谷子分蘖相关QTL定位及紧密连锁标记开发
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摘要
分蘖是与农作物产量相关的重要农艺性状之一,分蘖对于谷子产量的提高具有重要意义,但是目前谷子分蘖遗传分子机制还不清楚。利用简化基因组测序技术(RAD-seq),以2个F2群体(命名为Cross AJ和Cross HC)为研究对象,分别对2个F2群体的543个和131个单株及其亲本进行RAD-seq,利用MSTmap和Win QTLCart 2. 5软件进行遗传图谱构建和QTL分析,结果共鉴定出8个控制分蘖相关的QTL。其中,利用Cross AJ共鉴定了6个QTL,分别为qAJTN1、qAJTN5、qAJTN7-1、qAJTN7-2、qAJTN7-3和qAJTN9,可解释表型变异0. 7%～9. 8%;利用Cross HC群体共鉴定了2个QTL,分别为qHCTN5和qHCTN7,可解释表型变异1. 4%～8. 3%。在这8个QTL中,qAJTN1、qAJTN5、qAJTN7-2、qAJTN9和qHCTN5为该研究新鉴定的位点,其余3个QTL(qAJTN7-1、qAJTN7-3和qHCTN7)与前人研究结果相一致。另外,通过将亲本的测序结果与参考基因组进行比对,搜索插入缺失位点InDel(Insertion-deletion),新开发了谷子分蘖相关QTL(qAJTN7-3和qHCTN7)紧密相关的InDel标记。结果为谷子分蘖机制的研究奠定一定基础,所开发的分子标记对于分蘖型谷子的分子标记辅助育种具有重要意义。
Tillering is an important trait related to yield in many crops,and is the same for yield improvement of foxtail millet. However,the genetic mechanism of tillering in foxtail millet( Setaria italica) remains largely unknown. To accelerate mapping of relevant QTLs or genes,a restriction site-associated DNA sequencing( RAD-seq)approach,MSTmap and WinQTLCart 2. 5 were employed to identify QTLs responsible for tillering in two F2 populations called Cross AJ( 543 F2 individuals) and Cross HC( 131 F2 individuals). A total of six QTLs including qAJTN1,qAJTN5,qAJTN7-1,qAJTN7-2,qAJTN7-3 and qAJTN9,were identified in Cross AJ,explaining 0. 7%-9. 8% of the phenotypic variance,and two QTLs including qHCTN5 and qHCTN7 were identified in Cross HC,ex-plaining 1. 4%-8. 3% of the phenotypic variance. Of which qAJTN1,qAJTN5,qAJTN7-2,qAJTN9 and qHCTN5 were newly identified QTLs,and qAJTN7-1,qAJTN7-3 and qHCTN7 were consistent with previous reports. Meanwhile,we screened the insertions and deletions in the QTL regions compared with the reference genome,insertiondeletion( InDel) markers linked with tillering were developed. These results of this study will facilitate the revelation of the genetic mechanism of tillering and molecular marker-assisted breeding of foxtail millet.
Tillering is an important trait related to yield in many crops,and is the same for yield improvement of foxtail millet. However,the genetic mechanism of tillering in foxtail millet( Setaria italica) remains largely unknown. To accelerate mapping of relevant QTLs or genes,a restriction site-associated DNA sequencing( RAD-seq)approach,MSTmap and WinQTLCart 2. 5 were employed to identify QTLs responsible for tillering in two F2 populations called Cross AJ( 543 F2 individuals) and Cross HC( 131 F2 individuals). A total of six QTLs including qAJTN1,qAJTN5,qAJTN7-1,qAJTN7-2,qAJTN7-3 and qAJTN9,were identified in Cross AJ,explaining 0. 7%-9. 8% of the phenotypic variance,and two QTLs including qHCTN5 and qHCTN7 were identified in Cross HC,ex-plaining 1. 4%-8. 3% of the phenotypic variance. Of which qAJTN1,qAJTN5,qAJTN7-2,qAJTN9 and qHCTN5 were newly identified QTLs,and qAJTN7-1,qAJTN7-3 and qHCTN7 were consistent with previous reports. Meanwhile,we screened the insertions and deletions in the QTL regions compared with the reference genome,insertiondeletion( InDel) markers linked with tillering were developed. These results of this study will facilitate the revelation of the genetic mechanism of tillering and molecular marker-assisted breeding of foxtail millet.
