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| Molecular Diversity and Association Analysis of Drought and Salt Tolerance in Gossypium hirsutum L. Germplasm |
| JIA Yin-hua, SUN Jun-ling, WANG Xi-wen, ZHOU Zhong-li, PAN Zao-e, HE Shou-pu, PANG Bao-yin, WANG Li-ru , DU Xiong-ming |
| State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, P.R.China |
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摘要 Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium (LD). This study was carried out to estimate genetic diversity, population structure and the extent of LD to develop an association framework in order to identify genetic variations associated with drought and salt tolerance traits. 106 microsatellite marker primer pairs were used in 323 Gossypium hirsutum germplasms which were grown in the drought shed and salt pond for evaluation. Polymorphism (PIC=0.53) was found, and three groups were detected (K=3) with the second likelihood ΔK using STRUCTURE software. LD decay rates were estimated to be 13-15 cM at r2 0.20. Significant associations between polymorphic markers and drought and salt tolerance traits were observed using the general linear model (GLM) and mixed linear model (MLM) (P 0.01). The results also demonstrated that association mapping within the population structure as well as stratification existing in cotton germplasm resources could complement and enhance quantitative trait loci (QTLs) information for marker-assisted selection.
Abstract Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium (LD). This study was carried out to estimate genetic diversity, population structure and the extent of LD to develop an association framework in order to identify genetic variations associated with drought and salt tolerance traits. 106 microsatellite marker primer pairs were used in 323 Gossypium hirsutum germplasms which were grown in the drought shed and salt pond for evaluation. Polymorphism (PIC=0.53) was found, and three groups were detected (K=3) with the second likelihood ΔK using STRUCTURE software. LD decay rates were estimated to be 13-15 cM at r2 0.20. Significant associations between polymorphic markers and drought and salt tolerance traits were observed using the general linear model (GLM) and mixed linear model (MLM) (P 0.01). The results also demonstrated that association mapping within the population structure as well as stratification existing in cotton germplasm resources could complement and enhance quantitative trait loci (QTLs) information for marker-assisted selection.
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Received: 26 June 2013
Accepted:
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| Fund: This research was supported by the National Natural Science Foundation of China (31201246) and the Project of International Science and Technology Cooperation and Exchange from the Ministry of Science and Technology, China (2010DFR30620-3). |
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Corresponding Authors:
DU Xiong-ming, E-mail: dujeffrey8848@hotmail.com
E-mail: dujeffrey8848@hotmail.com
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| About author: JIA Yin-hua, E-mail: jia.yinhua@gmail.com |
Cite this article:
JIA Yin-hua, SUN Jun-ling, WANG Xi-wen, ZHOU Zhong-li, PAN Zao-e, HE Shou-pu, PANG Bao-yin, WANG Li-ru , DU Xiong-ming.
2014.
Molecular Diversity and Association Analysis of Drought and Salt Tolerance in Gossypium hirsutum L. Germplasm. Journal of Integrative Agriculture, 13(8): 1845-1853.
