摘要
由于长期的生殖隔离和人工选择,芸薹属植物中三个基本染色体组(A,B,C)在不同种内发生了深刻的变化。为了区分这种变化,本实验室提出用“亚基因组”来定义不同物种中的相同基因组,并用不同种拉丁文名的首写字母作为上标来区分不同的亚基因组。甘蓝型油菜(Brassica napus, AnAnCnCn)是世界上重要的油料作物之一,然而有限的栽培驯化历史和近期频繁的品种间杂交使得其遗传基础日益狭窄,杂种优势利用徘徊不前。为充分利用亚基因组间的分化差异进行油菜的遗传改良,本实验室通过种间杂交将白菜型油菜(B. rapa, ArAr)的Ar基因组和埃塞俄比亚芥(B.carinata, BcBcCcCc)的Cc基因组部分地替换了甘蓝型油菜的An和Cn基因组,创建出第一代“新型甘蓝型油菜”。将新型甘蓝型油菜与常规甘蓝型油菜配制的杂种称为“亚基因组间杂种”。已有的研究表明,用第一代新型甘蓝型油菜所配置的亚基因组间杂种具有较强的杂种优势,杂种优势的强弱与新型甘蓝型油菜中外源基因组成分的多少成正相关。
在前期研究的基础上,本课题经分子标记辅助选择和多次的遗传重组,进一步提高了第一代新型甘蓝型油菜中Ar/Cc基因组成分,并在多种环境条件下选育优良单株,培育出Ar/Cc成分得到提高、农艺性状得到改良的第二代新型甘蓝型油菜。用第二代新型甘蓝型油菜与常规甘蓝型油菜测验品系配制的杂种,其生长势和种子产量在两年田间试验中均优于第一代新型甘蓝型油菜所配制的杂种,表现出更强的杂种优势。第二代新型甘蓝型油菜株系已经被国内育种家用于培育新型油菜不育系,被国际育种公司用于培育新的育种材料,还作为轮回亲本用于创建第三代新型甘蓝型油菜基因资源库,以进一步开拓油菜亚基因组间杂种优势。
通过广泛分布在甘蓝型油菜遗传图谱上的117对SSR标记,对24份第一代新型新型甘蓝型油菜、79份第二代新型甘蓝型油菜、9份合成新型甘蓝型油菜的外源亲本、以及69份常规甘蓝型油菜品种进行遗传多样性分析。结果表明所有新型甘蓝型油菜与常规甘蓝型油菜品种差异明显,并且第二代新型甘蓝型油菜不同株系间遗传差异较第一代新型甘蓝型油菜株系间遗传差异更大。随着新型甘蓝型油菜中Ar/Cc成分的增加,它们与甘蓝型油菜亲本以及常规品种之间的遗传差异增大。用白菜型油菜和埃塞俄比亚芥同时改良甘蓝型油菜比单一用白菜型油菜引入的遗传变异更大,表明引入外源亚基因组成分同时改良甘蓝型油菜A、C基因组,是拓宽甘蓝型油菜遗传基础的有效途径。与常规品种相比,新型甘蓝型油菜(尤其是第二代新型甘蓝型油菜)每个SSR位点上含有更多的等位基因以及更为丰富的特异等位基因；新型甘蓝型油菜中原有连锁不平衡位点被打破,建立了更多新的连锁不平衡位点且与新型甘蓝型油菜的表型变异密切相关。这暗示着为创建新型甘蓝型油菜而开展的种间杂交使油菜基因组产生了深刻的变化。
为了进一步剖析新型甘蓝型油菜基因组的结构变化及其对表型的影响,本研究以甘/白种间杂交(甘蓝型油菜品种华双3号X白菜型油菜品种天门油菜白)衍生的重组自交系群体(简称TH RIL)为材料,采用基于SSR、内含子以及反转录转座子序列设计的分子标记对该群体进行遗传作图并评价新型甘蓝型油菜内发生的序列变异。试验结果表明,TH RIL群体中不仅可以直接导入所有来自亚基因组间存在的序列变异,而且还产生了大量新的序列变异。这些新的序列变异绝大多数都是在创建新型甘蓝型油菜的种间杂交过程中遗传下来的,其中一半以上新变异的分离比例正常,但有相当一部分新变异可能因为竞争劣势或者优势而呈现偏分离,且在反转录转座子区域要比在SSR和内含子区域更易发生具有竞争优势的新变异。测序结果表明,SSR新序列变异主要表现在重复单位模体(motif)数目的变化,但这些模体的变化很有可能与基因的功能有关；新出现的反转录转座子标记代表的是新产生的反转录转座子位点,暗示着基因组内反转录转座子的激活而导致反转录转座子新拷贝的插入。
在TH RIL遗传连锁图谱上定位了672个分子标记,检测到发生了各类序列变异的位点628个。将3个白菜型油菜遗传连锁图和2个常规甘蓝型油菜遗传连锁图分别进行了图谱整合。将整合遗传图谱与TH RIL遗传连锁图谱进行图谱比较分析,在新型甘蓝型油菜基因组中发现了大量的染色体重排事件。大约三分之一的重排事件是由于白菜型油菜Ar基因组与甘蓝型油菜的An基因组自身存在的结构差异而导致的,而大部分重排事件是由于种间杂交诱发的新的基因组结构变异。对TH RIL群体中所检测到的各类序列变异以及染色体重排事件之间的总体关系进行分析发现,新的SSR序列变异的发生与重排事件的发生以及新的反转录转座子序列变异的发生均呈显著相关(P<0.01)。虽然没有检测到反转录转座子新的序列变异与重排事件之间存在相关性,但很多重排事件都涉及到了新的反转录转座子位点的出现。这暗示着基因组内的染色体重排以及反转录转座子的活动会加速SSR的变异,而反转录转座子的活动与染色体重排密切相关。进一步分析了TH RIL群体的3个产量性状以及6个产量相关性状的两年田间数据,结果表明新型甘蓝型油菜基因组中新的结构变异对植株的农艺性状影响很大,其中新的反转录转座子位点的出现对农艺性状的影响最大。
根据本研究的分析结果,探讨了种间杂交导致各类基因组结构变异的可能机制及亚基因组间杂种优势产生的可能机制,提出了进一步进行新型甘蓝型油菜的遗传改良和开拓亚基因组间杂种优势的新途径。
As a result of long-term reproductive isolation and artificial selection, the three basic genomes (A, B, C) in different species have undergone profound changes in Brassica crops. In order to distinguish this differentiation, our laboratory previously proposed the concept of "subgenome" to define the same genome in different species, and used the initials of the Latin names of different species as a superscript to distinguish different subgenomes. B. napus (AnAnCnCn) is one of the world's most important oil crops, however, its limited history of cultivation and domestication, and the recent frequent intraspecific hybridization lead to an increasingly narrow genetic base and the stagnancy of heterosis utilization. To take full advantage of subgenomic differences for the genetic improvement of oilseed rape, we partially replaced the An and Cn genome of B. napus by the Ar genome of B. rapa (ArAr) and Cc genome of B. carinata (BcBcCcCc) resulting in the first generation of new type B. napus. Heterosis between "traditional" B. napus and the new type B. napus can therefore be defined as "intersubgenomic heterosis". Significant intersubgenomic heterosis was observed in the hybrids made with the first generation lines of new type B. napus over the past ten years of field trials, and positively related with the introgressed subgenomic components in the parental new type B. napus.
Based on the previous research basis, a second generation of new type B. napus was developed with improved agronomic traits and higher introgressed subgenomic components in this project, by selecting the plants with higher proportion of exotic-subgenomic components from segregated populations of first generation of new type B. napus and screenging the agronomic traits under different environments. The intersubgenomic hybrids made with the second generation lines of new type B. napus exhibited stronger heterosis than the intersubgenomic hybrids made with the first generatin lines in two years on the traits of seed yield and biomass. The excellent lines of the second generation of new type B. napus were selected for breeding new type of male sterile lines and bridge materials for the Chinese breeders and international company abroad, and used as the recurrent parents for the construction of the gene resource pool of the third generation lines of new type B. napus for broadening the avenue of intersubgenomic heterosis in rapeseed.