引文
[1] Kebrom T H,Spielmeyer W,Finnegan E J. Grasses provide new insights into regulation of shoot branching[J].Trends in Plant Science,2013,18(1):41-48.
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[3] Mauro-Herrera M,Doust A N. Development and genetic control of plant architecture and biomass in the panicoid grass,setaria[J]. PLo S One,2016,11(3):e0151346.
[4] McSteen P,Leyser O. Shoot branching[J]. Annual Review of Plant Biology,2005,56:353-374.
[5] Doust A N. Grass architecture:genetic and environmental control of branching[J]. Current Opinion in Plant Biology,2007,10(1):21-25.
[6]刘瑞华,崔贞玉,冯权.水稻分蘖期的温度条件与适宜移栽密度的研究[J].吉林农业科学,1993(3):40-43.
[7]丁艳锋.氮素营养调控水稻群体质量指标的研究[D].南京:南京农业大学,1997:20-24.
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[13] Arite T,Umehara M,Ishikawa S,et al. D14,a strigolactone-insensitive mutant of rice,shows an accelerated outgrowth of tillers[J]. Plant Cell Physiology,2009,50(8):1416-1424.
[14] Lin H,Wang R X,Qian Q,et al. DWARF27,an ironcontaining protein required for the biosynthesis of strigolactones,regulates rice tiller bud outgrowth[J]. The Plant Cell,2009,21(5):1512-1525.
[15] Xu C,Wang Y H,Yu Y C,et al. Degradation of MONOCULM 1 by APC/C(TAD1)regulates rice tillering[J]. Nature Communications,2012,3:750.
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[26] Jia G Q,Huang X H,Zhi H,et al. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet(Setaria italica)[J].Nature Genetics,2013,45(8):957-961.
[27] Zhang K,Fan G,Zhang X,et al. Identification of QTLs for 14 agronomically important traits in Setaria italica based on SNPs generated from high-throughput sequencing[J]. G3(Bethesda),2017,7(5):1587-1594.
[28] Bennetzen J L,Schmutz J,Wang H,et al. Reference genome sequence of the model plant Setaria[J]. Nature Biotechnology,2012,30(6):555-561.
[29] Zhang G Y,Liu X,Quan Z W,et al. Genome sequence of foxtail millet(Setaria italica)provides insights into grass evolution and biofuel potential[J]. Nature Biotechnology,2012,30:549-554.
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[31] Masumoto H,Takagi H,Mukainari Y,et al. Genetic analysis of NEKODE1 gene involved in panicle branching of foxtail millet,Setaria italica(L.)P. Beauv.,and mapping by using QTL-seq[J]. Molecular Breeding,2016,36:59.
[32] Zhang S,Tang C J,Zhao Q,et al. Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in foxtail millet(Setaria italica(L.)P. Beauv.)[J]. BMC Genomics,2014,15:78.
[33] Xue C X,Zhi H,Fang X J,et al. Characterization and fine mapping of Si DWARF2(D2)in foxtail millet[J].Crop Science,2016,56(1):95.
[34] Li W,Tang S,Zhang S,et al. Gene mapping and functional analysis of the novel leaf color gene Si YGL1 in foxtail millet(Setaria italica(L.)P. Beauv.)[J]. Physiologia Plantarum,2016,157(1):24-37.
[35] Liu X T,Tang S,Jia G Q,et al. The C-terminal motif of Si AGO1b is required for the regulation of growth,development and stress responses in foxtail millet(Setaria italica(L.)P. Beauv.)[J]. Joural of Experimental Botany,2016,67(11):3237-3249.
[36] Xiang J S,Tang S,Zhi H,et al. Loose Panicle1 encoding a novel WRKY transcription factor,regulates panicle development,stem elongation,and seed size in foxtail millet(Setaria italica(L.)P. Beauv.)[J]. PLo S One,2017,12(6):e0178730.
[37] Fan X K,Tang S,Zhi H,et al. Identification and fine mapping of Si DWARF3(D3),a pleiotropic locus controlling environment-independent dwarfism in foxtail millet[J]. Crop Science,2017,57(5):2431-2442.
