四倍体杂交群体的三点连锁分析模型
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摘要
多倍体在植物物种中分布广泛,约有半数以上的被子植物是多倍体或者进化史上发生过多倍体化。由于植物个体多倍化后出现新特点,使得其不仅在植物的遗传与进化上有着重要的研究价值,在农业的生产实践中也有着广泛的应用价值。连锁分析是基于孟德尔遗传定律,对标记之间的重组率与遗传距离进行推断的统计学方法,以连锁分析为基础制作的遗传图谱是遗传学领域最为重要的研究工具之一。然而,由于多倍体物种减数分裂时期存在的特殊细胞学现象----双减数分裂及配对倾向性使得传统的连锁分析模型不能适用多倍体物种。
在本文中,两个分别能够应用于同源四倍体与异源四倍体的连锁分析的统计学模型被提出。该系列模型基于三点连锁分析模型,整合了多倍体物种特有的细胞生物学现象。在最大似然法的框架下,结合EM最大期望估算法,该系列模型不仅可以对多倍体染色体组标记间的连锁进行准确的估算与检测,同时也能够获得衡量多倍体特有细胞生物学现象的参数。
一系列的模拟实验及真实数据分析表明,新的模型能够很好地应用到全信息分子标记以及部分信息分子标记数据中；此外研究还表明,与先前的多倍体两点连锁分析模型相比,基于三点分析的新模型能够得到更稳准确的重组率估算。
该系列三点模型为四倍体连锁分析提供了强有力的统计工具；同时,该模型可对四倍体特殊细胞学现象进行建模与量化,其估算结果在物种遗传多样性,多倍体起源方面的研究有着重要的意义。
Polyploidy is pervasive in plants and some estimates that more than50%of angiosperms are polyploidy, or experienced genome doubling in evolutionary history. Due to its special features, polyploidy not only display significant value in research on plant genetic evolution, but also in agricultural breeding practices. Linkage analysis is a statistical method for estimating the recombination fraction and genetic distance between markers. Genetic map, which is based on linkage analysis, is one of the most important tools in the field of genetics study. However, because of some special meiotic behavior---double reduction and preferential pairing, traditional method for estimating linkage cannot be deployed in polyploidy population.
In this thesis, two models were developed for linkage analysis in polyploidy species. These two models based on three points analysis and incorporated the important meiotic feature of polyploidy. By implementing the EM algorithm within the maximum likelihood framework, the models provides a procedure for simultaneous estimation of linkage and parameters measuring the meiotic behavior in polyploidy.
A series simulation studies and real data analysis has demonstrated the new models for polyploidy species can be well applied within fully informative markers and partially informative markers. Compare to the pervious method baseds on two points analysis, these two three points analysis method could provide more accurate estimation of recombination fraction.
The models provide robust statistical tools for linkage analysis in polyploidy population. The special meiotic behavior of polyploidy are modeled and measured in the models, therefore, the result from new models will help shed light on genetic diversity and origin of a polyploid population.
在本文中,两个分别能够应用于同源四倍体与异源四倍体的连锁分析的统计学模型被提出。该系列模型基于三点连锁分析模型,整合了多倍体物种特有的细胞生物学现象。在最大似然法的框架下,结合EM最大期望估算法,该系列模型不仅可以对多倍体染色体组标记间的连锁进行准确的估算与检测,同时也能够获得衡量多倍体特有细胞生物学现象的参数。
一系列的模拟实验及真实数据分析表明,新的模型能够很好地应用到全信息分子标记以及部分信息分子标记数据中；此外研究还表明,与先前的多倍体两点连锁分析模型相比,基于三点分析的新模型能够得到更稳准确的重组率估算。
该系列三点模型为四倍体连锁分析提供了强有力的统计工具；同时,该模型可对四倍体特殊细胞学现象进行建模与量化,其估算结果在物种遗传多样性,多倍体起源方面的研究有着重要的意义。
Polyploidy is pervasive in plants and some estimates that more than50%of angiosperms are polyploidy, or experienced genome doubling in evolutionary history. Due to its special features, polyploidy not only display significant value in research on plant genetic evolution, but also in agricultural breeding practices. Linkage analysis is a statistical method for estimating the recombination fraction and genetic distance between markers. Genetic map, which is based on linkage analysis, is one of the most important tools in the field of genetics study. However, because of some special meiotic behavior---double reduction and preferential pairing, traditional method for estimating linkage cannot be deployed in polyploidy population.
In this thesis, two models were developed for linkage analysis in polyploidy species. These two models based on three points analysis and incorporated the important meiotic feature of polyploidy. By implementing the EM algorithm within the maximum likelihood framework, the models provides a procedure for simultaneous estimation of linkage and parameters measuring the meiotic behavior in polyploidy.
A series simulation studies and real data analysis has demonstrated the new models for polyploidy species can be well applied within fully informative markers and partially informative markers. Compare to the pervious method baseds on two points analysis, these two three points analysis method could provide more accurate estimation of recombination fraction.
The models provide robust statistical tools for linkage analysis in polyploidy population. The special meiotic behavior of polyploidy are modeled and measured in the models, therefore, the result from new models will help shed light on genetic diversity and origin of a polyploid population.
引文
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2.刘爱民,常莉,薛建平.药用植物多倍体的诱导研究进展[J].中国中药杂志,2005,30(9)：645-652.
3.刘静.植物多倍体的形成及应用研究综述[J].安康学院学报,2011,23(4)：99-102.
4.匡全,梁国鲁,郭启高,等.秋水仙素诱导牛蒡多倍体[J].植物生理学通讯,2004,40(2)：157-158.
