玉米Bronze基因座位的分子和遗传特征
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摘要
玉米(Zea Mays)是遗传学研究的高等模式植物，有着很好的经典遗传学和细胞遗传学研究工作基础。然而，玉米分子遗传学的研究却不及它的经典遗传学和细胞遗传学的研究地位，这主要由于玉米复杂的基因组结构限制了其分子遗传学研究的深入开展。玉米基因组(2.3-2.7×10~9bp)分别是拟南芥(1.1×10~8bp)、水稻(4.3×10~8bp)和高粱(7.5×10~8bp)基因组的20倍、6倍和3倍。组成玉米基因组65-70％的DNA是具有长末端重复序列(Long Terminal Repeat, LTR)的反转座子(Retrotransposons)，其它的重复序列约占玉米基因组DNA的20％。玉米反转座子主要分属于几大类，它们在玉米基因组的拷贝数高达10000-30000拷贝／单倍体核基因组，这些反转座子之间的DNA序列一致性很高，有的达90％以上。庞大的基因组加上占基因组DNA总量85％以上的重复序列极大地增加了玉米基因组研究的难度。自二十世纪九十年代以来，随着克隆大段DNA(如YAC、BAC克隆)技术的发展，使得克隆、研究含有特定基因座位(locus)的大段基因组DNA(contig)成为可能。研究特定基因座位DNA的组织形式和结构特点，不仅将为剖析玉米全基因组的DNA序列结构积累有价值的数据，而且对于我们深入理解复杂基因组植物的分子遗传学特征和指导农作物育种研究也将具有重要意义。
Bronze(Bz)基因定位于玉米第九染色体短臂，编码UDPG-葡萄糖转移酶。Bz控制玉米糊粉层以及植株许多其它部位的花青素合成，从而控制玉米籽粒及植株某些营养器官的颜色，是研究植物分子遗传的极好的基因座位。本研究以玉米Bz-McC为材料，从分子遗传水平首次研究了Bz座位的DNA组织形式和结构特征，研究了同一等位基因座位内DNA物理距离与遗传距离之间的关系，提出了Bz基因座位不
同区段之间遗传重组率存在巨大差异的可能的分子机理。并应用比较基因组学的方
法研究了包括M心C和B73在内的十个不同玉米自交系间Bz座位的ONA分子组织
形式差异，为解释玉米杂种优势的显性学说提供了可能的分子依据。
本工作的主要研究结果如下:
1.以日矛拟陌C为材料，构建了一个基因富集的基因组BAC(BaCteriaIA比币cial
Chromosome)文库，从这个日AC文库箭选到两种Bz克隆，匹配了一个以Bz为中
心的240kb基因组片段(Contig)。
为了研究Bz基因座位的ONA分子组织形式和精细的结构特点，首先必须克隆
其基因组ONA。为研究同一等位基因座位内ONA物理距离与遗传距离之间的关系
必需克隆我们自己进行遗传距离研究的特定等位基因座位的ONA。从前人的研究结
果，我们知道Bz基因内部含有一个闪口tI核酸内切酶位点。NOtl是一个对甲基化敏
感的sbp辩认位点的限制性核酸内切酶，用Notl酶切的基因组 ONA，可望获得含Bz
基因的较大ONA片段(64kb以上)。以Bz基因为探针，我们首先进行了“诊断性”
的Southem杂交分析，结果表明，Bz探针检测到的两个NOtl片段分别约为1 1 Okb
和13Okb，其片段大小位于日AC载体可克隆的大小范围内。因此，我们决定构建一
个BAC文库以克隆这两个特定的Notl片段.