Genetic diversity analysis was conducted with 117 pairs of SSR markers distributed on published genetic map of B. napus, among 24 lines of the first generation of new type B. napus,79 lines of the second generation of new type B. napus,9 Brassica species as the original parents for the synthesis of new type B. napus, and 69 varieties of traditional B. napus. The results showed that there was significant genetic difference between new type B. napus and traditional B. napus, and bigger genetic distance was observed among the lines of the second generation of new type B. napus than the first generation of new type B. napus. Along with the increment of the genomic components of Ar/Cc in new type B. napus, the genetic difference between new type B. napus and traditional B. napus was enlarged. Introgressing of the genomic components from B. rapa and B. carinata synchronously into B. napus introduced more genetic variation than simply introgressing Ar component, which suggested that replacing the A and C genome of B. napus at the same time was an efficient way in broadening the genetic basis of B. napus. Compared with the traditional B. napus, the new type B. napus (especially the second generation lines) contained more alleles and group-special alleles per SSR locus, and constructed more new linkage disequilibrium loci pairs associated with the phenotypic variation. This implied the process of interspecific hybridization for the development of new type B. napus brought out profound genomic changes for new type B. napus.
To further dissect the genomic changes of new type B. napus and their impacts on the phenotypes, three kinds of molecular markers based on the SSR, intron, and retrotransposon were used to evaluate the sequence variation in a recombination inbred line population (TH RIL population) derived from an interspecific hybridization between B. rapa (Tianmenyoucaibai) and B. napus (Huashuang3). The results showed that abundant novel sequence variation was observed in TH RIL population along with the introgression of all specific sequence variation between subgenomes. The majority of the novel sequence variation was inherited from the process of interspecific hybridization, most of which showed normal segregation, however, a considerable portion of the novel sequence variation exhibited with distorted segregation possibly because of competitive disadvantages or advantages for the survival of the population. Novel sequence variation in retrotransposon showed advantages was much more than that in SSR and intron. The results on sequencing the novel variation showed that the novel sequence variation for SSR were mainly resulted from the changes of motifs, which was possibly associated with gene function; the newly appeared retrotransposon variation were detected in new retrotransposon loci, which was possibly resulted from the insertion of new copies of retrotransposon because of reactivation.
672 molecular markers were mapped on the genetic map of TH RIL population, representing 628 loci exhibited with various sequence variation. Three genetic maps of B. rapa and two genetic maps of B. napus was integrated, respectively. A lot of rearrangement events were detected in TH RIL population by the comparison among the two integrated maps and TH genetic map.Apporximately one third of the rearrangement events were resulted from the introgression of the pre-existed rearrangements between the genome of Ar and An, but most of the rearrangements were resulted from novel genomic structural variation induced by interspecific hybridization. The coefficient of correlation among various sequence variation and rearrangement events in TH RIL population was analyzed. The data showed that the novel sequence variation of SSR was positively and significantly (P<0.01) associated with the rearrangement events and new retrotransposon loci. Though no significant relativity was detected between the appearance of new retrotransposon loci and rearrangement events, considerable rearrangement events were involved with new retrotransposon loci. These resultes implied that the rearrangement evnents and reactivation of retrotransposon in new type B. napus prompted the mutation of SSR, and the reactivation of retrotransposon were intimately associated with rearrangement events. We further analyzed the two-year of field data about three yield traits and six yield related traits, which showed that the novel genomic structural variation had great impacts on the important agronomic traits of new type B. napus, and the novel retrotransposon loci showed the most significant impacts on the agronomic traits.
