12 27253671 TATAACAGCGACCACCCAGATGACC GAAGGTGACCAAGTTCATGCTATCACGTCCCCCGTTGTCA GAAGGTCGGAGTCAACGGATTATCACGTCCCCCGTTGTCG T C CC TT TT CC CAGAGGGAGGTTCGCGACCAAGGTAGCAGAACGGTGAGGGACGCCATTGGCCGAGACGGCGGAAGAAGGCAAGAGAAGGGGCACCGCGACAGGCGCCGGGATGACCGCGATGACCGTCGCGGGCGCAACAGGAGGTATAACAGCGACCACCCAGATGACCTCCGACGTGGAGGACGGCGCGACGACGACAATGATGATCG[C/T]GACAACGGGGGACGTGATGTCGCGCACGGAAGGGGCGGCGTTCGCGGCCCAGACGTCAACTTCAGGCGGGAACGCACGCACTCGCCGCGTGCCCGCGATCGCGGCGACACGGGAAGACGCGACGGGCAACGCCATCAAGCAAACTGCGGCGGCAAGGACGACGGGGCCAACGACCGCGACATGGGCAACCCACCCCCAGC
OS900129_K01 3 28890281 GCTCAGATTACTGGCTGTGTCA GAAGGTGACCAAGTTCATGCTCATCGATCGGTGTCATTCA GAAGGTCGGAGTCAACGGATTCCATCGATCGGTGTCATTCT A T TT AA AT AT AAATTGATCATTATGATTTTTTAAACAACTTTCGTATAGAAGCTTTTTACAAAAAGTATACCGTTTAGTAGTTTGAAAAACGTACGCGCGGAATACGAGTGAGAGAGGTTGGGAACAAGAAGCAACAAACATAGTACGCGTCCTATACCCCGGTGACCTCTATATATACCGTACCCCATCGCCATCGATCGGTGTCATTC[A/T]TTCTAAGCTTGACACAGCCAGTAATCTGAGCTAAATTAGTCCTAAACTCCAAGTTGATTATCCAACGAATCGTAGCCTCGAGGGGGTATCTGAATCTCCAACCACTTCAATTCAACGCGTCGCCATCGCCATCTTCGTGTAGAGGCGACCTCACCTACGCGCGCGGCGCGCCCCTGGCCATGCAGACGATAAGGTGGTCG
OS900130_K01 3 29290258 TGCATTATCCTCGAAAAACAA GAAGGTGACCAAGTTCATGCTAAAATTGTAATTGGTTGGGAAGAA GAAGGTCGGAGTCAACGGATTAAAATTGTAATTGGTTGGGAAGAG T C CC TT TC TC GAGAGTCCACATAATGTGTAAAAAATGTGCATGTTCCCTGCAAACTTAAGGTTCAACTTTACTTATGCGAAATTGCGGATAGGAAAAAAAAACTGTTTCTACGGATCGCAAGACTATGCATTATCCTCGAAAAACAATTTATACCTTGCATTGTAGCATTTAGAATTTGTTCCAACATATAACAACTTTATATTTAAAAT[C/T]TCTTCCCAACCAATTACAATTTTCCACCATTTATTTATTTTTTCATCCACTTCCTCTCTCCCATGTTTACTTACATATGTTTTTGATAACCATGTCCAATCTCAAAACTTCTTATCTTTTAAAACGGAGGTAGCAAGGCACATTCTTCTCATGATGTTAGATCGTCTTTCCTCATGTAAACAAGTACCATGGACAGTATC
OS900131_K01 3 29692468 GCACAGACATCCTCGTGTCA GAAGGTGACCAAGTTCATGCTAATCTTTAAATAGTTTCTTCTTTTCTTCTTCT GAAGGTCGGAGTCAACGGATTTCTTTAAATAGTTTCTTCTTTTCTTCTTCC T C CC TT TT CT CGCAGGTCCGGGATGCCGCCGACCATATCGTCCACAGCTTCGAGGGTTCGGCCCCTCGGCTCGCGTTCGCCCTCAACTCCGACGAGGAGGGCGATGACGGCGGTGTGGGCGACAGTGGCGACGAGGCTGGCGACCCGGGTGCATCGGAGTGAGCCCCCAGGCCCCCGCCAATCTTTAAATAGTTTCTTCTTTTCTTCTTC[C/T]GAGGCCTTCGGGCCCCCTTCTTGTATAGACTAATTTAATCTGCAATCAAATAAAGAGGAAATTTTTTGTGTCAATTCTATTTGTTGTGTGTATGACACGAGGATGTCTGTGCCGCGGTCCTTTTGTGTCTTGGCTTGAACAAGGGCTCGTGCCCAGGTCCTAGTCCTCAAATGGCTCGGGTCGGGGCTAGTGCCTGGGGA
OS900132_K01 3 30106408 CCACTAGCGAGTAGCGAAGC GAAGGTGACCAAGTTCATGCTATGGCCATGGTGAGCGTT GAAGGTCGGAGTCAACGGATTATGGCCATGGTGAGCGTC T C TT CC TC CC TTATCGAATCGCCACTGAAGTTGATGAGCTGGCTCCTCCCGTCGTCGTCGGTCCAAAGAGATAAGACGGAGACCTCACTCCACACGTCGAAATTGGCAGAGCTCAGATTGGGCGTCACCGCACAGGGGAGCGAGAGTGGAGGGAGGCATGGGGATCATGACCTTGTACTCCCACTCGAGGCGGATGGCCATGGTGAGCGT[C/T]TGCGACTGCAGCTTGTACGGATGCTTCGCTACTCGCTAGTGGCTTGAGGGTGCGGTAGCCGAGCATAACTGATGTGACCATGGCTACCACGGATGCAACCATTGCTCACATCATGGATGAACAAGAAGATATCAAGATCAAGTACTCCAAGTGCTAGAATCCGATTCGGCCACCTACTACACTGCTGACTTCAAACGGCC
OS900133_K01 3 30372501 GCTCCACCTTGAAAGCAATG GAAGGTGACCAAGTTCATGCTTTTCTAGCGTGGTGGAAGAGATA GAAGGTCGGAGTCAACGGATTTTCTAGCGTGGTGGAAGAGATT A T TT AA AT AT ACTTGTTGTCCATTTCCATCGTATGTTGTCTTCAATGTCTTGGGTTAGTGTGATGCCTGAGGTCCAGATTATCTCGAAGACCTTGAAGAAATCGGTGACGAGGACAGTTGTCAAGTTGTATCGGATGTCATCGATCCACTTGTTATCTTGTAGGGCTTCTGCGACCGTCCTTTTCTTTTTTCTAGCGTGGTGGAAGAGAT[T/A]GGGTGCCATTGCTTTCAAGGTGGAGCTGCAAGCCCATGGGGATTCCCAGAAGAGCGCCTTCCTACCATCTCCGATTGTCACTGACGTGGATGCTGCAAAGAGCTCGTTGTCCTGTTCATCACAGGGTGTTGGCATGCCGATCCATGGCTTGTCGGGGGAGGTCCATTCATACCATAGCCATCGCAGGCGAAGCGCCCTTC
