การพัฒนาเครื่องหมาย ILP จากยีนที่เกี่ยวข้องกับลักษณะทางลำต้นในอ้อย เพื่อศึกษาความหลากหลายทางพันธุกรรมและโครงสร้างทางพันธุกรรมในอ้อย
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Published:
Apr 23, 2018
Keywords:
sugarcane ILP marker genetic diversity genetic structure
Main Article Content
Abstract
Understanding genetic structure and diversity of sugarcanes is important for sugarcane breeding programs. In the present study, intron length polymorphism (ILP) markers were developed from 32 genes involving in stalk traits in sugarcane to assess genetic diversity and genetic structure of 200 sugarcanes cultivars. A total of 116 alleles were detected by ILP markers. The average polymorphism information content (PIC) value was 0.27. The analysis of genetic diversity based on geographic sources of sugarcanes indicated that the coefficient of gene differentiation and gene flow index revealed low level of genetic differentiation among the five groups, which corresponded to the result of analysis of molecular variance (AMOVA). The majority (97.7 %) of genetic variation was within populations. The analysis of population structure indicated that the number of subpopulations (K) of sugarcane germplasm was two (K = 2). The overall FST value of 0.04, suggesting the germplasm exchange among breeding programs around the world. The ILPs markers developed in present study have been proved to be useful for genetic diversity and genetic structure assessment in sugarcane, which could be advantageous for selecting parents with a greater combination capacity in breeding program.
Keywords: sugarcane; ILP marker; genetic diversity; genetic structure
Article Details
Section
Biological Sciences
References
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[18] Benbouza, H., Jacquemin, J.M., Baudoin, J.P. and Mergeai, G., 2006, Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels, Biol. Agron. Soc. Env. 10: 77-81.
[19] Botstein, D., White, R.L., Skolnick, M. and Davis, R.W., 1980, Construction of a genetic linkage map in man using restriction fragment length polymerphisms, Am. J. Hum, Genet. 32: 314-331.
[20] Nei, M. and Li, W.H., 1979, Mathematical model for studying genetic variation in terms of restriction endonucleases, Proc. Nat. Acad. Sci. USA. 76: 5269-5273.
[21] Liu, K. and Muse, S.V., 2005, PowerMarker: an integrated analysis environment for genetic marker analysis, Bioinformatics 21: 2128-2129.
[22] Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S., 2011, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol. 28: 2731-2739.
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[24] Excoffier, L., Laval, G. and Schneider, S., 2005, Arlequin (version 3.0): An integrated software package for population genetics data analysis, Evol. Bioinf. Online 1: 47-50.
[25] Pritchard, J.K., Stephens, M. and Donnelly, P., 2000, Inference of population structure using multilocus genotype data, Genetics 155: 945-959.
[26] Evanno, G., Regnaut, S. and Goudet, J., 2005, Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study, Mol. Ecol. 14: 2611-2620.
[27] Rohlf, F., 1998, NTSYS-pc Numerical taxonomy and multivariate analysis system (version 2.02), Exeter Software Publishers Ltd., Setauket., New York, 38 p.
[28] Guimarães, C.T., Sills, G.R. and Sobral, B.W., 1997, Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize, Proc. Nat. Acad. Sci. USA. 94: 14261-14266.
[29] Wang, J., Roe, B., Macmil, S., Yu, Q., Murray, J.E., Tang, H., Chen, C., Najar, F., Wiley, G. and Bowers, J., 2010, Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes, BMC Genom. 11: 261.
[30] Jaikishan, I., Rajendrakumar, P., Madhusudhana, R., Elangovan, M. and Patil, J.V., 2015, Development and utility of PCR-based intron polymorphism markers in sorghum [Sorghum bicolor (L.) Moench], J. Crop. Sci. Biotechnol. 18: 309-318.
[31] Zhou, R., Jia, J. and Gao, L., 2010, RGA-ILP, a new type of functional molecular markers in bread wheat, Euphytica 172: 263-273.