5.乔传卓,吴美枢,戴富宝,等.菘蓝多倍体育种的研究[J].植物学报,1989,31(9)：678-683.
6.邹道谦,崔丽华.秋水仙素诱导四倍体石刁柏的研究[J].河北农业大学学报,1990,13(1)：29-33.
7.杨继.植物多倍体基因组的形成与进化[J].植物分类学报,2001,39(4)：357-371.
8.郑思乡,王春桃,晏春耕,等.苎麻多倍体及其杂交后代的细胞学观察[J].农业现代化研究,1996,17(2)：108-111.
9.李铁军,王丽珍,杜雪.药用植物多倍体的研究概况[J].中药材,2009,32(9)：1481-1484.
10.张新忠,刘国俭.热激处理对桃,李离体花枝2n花粉产生的影响[J].园艺学报,1998,25(12)：133-138.
11.张自立,俞新大.植物细胞和体细胞遗传学技术与原理[M].北京：高等教育出版社,1990：224-230.
12.陶抵辉,刘明月,肖君泽,等.生物多倍体诱导方法研究进展[J].生命科学研究,2007,11(4)：6-13.
13.郭启高,宋明,梁国鲁.植物多倍体诱导育种研究进展[J].生物学通报.2000,35(2)：8-10.
14.晏春耕.植物多倍体及应用[J].生物科学通报.2007,42(4)：14-18
15.彭云霞,王宏霞,等.植物多倍体研究[J].甘肃农业科技.2012,11：29-32.
16. Blanc G, Hokamp K, Wolfe K.H. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genom[J]. Genome Research,2003,13:137-144.
17. Butruille DV, Boiteux LS. Selection-mutation balance in polysomic tetraploids:impact of double reduction and gametophytic selection on the frequency and subchromosomal localization of deleterious mutations[J]. Proc Natl Acad Sci USA,2000,97:6608-6613.
18. Chen ZJ. Molecular mechanisms of polyploidy and hybrid vigor[J]. Trends Plant Sci,2010,15:57-71.
19. Chester M, Gallagher JP, Symonds W, et al. Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogonmiscellus[J]. Proc Natl Acad Sci USA,2012, 109:1176-1181.
20. Comai L. The advantages and disadvantages of being polyploid[J]. Nat Rev Genet,2005,6:836-846.
21. Compton D, Grey J, et al. Identification of tetraploid regenerates from cotyledons of diploid watermelon cultured in vitro[J]. Euphytica,1996,87:165-172.
22. Darlington CD. Chromosome behaviour and structural hybridity in the Tradescantiae[J]. J Genet,1929, 21:207-86.
23. De Haan A, Maceira N O, Lumaret R, Delay J. Production of 2n gametes in diploid subspecies of Dactytis glomerata L.2. Occurrence and frequency of 2n eggs[J]. Ann Bot,1992,69:345-350
24. Fawcett JA, Maere S, Van de Peer Y. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci USA,2009,106:5737-5742.
25. Fisher RA. The theory of linkage in polysomic inheritance[J]. Phil Trans Roy Soc Ser, 1947,233:55-87.
26. Grant V. Plant speciation[M]. New York, USA:Columbia University Press.1981.
27. Grattapaglia D, Sederoff R. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophyylla using a pseudotestcross:mapping strategy and RAPD markers. Genetics,1994,137:1121-1137.
28. Guo W, Cai C, Wang C, et al. A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in gossypium. Genetics,2007,176:527-541.
29. Hagerup O. The spontaneous formation of haploid, polyploid and aneuploid embryos in some orchids[J].Kongel Danshe Videnskab Selskab Biol Meddelelser,1947,20:1-22
30. Hackett CA, Bradshaw JE, McNicol JW. Interval mapping of quantitative trait loci in multivalent tetraploid species[J]. Genetics,2001,159:1819-1832.
31. Haynes KG, Douches DS. Estimation of the coefficient of double reduction in the cultivated potato [J]. Theor Appl Genet,1993,85:857-862.
32. Hillers KJ. Crossover interference[J]. Curr Biol,2004,14:1036-1037.
33. Hou W, Liu T, Li Y, et al. Multilocus genomics of outcrossing plant populations[J]. Theor Pop Biol, 2009,76:68-76.
34. Jiao Y, Wickett NJ, Ayyampalayam S, et al. Ancestral polyploidy in seed plants and angiosperms Nature,2011,473:97-100.
35. Lagercrantz U, Lydiate DJ. Comparative genome mapping in Brassica[J]. Genetics,1996,144: 1903-1910.
36. Lander ES, Green P. Construction of multilocus genetic linkage maps in humans[J]. Proc Natl Acad Sci U S A,1987,84:2363-2367.
37. Lefon M, Grandont L, Eber F, et al. Crossovers get a boost in Brassica allotriploid and allotetraploid hybrids[J]. Plant Cell,2010,22:2253-2264.
38. Leitch AR, Leitch IJ. Genomic plasticity and the diversity of polyploid plants[J]. Science,2008, 320:481-483.
39. Li JH, Das K, Fu GF, et al. EM algorithm for mapping quantitative trait loci in multi-valent tetraploids[J]. Int J Plant Genom,2010, doh:10.1155/2010/216547.
40. Lu K, Kaeppler SM, Vogel KP, et al. Nuclear DNA content and chromosome numbers in switchgrass. Great Plains Res,1998,8:269-280.
41. Lu Q, Cui YH, Wu RL. A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family[J]. BMC Genetics,2004,5:20.
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