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推测QTL区间候选基因的方法

已有 10235 次阅读 2015-1-30 14:18 |个人分类:QTL精细定位|系统分类:科研笔记

这里有篇文章报道了相关内容

Prioritization of candidate genes in QTL regions based on associations between traits and biological processes

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274756/pdf/12870_2014_Article_330.pdf

我也是刚看到文章，没测试过，有兴趣的朋友可以试下。当然如果根据这篇文章的方法推得不准，可不要怪我，但可以告诉我。

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   这篇文章的附件中提供了一张抽穗期控制候选基因的表,我稍微整理下，加了一列Os那一列,这里共有82个基因

GeneExisting annotationOs
LOC_Os01g04750B3 DNA binding domain containing proteinOs01g0140700
LOC_Os01g04930MYB family transcription factorOs01g0142500
LOC_Os01g68620signal peptide peptidase-like 2BOs01g0914700
LOC_Os01g70920cullin-1, putativeOs01g0935300
LOC_Os01g74020MYB family transcription factor, putativeOs01g0971800
LOC_Os02g05510GATA transcription factor 25, putativeOs02g0148500
LOC_Os02g06910auxin response factor 6, putativeOs02g0164900
LOC_Os02g07430OsMADS29 - MADS-box family gene with MIKCc type-bo...Os02g0170300
LOC_Os02g07770Myb transcription factor, putativeOs02g0174000
LOC_Os02g07930B-box zinc finger family protein, putativeOs02g0176000
LOC_Os02g12790GATA zinc finger domain containing proteinOs02g0220400
LOC_Os02g13130KH domain-containing protein, putativeOs02g0224300
LOC_Os02g13830osFTL13 FT-Like13 homologous to Flowering Locus T ...Os02g0232300
LOC_Os02g30700MYB family transcription factor, putativeOs02g0511200
LOC_Os02g31140major ampullate spidroin 2-2, putativeOs02g0516400
LOC_Os02g32950RCN2 Centroradialis-like1 homologous to TFL1 gene;...Os02g0531600
LOC_Os02g42950YABBY domain containing protein, putativeOs02g0643200
LOC_Os02g43150GATA zinc finger domain containing proteinOs02g0645600
LOC_Os02g43170B-box zinc finger family protein, putativeOs02g0646200
LOC_Os02g45080MYB family transcription factor, putativeOs02g0672300
LOC_Os02g56250GATA zinc finger domain containing proteinOs02g0806400
LOC_Os02g57530ethylene receptor, putativeOs02g0820900
LOC_Os02g57530ethylene receptor, putativeOs02g0821100
LOC_Os02g57690kelch repeat protein, putativeOs02g0822800
LOC_Os02g57710signal peptide peptidase-like 2B, putativeOs02g0823000
LOC_Os03g01410Leucine Rich Repeat family proteinOs03g0104300
LOC_Os03g03070transcription factor, putativeOs03g0122600
LOC_Os03g03760MYB family transcription factor, putativeOs03g0129800
LOC_Os03g03850GATA zinc finger domain containing proteinOs03g0130600
LOC_Os03g06070la domain containing protein, putativeOs03g0156500
LOC_Os03g06654flavin monooxygenase, putativeOs03g0162000
LOC_Os03g54170OsMADS34 - MADS-box family gene with MIKCc type-bo...Os03g0753100
LOC_Os03g61570ProteinOs03g0831200
LOC_Os04g54400BTBN12 - Bric-a-Brac, Tramtrack, Broad Complex BTB...Os04g0636500
LOC_Os04g54420protein of unknown function, DUF618 domain contain...Os04g0636700
LOC_Os05g02300Core histone H2A/H2B/H3/H4 domain containing prote...Os05g0113900
LOC_Os05g10580cullin family domain containing protein, putativeOs05g0193900
LOC_Os05g11380OsMADS66 - MADS-box family gene with MIKCc type-bo...Os05g0203600
LOC_Os05g11414OsMADS58 - MADS-box family gene with MIKCc type-bo...Os05g0203800
LOC_Os05g11510B-box zinc finger family protein, putativeOs05g0204600
LOC_Os05g32880response regulator receiver domain containing prot...Os05g0395600
LOC_Os05g32890response regulator receiver domain containing prot...Os05g0395700
LOC_Os05g33570pyruvate, phosphate dikinase, chloroplast precurso...Os05g0405000
LOC_Os05g34110homeodomain-related, putativeOs05g0412000
LOC_Os05g34940OsMADS4 - MADS-box family gene with MIKCc type-box...Os05g0423400
LOC_Os06g06300osFTL3 FT-Like3 homologous to Flowering Locus T ge...Os06g0157500
LOC_Os06g06320osFTL2 FT-Like2 homologous to Flowering Locus T ge...Os06g0157700
LOC_Os06g06750OsMADS5 - MADS-box family gene with MIKCc type-boxOs06g0162800
LOC_Os06g11330OsMADS55 - MADS-box family gene with MIKCc type-bo...Os06g0217300
LOC_Os06g11440transposon protein, putative, Mutator sub-classOs06g0218150
LOC_Os06g11440transposon protein, putative, Mutator sub-classOs06g0218200
LOC_Os06g44410histidine kinase, putativeOs06g0654300
LOC_Os06g44450CCT/B-box zinc finger protein, putativeOs06g0654900
LOC_Os06g45410MYB family transcription factor, putativeOs06g0664800
LOC_Os06g45650OsMADS30 - MADS-box family gene with MIKCc type-bo...Os06g0667200
LOC_Os06g45900peptidyl-prolyl cis-trans isomerase-like 4, putati...Os06g0670400
LOC_Os06g46410auxin response factor, putative, LOC_Os06g46410.2 ...Os06g0677800
LOC_Os06g47150auxin response factor 18, putativeOs06g0685700
LOC_Os07g08520auxin response factor, putativeOs07g0183100
LOC_Os07g08540auxin response factor 20, putativeOs07g0183300
LOC_Os07g08540auxin response factor 20, putativeOs07g0183600
LOC_Os07g08600auxin response factor, putativeOs07g0183866
LOC_Os07g08600auxin response factor, putativeOs07g0183932
LOC_Os07g08880ES43 protein, putativeOs07g0186400
LOC_Os07g41370OsMADS18 - MADS-box family gene with MIKCc type-bo...Os07g0605200
LOC_Os07g46180PWWP domain containing proteinOs07g0655500
LOC_Os07g47140CCT/B-box zinc finger protein, putativeOs07g0667300
LOC_Os07g48596Myb transcription factor, putativeOs07g0685300
LOC_Os08g06370MYB family transcription factor, putativeOs08g0160300
LOC_Os08g08830proteinOs08g0187700
LOC_Os08g32620ES43 protein, putativeOs08g0421900
LOC_Os08g33488OsMADS23 - MADS-box family gene with MIKCc type-bo...Os08g0431900
LOC_Os08g34370SET domain containing proteinOs08g0442500
LOC_Os09g39270ZOS9-20 - C2H2 zinc finger proteinOs09g0566100
LOC_Os10g40810GATA zinc finger domain containing protein,Os10g0557600
LOC_Os10g39550MYB family transcription factor, putativeOs10g0541500
LOC_Os10g39130OsMADS56 - MADS-box family gene with MIKCc type-bo...Os10g0536100
LOC_Os12g06850transcription elongation factor protein, putativeOs12g0165700
LOC_Os12g07120GATA zinc finger domain containing proteinOs12g0168800
LOC_Os12g42310serine/threonine-protein phosphatase BSL2, putativ...Os12g0617900
LOC_Os12g42610YABBY domain containing protein, putativeOs12g0621100
LOC_Os12g42970GATA zinc finger domain containing proteinOs12g0624900