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| Abdurakhmonovn I Y, Kohe R J, Yu J Z, Pepper A E,Abdullaev A A, Kushanov F N, Salakhutdinov I B, BurievZ T, Saha S, Scheffler B E, Jenkins J N, AbdukarimovA. 2008. Molecular diversity and association mapping offiber quality traits in exotic G. hirsutum L. germplasm.Genomics, 92, 478-487Abdurakhmonov I Y, Saha S, Jenkins J N, Buriev Z T,Shermatov S E, Scheffler B E, Pepper A E, Yu J Z, KohelR Z, Abdukarimov A. 2009. Linkage disequilibrium basedassociation mapping of fiber quality traits in G. hirsutumL. variety germplasm. Genetica, 136, 401-417Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape J M, YuJ Z, Jesudurai C, Jung S, Muthukumar S, Yellambalase P,Ficklin S, Staton M, Eshelman R, Ulloa M, Saha S, BurrB, Liu S, Zhang T Z, Fang D Q, Pepper A. 2006. CMD:A cotton microsatellite database resource for Gossypiumgenomics. BMC Genomics, 7, 132.Breseghello F, Sorrells M E. 2006. Association mapping ofkernel size and milling quality in wheat (Triticum aestivumL.) cultivars. Genetics, 172, 1165-1177Doebley J, Stec A, Hubbard L. 1997. The evolution of apicaldominance in maize. Nature, 386, 485-488Evanno G, Regnaut S, Goudet J. 2005. Detecting the numberof clusters of individuals using the software structure:A simulation study. Molecular Ecology, 14, 2611-2620Goldstein D B, Tate S K, Sisodiya S M. 2003. Pharmacogeneticsgoes genomic. Nature Reviews Genetics, 4, 937-947Hardy O J, Vekemans X. 2002. SpaGeDi: A versatile computerprogramto analyze spatial genetic structure at the individualor population levels. Molecular Ecology Notes, 2, 618-620Ivandic V, Thomas W T B, Nevo E, Zhang Z, Forster BP. 2003. Associations of simple sequence repeats withquantitative trait variation including biotic and abioticstress tolerance in Hordeum spontaneum. Plant Breeding,122, 300-304Kantartzi S K, Stewart J M. 2008. Association analysis of fibretraits in Gossypium arboreum accessions. Plant Breeding,127, 173-179Kohel R J, Yu J, Park Y H, Lazo G R. 2001. Molecular mappingand characterization of traits controlling fiber quality incotton. Euphytica, 121, 163-172Kraakman A T W, Rients E N, Petra M M, van den B M, StamP, van E F A. 2004. Linkage disequilibrium mapping ofyield and yield stability in modern spring barley cultivars.Genetics, 168, 435-446Lacape J M, Dessauw D, Rajab M, Noyer J L, Hau B.2007. Microsatellite diversity in tetraploid Gossypiumgermplasm: assembling a highly informative genotypingset of cotton SSRs. Molecular Breeding, 19, 45-58Lacape J M, Llewellyn D, Jacobs J, Arioli T, Becker D,Calhoun S, Al-Ghazi Y, Liu S, Georges O P S, GibandM, Giband M, de Assuncao H, Barroso P, Claverie M,Gawryziak G, Jean J, Vialle M, Viot C. 2010. Metaanalysisof cotton fiber quality QTLs across diverseenvironments in a Gossypium hirsutum×G. barbadenseRIL population. BMC Plant Biology, 10, 132.Levi A, Ovnat L, Paterson A H, Saranga Y. 2009a.Photosynthesis of cotton near-isogenic lines introgressedwith QTLs for productivity and drought related traits. PlantScience, 177, 88-96Levi A, Paterson A H, Barak V, Yakir D, Wang B, Chee P W,Saranga Y. 2009b. Field evaluation of cotton near-isogeniclines introgressed with QTLs for productivity and droughtrelated traits. Molecular Breeding, 23, 179-195Lilley J M, Ludlow M M, Mccouch S R, O’Toole J C. 1996.Locating QTL for osmotic adjustment and dehydrationtolerance in rice. Journal of Experimental Botany, 47,1427-1436Liu J, Ye W, Fan B. 1998. Studying and utilization of resistance of cotton in China. China Cotton, 25, 5-6Liu K, Muse S V. 2005. PowerMarker: An integrated analysisenvironment for genetic marker analysis. Bioinformatics,21, 2128-2129Ma X X, Ding Y Z, Zhou B L, Guo W Z, Lv Y L, Zhu X F,Zhang T Z. 2008. QTL mapping in A-genome diploidAsiatic cotton and their congruence analysis with ADgenometetraploid cotton in genus Gossypium. Journal ofGenetics and Genomics, 35, 751-762Mansur L M, Lark K G, Kross H, Oliveira A. 1993. Intervalmapping of quantitative trait loci for reproductive,morphological, and seed traits of soybean (Glycine maxL.). Theoretical and Applied Genetics, 86, 907-913Muhammad B, Yehoshua S, Zafar I, Muhammad A, Yusuf Z,Edward L, Peng C. 2009. Identification of QTLs and impactof selection from various environments (dry vs. irrigated)on the genetic relationships among the selected cotton linesfrom f6 population using a phylogenetic approach. AfricanJournal of Biotechnology, 8, 