OS900134_K01 3 30668336 GCCTTGGTAGCTCGGAAAA GAAGGTGACCAAGTTCATGCTAGATTCGATGTAAAGTTGAGGGAC GAAGGTCGGAGTCAACGGATTAGATTCGATGTAAAGTTGAGGGAT G A GG AA GA AA GGGACTACCCTTAGCCCGCTGTACCTGCTCTTTCCTTGCCCTGCCCTGCGCGGCCTTCTTTTCCTCCCAGCCCCAAGCTCTTCTACGCGGTCCGTTTACTTGCTTGGGATCCTCCCAGGCTCCCAGGCCATGTCTCATCTGTCCGACTGTCCGCGCCCTAATCGCCTTGGTAGCTCGGAAAAAAAATAAGTTCAGATACC[A/G]TCCCTCAACTTTACATCGAATCTGTATGATATCCCCAATATCAGATAGGGTTAATTGGATCCATGCTATTATAACTTTACCACTTTTCCCAAAAAAAAAAAACTTTACCACTTTTGATAAATGCTACTACTATTTGTTGAATTGCAAACATGCCATTATAAATCAGCTAATTTTGGAACCATGCCACTCTCTACATCCTG
OS900135_K01 3 31027370 ACTAGCCCCACACAGACCAC GAAGGTGACCAAGTTCATGCTGGATTTTATGGGCTTTTCCA GAAGGTCGGAGTCAACGGATTGGATTTTATGGGCTTTTCCG T C TT CC CT CT TACGGGGGAGATGCAGCCTGAGTCCGTCCTGATTCTAGGAGACGGTATCCCGTCCTTCCCGTTTCACGTGCACCAGCTGCGAGGGGGAACGCCCGCTGCGCGCGGGCAAAATCGCTCGCTTGCGGCCTTCTGGTCCATCATTCGTACTAGCCCCACACAGACCACAGCGGCGGCACGCTGCACGCACGCAAAATTTCCAC[T/C]GGAAAAGCCCATAAAATCCAGGAAAACGTGGTGGTTTTGCCAACCTCCCGCCCCTCGTCCAAAAAAAAGGCCCGGAAATAAAAGCGGATTGGAATCTGGTGGCTCCGGGTCCGTGCGGTGCGGGTGCGGCTCGCTCGACTTGGCGTCGTTGGAGTCCACCTGACCTCCTGTCCTCCACCGCCCGCTTCCCCTCGCCTCGG
OS900136_K01 3 31391306 GGAACGATGTGACGGAAAAA GAAGGTGACCAAGTTCATGCTGGACTTCGTCAAACTTCCAAC GAAGGTCGGAGTCAACGGATTGGACTTCGTCAAACTTCCAAA G T GG TT GT TT AGCCAAAAGGTTTATATTTAAAAATACTTTAGAAAAAGACTATTAATAAAATTAAAAATAAAGAGTCTAAAAAATAAAAATATTTTTAAGTTTGGATGTGTTTGCTTCATGCTAAAATTGGAAGTTTGGTTGAAATTGGAACGATGTGACGGAAAAATTGGAAGTTTATGCATGTAGAAAAGTTTCGATGCGATAGAAAC[T/G]TTGGAAGTTTGACGAAGTCCGTGTGCGTCACCGACATATGGGTCCCTTCTAGCGGTGCAGAAAGTGATAAGGTTCAACCAAAGTCGCAAGTCCGCAACGCGACTGTGCACACGAGGCCACTCCACTCCTCTCCTTTGCGCTCGCTCTGCTCTGCCATGGCGGAGGCGCTCGTCGCCGTCCTCCGGCTCGCGGCGTCCGCC
OS900137_K01 3 31783291 CCATGGACTATATGGGGTGTG GAAGGTGACCAAGTTCATGCTGTTTCACAAAGCAACACAGCAT GAAGGTCGGAGTCAACGGATTTTTCACAAAGCAACACAGCAC T C CC TT TC TC TGCAAGCTACTGCACTAGGAAGTATGTAATCTGGTGAATGCAAAGAGTACAAAGATTGTTTAAGCATGCACACTCATTACCTGAAGATTAGGAAAGGCAATGGATGAACAAAAGGCTCGGGAAAAGGTTGCTTGGAGCAGGACCGCATGAAATTGACTCTTTCTGTTACTTCCATAAAGGTTTCACAAAGCAACACAGCA[C/T]TAGTTGCTCACACCCCATATAGTCCATGGCTCCATGCCTTGTCTCGCCAAGATTGCCAGCTTCTGCACTGTTATCTATAACAAAAAACAGCTTCCATATTAATGTGTCGCTGCTGATTTTTCTTTTTAACATAACATAAGGATAGAAGATGTGGATGTAGAGCGAACAAGAAGCAAAAGGGACAGACCGAACAACACGTT
OS900138_K01 3 32205877 AGGAAAGATCTGGCCTTGTG GAAGGTGACCAAGTTCATGCTCGAGTGATCGGCTGTCTTT GAAGGTCGGAGTCAACGGATTCGAGTGATCGGCTGTCTTC T C TT CC TC CC CCTCGGGATTGAAGTTGATCAGGGAGAAAATGGAACCACGCTCAAGCAAACTGCCTATGCCAGAAAAGTGCTTTCTCAGTTCGGGATGCTGGAGTGTAATTCAACCTCAATTCCGATTGATCCAAGGATGCAGCTGAACAAAGATGCAGATGGTCACCCGGTGGGATGTAACTGAGTATCGGCGAGTGATCGGCTGTCTT[C/T]GATATCTGTTACACACAAGGCCAGATCTTTCCTTTGCTGTTGGAGTGGCAAGCAGATTTATGGAGCGGCCAACTCTTATGCACTTCAAAGCAGTGACACAAATTCTCAGATATCTGAAAGGTACAATTGATTGCGGCCTTGTGTATGCAGCTTGAAATGGTGATATGCAGATTACTGGGTATACAGACAGCGACCCGCTG
OS900139_K01 3 32341783 GCATTGGGTTTGTTGCTAGA GAAGGTGACCAAGTTCATGCTCCAAAAAAAGCTAATAACTCTCTCATATTT GAAGGTCGGAGTCAACGGATTCCAAAAAAAGCTAATAACTCTCTCATATTA T A TT AA TT AT GGTGATGAGGTGGAGGAGAGAAGTGAGGACAGAGATGATGAACCACCCCCCACACAAACTTCAAGAAGGATGTGAGAGTACTAAAGTCATTGATATTTGTGTATTAGAGGTGACCTATTGTATACTCTCTCCATTCCAAATTGATCTACATATTTCATAGGTACACCAAGACCAAAAAAAGCTAATAACTCTCTCATATT[T/A]TATTTACTCTAGCAACAAACCCAATGCATGCACCATCCCCACTATTTCCTAGCCAATAGCAAATTAAGATATTGCATGTGGGTTATAAATACTTGTGTGCATGGATGCATGCATCAATGTCCATTTACTCCAATGGACAAATAACGAATAGACTTAATAAATAAACACAAATATGTAGATCATTTAGGAATAACCTCAAA
OS900140_K01 3 32789243 GAGACAGCGTGAGATTGTGC GAAGGTGACCAAGTTCATGCTTCCCTTCTTTTTTTTTTTCGTTACT GAAGGTCGGAGTCAACGGATTCCCTTCTTTTTTTTTTTCGTTACC T C TT CC TC CC ATCCTTCTCGTCGTCTGGGAGATACAGAAGAAGTGGAACCAACGAATTTTTGAGCACAACGAGAGCATGACAATCACCCTCCTAGCAAAAATTAAGGAAGAAGCCAAAATTTAACCCTAGGAGGAGCTAAACCACAGTTAATTCCTAAGAGCGTATAATCTGTAAAGACGGGCTTTTCCCTTCTTTTTTTTTTTCGTTAC[C/T]AGGGGTGTATTTTTTTCCTCTCTATCTAACGAAAGATAAAGCACAATCTCACGCTGTCTCCTTTTAAAAAACACTTTCTTTACGCTGTTCATTGGCTGTAGCGGGTAGAATTCGCAAGGAATATGAATTAAATTTGGTTATAAATGAACGTACTTTTGTAATCACAACAAAGGGTCCATAGCTCAGTGGTAGAGCAATTG