(1).为了构建NOtl BAC文库，我们在现有BAC克隆载体pBel。日ACll的基础
上，通过直接的位点诱变修饰(site一directedm川Lagenesis)，将一个新的NOtl识别
位点插入到pBeloBACll的多克隆位点(polylinker)，移去了两个以前位于多克隆位
点两侧的NOtl识别位点。新的BAC克隆载体pNOBACI除了含有一个NOtl克隆位
点适合于克隆NOtl片段外，保留了原有的月加dII和BamHI克隆位点以及蓝白斑筛
选的特征，是一个非常有应用价值的BAC克隆载体，己被英美等国的多个实验室索
用。
(2).为了经济高效地克隆这两个含Bz的Notl基因组ONA片段，我们巧妙地
应用了闪口tI完全酶消化基因组ONA的研究方案。通过片段化富集川Otl完全酶切的
基因组ONA片段在1 00一1 SOkb范围，Bz Notl片段被大大地富集。所构建的BAC文
库仅含有相当于三分之二玉米基因组的ONA(20，000个克隆，平均插入片段为
106kb)，却富集了Bz片段15-24倍。这使我们非常经济有效地获得了我们的目的
ONA片段。为了验证我们的研究途经是否具有普遍的实用意义，我们用几个其它的
基因探针筛选了这个BAC文库，结果表明所有其NOtl片段位于1 00一1 SOkb范围内
的基因都都筛选到了1至多个相应的克隆。我们的结果也表明我们的这个日AC文库
是一个基因大大富集的BAC文库。我们的成功为克隆特殊基因组座位的ONA大片
段提供了一个经济、省时、高效的模式。
(3).从以上构建的日AC文库，我们筛选到两种日之克隆，以Bz Nbtl位点为
中心，近着丝粒侧的克隆为1 30kb，远着丝粒侧的克隆为 11Okb。这两个克隆组成了
一个含8z基因座位的240kb的基因组片段(Contig)。
2.分析了以上克隆的以Bz基因为中心的24Okb ONA的序列和分子组织形式，
结果表明Bz基因位于一个不寻常的基因密集程度极高的基因岛(gene island)，整
个24Okb的基因组ONA是以“基因岛一反转座子串(retrotransposon cluster，)一基
因岛一反转座子串一基因岛”的组织形式存在。
为了讨论方便，我们称含有Bz基因的基因岛为日全基因岛，以此为起始点，整
个这240kb的基因组ONA的组织结
Most agriculturally important plants have complex genotypes, consisting of islands of hypomethylated, single-to low copy DNA, where most genes are found, surrounded by repetitive, methylated DNA of unknown function. Little is known about the organization of the key genie regions in such plants. Maize is prototype of higher plant with a complex genome, for which there exists an excellent genetic and cytogenetic knowledge a base. Characterization of well-studied genie regions should help us to understand how the genome is organized at a supragenic level.
The bz locus is ideally suited for studying genetic organization in plants. This locus conditions anthocyanin pigmentation in the aleurone layer of the seed and in many parts of the plant. Bz intragenic recombinants occurring at meiosis in bz heteroallelic plants can be selected easily as exceptional purple seeds among the bronze testcross progeny and subjected to a genetic and molecular analysis. A series of Ac elements that transposed from the bz locus to its vicinity have been mapped fairly precisely and have been used as genetic markers. To study the molecular organization of the bz genomic region, we constructed a gene-rich partial bacterial artificial chromosome (BAC) genomic library of maize. Two adjacent BAC clones, which made up a 240kb contig of maize genome centered around the bz locus, were isolated and sequenced. We have found the bz locus lies in an unusually gene-rich region of the maize genome. Ten genes are contained in a 32-kb stretch of DNA that is uninterrupted by retrotransposons. The av
erage intertranscript distance between genes is just lkb, revealing a surprisingly compact packaging of adjacent genes in this part of the genome. The gene-rich region is flanked by the 94kb proximal retrotransposon cluster and the approximately 100kb distal retrotransposon clusters. Recombination is almost 2 orders of magnitude higher in the gene-rich region.
The repetitive retrotransposon DNA contributes little if any to genetic length.
We sequenced and compared over 100kb from the bz genomic region of two different maize lines and found dramatic differences between them not only in the intergenic retrotransposon cluster make up and location relative to the genes in the bz region, but also in the genes themselves. We also surveyed the organization of the bz region in other inbred lines. Our finding has bearing on the underlying genetic basis of hybrid vigor in maize, and possibly other organisms, and on the measurement of genetic distances in different backgrounds.