Based on the results of this paper, the mechanism of various genomic structural variation and intersubgenomic heterosis was discussed, and new approaches in improving the new type B. napus and exploring intersubgenomic heterosis was put forward.
引文
1. 陈新.油菜亚基因组杂种和亲本的基因差异表达研究.[博士学位论文].武汉：华中农业大学图书馆,2008
2. 傅廷栋.杂交油菜的育种与利用.湖北科学技术出版社,2000,1-5
3. 黄顺谋.油菜亚基因组间杂种优势的表现及其遗传基础分析.[硕士学位论文].武汉：华中农业大学图书馆,2008
4. 黄镇.分子标记辅助选择培育新型甘蓝型油菜隐性细胞核雄性不育系.[博士学位论文].武汉,华中农业大学图书馆,2008
5. 栗茂腾.甘蓝型油菜新类型创建及油菜亚基因组间杂种优势研究.[博士学位论文].武汉：华中农业大学图书馆,2003
6. 李媛媛,傅廷栋,马朝芝.芸薹属植物比较基因组学研究进展.植物学通报,2007,24：200—207
7. 钱伟.甘蓝型油菜与白菜型油菜亚基因组间杂种优势的研究.[博士学位论文].武汉：华中农业大学图书馆,2003
8. 孙逢吉.芸薹属之杂种优势.中华农学会会报,1943,175：35—38
9. 宋来强.甘蓝型油菜显性细胞核雄性不育的遗传与应用模式.[博士学位论文].武：华中农业大学图书馆,2006
10.萨姆布鲁克J,D.W.拉塞尔.分子克隆实验指南(第三版).黄培堂等译.北京：科学出版社,2002,96—99
11.肖麓.新型甘蓝型油菜核不育系的选育及隐性上位基因BnRf的定位.[博士学位论文].武汉：华中农业大学图书馆,2008
12.袁隆平.杂交水稻的育种战略设想.杂交水稻,1987,1：1—3
13. Alix K, Ryder C D, Moore J, King G J, Heslop-Harrison J S. The genomic organization of retrotransposons in Brassica oleracea. Plant Molecular Biology,2005,59:839-851
14. Allard R W. Principles of Plant Breeding. John Wiley & Sons, IncNew York,1960:68
15. Allnutt TR, Roper K, Henry C. Development and application of SINE multilocus and quantitative genetic markers to study oilseed rape(Brassica napus L.) crops. J Agric Food Chem,2008,56: 426-432
16. Ammiraju J S, Zuccolo A, Yu Y, Song X, Piegu B, Chevalier F, Walling J G, Ma J, Talag J, Brar D S, SanMiguel P J, Jiang N, Jackson S A, Panaud O, Wing R A. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J,2007,52:342-351
17. Antonius-Klemola K, Kalendar R, Schulman A H.TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports. Theor Appl Genet,2006,112:999-1008
18. Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J. BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics,2004, 202:324-2326
19. Axelsson T, Shavorskaya O, Lagercrantz U. Multiple flowering time QTLs within several Brassica species could be the result of duplicated copies of one ancestral gene. Genome,2001,44: 856-864
20. Babula D, Ruminska M,Sadowski J. Using Arabidopsis thaliana genetic and physical maps as tools to study Brassica genomes. Pfluegers Archiv European Journal of Physiology,2000,439: R23
21. Barnes S. Comparing Arabidopsis to other flowering plants. Current Opinion in Plant Biology, 2002,5:128-133
22. Becker H C, Engqvist G M, Karlsson B. Comparison of rapeseed cultivars and resynthesized lines based on allozyme and RFLP markers. Theor Appl Genet,1995,91:62-67
23. Bennett R A, Thiagarajah M R, King JR., Rahman M H. Interspecific cross of Brassica oleracea var. alboglabra and B. napus:effects of growth condition and silique age on the efficiency of hybrid production, and inheritance of erucic acid in the self-pollinated backcross generation. Euphytica,2008,164:593-601
24. Bennetzen J L. The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol,1996,4:347-353
25. Bennetzen J L. Transposable elements, gene creation and genome rearrangement in flowering plants. Current Opinion in Genetics& Development,2005,15:621-627
26. Bennetzen J L, SanMiguel P, Chen M, Tikhonov A, Francki M, Avramova Z. Grass genomes. Proc Natl Acad Sci U S A,1998,95:1975-1978
27. Bento M, Pereira H S, Rocheta M, Gustafson P, Viegas W, Silva M. Polyploidization as a retraction force in plant genome evolution:sequence rearrangements in Triticale. PLoS ONE, 2008,3:e1402
28. Boivin K, Acarkan A, Mbulu R S, Clarenz O, Schmidt R. The Arabidopsis genome sequence as a tool for genome analysis in Brassicaceae. A comparison of the Arabidopsis and Capsella rubella genomes. Plant Physiology,2004,135:735-744
29. Bouck A, Peeler R, Arnold M L, Wessler SR. Genetic mapping of species boundaries in Louisiana irises using IRRE retrotransposon display markers. Genetics,2005,171:1289-1303
30. Camirand A, Brisson N. The complete nucleotide sequence of the Tst1 retrotransposon of potato. Nucleic Acids Res,1990,18:4929
31. Camussi A, Ottaviano E, Calinski T, Kaczmarek Z. Genetic distances based on quantitative traits. Genetics,1985,111:945-962
32. Cavell A C, Lydiate D J, Parkin I A P, Dean C, Trick M. Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome. Genome,1998,41:62-69
33. Chen X, Li M T, Shi J Q, Fu D H, Qian W, Zou J, Zhang C Y, Meng J L. Gene expression profiles associated with intersubgenomic heterosis in Brassica napus. Theor Appl Genet,2008,117: 1031-1040
34. Choi S R, Teakle G R, Plaha P, Kim J H, Allender C J, Beynon E, Piao Z Y, Soengas P, Han T H, King G J, Barker G C, Hand P, Lydiate D J, Batley J, Edwards D, Koo D H, Bang J W, Park B S, Lim Y P. The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theor Appl Genet,2007,115:777-792
35. Cowling W A. Genetic diversity in Australian canola and implications for crop breeding for changing future environments. Field Crops Research,2007,104:103-111