[38]王冠杰,周波,李玉花. RAD标记测序及其在分子育种中的应用[J].中国生物化学与分子生物学报,2012,28(9):797-803.
[39] Wang J,Wang Z L,Du X F,et al. A high-density genetic map and QTL analysis of agronomic traits in foxtail millet(Setaria italica(L.)P. Beauv.)using RAD-seq[J]. PLo S One,2017,12(6):e0179717.
[40] Wang J,Yang H Q,Du G H,et al. Mapping of Sihc1,which controls hull color,using a high-density genetic map based on restriction site-associated DNA sequencing in foxtail millet(Setaria italica(L.)P. Beauv.)[J].Molecular Breeding,2017,37:128.
[41] Chen D H,Ronald P C. A rapid DNA minipreparation method suitable for AFLP and other PCR applications[J]. Plant Molecular Biology Reporter,1999,17(1):53-57.
[42] Baird N A,Etter P D,Atwood T S,et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers[J]. PLo S One,2008,3(10):e3376.
[43] Li H,Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform[J]. Bioinformatics,2009,25(14):1754-1760.
[44] McKenna A,Hanna M,Banks E,et al. The Genome Analysis Toolkit:a MapReduce framework for analyzing next-generation DNA sequencing data[J]. Genome Research,2010,28(1):1297-1303.
[45] Li H,Handsaker B,Wysoker A,et al. The Sequence Alignment/Map format and SAMtools[J]. Bioinformatics,2009,25(16):2078-2079.
[46] Wu Y H,Bhat P R,Close T J,et al. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph[J]. PLo S Genetics,2008,4(10):e1000212.
[47] Wang S,Basten C J,Zeng Z B. Windows QTL cartographer 2. 5. Department of Statistics,North Carolina State University,Raleigh,NC[EB/OL].[2012-02-05].http://statgen. ncsu. edu/qtlcart/WQTLCart. htm.
[48] Marklund S,Chaudhary R,Marklund L,et al. Extensive mt DNA diversity in horses revealed by PCR-SSCP analysis[J]. Animal Genetics,1995,26(3):193-196.
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[50] Tomaszewski C,Byrne S L,Foito A,K et al. Genetic linkage mapping in an F2perennial ryegrass population using DAr T markers[J]. Plant Breeding,2012,131(2):345-349.
[51] Barakat M N,Wahba L E,Milad S I. Molecular mapping of QTLs for wheat flag leaf senescence under waterstress[J]. Biologia Plantarum,2013,57(1):79-84.
[52] Herlina L,Sobir S,Trijatmiko K R. Identification of quantitative trait loci(QTL)for awn,incomplete panicle exertion and total spikelet number in an F2population derived from a backcross inbred line,Bio-148,and the recurrent parent,IR64[J]. Makara Journal of Science,2016,20(1):17-27.
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[2] Kuraparthy V,Sood S,Dhaliwal H S,et al. Identification and mapping of a tiller inhibition gene(tin3)in wheat[J]. Theoretical and Applied Genetics,2007,114(2):285-294.
[3] Mauro-Herrera M,Doust A N. Development and genetic control of plant architecture and biomass in the panicoid grass,setaria[J]. PLo S One,2016,11(3):e0151346.
[4] McSteen P,Leyser O. Shoot branching[J]. Annual Review of Plant Biology,2005,56:353-374.
[5] Doust A N. Grass architecture:genetic and environmental control of branching[J]. Current Opinion in Plant Biology,2007,10(1):21-25.
[6]刘瑞华,崔贞玉,冯权.水稻分蘖期的温度条件与适宜移栽密度的研究[J].吉林农业科学,1993(3):40-43.
[7]丁艳锋.氮素营养调控水稻群体质量指标的研究[D].南京:南京农业大学,1997:20-24.
[8] Dun E A,de Saint Germain A,Rameau C,et al. Antagonistic action of strigolactone and cytokinin in bud outgrowth control[J]. Plant Physiology,2012,158(1):487-498.
[9] Li X Y,Qian Q,Fu Z M,et al. Control of tillering in rice[J]. Nature,2003,422(6932):618-621.
[10] Ishikawa S,Maekawa M,Arite T,et al. Suppression of tiller bud activity in tillering dwarf mutants of rice[J].Plant Cell Physiology,2005,46(1):79-86.