Bronze(Bz)基因定位于玉米第九染色体短臂，编码UDPG-葡萄糖转移酶。Bz控制玉米糊粉层以及植株许多其它部位的花青素合成，从而控制玉米籽粒及植株某些营养器官的颜色，是研究植物分子遗传的极好的基因座位。本研究以玉米Bz-McC为材料，从分子遗传水平首次研究了Bz座位的DNA组织形式和结构特征，研究了同一等位基因座位内DNA物理距离与遗传距离之间的关系，提出了Bz基因座位不
同区段之间遗传重组率存在巨大差异的可能的分子机理。并应用比较基因组学的方
法研究了包括M心C和B73在内的十个不同玉米自交系间Bz座位的ONA分子组织
形式差异，为解释玉米杂种优势的显性学说提供了可能的分子依据。
本工作的主要研究结果如下:
1.以日矛拟陌C为材料，构建了一个基因富集的基因组BAC(BaCteriaIA比币cial
Chromosome)文库，从这个日AC文库箭选到两种Bz克隆，匹配了一个以Bz为中
心的240kb基因组片段(Contig)。
为了研究Bz基因座位的ONA分子组织形式和精细的结构特点，首先必须克隆
其基因组ONA。为研究同一等位基因座位内ONA物理距离与遗传距离之间的关系
必需克隆我们自己进行遗传距离研究的特定等位基因座位的ONA。从前人的研究结
果，我们知道Bz基因内部含有一个闪口tI核酸内切酶位点。NOtl是一个对甲基化敏
感的sbp辩认位点的限制性核酸内切酶，用Notl酶切的基因组 ONA，可望获得含Bz
基因的较大ONA片段(64kb以上)。以Bz基因为探针，我们首先进行了“诊断性”
的Southem杂交分析，结果表明，Bz探针检测到的两个NOtl片段分别约为1 1 Okb
和13Okb，其片段大小位于日AC载体可克隆的大小范围内。因此，我们决定构建一
个BAC文库以克隆这两个特定的Notl片段.
(1).为了构建NOtl BAC文库，我们在现有BAC克隆载体pBel。日ACll的基础
上，通过直接的位点诱变修饰(site一directedm川Lagenesis)，将一个新的NOtl识别
位点插入到pBeloBACll的多克隆位点(polylinker)，移去了两个以前位于多克隆位
点两侧的NOtl识别位点。新的BAC克隆载体pNOBACI除了含有一个NOtl克隆位
点适合于克隆NOtl片段外，保留了原有的月加dII和BamHI克隆位点以及蓝白斑筛
选的特征，是一个非常有应用价值的BAC克隆载体，己被英美等国的多个实验室索
用。
(2).为了经济高效地克隆这两个含Bz的Notl基因组ONA片段，我们巧妙地
应用了闪口tI完全酶消化基因组ONA的研究方案。通过片段化富集川Otl完全酶切的
基因组ONA片段在1 00一1 SOkb范围，Bz Notl片段被大大地富集。所构建的BAC文
库仅含有相当于三分之二玉米基因组的ONA(20，000个克隆，平均插入片段为
106kb)，却富集了Bz片段15-24倍。这使我们非常经济有效地获得了我们的目的
ONA片段。为了验证我们的研究途经是否具有普遍的实用意义，我们用几个其它的
基因探针筛选了这个BAC文库，结果表明所有其NOtl片段位于1 00一1 SOkb范围内
的基因都都筛选到了1至多个相应的克隆。我们的结果也表明我们的这个日AC文库
是一个基因大大富集的BAC文库。我们的成功为克隆特殊基因组座位的ONA大片
段提供了一个经济、省时、高效的模式。
(3).从以上构建的日AC文库，我们筛选到两种日之克隆，以Bz Nbtl位点为
中心，近着丝粒侧的克隆为1 30kb，远着丝粒侧的克隆为 11Okb。这两个克隆组成了
一个含8z基因座位的240kb的基因组片段(Contig)。
2.分析了以上克隆的以Bz基因为中心的24Okb ONA的序列和分子组织形式，
结果表明Bz基因位于一个不寻常的基因密集程度极高的基因岛(gene island)，整
个24Okb的基因组ONA是以“基因岛一反转座子串(retrotransposon cluster，)一基
因岛一反转座子串一基因岛”的组织形式存在。
为了讨论方便，我们称含有Bz基因的基因岛为日全基因岛，以此为起始点，整
个这240kb的基因组ONA的组织结
Most agriculturally important plants have complex genotypes, consisting of islands of hypomethylated, single-to low copy DNA, where most genes are found, surrounded by repetitive, methylated DNA of unknown function. Little is known about the organization of the key genie regions in such plants. Maize is prototype of higher plant with a complex genome, for which there exists an excellent genetic and cytogenetic knowledge a base. Characterization of well-studied genie regions should help us to understand how the genome is organized at a supragenic level.