OS900141_K01 3 33203208 CGCATAACCCTGATGGAGTC GAAGGTGACCAAGTTCATGCTCTCGCTGTGAAGGAGACGA GAAGGTCGGAGTCAACGGATTTCGCTGTGAAGGAGACGG T C CC TT TC TC TACCTTGCTTTCCTCGATCGGAGCGCCCAGAGTGACCAGCGTGGTGACCAGGTTGTTGAGGCGTAGCGAGAAGTCCTCGACGGACTCCCCCTCCTTGAACTCGATGGCGTCGTACTGCCGTAGAAACAGTTGCGCCTTGGACTTGCGCACTCGATCAACGCCGACTCGCATAACCCTGATGGAGTCCCACGCCTCCTTTG[C/T]CGTCTCCTTCACAGCGAGCGTCAACAGCATCTCCTGCGGCACTGCACGGAGGATGGCCTCCAGCGCCATTCTGTCTTCCTGAAAGTCTGCGTCGCCGTGCTAGACGGCTTCCCACAGACCACGGGCTTGGAGCATAACTTTCATCATCAGGGACCAGTCACCATAGTTTGTCTTCGTGAGGGTAGGATAGTTTGCTGAGC
OS900171_K01 3 14489983 GGTGACCTCGATACAAACTCGGTGA GAAGGTGACCAAGTTCATGCTCTTCCGTATGATTTTTCGTCTGTCA GAAGGTCGGAGTCAACGGATTCTTCCGTATGATTTTTCGTCTGTCG T C CT T/C CT CC ACGACGGTTGGTGGCGGCCCGGAGGAGATCGGTAGTGGCCACTAATTGGGAAGGGGAGGGAGCACGGGAAGAAAGGTGGGAGGTGGAAGAGATTAGGAGAGGGAGTGCGTGCATGAATCAGGGGATGTGATCAAGGGACCGTGATTAGGGGATCCAGATCGCTCTCTCTTAAAAGGGTGACCTCGATACAAACTCGGTGA[T/C]GACAGACGAAAAATCATACGGAAGCCTTACGTATGTTTTAAGTAGGTATAGATGTCATGTATCCTATAGATACAGATCTACTACTACGATATGTATTTAATATTTTAATATGTGACCAAATGTTATATTTTTGGGACATGTTTTGATATATCCAACTGATATGCAACTGATCTATGCAATCATTTAAAGTATGATATAAT
OS900172_K01 4 35335719 ACGGGCTGCTGGATTTACATAAGGT GAAGGTGACCAAGTTCATGCTTGCTTCAAACATATATTCATAGAGTCG GAAGGTCGGAGTCAACGGATTGCTTCAAACATATATTCATAGAGTCA G A GG AA AA GG TTTTGTAACCCTGGAAACCGCGAGACGAATTTATTAAGCCTAATTAATATGTCATTAGCACATGTAGGTTACTATAGCACTTATGGCTAATCATGGACTAATTAGGCTCAAAAGATTCGTCTCGCGATTTCCATACGAACTGTGCAATTAGTTTTTTATTTTATCATTATTTAATGCTTCAAACATATATTCATAGAGTC[G/A]ATGTGACGTTTTTCGGAAAAAAAATTAGGAACTACACAAGACCTTATGTAAATCCAGCAGCCCGTACTATTCGGGGATGACAGAAGGATGTCGATCTACACGGTTTATTAACAAGCTTTGGAGTTAAATTTCACCATTTAGCATTTTACCTTGAGCATTGGGAAAAGTAAGAAAACCCTTCGTGCAATGGAGAAATTCAT
OS900173_K01 6 29173606 AGCACAAAGGGAGTTGACATCATCA GAAGGTGACCAAGTTCATGCTGTCCTGTATCAAGTTTATTTTTAACA GAAGGTCGGAGTCAACGGATTGTCCTGTATCAAGTTTATTTTTAACG T C CC TT TT CC TAGATAGTGCATCTACACCTTTCGAATGAGGAGGAACAGCCTCTGGTCCAGCTCAAAGCTAGCGGCACTGGAGGGGTCACCCTTGAGCATCATCAGAAGGCCACCAAACGATGCATAGATCTCCCTAGAATGGAAAAGAATGCAATTCATTAAAATTCATAGCACAAAGGGAGTTGACATCATCACATGATACAGGATTA[C/T]GTTAAAAATAAACTTGATACAGGACTAACAGTAGTCTAGTACAAGCTGTGTAGCTGTAGGCCAGATTTACATATTGGCAAGGCGAAAAATTGTTCTTTGAAGGTACTTATCTTCGTATAACATGATTCACATAACAATGATACAATTAATTAAGTAAATGCACTTGAATTGAATTAACCAAGTAGCTGAAACAGTACAGA
OS900174_K01 7 23668282 AACATCTTCAGCCCTTGCAACCCTA GAAGGTGACCAAGTTCATGCTGTTCATGTTGTTGCTGGTGGGTCTA GAAGGTCGGAGTCAACGGATTGTTCATGTTGTTGCTGGTGGGTCTG T C CC TT TT CC TATTTCTTGTTCATTACATGATCAAATCAACTGGCACGCTCATACATTCGAAGGCGAGCTTTGGACCTGCACTAGAGTTAAACAGATCTCCCAGGCCTCGTGTTTTCTGTCAACAACAACACCAGCCCCAATGCCTACACCATCTTGACCAGCACCAATTGGAACATCTTCAGCCCTTGCAACCCTAGCATTCTCAGCCT[C/T]AGACCCACCAGCAACAACATGAACTTGGGCTAGATATGGGATCTCATTCTGTGGACGGAACTGAAGAAATAAAAAGATGAAACATAGTCTTAGTAAGTGGTGAAACACAAAATGTATATATACTAAAACATTCATAGTTGTGAAACATACCGGGCGAGACCCATATGTGACATAGCCAAGGTTCATCCTACAACGGTCTA
OS900175_K01 9 6324514 GCATCTCTTGACCCTATAAAATTGA GAAGGTGACCAAGTTCATGCTATGCAAGCAATGTGATTGGGAGA GAAGGTCGGAGTCAACGGATTGCAAGCAATGTGATTGGGAGG T C CC TT TT CC TAGAAACAGAAAGTTGGGGGACTCAACATACCGAGTACATCGACATAAAAACATAATCTCAATACTCCCTCCATCCCAAAATATAAGGCACAACCATTTTTCTCTCATGTCACATAATATAAGGCGTGTATGCATGTATATATTAACTAGCATCTCTTGACCCTATAAAATTGATTTGTTTTAAATCTTATACCATTAAA[C/T]CTCCCAATCACATTGCTTGCATGCATCCAAGTGATCCAACCATGAAGATGATAAAATATTTTCTTGGTCTTTGTGTTTTGAGTGTTATACCTTATATTTTAGGATGGAGGGAGTATTAAACTATACTAAAATACTATTAGGAGACCTTTAGCACCTCCTATCTTATCAACTATGACGAAAAATTTGAAGGGGGGACTCAG