[11] Booker J,Auldridge M,Wills S,et al. MAX3/CCD7 is a carotenoid cleavage dioxygenase required for the synthesis of a novel plant signaling molecule[J]. Current Biology,2004,14(14):1232-1238.
[12] Arite T,Iwata H,Ohshima K,et al. DWARF10,an RMS1/MAX4/DAD1 ortholog,controls lateral bud outgrowth in rice[J]. The Plant Journal,2007,51(6):1019-1029.
[13] Arite T,Umehara M,Ishikawa S,et al. D14,a strigolactone-insensitive mutant of rice,shows an accelerated outgrowth of tillers[J]. Plant Cell Physiology,2009,50(8):1416-1424.
[14] Lin H,Wang R X,Qian Q,et al. DWARF27,an ironcontaining protein required for the biosynthesis of strigolactones,regulates rice tiller bud outgrowth[J]. The Plant Cell,2009,21(5):1512-1525.
[15] Xu C,Wang Y H,Yu Y C,et al. Degradation of MONOCULM 1 by APC/C(TAD1)regulates rice tillering[J]. Nature Communications,2012,3:750.
[16] Lin Q B,Wang D,Dong H,et al. Rice APC/C(TE)controls tillering by mediating the degradation of MONOCULM 1[J]. Nature Communications, 2012,3:752.
[17] Jiang L,Liu X,Xiong G S,et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature,2013,504:401-405.
[18] Tanaka W,Ohmori Y,Ushijima T,et al. Axillary meristem formation in rice requires the WUSCHEL ortholog TILLERS ABSENT1[J]. The Plant Cell,2015,27(4):1173-1184.
[19] Xu J X,Zha M R,Li Y,et al. The interaction between nitrogen availability and auxin,cytokinin,and strigolactone in the control of shoot branching in rice(Oryza sativa L.)[J]. Plant Cell Reports,2015,34(9):1647-1662.
[20] Zuo J R,Li J Y. Molecular dissection of complex agronomic traits of rice:a team effort by Chinese scientists in recent years[J]. National Science Review,2014,1(2):253-276.
[21] Li W L,Nelson J C,Chu C Y,et al. Chromosomal locations and genetic relationships of tiller and spike characters in wheat[J]. Euphytica,2002,125(3):357-366.
[22] Li Z K,Peng T,Xie Q G,et al. Mapping of QTL for tiller number at different stages of growth in wheat using double haploid and immortalized F2populations[J]. Indian Academy of Sciences,2010,89(4):409-415.
[23] Naruoka Y,Talbert L E,Lanning S P,et al. Identification of quantitative trait loci for productive tiller number and its relationship to agronomic traits in spring wheat[J]. Theoretical and Applied Genetics,2011,123(6):1043-1053.
[24] Doust A N,Devos K M,Gadberry M D,et al. Genetic control of branching in foxtail millet[J]. Proceeding of National Academy of Sciences of the United States of American,2004,101(24):9045-9050.
[25] Doust A N,Kellogg E A. Effect of genotype and environment on branching in weedy green millet(Setaria viridis)and domesticated foxtail millet(Setaria italica)(Poaceae)[J]. Molecular Ecology,2006,15(5):1335-1349.
[26] Jia G Q,Huang X H,Zhi H,et al. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet(Setaria italica)[J].Nature Genetics,2013,45(8):957-961.
[27] Zhang K,Fan G,Zhang X,et al. Identification of QTLs for 14 agronomically important traits in Setaria italica based on SNPs generated from high-throughput sequencing[J]. G3(Bethesda),2017,7(5):1587-1594.
[28] Bennetzen J L,Schmutz J,Wang H,et al. Reference genome sequence of the model plant Setaria[J]. Nature Biotechnology,2012,30(6):555-561.
[29] Zhang G Y,Liu X,Quan Z W,et al. Genome sequence of foxtail millet(Setaria italica)provides insights into grass evolution and biofuel potential[J]. Nature Biotechnology,2012,30:549-554.
[30] Sato K,Mukainari Y,Naito K,et al. Construction of afoxtail millet linkage map and mapping of spikelet-tipped bristles 1(stb1)by using transposon display markers and simple sequence repeat markers with genome sequence information[J]. Molecular Breeding,2013,31(3):675-684.