The bz locus is ideally suited for studying genetic organization in plants. This locus conditions anthocyanin pigmentation in the aleurone layer of the seed and in many parts of the plant. Bz intragenic recombinants occurring at meiosis in bz heteroallelic plants can be selected easily as exceptional purple seeds among the bronze testcross progeny and subjected to a genetic and molecular analysis. A series of Ac elements that transposed from the bz locus to its vicinity have been mapped fairly precisely and have been used as genetic markers. To study the molecular organization of the bz genomic region, we constructed a gene-rich partial bacterial artificial chromosome (BAC) genomic library of maize. Two adjacent BAC clones, which made up a 240kb contig of maize genome centered around the bz locus, were isolated and sequenced. We have found the bz locus lies in an unusually gene-rich region of the maize genome. Ten genes are contained in a 32-kb stretch of DNA that is uninterrupted by retrotransposons. The av
erage intertranscript distance between genes is just lkb, revealing a surprisingly compact packaging of adjacent genes in this part of the genome. The gene-rich region is flanked by the 94kb proximal retrotransposon cluster and the approximately 100kb distal retrotransposon clusters. Recombination is almost 2 orders of magnitude higher in the gene-rich region.
The repetitive retrotransposon DNA contributes little if any to genetic length.
We sequenced and compared over 100kb from the bz genomic region of two different maize lines and found dramatic differences between them not only in the intergenic retrotransposon cluster make up and location relative to the genes in the bz region, but also in the genes themselves. We also surveyed the organization of the bz region in other inbred lines. Our finding has bearing on the underlying genetic basis of hybrid vigor in maize, and possibly other organisms, and on the measurement of genetic distances in different backgrounds.
引文
1. Food and agriculture organization of the united nations, Statistical Databases,FAOSTAT, Agriculture, 2002., Provisional 2002 Production and Production Indices Data. http://apps.fao.org/page/collections/subset=agriculture.
2. Salvador, R. J., Maize. in The Encyclopedia of Mexico: History Culture and Society (ed. Wemer, Michael S.), 1997. Fitzroy Dearborn Publishers,
3. Maguire, M. P., 1966. The relationship of crossing over to chromosome synapsis in a short paracentric inversion. Genetics, 53(6): p.1071-1077.
4. Smith, H. H., 1967. Relative biological effectiveness of different type of ionizing radiations: cytogenetics effects in maize. Radiat Res Suppl., 7: p. 190-195.
5. Coe, E.., 1968. Heritable repression due to paramutation in maize. Science, 162(856): p. 925.
6. Maguire, M. P., 1968. Chromosome pairing in altered constitutions and models of synapsis and crossing-over. Genet Res, 12(1): p. 21-27.
7. Ghidoni, A., 1968. Transmission and phenotypic effect of a duplicate chromosome segment in maize. Mol. Gen Genet, 101(4): p. 317-332.
8. Mottinger, J.P., 1970. The effects of X-rays on the bronze and shrunken loci in maize. Genetics, 64: p. 259-271.
9. Thomas, C.A., 1971. The genetic organization of chromosome. Annu. Rev. Genet., 5: p. 237-256.
10. Ralston, E.J., English, J. & Dooner, H. K., 1989. Chromosome-Breaking Structure in Maize Involving a Fractured Ac Element. Proc. Natl. Acad. Sci. USA, 86: p. 9451-9455.