OS900176_K01 9 10024501 TCGGATGTTACGTGTGTATGCAACC GAAGGTGACCAAGTTCATGCTTGGACCTCATATTCATGTTGTTTGGT GAAGGTCGGAGTCAACGGATTGGACCTCATATTCATGTTGTTTGGC T C CC TT TT CC TCTGATAGGCCACTTTCCGGATAATCCGAAATTATCAACATATGTGATATCTCTATCTATTGCATATAACATAAATTGGTTCCTTCAATGATCTAATTCATCAATTAACCTAGATTTCTTAGTCTGAGGCTTTCACCGTTTCTTGTCAGACTTGCCTAGCTGTATTTTTATATTATGGACCTCATATTCATGTTGTTTGG[C/T]ACTTAAGCATATAATTATTACGATGGATCGTTTATTGATTATTATATTATTGTTCATTGCATTACTAACTTGATATTATATTGGTTGCATACACACGTAACATCCGATAAATTTATTCCATTCCCGAACTGATTCCGCACCATTTCCGACATCCAAAATAATCCGTTCCGCATCCGCGTCCGTACACTATCCGCACCCGC
OS900177_K01 9 15799081 ACTAGCTTTCGTGCAAGGATCAACG GAAGGTGACCAAGTTCATGCTCCAAGGTACGTTATCTCCTTTAGTTG GAAGGTCGGAGTCAACGGATTCCAAGGTACGTTATCTCCTTTAGTTT G T GG TT TT GG CAGATTGTCTTGAATGATCCTGTTGAGAAGTATATGATTCCATTTCAAGAAACCCAGCCATTGCATGCTGACTTAATCTTGGAGGAGGTTGTCATGCGATTCTTCAAGGATCCTGTAGTTCCTATTGTTGATGACTGGGGAAGCTGCGTGGGTATTGTTCACCGACAGGATTGTACCAAGGTACGTTATCTCCTTTAGTT[G/T]GTACCAGCAATAATAGCGTTGATCCTTGCACGAAAGCTAGTGGAATGGTTAGCACTTGTTTTAGCGGCAGGGACCAGTCACCAGTGTTAGGATAAAAAAAATCAACCACCTTAGCTTCTCTTCCAAACAGTTCAAGTTTGGTCAAGGATTATATTACAAGGAGGAAACCAATAACAAATTTTGGTCGTTTTTCATTTTCA
OS900178_K01 10 8923315 CAGACATGGGGATGGATGCATATAGA GAAGGTGACCAAGTTCATGCTTGCAAAATAATGAAGAGATACAAGTGGAAA GAAGGTCGGAGTCAACGGATTTGCAAAATAATGAAGAGATACAAGTGGAAG T C TT CC CC TT TAACACAGAAAGTGAAAGTATATCTATCTATTTTTTTTGATCGAGTTCAAATTTTGAGATTACTGTGCTTGTCATATCAATATTTCAGGAAGATATTCAGCTTATGGCAGACATGGGGATGGATGCATATAGATTCTCAATTTCATGGTCTAGGATTTTCCCAAGTATGTAATATAATAATTCATTGGTTAATATGGGTA[T/C]TTCCACTTGTATCTCTTCATTATTTTGCATCTTTATGTTAACTTAATGGTCACACATAACCTTTGAAGTTTTTCTTCATTATGAAATGTTTTATCTGTGGATAAACAGACCTGCACTACTAACAATAATCATATCTGCACTCTTATTCAGATGGCACTGGTGAGGTCAACCAGGCAGGCATTGATCACTACAACAAGCTA
OS900179_K01 10 12020045 TTCAAGTTTTAGTTTGGACACTCTG GAAGGTGACCAAGTTCATGCTCAGCTGGTGAGTTCAAAGTGAAAAGATA GAAGGTCGGAGTCAACGGATTGCTGGTGAGTTCAAAGTGAAAAGATG T C CC TT TT CC GTCACGCATGAAGTACTATTCACATTTTATCATCTAATAACAATAAAAAATACTAATTATAAACAAATTAAATAAGACGGTGAAACGTTGGACATTGAAACCCACAACTACACTTAAAATGATACGGGGAAATAAATTGAGTAAATTGCAATTTGGACCATCTTTTATTATTCAAGTTTTAGTTTGGACACTCTGTATTT[C/T]ATCTTTTCACTTTGAACTCACCAGCTGATCAGAGTTGCGCTTAGCCATCGTTGTAGTTTTTTTTTCTCCTTTTCCTTGCTGCAGCTTTTGTTTTGCTTTTTCTCTCTTCCCCTGGTTTGGTTTGGACCGGTCTGCGGGTGAAGTAAAAAGATGACCGGTCTAATTAAACCAGGGAAAGGGAGAAAAAGAGTTTTTGTTAC
OS900180_K01 10 22817323 ATATGAATGTTGTGCCGGTGGTGAC GAAGGTGACCAAGTTCATGCTGATGACTCCCTATGTTAACCGATCCT GAAGGTCGGAGTCAACGGATTATGACTCCCTATGTTAACCGATCCC T C CC TT TT CC TTTCCATTCTCGCGAACCTTCCACACACCGAGAGCTTAGAATCTCACCCAGGGCCCCCGGCCGAACCGGCAAAGGGGGGCCTGCGCGGTCTCCCGGTGAGGAGCCTCACGCTCCGTCAGGTACACTAGCCGGTTTTGACAAGTCTTAGCTTAGATCACCGCAATAATCTTTAAGGGATGACTCCCTATGTTAACCGATCC[C/T]GCCTCAGATCCGCGCTCGTCACCACCGGCACAACATTCATATCCGGCCGATATGGCGATTTAATATATGCTACTATCTTCCTTCCAAAATATAAGGAATATAAGGAGTTATATTTTGAGATGGAGAAAGTACTAGTGATGATGAGGAAGATACACTAGTGCTTGAAGGCTTAGTTGTTTTGTTCTTTTTCCCAACTCACC
OS900181_K01 11 11901489 CATTAGGGGTAATTCCATTGTAGGG GAAGGTGACCAAGTTCATGCTGACTACCTATTATTGTTTTCAGTCAATTCT GAAGGTCGGAGTCAACGGATTCCTATTATTGTTTTCAGTCAATTCC T C CC TT TT CC CTCTCTGGGTCCATCCATAAGCATGCATACTGGCGCTCTCTTATTGGCTATACACACACACACACACACATATATATACATATATATATATATATATGTGTGTGTGTGTGTGTGTATAGTACTTTTAGATTTGATTAAATTACTTCCTATACATTCATAATGCTACGAGGTGACTACCTATTATTGTTTTCAGTCAATTC[C/T]GTAATTTGTGCTGATTAATTTAGTTTCTAGATAGAGTTATGTTTTTATCCCTACAATGGAATTACCCCTAATGTTATGACAAAGTTACTTTCGTTTTGTCTGAAGTTACTTCTATAATATATGTAAATTACATTTAAACTTTATTAAATTTACTTTTGTATGTCTAAGAAGTAATTTAGTGATATCCAAAAGTAATTTAG
OS900196_K01 1 38383221 TAGTAGTTGCACCGCATGATTGAGC GAAGGTGACCAAGTTCATGCTGGCGTGGAGCGAGGCTACTAT GAAGGTCGGAGTCAACGGATTGGCGTGGAGCGAGGCTACTAC T C C T GATGAAGGAGCTGTCGCTGACGATCATGGAACTCCTGGAGCTGAGCCTGGGCGTGGAGCGAGGCTACTA[C/T]AGGGAGTTCTTCGCGGACAGCAGCTCAATCATGCGGTGCAACTACTACCCGCCATGCCCGGAGCCGGAGCGGACGCTCGGCAC