[32] โสณิชา อุทุมพร, 2559, การวิเคราะห์ยีนลักษณะปริมาณที่เกี่ยวข้องกับผลผลิตปาล์มน้ำมันโดยใช้เครื่องหมาย Intron Length Polymorphism, วิทยานิพนธ์ปริญญาโท, มหาวิทยาลัยธรรมศาสตร์, ปทุมธานี, 131 น.
[33] ณัฐภัทร พงศ์ศิริพัฒน์ และกิตติพัฒน์ อุโฆษกิจ, 2015, การพัฒนาเครื่องหมาย ILP จากยีนที่มีความเกี่ยวข้องกับการสังเคราะห์น้ำตาลซูโครสในอ้อย และการศึกษาโครงสร้างพันธุกรรมอ้อย, Thai J. Genet. 8: 111-122.
[34] Ukoskit, K., Thipmongkolcharoen, P. and Chatwachirawong, P., 2012, Novel expressed sequence tag-simple sequence repeats (EST-SSR) markers characterized by new bioinformatic criteria reveal high genetic similarity in sugarcane (Saccha-rum spp.) breeding lines, Afr. J. Biotechnol. 11: 1337-1363.
[35] Singh, R.K., Jena, S.N., Khan, S., Yadav, S., Banarjee, N., Raghuvanshi, S., Bhardwaj, V., Dattamajumder, S.K., Kapur, R. and Solomon, S., 2013, Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane, Gene 524: 309-329.
[36] Wang, X., Zhao, X., Zhu, J. and Wu, W., 2005, Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice, DNA Res. 12: 417-427.
[37] Zeid, M., Yu, J., Goldowitz, I., Denton, M., Costich, D.E., Jayasuriya, C., Sahac, M., Elshire, R. Benscher, D. and Breseghello, F., 2010, Cross-amplification of EST-derived markers among 16 grass species, Field Crop Res. 118: 28-35.
[38] Parra, G., Bradnam, K., Rose, A.B. and Korf, I., 2011, Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants, Nucl. Acids Res. 39: 5328-5337.
[39] Yang, Y., Zhao, X., Xia, L., Chen, X., Xia, X., Yu, Z. and Röder, M., 2007, Development and validation of a Viviparous-1 STS marker for pre-harvest sprouting tolerance in Chinese wheats, Theor. Appl. Genet. 115: 971-980.
[40] Wongpraneekul, A., 2008, Pedigree analysis of Thai sugarcane germplasm, M.S. Thesis, Kasetsart University, Bangkok, 135 p.
[41] Deren, C., 1995, Genetic base of US mainland sugarcane, Crop Sci. 35: 1195-1199.
[42] Raboin, L.M., Pauquet, J., Butterfield, M., D’Hont, A. and Glaszmann, J.C., 2008, Analysis of genome-wide linkage disequilibrium in the highly polyploid sugarcane, Theor. Appl. Genet. 116: 701-714.
[2] Wei, H., Fu, Y. and Arora, R., 2005, Intron-flanking EST-PCR markers: From genetic marker development to gene structure analysis in Rhododendron, Theor. Appl. Genet. 111: 1347-1356.
[3] Shu, Y., Li, Y., Zhu, Y., Zhu, Z., Lv, D., Bai, X., Cai, H., Ji, W. and Guo, D., 2010, Genome-wide identification of intron fragment insertion mutations and their potential use as SCAR molecular markers in the soybean, Theor. Appl. Genet. 121: 1-8.
[4] Li, D., Xia, Z., Deng, Z., Liu, X., Dong, J. and Feng, F., 2012, Development and characterization of intron-flanking EST-PCR markers in rubber tree (Hevea brasiliensis Muell. Arg.), Mol. Biotechnol. 51: 148-159.
[5] Liu, H., Lin, Y., Chen, G., Shen, Y., Liu, J. and Zhang, S., 2012, Genome-scale identification of resistance gene analogs and the development of their intron length polymorphism markers in maize, Mol. Breed. 29: 437-447.
[6] SaiSug, W. and Ukoskit, K., 2013, Comparative analysis of EST-derived markers for allelic variation in Jatropha curcas L. and cross transferability among economically important species of Euphorbiaceae, Genes Genom. 35: 1-12.