36. Crombach A, Hogeweg P. Chromosome rearrangements and the evolution of genome structuring and adaptability. Mol Biol Evol,2007,24:1130-1139
37. Darwin C R. The Effects of Cross-and Self-fertilization in the Vegetable Kingdom. John Murray, 1876
38. Dodds K S. Hybrid vigour in plant breeding. Proceedings of the Royal Society of London Series B-Biological Sciences,1955,144:185-192
39. Dolgin E S, Charlesworth B. The effects of recombination rate on the distribution and abundance of transposable elements. Genetics,2008,178:2169-2177
40. Dooner H K, He L. Maize genome structure variation:interplay between retrotransposon polymorphisms and genic recombination. Plant Cell,2008,20:249-258
41. Falush D, Stephens M, Pritchard J K. Inference of population structure using multilocus genotype data:dominant markers and null alleles. Molecular Ecology Notes,2007,7:574-578
42. Flavell A J, Knox M R, Pearce S R, Ellis T H. Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J,1998,16:643-650
43. Flavell A J, Pearce S R, Heslop-Harrison P, Kumar A. The evolution of Tyl-copia group retrotransposons in eukaryote genomes. Genetica,1997,100:185-195
44. Fourmann M, Barret P, Froger N, Baron C, Charlot F, Delourme R, Brunel D. From Arabidopsis thaliana to Brassica napus:development of amplified consensus genetic markers (ACGM) for construction of a gene map. Theor Appl Genet,2002,105:1196-1206
45. Friesen N, Brandes A, Heslop-Harrison J S. Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers. Mol Biol Evol,2001,18:1176-1188
46.34. Fujimoto R, Sasaki T, Inoue H, Nishio T. Hypomethylation and transcriptional reactivation of retrotransposon-like sequences in ddml transgenic plants of Brassica rapa. Plant Mol Biol, 2008,66:463-473
47. Gaeta R T, Pires J C, Iniguez-Luy F, Leon E, Osborn T C. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell,2007,19: 3403-3417
48. Gale M D, Devos K M. Plant comparative genetics after 10 years. Science,1998,282:656-659
49. Gao M Q, Li G Y, McCombie W R, Quiros C F. Comparative analysis of a transposon-rich Brassica oleracea BAC clone with its corresponding sequence in A. thaliana. Theor Appl Genet, 2005,111:949-955
50. Geregory T R. The evolution of the genome. Elsevier Academic Press, Inc., London, UK,2005
51. Grandbastien M A, Audeon C, Bonnivard E, Casacuberta J M, Chalhoub B, Costa A P, Le Q H, Melayah D, Petit M, Poncet C, Tam S M, Van Sluys M A, Mhiri C. Stress activation and genomic impact of Tntl retrotransposons in Solanaceae. Cytogenet Genome Res,2005,110:229-241
52. Gray Y H. It takes two transposons to tango:transposable-element-mediated chromosomal rearrangements. Trends Genet,2000,16:461-468
53. Hamilton A, Voinnet O, Chappell L, Baulcombe D. Two classes of short interfering RNA in RNA silencing. EMBO J,2002,21:4671-4679
54. Han F P, Fedak G, Guo W L, Liu B. Rapid and repeatable elimination of a parental genome-specific DNA repeat (pGcIR-1a) in newly synthesized wheat allopolyploids. Genetics, 2005,170:1239-1245
55. Handa H. The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed(Brassica napus L.):comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana. Nucleic Acids Research,2003,31:5907-5916
56. Hilbricht T, Varotto S, Sgaramella V, Bartels D, Salamini F, Furini A. Retrotransposons and siRNA have a role in the evolution of desiccation tolerance leading to resurrection of the plant Craterostigma plantagineum. New Phytol,2008,179:877-887
57. Hirochika H. Retrotransposons of rice:their regulation and use for genome analysis. Plant Mol Biol,1997,35:231-240
58. Hirochika H, Okamoto H, Kakutani T. Silencing of retrotransposons in Arabidopsis and reactivation by the ddml mutation. Plant Cell,2000,12:357-369
59. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M. Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci,1996,93:7783-7788
60. Hong C P, Kwon S J, Kim J S, Yang T J, Park B S, Lim Y P. Progress in understanding and sequencing the genome of Brassica rapa. Int J Plant Genomics,2008,2008:582837
61. Hong C P, Piao Z Y, Kang T W, Batley J, Yang T J, Hur Y K, Bhak J, Park B S, Edwards D, Lim Y P. Genomic distribution of simple sequence repeats in Brassica rapa. Molecules and Cells, 2007,23:349-356
62. Jaccard P. Nouvelles recherches sur la distribution florale. Bulletin de la Societe Vaudoise des lles. Sciences Nature,1908,44:223-270
63. Jackson S A, Cheng Z K, Wang M L, Goodman H M, Jiang J M. Comparative fluorescence in situ hybridization mapping of a 431-kb Arabidopsis thaliana bacterial artificial chromosome contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome. Genetics,2000,156:833-838
64. Kajikawa M, Okada N. LINEs mobilize SINEs in the eel through a shared 3'sequence. Cell,2002, 111:433-444
65. Kalendar R, Schulman A H. IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nature protocols,2006b,1:2478-2484