Table S2

Primer information for Candidate gene"

基因名称Gene name 起始Start(bp) 终止End(bp) 正向引物Forward primer(5'-3') 反向引物Reverse primer (5'-3')
β-Actin AGTGTCTGGATTGGAGGAT TCTTGGCTTAGCATTCTTG
GAPDH AAGCCAGCATCCTATGATCAGATT CGTAACCCAGAATACCCTTGAGTTT
UBC1 CCGTTTGTAGAGCCATAATTGCA AGGTTGCCTGAGTCACAGTTAAGTG
LOC_Os03g49400 28116620 28124217 TCTTTCCCGTACCCTTGGAC TGCCGATACACATCGACAGA
LOC_Os03g49500 28169807 28173984 AGCCCTCAGGATCTACCTCA AGATGTGCCCTCCCATCAAA
LOC_Os03g49620 28254419 28259880 CCAACGTCCTGCTTGATGAG GCGCAATGTGACCCATAGTT
LOC_Os03g53150 30480660 30483331 GGTGAATGGCTCTGATGCTG CCTCAAGCGTTTGCATGACT
LOC_Os03g56050 31921933 31925513 TTCCACGCACATCAACTTCC CCTGCCTGCTCATGTTCTTC
LOC_Os03g57640 32851425 32852782 CAAACTGAGCTGCCTGAGTC TAGTCCTCGAAGCGGATCAC
LOC_Os03g52450 30094292 30099092 AAAGGCCAGTTTGCTGGAAG CCACAGGCATTACAGAGGGA
LOC_Os03g56060 31930541 31934624 CGTCGAGTGCCAATGTGAAT GAGCTTCCGGAGAAGGAAGA
LOC_Os03g53880 30890100 30899911 TACAGACTTTGGCCTCAGCA GTTCCAGCTCCCTGAGAAGT
LOC_Os03g55290 31465625 31464840 CCTCCTCTTCCCTCCAAGTT TACTTGAGGCAGTCGTCGTG
LOC_Os03g58260 33193735 33198078 CAGGTGCACGCTCAAATGTA CCGATGATCACACCATCTGC
LOC_Os03g58290 33207531 33210400 AAAGAAGCTGGTGTGCAAGG TCATCCTCTCTCCCGGTGTA
LOC_Os03g58300 33217418 33214533 GGCATGCTCTTTCAGGAGTG CCTTCATCCTGTCTGGTGGT
LOC_Os03g58320 33226460 33228543 GCTGGTGCTGCTTACTACAC AAAGCCAACACACACAGCTT

Fig. 1

Comparation of mesocotyl length between ‘IR 145’ and ‘Changai’ The mesocotyl section is marked by red mark. The left is ‘IR 145’ with a mesocotyl length of about 0.18 cm. The right is ‘Changai’ with a mesocotyl length of about 4.75 cm."

Fig. 2

Distribution frequency of mesocotyl length in F2 population derived from ‘IR 145’ × ‘Changai The X-axis represents the mesocotyl length of the F2 population, which is divided into five levels: 0.18-1.21, 1.21-2.23, 2.23-3.26, 3.26-4.29, and 4.29-5.32 cm. The Y-axis denotes the number of individuals at each level."

Table S3

Basic statistical for NGS"

样品编号 Changai L-Pool S-Pool IR 145
Clean reads 160733360 189587718 223654650 145947156
Clean bases(bp) 24110004000 28438157700 33548197500 21892073400
Mapped reads 157946429 186412438 220135923 142034376
Mapped bases(bp) 23691964350 27762740240 32098485368 21305156400
Mapping rate 98.27% 98.33% 98.43% 97.32%
Duplicate reads 26216469 35168893 38980737 18236886
Duplicate rate 16.60% 18.87% 17.71% 12.84%
Mismatch bases(bp) 309119777 369422281 396469736 310450630
Mismatch rate 1.30% 1.33% 1.24% 1.46%
Average sequencing depth 51.32 57.83 66.53 47.49
Coverage 91.95% 95.90% 98.82% 92.53%
Coverage at least 4X 88.98% 93.47% 95.62% 89.25%
Coverage at least 10X 85.93% 90.72% 91.91% 86.24%
Coverage at least 20X 82.13% 86.27% 87.90% 82.48%
Coverage at least 50X 36.81% 46.49% 61.40% 15.04%

Fig. 3

Genomic distribution of Δ(SNP-index) and G-value between two extreme pools for mesocotyl length"

Fig. 4

Location of KASP markers in the genetic map The genetic map constructed by KASP markers is on the left, whereas the corresponding LOD curve (LOD > 2.5) is on the right."

Fig. 5

Relative expression levels of candidate genes between IR 145 × Changai Figure A-N shows the relative expression levels of 14 candidate genes in the mesocotyl tissues of ‘IR 145’ and ‘Changai’, respectively. The internal reference gene is GAPDH. The relative expression levels of LOC_Os03g56050, LOC_Os03g57640, LOC_Os03g52450, LOC_Os03g56060, LOC_Os03g58290, LOC_Os03g58300, and LOC_Os03g58320 were significantly different between the short-mesocotyl variety ‘IR 145’ and long-mesocotyl variety ‘Changai’ at P < 0.05."

Fig. S1

Relative expression levels of 14 candidate genes with housekeeper β-Actin, GAPDH, and UBC1 as reference in the mesocotyl tissues of ‘IR 145’and‘Changai’ The X-axis represents different housekeeping genes, namely -actin, GAPDH and UBC1.The Y-axis represents the relative expression of each gene in the mesocotyl tissues of ‘IR 145’ and ‘Changai’."

Table 1

Candidate genes for mesocotyl elongation in rice"

候选基因
Candidate gene
基因名称
Gene name
注释信息
Annotation
LOC_Os03g56050 OsAP23 AP2-like ethylene-responsive transcription factor Aintegumenta
LOC_Os03g57640 OsGID1L2 Gibberellin receptor GID1L2
LOC_Os03g52450 OsGATA19a GATA transcription factor 25
LOC_Os03g56060 OsCSLC9 CSLC9 - cellulose synthase-like family C
LOC_Os03g58300 OsIGL1 indole-3-glycerol phosphate lyase, chloroplast precursor
LOC_Os03g58320 OsIGL2 indole-3-glycerol phosphate lyase, chloroplast precursor
LOC_Os03g58290 OsIGL3 indole-3-glycerol phosphate lyase, chloroplast precursor

Table S4

QTLs or genes reported to be related to rice mesocotyl elongation in rice chromosome 3"

位点/基因 标记区间 位置(bp) LOD值 解释变异 群体 参考文献
QTL/Gene Marker interval Position LOD value R2(%) Population Reference
- RZ403-RZ448 - 4.73 17.5 - Redona et al., 1996
- RZ403-RZ630 - 3.33 10.3 - Redona et al., 1996
qml3 RZ403-RG179 - 3.67 11.32 DH Cao et al., 2002
- G232-R1927 - 3.11 -0.59 RILs Cai et al., 2002
- R1927-BCD450 - 5.51 0.67 RILs Cai et al., 2002
- BCD450-RZ393 - 3.04 -0.56 RILs Cai et al., 2002
qml3-1 RZ517-RZ399 - 4.67 7.1 RILs OUYANG et al., 2005
qml3-2 RZ328-RZ575 - 3.45 6 RILs OUYANG et al., 2005
qml3-3 RZ696-RZ22 - 4.43 8.1 RILs OUYANG et al., 2005
qLOE-3 RM3919-RM520 - 2.548 10.7 DH Zhang et al., 2006
- RM426-RM448 - 8.93 24.97 RILs Huang et al., 2010
- RM426-RM514 - 15.52 33.36 RILs Huang et al., 2010
- R3226/R1927/R1925 - 4.2 11.5 BILs Lee et al., 2012b
- C595/R1927/R1925 - 7.5 20.8 BILs Lee et al., 2012b
- RM8208-RM8277 - 2.8 6.5 - Lee et al., 2012a
- R1618 - 12.09 37.56 BILs Lee et al., 2017
- R1618 - 7.18 26.97 BILs Lee et al., 2017
LOC_Os03g51340 - 29376077-29378021 - - - Zhao et al., 2018
LOC_Os03g53320 - 30603235-30602885 - - - Zhao et al., 2018
LOC_Os03g53340 - 30607159-30604067 - - - Zhao et al., 2018
LOC_Os03g06070 - 3039736-3045376 - - - Wu et al., 2015
LOC_Os03g06139 - 3085989-3075919 - - - Wu et al., 2015
LOC_Os03g39790 - 22138216-22135801 - - - Wu et al., 2015
LOC_Os03g40040 - 22244649-22243187 - - - Wu et al., 2015
LOC_Os03g40084 - 22268809-22270021 - - - Wu et al., 2015
LOC_Os03g40110 - 22292562-22285683 - - - Wu et al., 2015
LOC_Os03g40194 - 22351524-22347660 - - - Wu et al., 2015
LOC_Os03g40390 - 22440834-2248628 - - - Wu et al., 2015