11. Gierl, A., Saedler, H. & Peterson, P. A., 1989. Maize transposable elements. An. Rev. Genet.. 23: p. 71-85.
12. Das, O., Levi-Minzi, Simona., Koury, Michelle, Benner, M., Messing, J, 1990.A somatic gene rearrangement contributing to genetic diversity in maize. Proc. Natl. Acad. Sci. USA, 87(20): p. 7809-7813.
13. Arumuganathan, K.E., E. D., 1991. Nuclear DNA content of some important plant species. Plant Mol. Bio. Rep., 9: p. 208-218.
14. Robbins, T.P., Walker, E. L., Kermicle, J. L., Alleman, M. & Dellaporta, S. L., 1991. Meiotic instability of the R-r complex arising from displaced intragenic exchange and intrachromosomal. Genetics, 129: p. 271-283.
15. Dooner, H.K. & Belachew., A, 1991, Chromosome breakage by pairs of closely linked transposable elements of the Ac-Ds family in maize. Genetics,. 129: p. 855-862.
16. Barnes, T.M., Kohara, Y., Coulson, A. & Hekimi, S.,1995. Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans,. Genetics, 141 : p. 159-179.
17. Ananiev, E.V., Phillips, R. L. & Rines, H. W., 1998. Complex structure of knob DNA on maize chromosome 9: Retrotransposon invasion into heterochromatin,. Genetics, 149.: p. 2025-2037.
18. Eyre-Walker, A., Gaut, R. L., Hilton, H., Feldman, D. L. & Gaut, B. S., 1998. Investigation of the bottleneck leading to the domestication of maize. Proc. Natl. Acad. Sci. USA, 95: p.4441-4446.
19. Wade, P.A., Gegonne, A., Jones, P. L., Ballestar, E., Aubry, F. & Wolffe, A. P., 1999. Mi-2 complex couples DNA methulation to chromatin remodelling and histone deacetylation,. Nature Genetics., 23: p. 62-6.
20. Gaut, B.S., Le Thierry d'Ennequin, M., Peek, A. S. & Sawkins, M. C., 2000. Maize as a model for the evolution of plant nuclear genomes. Proc. Natl. Acad. Sci. USA, 97: p. 7008-7015.
21. Gaut, B.S., 2001. Patterns of chromosomal duplication in maize and their implication for comparative maps of the grasses. Gen. Research., 11: p. 55-66.
22. Martinez-Perez, E., and Moore, G, 2004. Promiscuous maize chromosomes. Science, 303: p. 49-50.
23. Pawlowski W. P. et al, 2004. Coordination of meiotic recombination, pairing, and synapsis by PHS1. Science, 303: p. 89-92.
24. Fang, Z., Cone, K., Sanchez-Villeda, H., Polacco, M., McMullen, M.,Schroeder, S., Gardiner, J., Ddavis, G., Havermann, S., Yim, Y., Vroh Bi I. and Coe, E., 2003. iMap: a database-driven utility to integrate and access the genetic and physical maps of maize. Bioinformatics, Vol. 19(no.16): p. 2105-2111.
25. Maize Genetics and Genomics Database Team,., Map Data In MaizeGDB. http://www.maizegdb.org/map.php.
26. Lee, M., Sharopova, N., Beavis, W., Grant, D., Katt, M., Blair, D., and Hallauer, A., 2002. Expanding the genetic map of maize with the intermated B73×Mo17 (IBM) population. Plant Mol. Biol., Vol. 48: p.453-461.
27. Sharopova, N., McMullen, M.D., Schultz, I., Schroeder, S., Sanchez-Villeda,H.,Gardiner, J., Bergstrom, D., Houchins, K., Melia-Hancock, S., Musket, T., et al. 2002. Development and mapping of SSR markers for maize. Plant Mol. Biol., Vol.48: p. 463-481.
28. Cone, K., McMullen,M., Vroh Bi,I., Davis,G, Yim,Y., Gardiner, J., Polacco,M.,Sanchez-Villeda, H., Fang,Z., Schroeder, S. et al, 2002. Genetic, physical and informatics resoumes for maize: On the road to an integrated map. Plant Physiol., Vol. 130: p. 1598-1605.