66. Kalendar R, Vicient C M, Peleg O, Anamthawat-Jonsson K, Bolshoy A, Schulman A H. Large retrotransposon derivatives:abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics,2004,166:1437-1450
67. Kashi Y, King D G. Simple sequence repeats as advantageous mutators in evolution. Trends in Genetics,2006,22:253-259
68. Kashkush K, Feldman M, Levy A A. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nature Genetics,2003,33:102-106
69. Kenward K D, Bai D, Ban M R, Brandle J E. Isolation and characterization of Tnd-1, a retrotransposon marker linked to black root rot resistance in tobacco. Theor Appl Genet,1999,98: 387-395
70. Kimura Y, Tosa Y, Shimada S, Sogo R, Kusaba M, Sunaga T, Betsuyaku S, Eto Y, Nakayashiki H, Mayama S. OARE-1, a Tyl-copia retrotransposon in oat activated by abiotic and biotic stresses. Plant Cell Physiol,2001,42:1345-1354
71. Knoop V, Unseld M, Marienfeld J, Brandt P, Sunkel S, Ullrich H, Brennicke A. copia-, gypsy-and LINE-like retrotransposon fragments in the mitochondrial genome of Arabidopsis thaliana. Genetics,1996,142:579-585
72. Kole C, Quijada P, Michaels S,D, Amasino R M, Osborn T C. Evidence for homology of flowering-time genes VFR2 from Brassica rapa and FLC from Arabidopsis thaliana. Theor Appl Genet,2001,102:425-430
73. Kole C, Williams P H, Rimmer S R, Osborn T C. Linkage mapping of genes controlling resistance to white rust(Albugo candida) in Brassica rapa (syn. campestris) and comparative mapping to Brassica napus and Arabidopsis thaliana. Genome,2002,45:22-27
74. Komatsu M, Shimamoto K, Kyozuka J. Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma. Plant Cell,2003,15:1934-1944
75. Kovarik A, Pires JC, Leitch A R, Lim K Y, Sherwood A M, Matyasek R, Rocca J, Soltis D E, Soltis P S. Rapid concerted evolution of nuclear ribosomal DNA in two tragopogon allopolyploids of recent and recurrent origin. Genetics,2005,169:931-944
76. Kowalski S P, Lan T H, Feldmann K A, Paterson A H. Comparative mapping of Arabidopsis-Thaliana and Brassica-Oleracea chromosomes reveals islands of conserved organization. Genetics,1994,138:499-510
77. Krom N, Recla J, Ramakrishna W. Analysis of genes associated with retrotransposons in the rice genome. Genetica,2008,134:297-310
78. Kwon S J, Kim D H, Lim M H, Long Y, Meng J L, Lim KB, Kim J A, Kim J S, Jin M, Kim H I, Ahn S N, Wessler S R, Yang T J, Park B S. Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives. Mol Genet Genomics,2007,278:361-370
79. Labrador M, Farre M, Utzet F, Fontdevila A. Interspecific hybridization increases transposition rates of Osvaldo. Molecular Biology and Evolution,1999,16:931-937
80. Lagercrantz U. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics,1998,150:1217-1228
81. Lagercrantz U, Lydiate D J. Comparative genome mapping in Brassica. Genetics,1996,144: 1903-1910
82. Lagercrantz U, Putterill J, Coupland G, Lydiate D. Comparative mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time. Plant Journal,1996,9:13-20
83. Lan T H, DelMonte T A, Reischmann K P, Hyman J, Kowalski S P, McFerson J, Kresovich S, Paterson A H. An EST-enriched comparative map of Brassica oleracea and Arabidopsis thaliana. Genome Research,2000,10:776-788
84. Lan T H, Paterson A H. Comparative mapping of quantitative trait loci sculpting the curd of Brassica oleracea. Genetics,2000,155:1927-1954
85. Lan T H, Paterson A H. Comparative mapping of QTLs determining the plant size of Brassica oleracea. Theor Appl Genet,2001,103:383-397
86. Le Rouzic A, Boutin TS, Capy P. Long-term evolution of transposable elements. Proc Natl Acad Sci,2007,104:19375-19380
87. Leeton P R, Smyth D R. An abundant LINE-like element amplified in the genome of Lilium speciosum. Mol Gen Genet,1993,237:97-104
88. Leflon M, Eber F, Letanneur J C, Chelysheva L, Coriton O, Huteau V, Ryder C D, Barker G, Jenczewski E, Chevre AM. Pairing and recombination at meiosis of Brassica rapa (AA) x Brassica napus (AACC) hybrids. Theor Appl Genet,2006,113:1467-1480
89. Lenoir A, Pelissier T, Bousquet-Antonelli C, Deragon J M. Comparative evolution history of SINEs in Arabidopsis thaliana and Brassica oleracea:evidence for a high rate of SINE loss. Cytogenetic and Genome Research,2005,110:441-447
90. Levy A A, Feldman M. Genetic and epigenetic reprogramming of the wheat genome upon allopolyploidization. Biological Journal of the Linnean Society,2004,82:607-613
91. Li M T, Chen X, Meng J L. Intersubgenomic heterosis in rapeseed production with a partial new-typed Brassica napus containing subgenome A(r) firom B. rapa and C-c from Brassica carinata. Crop Science,2006,46:234-242
92. Li M T, Li Z Y, Zhang C Y, Qian W, Meng J L. Reproduction and cytogenetic characterization of interspecific hybrids derived from crosses between Brassica carinata and B. rapa. Theor Appl Genet,2005,110:1284-1289