Table S5

Cloned genes regulating mesocotyl elongation"

染色体 基因名称 基因登录号 位置(bp) 参考文献
Chromosome Gene name Gene accession Position Reference
1 OsGY1 LOC_Os01g67430 39177169-39178676 Xiong et al., 2017
5 OsGSK2 LOC_Os05g11730 6661493-6657481 Sun et al., 2018
8 OsSMAX1 LOC_Os08g15230 9228110-9224161 Zheng et al., 2020
[1] Zhao G, Fu J, Wang G, Ma P, Wu L, Wang J. Gibberellin-induced mesocotyl elongation in deep-sowing tolerant maize inbred line 3681-3684. Plant Breed, 2010, 129:87-91.
doi: 10.1111/pbr.2010.129.issue-1
[2] Liu H, Hussain S, Zheng M, Peng S, Huang J, Cui K, Nie L. Dry direct-seeded rice as an alternative to transplanted-flooded rice in central China. Agron Sustain Dev, 2015, 35:285-294.
doi: 10.1007/s13593-014-0239-0
[3] Chen Z, Tang Y T, Zhou C, Xie S T, Xiao S, Baker A J M, Qiu R L. Mechanisms of Fe biofortification and mitigation of Cd accumulation in rice (Oryza sativa L.) grown hydroponically with Fe chelate fertilization. Chemosphere, 2017, 175:275-285.
doi: S0045-6535(17)30231-X pmid: 28232138
[4] Matloob A, Khaliq A, Chauhan B S. Weeds of direct-seeded rice in Asia: problems and opportunities. Adv Agron, 2015, 130:291-336.
[5] Turner F T, Chen C C, Bollich C N. Coleoptile and mesocotyl lengths in semidwarf rice seedlings. Crop Sci, 1982, 22:43-46.
doi: 10.2135/cropsci1982.0011183X002200010010x
[6] Chung N J. Elongation habit of mesocotyls and coleoptiles in weedy rice with high emergence ability in direct-seeding on dry paddy fields. Crop Pasture Sci, 2010, 61:911-917.
doi: 10.1071/CP10099
[7] Zhang H, Ma P, Zhao Z, Zhao G, Tian B, Wang J, Wang G. Mapping QTL controlling maize deep-seeding tolerance-related traits and confirmation of a major QTL for mesocotyl length. Theor Appl Genet, 2012, 124:223-232.
doi: 10.1007/s00122-011-1700-y
[8] Xiong Q, Ma B, Lu X, Huang Y H, He S J, Yang C, Yin C C, Zhao H, Zhou Y, Zhang W K, Wang W S, Li Z K, Chen S Y, Zhang J S. Ethylene-inhibited jasmonic acid biosynthesis promotes mesocotyl/coleoptile elongation of etiolated rice seedlings. Plant Cell, 2017, 29:1053-1072.
doi: 10.1105/tpc.16.00981
[9] 曹立勇, 朱军, 颜启传, 何立斌, 魏兴华, 程式华. 水稻籼粳交DH群体幼苗中胚轴长度的QTLs定位和上位性分析. 中国水稻科学, 2002, 16(3):24-27.
Cao L Y, Zhu J, Yan Q C, He L B, Wei X H, Cheng S H. Mapping QTLs with Epistasis for mesocotyl length in a DH population from indica-japonica cross of rice(Oryza sativa). Chin J Rice Sci, 2002, 16(3):24-27 (in Chinese with English abstract).
[10] Liu H, Zhan J, Li J, Lu X, Liu J, Wang Y, Zhao Q, Ye G. Genome-wide association study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions. Genes, 2019, 11:49-64.
doi: 10.3390/genes11010049
[11] Zhan J, Lu X, Liu H, Zhao Q, Ye G. Mesocotyl elongation, an essential trait for dry-seeded rice (Oryza sativa L.): a review of physiological and genetic basis. Planta, 2020, 251:1-14.
doi: 10.1007/s00425-019-03297-x
[12] Zhao Y, Zhao W, Jiang C, Wang X, Xiong H, Todorovska E G, Yin Z, Chen Y, Wang X, Xie J, Pan Y, Rashid M A R, Zhang H, Li J, Li Z. Genetic architecture and candidate genes for deep-sowing tolerance in rice revealed by non-syn GWAS. Front Plant Sci, 2018, 9:332-345.
doi: 10.3389/fpls.2018.00332 pmid: 29616055
[13] Sun S, Wang T, Wang L, Li X, Jia Y, Liu C, Huang X, Xie W, Wang X. Natural selection of a GSK3 determines rice mesocotyl domestication by coordinating strigolactone and brassinosteroid signaling. Nat Commun, 2018, 9:2523-2535.
doi: 10.1038/s41467-018-04952-9
[14] Zheng J, Hong K, Zeng L, Wang L, Kang S, Qu M, Dai J, Zou L, Zhu L, Tang Z, Meng X, Wang B, Hu J, Zeng D, Zhao Y, Cui P, Wang Q, Qian Q, Wang Y, Li J, Xiong G. Karrikin signaling acts parallel to and additively with Strigolactone signaling to regulate rice mesocotyl elongation in darkness. Plant Cell, 2020, 32:2780-2805.
doi: 10.1105/tpc.20.00123
[15] Lee H S, Sasaki K, Kang J, Sato T, Song W, Ahn S. Mesocotyl elongation is essential for seedling emergence under deep- seeding condition in rice. Rice, 2017, 10:32-42.
doi: 10.1186/s12284-017-0173-2
[16] Das S, Upadhyaya H D, Baiai D, Kujur A, Badoni S, Narnoliya L, Kumar V, Tripathi S, Gowda C L, Sharma S, Sube S, Tyagi A K, Parida S. Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea. DNA Res, 2015, 22:193-203.
doi: 10.1093/dnares/dsv004
[17] Lee H S, Sasaki K, Higashitani A, Ahn S N, Sato T. Mapping and characterization of quantitative trait loci for mesocotyl elongation in rice (Oryza sativa L.). Rice, 2012, 5:13-22.
doi: 10.1186/1939-8433-5-13
[18] Zou C, Wang P, Xu Y. Bulked sample analysis in genetics, genomics and crop improvement. Plant Biotechnol J, 2016, 14:1941-1955.
doi: 10.1111/pbi.2016.14.issue-10
[19] Sun J, Yang L, Wang J, Liu H, Zheng H, Xie D, Zhang M, Feng M, Jia Y, Zhao H, Zou D. Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy. Rice, 2018, 11:1-12.
doi: 10.1186/s12284-017-0196-8
[20] Farooqi M Q U, Ma S, Lee J K. Bulk segregant analysis for the improvement of drought resistance in maize (Zea mays L.) inbred lines as revealed by SSR molecular markers. Res J Biotechnol, 2018, 13:34-51.
[21] Xu X, Li Q, Ma Z, Fan J, Zhou Y. Molecular mapping of powdery mildew resistance gene PmSGD in Chinese wheat landrace Shangeda using RNA-seq with bulk segregant analysis. Mol Breed, 2018, 38:23-34.
doi: 10.1007/s11032-018-0783-4
[22] Li C, Ling F, Su G, Sun W, Liu H, Su Y, Xin Q. Location and mapping of the NCLB resistance genes in maize by bulked segregant analysis (BSA) using whole genome re-sequencing. Mol Breed, 2020, 40:1-12.