4802-4810Muhammad S, Guo W Z, Ihsan U, Tabbasam N, ZafarY, Rahman M, Zhang T Z. 2011. QTL mapping forphysiology, yield and plant architecture traits in cotton(Gossypium hirsutum L.) grown under well-wateredversus water-stress conditions. Electronic Journal ofBiotechnology, 14, 1-13Muhammad S, Guo W Z, Zhang T Z. 2014. Associationmapping for salinity tolerance in cotton (Gossypiumhirsutum L.) germplasm from US and diverse regions ofChina. Australian Journal of Crop Science, 8, 338-346Paterson A H, Smith R H. 1999. Future horizons: Biotechnologyfor cotton improvement. In: Smith C W, Cothren J T, eds.,Cotton: Origin, History, Technology, and Production.John Wiley&Sons, Inc., New York. pp. 415-432Pritchard J K, Stephens M, Donnelly P. 2000a. Inferenceof population structure using multilocus genotype data.Genetics, 155, 945-959Pritchard J K, Stephens M, Rosenberg N A, Donnelly P.2000b. Association mapping in structured populations.The American Journal of Human Genetics, 67, 170-181Pritchard J K, Wen W. 2003. Documentation for StructureSoftware. ver. 2. Department of Human Genetics,University of Chicago, Chicago.Rong J K, Feltus F A, Waghmare V N, Pierce G J, Chee PW, Draye X, Saranga Y, Wright R J, Wilkins T A, MayO L, Smith C W, Gannaway J R, Wendel J F, Paterson AH. 2007. Meta-analysis of polyploid cotton QTL showsunequal contributions of subgenomes to a complexnetwork of genes and gene clusters implicated in lintfiber development. The Genetics Society of America, 176,2577-2588Rungis D, Llewellyn D, Dennis E S, Lyon B R. 2005. Simplesequence repeat (SSR) markers reveal low levels ofpolymorphism between cotton (Gossypium hirsutum L.)cultivars. Australian Journal of Agricultural Research,56, 301-307Sambrook J, Fritsch E F, Maniatis T. 1989. Molecular Cloning,vol. 2. Cold Spring Harbor Laboratory Press, New York.Saranga Y, Menz M, Jiang C X, Wright R J, Yakir D, PatersonA H. 2001. Genomic dissection of genotype x environmentinteractions conferring adaptation of cotton to aridconditions. Genome Research, 11, 1988-1995Stich B, Melchinger A E, Frisch M, Maurer H P, HeckenbergerM, Reif J C. 2005. Linkage disequilibrium in Europeanelite maize germplasm investigated with SSRs. Theoreticaland Applied Genetics, 111, 723-730Thornsberry J M, Goodman M M, Doebley J, Kresovich S,Nielsen D, Buckler E S. 2001. Dwarf8 polymorphismsassociate with variation in flowering time. Nature Genetic,28, 286-289Tuberrosa R, Sanguineti M C, Landi P, Salvi S, Casarini E,Conti S. 1998. RFLP mapping of quantitative trait locicontrolling abscisic acid concentration in leaves of droughtstressedmaize (Zea mays L.). Theoretical and AppliedGenetics, 97, 744-755Viviane J D, Ed S B, Bruce D S, Thomas P G, Alan C,Doebley J, Pääbo S. 2003. Early allelic selection in maizeas revealed by ancient DNA. Science, 302, 1206-1208Wang R L, Stec A, Hey J, Lukens L, Doebley J. 1999. Thelimits of selection during maize domestication. Nature,398, 236-239Weiss K M, Clark A G. 2002. Linkage disequilibrium and themapping of complex human traits. Trends in Genetics,18, 19-24Ye W, Liu J. 1998. The method of evaluating the salt stressin cotton and utilization. China Cotton, 25, 34-38 (inChinese)Zhang H B, Li Y, Wang B, Chee P W. 2008. Recent advances incotton genomics. International Journal of Plant Genomics,2008, 742304.Zhang J, Wu Y T, Guo W Z, Zhang T Z. 2000. Fast screening ofmicrosatellite markers in cotton with PAGE/silver staining.Cotton Science, 12, 267-269 (in Chinese)Zhang X, Zhen J B, Li Z H, Kang D M, Yang Y M, Kong J,Hua J P. 2011. Expression profile of early responsive genesunder salt stress in upland cotton (Gossypium hirsutum L.).Plant Molecular Biology Reporter, 29, 626-637Zhang Z S, Hu M H, Zhang J, Liu D J, Zheng J, Zhang K,Wang W, Wan Q. 2009. Construction of a comprehensivePCR-based marker linkage map and QTL mapping for fiberquality traits in upland cotton (Gossypium hirsutum L.).Molecular Breeding, 24, 49-61. |
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