93. Li M T, Qian W, Meng J L, Li Z Y. Construction of novel Brassica napus genotypes through chromosomal substitution and elimination using interploid species hybridization. Chromosome Research,2004,12:417-426
94. Lim K B, Yang T J, Hwang Y J, Kim J S, Park J Y, Kwon S J, Kim J A, Choi B S, Lim M H, Jin M, Kim H I, de Jong H, Bancroft I, Lim Y, Park B S. Characterization of the centromere and peri-centromere retrotransposons in Brassica rapa and their distribution in related Brassica species. Plant Journal,2007,49:765-765
95. Lim Y P, Choi S R, Kim J H, Piao Z Y, Plaha P, Han T H, Koo D H, Bang J W, King G J, Teakle G R, Allender C J, Lydiate D J, Beynon E, Osborn T C. Construction of genetic linkage map based on molecular markers and analysis of QTLs controlling morphological traits in Chinese cabbage(Brassica rapa L.ssp.pekinensis). Plant Biology (Rockville),2004,2004:183
96. Liu B, Wendel J F. Retrotransposon activation followed by rapid repression in introgressed rice plants. Genome,2000,43:874-880
97. Liu K J, Muse S V. PowerMarker:an integrated analysis environment for genetic marker analysis. Bioinformatics,2005,21:2128-2129
98. Liu R, Qian W, Meng J. Association of RFLP markers and biomass heterosis in trigenomic hybrids of oilseed rape (Brassica napus x B-campestris). Theor Appl Genet,2002,105: 1050-1057
99. Long Y, Shi J, Qiu D, Li R, Zhang C, Wang J, Hou J, Zhao J, Shi L, Park B S, Choi S R, Lim Y P, Meng J. Flowering time quantitative trait loci analysis of oilseed Brassica in multiple environments and genomewide alignment with Arabidopsis. Genetics,2007,177:2433-2444
100. Lukens L, Zou F, Lydiate D, Parkin I, Osborn T. Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana. Genetics,2003,164:359-372
101. Maloof JN. QTL for plant growth and morphology. Current Opinion in Plant Biology,2003,6: 85-90
102. Malysheva-Otto LV, Ganal MW, Roder MS. Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). Bmc Genetics,2006,7
103. Manninen O, Kalendar R, Robinson J, Schulman A H. Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley. Mol Gen Genet,2000, 264:325-334
104. Martinsen G D, Whitham T G, Turek R J, Keim P. Hybrid populations selectively filter gene introgression between species. Evolution,2001,55:1325-1335
105. McClintock B. The Significance of Responses of the Genome to Challenge. Science,1984,226: 792-801
106. McGrath J M, Quiros C F, Harada J J, Landry B S. Identification of Brassica-Oleracea monosomic alien chromosome addition Lines with molecular markers reveals extensive gene duplication. Molecular & General Genetics,1990,223:198-204
107. Mieczkowski P A, Lemoine F J, Petes T D. Recombination between retrotransposons as a source of chromosome rearrangements in the yeast Saccharomyces cerevisiae. DNA Repair (Amst),2006, 5:1010-1020
108. Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nature Genetics,2002,30:194-200
109. Neumann P, Yan H, Jiang J. The centromeric retrotransposons of rice are transcribed and differentially processed by RNA interference. Genetics,2007,176:749-761
110. Nicolas S D, Le Mignon G, Eber F, Coriton O, Monod H, Clouet V, Huteau V, Lostanlen A, Delourme R, Chalhoub B, Ryder C D, Chevre A M, Jenczewski E. Homeologous recombination plays a major role in chromosome rearrangements that occur during meiosis of Brassica napus haploids. Genetics,2007,175:487-503
111. Nishio T. Polyploidy and genome analysis of Brassicaceae. Genes and Genetic Systems,2000,75: 360
112. Oliveira E, Padua J G, Zucchi M I, Vencovsky R, Vieira M L C. Origin, evolution and genome distribution of microsatellites. Genetics and Molecular Biology,2006,29:294-307
113. Osborn T C, Butrulle D V, Sharpe A G, Pickering K J, Parkin I A P, Parker J S, Lydiate D J. Detection and effects of a homeologous reciprocal transposition in Brassica napus. Genetics, 2003,165:1569-1577
114. Ozkan H, Levy A A, Feldman M. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell,2001,13:1735-1747
115. Parkin I A P, Gulden S M, Sharpe A G, Lukens L, Trick M, Osborn T C, Lydiate D J. Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics,2005,171:765-781
116. Parkin I A P, Sharpe A G, Keith. D J, Lydiate D J. Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome,1995,38:1122-1131
117. Parkin I A P, Sharpe A G, Lydiate D J. Patterns of genome duplication within the Brassica napus genome. Genome,2003,46:291-303
118. Pearce S R, Knox M, Ellis T H, Flavell A J, Kumar A. Pea Tyl-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum. Mol Gen Genet, 2000,263:898-907
119. Pereira V. Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biol,2004,5:R79
120. Petit M, Lim K Y, Julio E, Poncet C, de Borne F D, Kovarik A, Leitch A R, Grandbastien M A, Mhiri C. Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum). Molecular Genetics and Genomics,2007,278:1-15
121. Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, Kim H, Collura K, Brar D S, Jackson S, Wing R A, Panaud O. Doubling genome size without polyploidization:Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Research,2006,16:1262-1269