doi: 10.1007/s11032-019-1080-6
[23] Miao L, Chao H, Chen L, Wang H, Zhao W, Li B, Zhang L, Li H, Wang B, Li M. Stable and novel QTL identification and new insights into the genetic networks affecting seed fiber traits in Brassica napus. Theor Appl Genet, 2019, 132:1761-1775.
doi: 10.1007/s00122-019-03313-4
[24] Wang H, Cheng H, Wang W, Liu J, Hao M, Mei D, Zhou R, Fu L, Hu Q. Identification of BnaYUCCA6 as a candidate gene for branch angle in Brassica napus by QTL-seq. Sci Rep, 2016, 6:38493-38502.
doi: 10.1038/srep38493 pmid: 27922076
[25] Lu H, Lin T, Klein J, Wang S, Qi J, Zhou Q, Sun J, Zhang Z, Weng Y, Huang S. QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber. Theor Appl Genet, 2014, 127:1491-1499.
doi: 10.1007/s00122-014-2313-z
[26] Lei L, Zheng H, Bi Y, Yang L, Liu H, Wang J, Sun J, Zhao H, Li X, Li J, Lai Y, Zou D. Identification of a major QTL and candidate gene analysis of salt tolerance at the bud burst stage in rice (Oryza sativa L.) using QTL-Seq and RNA-Seq. Rice, 2020, 13:55-68.
doi: 10.1186/s12284-020-00416-1 pmid: 32778977
[27] Ehrenreich I M, Torabi N, Jia Y, Kent J, Martis S, Shapiro J A, Gresham D, Caudy A A, Kruglyak L. Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature, 2020, 464:1039-1042.
doi: 10.1038/nature08923
[28] Abe A, Shunichi K, Kentaro Y, Satoshi N, Hiroki T, Hiroyuki K, Hideo M, Kakoto Y, Chikako M, Muluneh T, Hideki I, Liliana C, Sophien K, Ryohei T. Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol, 2012, 30:174-178.
doi: 10.1038/nbt.2095
[29] Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano L M, Kamoun S, Terauchi R. QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J, 2013, 74:174-183.
doi: 10.1111/tpj.2013.74.issue-1
[30] Mansfeld B N, Grumet R. QTLseqr: an R package for bulk segregant analysis with next-generation sequencing. Plant Genome, 2018, 11:1-5.
[31] Kosambi D D. The estimation of map distance from recombination values. Ann Eugen, 1943, 12:172-175.
doi: 10.1111/j.1469-1809.1943.tb02321.x
[32] Meng L, Li H, Zhang L, Wang J. QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J, 2015, 3:269-283.
doi: 10.1016/j.cj.2015.01.001
[33] Watanabe H, Hase S, Saigusa M. Effects of the combined application of ethephon and gibberellin on growth of rice (Oryza sativa L.) seedlings. Plant Prod Sci, 2007, 10:468-472.
doi: 10.1626/pps.10.468
[34] Gray W M, Ostin A, Sandberg G, Romano C P, Estelle M. High temperature promotes auxin-mediated hypocotyl elongation in Arabidopsis. Proc Natl Acad Sci USA, 1998, 95:7197-7202.
doi: 10.1073/pnas.95.12.7197
[35] Romano C P, Robson P R H, Smith H, Estelle M, Klee H. Transgene-mediated auxin overproduction in Arabidopsis: hypocotyl elongation phenotype and interactions with the hy6-1 hypocotyl elongation and axr1 auxin-resistant mutants. Plant Mol Biol, 1995, 27:1071-1083.
pmid: 7766890
[36] Watanabe H, Takahashi K, Saigusa M. Morphological and anatomical effects of abscisic acid (ABA) and fluridone (FLU) on the growth of rice mesocotyls. Plant Growth Regul, 2001, 34:273-275.
doi: 10.1023/A:1013333718573
[37] Hu Z, Yamauchi T, Yang J, Jikumaru Y, Tsuchida-Mayama T, Ichikawa H, Takamure I, Nagamura Y, Tsutsumi N, Yamaguchi S, Kyozuka J, Nakazono M. Strigolactone and cytokinin act antagonistically in regulating rice mesocotyl elongation in darkness. Plant Cell Physiol, 2014, 55:30-41.
doi: 10.1093/pcp/pct150
[38] Redona E D, Mackill D J. Mapping quantitative trait loci for seeding vigor in rice using RFLPs. Theor Appl Genet, 1996, 92:395-402.
doi: 10.1007/BF00223685
[39] Katsuta-Seki M, Ebana K, Okuno K. QTL analysis for mesocotyl elongation in rice. Rice Genet Newsl, 1996, 13:126.
[40] Wu J, Feng F, Lian X, Teng X, Wei H, Yu H, Xie W, Yan M, Fan P, Li Y, Ma X, Liu H, Yu S, Wang G, Zhou F, Luo L, Mei H. Genome-wide association study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice. BMC Plant Biol, 2015, 15:218-227.
doi: 10.1186/s12870-015-0608-0
[41] Zhao G, Wang J. Effect of gibberellin and uniconazole on mesocotyl elongation of dark-grown maize under different seeding depths. Plant Prod Sci, 2008, 11:423-429.
doi: 10.1626/pps.11.423
[42] Masuda Y. Auxin-induced cell elongation and cell wall changes. J Plant Res, 1990, 103:345-370.
[43] Watanabe H, Takahashi K, Saigusa M. Morphological and anatomical effects of abscisic acid (ABA) and fluridone (FLU) on the growth of rice mesocotyls. Plant Growth Regul, 2001, 34:273-275.
doi: 10.1023/A:1013333718573
[44] Zhang C, Huang Y, Xiao Z, Yang H, Hao Q, Yuan S, Chen H, Chen L, Chen S, Zhou X, Huang W. A GATA transcription factor from soybean (Glycine max) regulates chlorophyll biosynthesis and suppresses growth in the transgenic Arabidopsis thaliana. Plants, 2020, 9:1036-1041.
doi: 10.3390/plants9081036
[45] Ye H, Du H, Tang N, Li X, Xiong L. Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. Plant Mol Biol, 2009, 71:291-305.
doi: 10.1007/s11103-009-9524-8
[46] Nutan K K, Singla-Pareek S L, Pareek A. The Saltol QTL-localized transcription factor OsGATA8 plays an important role in stress tolerance and seed development in Arabidopsis and rice. J Exp Bot, 2019, 71:684-698.
[47] Zhang L, Li Q, Dong H, He Q, Liang L, Tan C, Han Z, Yao W, Li G, Zhao H, Xie W, Xing Y. Three CCT domain-containing genes were identified to regulate heading date by candidate gene-based association mapping and transformation in rice. Sci Rep, 2015, 5:7663-7673.
doi: 10.1038/srep07663 pmid: 25563494