[7] โสณิชา อุทุมพร และกิตติพัฒน์ อุโฆษกิจ, 2016, การพัฒนาเครื่องหมาย ILP จากกลุ่มยีนที่เกี่ยวข้องกับการสร้างดอกปาล์มน้ำมัน (Elaeis guineensis Jacq.), ว.วิทยาศาสตร์และเทคโนโลยี 24: 299-308.
[8] Wang, Y. and Li, J., 2008, Molecular basis of plant architecture, Plant Biol. 59: 253-279.
[9] Hussien, A., Tavakol, E., Horner, D.S., Muñoz-Amatriaín, M., Muehlbauer, G.J. and Rossini, L., 2014, Genetics of tillering in rice and barley, Plant Genom. 7: 1-20.
[10] Kong, W., Guo, H., Goff, V.H., Lee, T.H., Kim, C. and Paterson, A.H., 2014, Genetic analysis of vegetative branching in sorghum, Theor. Appl. Genet. 127: 2387-2403.
[11] Gawal, N. and Jarret, R., 1991, A modified CTAB DNA extraction procedure for Musa and Ipomea, Plant Mol. Biol. Rep. 9: 262-266.
[12] Telles, G.P., Braga, M.D., Dias, Z., Tzy-Li, L., Quitzau, J.A., da Silva, F.R. and Meidanis, J., 2001, Bioinformatics of the sugarcane EST project, Genet. Mol. Biol. 24: 9-15.
[13] Goodstein, D.M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U. and Putnam, N., 2011, Phytozome: a comparative platform for green plant genomics, Nucl. Acids Res. 40: 1178-1186.
[14] Jannoo, N., Grivet, L., Chantret, N., Garsmeur, O., Glaszmann, J.C., Arruda, P. and D’Hont, A., 2007, Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome, Plant J. 50: 574-585.
[15] Schlueter, S.D., Dong, Q. and Brendel, V., 2003, GeneSeqer@PlantGDB: Gene structure prediction in plant genomes, Nucl. Acids Res. 31: 3597-3600.
[16] Rozen, S. and Skaletsky, H., 1999, Primer3 on the WWW for general users and for biologist programmers, Meth. Mol. Biol. 132: 365-386.
[17] Owczarzy, R., Tataurov, A.V., Wu, Y., Manthey, J.A., McQuisten, K.A., Almabrazi, H.G., Pedersen, K.F., Lin, Y., Garretson, J. and McEntaggart, N.O., 2008, IDT SciTools: A suite for analysis and design of nucleic acid oligomers, Nucl. Acids Res. 36: 163-169.
[18] Benbouza, H., Jacquemin, J.M., Baudoin, J.P. and Mergeai, G., 2006, Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels, Biol. Agron. Soc. Env. 10: 77-81.
[19] Botstein, D., White, R.L., Skolnick, M. and Davis, R.W., 1980, Construction of a genetic linkage map in man using restriction fragment length polymerphisms, Am. J. Hum, Genet. 32: 314-331.
[20] Nei, M. and Li, W.H., 1979, Mathematical model for studying genetic variation in terms of restriction endonucleases, Proc. Nat. Acad. Sci. USA. 76: 5269-5273.
[21] Liu, K. and Muse, S.V., 2005, PowerMarker: an integrated analysis environment for genetic marker analysis, Bioinformatics 21: 2128-2129.
[22] Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S., 2011, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol. 28: 2731-2739.
[23] Yeh, F., Yang, R., Boyle, T., Ye, Z. and Xiyan, J., 2000, PopGene32; Microsoft Windows-based freeware for population genetic analysis, Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, 28 p.
[24] Excoffier, L., Laval, G. and Schneider, S., 2005, Arlequin (version 3.0): An integrated software package for population genetics data analysis, Evol. Bioinf. Online 1: 47-50.
[25] Pritchard, J.K., Stephens, M. and Donnelly, P., 2000, Inference of population structure using multilocus genotype data, Genetics 155: 945-959.