122. Piquemal J, Cinquin E, Couton F, Rondeau C, Seignoret E, Doucet I, Perret D, Villeger M J, Vincourt P, Blanchard P. Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers. Theor Appl Genet,2005,111:1514-1523
123. Pires J C, Zhao J W, Schranz M E, Leon E J, Quijada P A, Lukens L N, Osborn T C. Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biological Journal of the Linnean Society,2004,82:675-688
124. Pontes O, Neves N, Silva M, Lewis M S, Madlung A, Comai L, Viegas W, Pikaard C S. Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proc Natl Acad Sci,2004,101:18240-18245
125. Pouch-Pelissier M N, Pelissier T, Elmayan T, Vaucheret H, Boko D, Jantsch M F, Deragon J M. SINE RNA induces severe developmental defects in Arabidopsis thaliana and interacts with HYL1 (DRB1), a key member of the DCL1 complex. PLoS Genet,2008,4:e1000096
126. Pouilly N, Delourme R, Alix K, Jenczewski E. Repetitive sequence-derived markers tag centromeres and telomeres and provide insights into chromosome evolution in Brassica napus. Chromosome Research,2008,16:683-700
127. Qian W, Chen X, Fu D, Zou J, Meng J. Intersubgenomic heterosis in seed yield potential observed in a new type of Brassica napus introgressed with partial Brassica rapa genome. Theor Appl Genet,2005,110:1187-1194
128. Qian W, Sass O, Meng J, Li M, Frauen M, Jung C. Heterotic patterns in rapeseed (Brassica napus L.):Ⅰ. Crosses between spring and Chinese semi-winter lines. Theor Appl Genet,2007,115: 27-34
129. Qiu D, Morgan C, Shi J, Long Y, Liu J, Li R, Zhuang X, Wang Y, Tan X, Dietrich E, Weihmann T, Everett C, Vanstraelen S, Beckett P, Fraser F, Trick M, Barnes S, Wilmer J, Schmidt R, Li J, Li D, Meng J, Bancroft I. A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content. Theor Appl Genet,2006,114:67-80
130. Queen R A, Gribbon B M, James C, Jack P, Flavell A J. Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat. Mol Genet Genomics,2004,271: 91-97
131. Quijada P A, Udall J A, Lambert B, Osborn T C. Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.):1. Identification of genomic regions from winter germplasm. Theor Appl Genet,2006,113:549-561
132. Ramsay L, Macaulay M, Cardle L, Morgante M, degli Ivanissevich S, Maestri E, Powell W, Waugh R. Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant Journal,1999,17:415-425
133. Rana D, Boogaart T, O'Neill C M, Hynes L, Bent E, Macpherson L, Park J Y, Lim Y P, Bancroft I. Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives. Plant Journal,2004,40:725-733
134. Rohlf FJ. NTSYS-PC 2.1. Numerical taxonomy and multivariate analysis system. Exeter Software, Setauket, NY.,1997,
135. Sadowski J, Gaubier P, Delseny M, Quiros C F. Genetic and physical mapping in Brassica diploid species of a gene cluster defined in Arabidopsis thaliana. Molecular & General Genetics,1996, 251:298-306
136. Sadowski J, Quiros C F. Organization of an Arabidopsis thaliana gene cluster on chromosome 4 including the RPS2 gene, in the Brassica nigra genome. Theor Appl Genet,1998,96:468-474
137. SASInstitute. SAS Online Doc (R), version 8.0, Cary, IVC, USA,1999,
138. Schmidt A L, Anderson L M. Repetitive DNA elements as mediators of genomic change in response to environmental cues. Biological Reviews,2006,81:531-543
139. Schmidt R, Acarkan A, Boivin K. Comparative structural genomics in the Brassicaceae family. Plant Physiology and Biochemistry,2001,39:253-262
140. Schranz M E, Lysak M A, Mitchell-Olds T. The ABC's of comparative genomics in the Brassicaceae:building blocks of crucifer genomes. Trends in Plant Science,2006,11:535-542
141. Schwarz-Sommer Z, Leclercq L, Gobel E, Saedler H.Cin4, an insert altering the structure of the Al gene in Zea mays, exhibits properties of nonviral retrotransposons. EMBO J,1987,6: 3873-3880
142. Sensoz S, Angin D, Yorgun S, Kockar O M. Biooil production from an oilseed crop:Fixed-bed pyrolysis of rapeseed (Brassica napus L.). Energy Sources,2000,22:891-899
143. Seyis F, Friedt W, Luhs W. Yield of Brassica napus L. hybrids developed using resynthesized rapeseed material sown at different locations. Field Crops Research,2006,96:176-180
144. Shaked H, Kashkush K, Ozkan H, Feldman M, Levy A A. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell,2001,13:1749-1759
145. Sharma A, Presting G G. Centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity. Mol Genet Genomics,2008,279:133-147
146. Shepherd N S, Schwarz-Sommer Z, Blumberg vel Spalve J, Gupta M, Wienand U, Saedler H. Similarity of the Cinl repetitive family of Zea mays to eukaryotic transposable elements. Nature, 1984,307:185-187
147. Slocum M K, Figdore S S, Kennard W C, Suzuki J Y, Osborn T C. Linkage arrangement of restriction fragment length polymorphism loci in Brassica oleracea. Theor Appl Genet,1990,80: 57-64