[48] Liu D, Zehfroosh N, Hancock B L, Hines K, Fang W, Kilfoil M, Learned-Miller E, Sanguinet K A, Goldner L S, Baskin T I. Imaging cellulose synthase motility during primary cell wall synthesis in the grass Brachypodium distachyon. Sci Rep, 2017, 7:15111-15122.
doi: 10.1038/s41598-017-14988-4
[49] Inouhe M, Inada G, Thomas B R, Nevins D J. Cell wall autolytic activities and distribution of cell wall glucanases in Zea mays L. seedlings. Int J Biol Macromol, 2000, 27:151-156.
pmid: 10771065
[50] Erp H V, Walton J D. Regulation of the cellulose synthase-like gene family by light in the maize mesocotyl. Planta, 2009, 229:885-897.
doi: 10.1007/s00425-008-0881-3
[51] Zhuang J, Jiang H H, Wang F, Peng R H, Yao Q H, Xiong A S. A rice OsAP23, functioning as an AP2/ERF transcription factor, reduces salt tolerance in transgenic Arabidopsis. Plant Mol Biol Rep, 2013, 31:1336-1345.
doi: 10.1007/s11105-013-0610-3
[52] Hwang S G, Kim D S, Hwang J E, Han A R, Jang C S. Identification of rice genes associated with cosmic-ray response via co-expression gene network analysis. Gene, 2014, 541:82-91.
doi: 10.1016/j.gene.2014.02.060
[53] Li X, Yang D L, Sun L, Li Q, Mao B, He Z. The systemic acquired resistance regulator OsNPR1 attenuates growth by repressing auxin signaling through promoting IAA-amido synthase expression. Plant Physiol, 2016, 172:546-558.
doi: 10.1104/pp.16.00129
[1] TIAN Tian, CHEN Li-Juan, HE Hua-Qin. Identification of rice blast resistance candidate genes based on integrating Meta-QTL and RNA-seq analysis [J]. Acta Agronomica Sinica, 2022, 48(6): 1372-1388.
[2] YU Chun-Miao, ZHANG Yong, WANG Hao-Rang, YANG Xing-Yong, DONG Quan-Zhong, XUE Hong, ZHANG Ming-Ming, LI Wei-Wei, WANG Lei, HU Kai-Feng, GU Yong-Zhe, QIU Li-Juan. Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height [J]. Acta Agronomica Sinica, 2022, 48(5): 1091-1102.
[3] YU Rui-Su, TIAN Xiao-Kang, LIU Bin-Bin, DUAN Ying-Xin, LI Ting, ZHANG Xiu-Ying, ZHANG Xing-Hua, HAO Yin-Chuan, LI Qin, XUE Ji-Quan, XU Shu-Tu. Dissecting the genetic architecture of lodging related traits by genome-wide association study and linkage analysis in maize [J]. Acta Agronomica Sinica, 2022, 48(1): 138-150.
[4] ZENG Wei-Ying, LAI Zhen-Guang, SUN Zu-Dong, YANG Shou-Zhen, CHEN Huai-Zhu, TANG Xiang-Min. Identification of the candidate genes of soybean resistance to bean pyralid (Lamprosema indicata Fabricius) by BSA-Seq and RNA-Seq [J]. Acta Agronomica Sinica, 2021, 47(8): 1460-1471.
[5] CHEN Can, NONG Bao-Xuan, XIA Xiu-Zhong, ZHANG Zong-Qiong, ZENG Yu, FENG Rui, GUO Hui, DENG Guo-Fu, LI Dan-Ting, YANG Xing-Hai. Genome-wide association study of blast resistance loci in the core germplasm of rice landraces from Guangxi [J]. Acta Agronomica Sinica, 2021, 47(6): 1114-1123.
[6] LI Shu-Yu, HUANG Yang, XIONG Jie, DING Ge, CHEN Lun-Lin, SONG Lai-Qiang. QTL mapping and candidate genes screening of earliness traits in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(4): 626-637.
[7] ZENG Jian, XU Xian-Chao, XU Yu-Fei, WANG Xiu-Cheng, YU Hai-Yan, FENG Bei-Bei, XING Guang-Nan. Utilization of dynamic transcriptomics analysis for candidate gene mining of 100-seed weight in soybean [J]. Acta Agronomica Sinica, 2021, 47(11): 2121-2133.
[8] XIE Lei, REN Yi, ZHANG Xin-Zhong, WANG Ji-Qing, ZHANG Zhi-Hui, SHI Shu-Bing, GENG Hong-Wei. Genome-wide association study of pre-harvest sprouting traits in wheat [J]. Acta Agronomica Sinica, 2021, 47(10): 1891-1902.
[9] LI Jing-Cai, WANG Qiang-Lin, SONG Wei-Wu, HUANG Wei, XIAO Gui-Lin, WU Cheng-Jin, GU Qin, SONG Bo-Tao. Association analysis of dormancy QTL in tetraploid potato via candidate gene markers [J]. Acta Agronomica Sinica, 2020, 46(9): 1380-1387.
[10] WANG Rui-Li,WANG Liu-Yan,YE Sang,Gao Huan-Huan,LEI Wei,WU Jia-Yi,YUAN Fang,MENG Li-Jiao,TANG Zhang-Lin,LI Jia-Na,ZHOU Qing-Yuan,CUI Cui. QTL mapping of seed germination-related traits in Brassica napus L. under aluminum toxicity stress [J]. Acta Agronomica Sinica, 2020, 46(6): 832-843.
[11] WU Hai-Tao, ZHANG Yong, SU Bo-Hong, Lamlom F Sobhi, QIU Li-Juan. Development of molecular markers and fine mapping of qBN-18 locus related to branch number in soybean (Glycine max L.) [J]. Acta Agronomica Sinica, 2020, 46(11): 1667-1677.
[12] JIAN Hong-Ju, HUO Qiang, GAO Yu-Min, LI Yang-Yang, XIE Ling, WEI Li-Juan, LIU Lie-Zhao, LU Kun, LI Jia-Na. Selection of candidate genes for chlorophyll content in leaves of Brassica napus using genome-wide association analysis [J]. Acta Agronomica Sinica, 2020, 46(10): 1557-1565.
[13] HUO Qiang,YANG Hong,CHEN Zhi-You,JIAN Hong-Ju,QU Cun-Min,LU Kun,LI Jia-Na. Candidate genes screening for plant height and the first branch height based on QTL mapping and genome-wide association study in rapessed (Brassica napus L.) [J]. Acta Agronomica Sinica, 2020, 46(02): 214-227.
[14] Cun-Min QU,Guo-Qiang MA,Mei-Chen ZHU,Xiao-Hu HUANG,Le-Dong JIA,Shu-Xian WANG,Hui-Yan ZHAO,Xin-Fu XU,Kun LU,Jia-Na LI,Rui WANG. Genome-wide association of roots, hypocotyls and fresh weight at germination stage under as stress in Brassica napus L. [J]. Acta Agronomica Sinica, 2019, 45(2): 175-187.
[15] Yang-Yang LI,Rong-Rong JING,Rong-Rong LYU,Peng-Cheng SHI,Xin LI,Qin WANG,Dan WU,Qing-Yuan ZHOU,Jia-Na LI,Zhang-Lin TANG. Genome-wide association analysis and candidate genes prediction of waterlogging-responding traits in Brassica napus L. [J]. Acta Agronomica Sinica, 2019, 45(12): 1806-1821.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!