[26] Evanno, G., Regnaut, S. and Goudet, J., 2005, Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study, Mol. Ecol. 14: 2611-2620.
[27] Rohlf, F., 1998, NTSYS-pc Numerical taxonomy and multivariate analysis system (version 2.02), Exeter Software Publishers Ltd., Setauket., New York, 38 p.
[28] Guimarães, C.T., Sills, G.R. and Sobral, B.W., 1997, Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize, Proc. Nat. Acad. Sci. USA. 94: 14261-14266.
[29] Wang, J., Roe, B., Macmil, S., Yu, Q., Murray, J.E., Tang, H., Chen, C., Najar, F., Wiley, G. and Bowers, J., 2010, Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes, BMC Genom. 11: 261.
[30] Jaikishan, I., Rajendrakumar, P., Madhusudhana, R., Elangovan, M. and Patil, J.V., 2015, Development and utility of PCR-based intron polymorphism markers in sorghum [Sorghum bicolor (L.) Moench], J. Crop. Sci. Biotechnol. 18: 309-318.
[31] Zhou, R., Jia, J. and Gao, L., 2010, RGA-ILP, a new type of functional molecular markers in bread wheat, Euphytica 172: 263-273.
[32] โสณิชา อุทุมพร, 2559, การวิเคราะห์ยีนลักษณะปริมาณที่เกี่ยวข้องกับผลผลิตปาล์มน้ำมันโดยใช้เครื่องหมาย Intron Length Polymorphism, วิทยานิพนธ์ปริญญาโท, มหาวิทยาลัยธรรมศาสตร์, ปทุมธานี, 131 น.
[33] ณัฐภัทร พงศ์ศิริพัฒน์ และกิตติพัฒน์ อุโฆษกิจ, 2015, การพัฒนาเครื่องหมาย ILP จากยีนที่มีความเกี่ยวข้องกับการสังเคราะห์น้ำตาลซูโครสในอ้อย และการศึกษาโครงสร้างพันธุกรรมอ้อย, Thai J. Genet. 8: 111-122.
[34] Ukoskit, K., Thipmongkolcharoen, P. and Chatwachirawong, P., 2012, Novel expressed sequence tag-simple sequence repeats (EST-SSR) markers characterized by new bioinformatic criteria reveal high genetic similarity in sugarcane (Saccha-rum spp.) breeding lines, Afr. J. Biotechnol. 11: 1337-1363.
[35] Singh, R.K., Jena, S.N., Khan, S., Yadav, S., Banarjee, N., Raghuvanshi, S., Bhardwaj, V., Dattamajumder, S.K., Kapur, R. and Solomon, S., 2013, Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane, Gene 524: 309-329.
[36] Wang, X., Zhao, X., Zhu, J. and Wu, W., 2005, Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice, DNA Res. 12: 417-427.
[37] Zeid, M., Yu, J., Goldowitz, I., Denton, M., Costich, D.E., Jayasuriya, C., Sahac, M., Elshire, R. Benscher, D. and Breseghello, F., 2010, Cross-amplification of EST-derived markers among 16 grass species, Field Crop Res. 118: 28-35.
[38] Parra, G., Bradnam, K., Rose, A.B. and Korf, I., 2011, Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants, Nucl. Acids Res. 39: 5328-5337.
[39] Yang, Y., Zhao, X., Xia, L., Chen, X., Xia, X., Yu, Z. and Röder, M., 2007, Development and validation of a Viviparous-1 STS marker for pre-harvest sprouting tolerance in Chinese wheats, Theor. Appl. Genet. 115: 971-980.
[40] Wongpraneekul, A., 2008, Pedigree analysis of Thai sugarcane germplasm, M.S. Thesis, Kasetsart University, Bangkok, 135 p.
[41] Deren, C., 1995, Genetic base of US mainland sugarcane, Crop Sci. 35: 1195-1199.
[42] Raboin, L.M., Pauquet, J., Butterfield, M., D’Hont, A. and Glaszmann, J.C., 2008, Analysis of genome-wide linkage disequilibrium in the highly polyploid sugarcane, Theor. Appl. Genet. 116: 701-714.