148. Smykal P, Hybl M, Corander J, Jarkovsky J, Flavell AJ, Griga M. Genetic diversity and population structure of pea(Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis. Theor Appl Genet,2008,117:413-424
149. Soifer H S, Rossi J J. Small interfering RNAs to the rescue:blocking L1 retrotransposition. Nat Struct Mol Biol,2006,13:758-759
150. Song K M, Lu P, Tang K L, Osborn T C. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc Natl Acad Sci,1995,92:7719-7723
151. Struss D, Quiros C F, Plieske J, Robbelen G. Construction of Brassica B genome synteny groups based on chromosomes extracted from three different sources by phenotypic, isozyme and molecular markers. Theor Appl Genet,1996,93:1026-1032
152. Suwabe K, Morgan C, Bancroft I. Integration of Brassica A genome genetic linkage map between Brassica napus and B. rapa. Genome,2008,51:169-176
153. Syed N H, Sorensen A P, Antonise R, van de Wiel C, van der Linden C G, van't Westende W, Hooftman D A, den Nijs H C, Flavell A J. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers. Theor Appl Genet,2006,112:517-527
154. Tadege M, Wen J, He J, Tu H, Kwak Y, Eschstruth A, Cayrel A, Endre G, Zhao PX, Chabaud M, Ratet P, Mysore K S. Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant J,2008,54:335-347
155. Takata M, Kiyohara A, Takasu A, Kishima Y, Ohtsubo H, Sano Y. Rice transposable elements are characterized by various methylation environments in the genome. BMC Genomics,2007,8:469
156. Town C D, Cheung F, Maiti R, Crabtree J, Haas B J, Wortman J R, Hine E E, Althoff R, Arbogast T S, Tallon L J, Vigouroux M, Trick M, Bancroft I. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell,2006,18:1348-1359
157. U N. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn J Bot,1935,7:389-452
158. Vershinin A V, Druka A, Alkhimova A G, Kleinhofs A, Heslop-Harrison J S. LINEs and gypsy-like retrotransposons in Hordeum species. Plant Mol Biol,2002,49:1-14
159. Vicient C M, Jaaskelainen M J,Kalendar R, Schulman A H. Active retrotransposons are a common feature of grass genomes. Plant Physiol,2001,125:1283-1292
160. Vitte C, Panaud O, Quesneville H. LTR retrotransposons in rice (Oryza sativa, L.):recent burst amplifications followed by rapid DNA loss. Bmc Genomics,2007,8
161. Wang D L, Zhu J, Li Z K L, Paterson A H. Mapping QTLs with epistatic effects and QTL×environment interactions by mixed linear model approaches. Theor Appl Genet,1999,99: 1255-1264
162. Wang Y M, Dong Z Y, Zhang Z J, Lin X Y, Shen Y, Zhou D W, Liu B. Extensive de novo genomic variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.). Genetics,2005,170:1945-1956
163. Wendel J F, Schnabel A, Seelanan T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc Natl Acad Sci,1995,92:280-284
164. Wicker T, Keller B. Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res,2007,17:1072-1081
165. Witte C P, Le Q H, Bureau T, Kumar A. Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc Natl Acad Sci,2001,98:13778-13783
166. Wright D A, Ke N, Smalle J, Hauge B M, Goodman H M, Voytas D F. Multiple non-LTR retrotransposons in the genome of Arabidopsis thaliana. Genetics,1996,142:569-578
167. Xiong Y, Eickbush T H. Origin; and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J,1990,9:3353-3362
168. Xu Z, Ramakrishna W. Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history. Gene,2008,412:50-58
169. Yang T J, Kim J S, Kwon S J, Lim K B, Choi B S, Kim J A, Jin M, Park J Y, Lim M H, Kim H I, Lim Y P, Kang J J, Hong J H, Kim C B, Bhak J, Bancroft I, Parka B S. Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell,2006,18:1339-1347
170. Yang T J, Kim J S, Lim K B, Kwon S J, Kim J A, Jin M, Park J Y, Lim M H, Kim H I, Kim S H, Lim YP, Park BS. The Korea Brassica Genome Project:A glimpse of the Brassica genome based on comparative genome analysis with Arabidopsis. Comparative and Functional Genomics,2005, 6:138-146
171. Yang X, Yu Y J, Zhang F L, Zoul Z R, Zha X Y, Zhang D S, Xu J B. Linkage map construction and quantitative trait loci analysis for bolting based on a double haploid population of Brassica rapa. Journal of Integrative Plant Biology,2007,49:664-671
172. Yap I V, Nelson R J. WINBOOT, a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. IRRI, Manila, Philippines., 1996,
173. Zhang X, Wessler S R. Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proc Natl Acad Sci,2004,101: 5589-5594
174. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan S W, Chen H, Henderson I R, Shinn P, Pellegrini M, Jacobsen S E, Ecker J R. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell,2006,126:1189-1201
175. Zilberman D, Gehring M, Tran R K, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet,2007,39:61-69
176. Zuccolo A, Sebastian A, Talag J, Yu Y, Kim H, Collura K, Kudrna D, Wing R A. Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evol Biol,2007,7:152