[31] Masumoto H,Takagi H,Mukainari Y,et al. Genetic analysis of NEKODE1 gene involved in panicle branching of foxtail millet,Setaria italica(L.)P. Beauv.,and mapping by using QTL-seq[J]. Molecular Breeding,2016,36:59.
[32] Zhang S,Tang C J,Zhao Q,et al. Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in foxtail millet(Setaria italica(L.)P. Beauv.)[J]. BMC Genomics,2014,15:78.
[33] Xue C X,Zhi H,Fang X J,et al. Characterization and fine mapping of Si DWARF2(D2)in foxtail millet[J].Crop Science,2016,56(1):95.
[34] Li W,Tang S,Zhang S,et al. Gene mapping and functional analysis of the novel leaf color gene Si YGL1 in foxtail millet(Setaria italica(L.)P. Beauv.)[J]. Physiologia Plantarum,2016,157(1):24-37.
[35] Liu X T,Tang S,Jia G Q,et al. The C-terminal motif of Si AGO1b is required for the regulation of growth,development and stress responses in foxtail millet(Setaria italica(L.)P. Beauv.)[J]. Joural of Experimental Botany,2016,67(11):3237-3249.
[36] Xiang J S,Tang S,Zhi H,et al. Loose Panicle1 encoding a novel WRKY transcription factor,regulates panicle development,stem elongation,and seed size in foxtail millet(Setaria italica(L.)P. Beauv.)[J]. PLo S One,2017,12(6):e0178730.
[37] Fan X K,Tang S,Zhi H,et al. Identification and fine mapping of Si DWARF3(D3),a pleiotropic locus controlling environment-independent dwarfism in foxtail millet[J]. Crop Science,2017,57(5):2431-2442.
[38]王冠杰,周波,李玉花. RAD标记测序及其在分子育种中的应用[J].中国生物化学与分子生物学报,2012,28(9):797-803.
[39] Wang J,Wang Z L,Du X F,et al. A high-density genetic map and QTL analysis of agronomic traits in foxtail millet(Setaria italica(L.)P. Beauv.)using RAD-seq[J]. PLo S One,2017,12(6):e0179717.
[40] Wang J,Yang H Q,Du G H,et al. Mapping of Sihc1,which controls hull color,using a high-density genetic map based on restriction site-associated DNA sequencing in foxtail millet(Setaria italica(L.)P. Beauv.)[J].Molecular Breeding,2017,37:128.
[41] Chen D H,Ronald P C. A rapid DNA minipreparation method suitable for AFLP and other PCR applications[J]. Plant Molecular Biology Reporter,1999,17(1):53-57.
[42] Baird N A,Etter P D,Atwood T S,et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers[J]. PLo S One,2008,3(10):e3376.
[43] Li H,Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform[J]. Bioinformatics,2009,25(14):1754-1760.
[44] McKenna A,Hanna M,Banks E,et al. The Genome Analysis Toolkit:a MapReduce framework for analyzing next-generation DNA sequencing data[J]. Genome Research,2010,28(1):1297-1303.
[45] Li H,Handsaker B,Wysoker A,et al. The Sequence Alignment/Map format and SAMtools[J]. Bioinformatics,2009,25(16):2078-2079.
[46] Wu Y H,Bhat P R,Close T J,et al. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph[J]. PLo S Genetics,2008,4(10):e1000212.
[47] Wang S,Basten C J,Zeng Z B. Windows QTL cartographer 2. 5. Department of Statistics,North Carolina State University,Raleigh,NC[EB/OL].[2012-02-05].http://statgen. ncsu. edu/qtlcart/WQTLCart. htm.
[48] Marklund S,Chaudhary R,Marklund L,et al. Extensive mt DNA diversity in horses revealed by PCR-SSCP analysis[J]. Animal Genetics,1995,26(3):193-196.
[49] Weng Y Q,Colle M,Wang Y H,et al. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes[J]. Theoretical and Applied Genetics,2015,128(9):1747-1763.
[50] Tomaszewski C,Byrne S L,Foito A,K et al. Genetic linkage mapping in an F2perennial ryegrass population using DAr T markers[J]. Plant Breeding,2012,131(2):345-349.
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