其中文献中出现过的基因有41个


Os		geneGene.symbol.name
Os05g0423400LOC_Os05g34940OsMADS4, PI1
Os06g0162800LOC_Os06g06750OsMADS5, FDRMADS2
Os07g0605200LOC_Os07g41370OsMADS18, MADS2, OsMADS2, MADS28, OsMADS28, FDRMADS7, OsMADS18/28
Os08g0431900LOC_Os08g33488OsMADS23, MADS-23
Os02g0170300LOC_Os02g07430OsMADS29
Os06g0667200LOC_Os06g45650OsMADS30
Os03g0753100LOC_Os03g54170MADS34, OsMADS34, RMADS212/RMADS217/RMADS221
Os03g0122600LOC_Os03g03070OsMADS50, AGL20, SOC1, OsSOC1, RMADS208
Os06g0217300LOC_Os06g11330OsMADS55
Os10g0536100LOC_Os10g39130OsMADS56, FDRMADS8, RMADS214
Os05g0405000LOC_Os05g33570flo4, flo4-2, flo4-3, ppdk, OsPPDK, PPDK1, CPDK1, PPDKB, OsPPDKB, cyOsPPDKB, OsPBDK, PBDK
Os02g0531600LOC_Os02g32950Rcn2
Os05g0203800LOC_Os05g11414OsMADS58
Os06g0157700LOC_Os06g06320Hd3a, FT, qHD3(t)*, FT-L 2, OsFTL2, FT-L2
Os01g0971800LOC_Os01g74020OsPCL1
Os03g0162000LOC_Os03g06654OsCOW1, oscow1, OsYUC8, NAL7, OsYUCCA8, FMO, OsFMO(t)
Os06g0157500LOC_Os06g06300FT-L 3, OsFTL3, FT-L3, RFT
Os05g0395600LOC_Os05g32880OsRR27, Rra16, OsPRR5, OsRRA16
Os05g0395700LOC_Os05g32890OsPRR10, Rra18, OsRRA18
Os06g0654300LOC_Os06g44410OsHK1, OHK1
Os02g0820900LOC_Os02g57530OsETR3, OsERS4, OS-ETR3, OsETR3a, OsETR3b, PK2, OsPK2
Os02g0164900LOC_Os02g06910OsARF6a, OsARF6, ARF6
Os06g0685700LOC_Os06g47150OsARF10, OsARF18
Os06g0677800LOC_Os06g46410OsARF17
Os07g0183100LOC_Os07g08520OsARF20
Os06g0670400LOC_Os06g45900OsCYP59a, OsCYP-14
Os02g0643200LOC_Os02g42950OsYAB4, OsYAB7
Os12g0621100LOC_Os12g42610OsYAB6, OsYAB5
Os02g0516400LOC_Os02g31140CFL1
Os01g0140700LOC_Os01g04750AP2/EREBP#077
Os02g0232300LOC_Os02g13830OsFTL13
Os02g0176000LOC_Os02g07930OsBBX2
Os02g0646200LOC_Os02g43170OsBBX6
Os05g0204600LOC_Os05g11510OsBBX14, OsDBB3b
Os06g0654900LOC_Os06g44450OsBBX20, OsE
Os07g0667300LOC_Os07g47140OsBBX23
Os12g0617900LOC_Os12g42310OsPPKL3
Os05g0113900LOC_Os05g02300
Os12g0165700LOC_Os12g06850OsTFIIS-like gene
Os02g0148500LOC_Os02g05510OsTIFY2a
Os01g0142500LOC_Os01g04930
这里面有功能明确抽穗期控制基因。其它基因是不是预测得准，看后续报道。



https://blog.sciencenet.cn/blog-479743-864099.html

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