29. Vroh Bi, I. et.al., 2004 manuscript in preparation.
30. Sodedund, C., Humphray, D., and French,L., 2000. Contigs built with fingerprints, markers and FPC V4.7. Genome Research, Vol. 10: p. 1772-1787.
31. Davis, G., McMullen,M., Baysdorfer, C.,Musket,T., Grant, D., Staebell,M.S.,Xu,G., Polacco,M., Koster, L., Melia-Hancock,S. et al, 1999. A maize map standard with sequenced core markers, grass genome reference points, and 932 ESTs in a 1736-locus map. Genetics, Vol. 152: p.1137-1172.
32. Sharopova, N., McMullen, M.D., Schultz, I., Schroeder, S., Sanchez-Villeda, H.,Gardiner, J., Bergstrom, D., Houchins, K., Melia-Hancock, S., Musket, T., et al, 2002. Development and mapping of SSR markers for maize. Plant Mol. Biol.,
Vol. 48: p. 463-481.
33. Yim, Y., Davis,G, Duru,N., Musket,T., McMullen,M., Soderlund,C., Polacco,M. Gardiner, J., Cone,K. and Coe,E., 2002. Characterization of maize BAC libraries and anchoring of the physical map to the genetic map using high density BAC filter hybridization. Plant Physiol., Vol. 130: p.1686-1696.
34. Arabidopsis-Genome-Initiative, 2000. Analysis of the genome sequence of the flowedng plant arabidopsis thaliana. Nature Genetics, 408: p. 796-815.
35. Yu, J., Hu, S., et al, 2002. A draft sequence of the rice genome (Oryza sativa L.ssp. indica). Science, 296: p. 79-92.
36. Goff, S.A., Ricke, D. et al, 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296: p. 92-100.
37. Feng, Q., Zhang, Y., et al, 2002. Sequence and analysis of rice chromosome 4. Nature, 420: p. 316-320.
38. Sasaki, T., Matsumoto, T. et al, 2002. The genome sequence and structure of rice chromosome 1. Nature, 420(312-316).
39. Bennetzen, J.L., Schrick, K., Springer, P. S., Brown, W. E., SanMiguel, P., 1994. Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome, 37: p.565-576.
40. SanMiguel, P., Alexander Tikhonov, Young-Kwan Jin, Natasha Motchoulskaia, Dmitrii Zakharov, Admasu Melake-Berhan, Patricia Springer, Keith J. Edwards, Michael Lee, Zoya Avramova, Jeffrey L. 1996. Bennetzen, Nested Retrotransposons in the intergenic regions of maize Genome. Science, 274(5288): p.765-768.
41. Vicient, C.M., Jaaskelainen, M. J., Kalendar, R. & Schulman, A. H., 2001. Active retrotransposons are a common feature of grass genome. Plant Physiology, 125: p. 1283-92.
42. Meyers, B., "Tingey, SV., Morgante, M., 2001. Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Research, 11: p. 1660.
43. Tikhonow, A.P., SaMiguel, P.J., Nakajima, Y., Georenstein, N.M., Bennetsen,J.L. & Avramova, Z., 1999. Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc. Natl. Acad. Sci. USA, 96: p. 7409-7414.
44. Civardi, L., Xia, Y., Edwards, KJ., Schnable, PS., Nikolau, BJ., 1994. The relationship between genetic and physical distances in the cloned a1-sh2 interval of th Zea Mays L. genome. Proc. Natl. Acad. Sci. USA, 91(17): p. 8268-8272.
45. Yao, H., Zhou, Q., Li, Jin., Smith, H., Yandeau, M., Nikolau, BJ., Schnable, PS.,2002. Molecular characterization of meiotic recombination across the 140-kb multigenic al-sh2 interval. Proc. Natl. Acad. Sci. USA, 99(9): p. 6157-6162.
46. Dooner, H.K. & Nelson, OE, 1977. Controlling element-induced alterations in UDPglucose: Flavonoid glucosyltransferase, the enzyme specified by the bronze locus in maize. Proc. Natl. Acad. Sci. USA, 74(12): p.5623-5627.
47. Dooner, H. K. & Nelson OE.,1979.Heterogeneous flavonoid glucosyltransferases in purple derivatives from a controlling element-suppressed bronze mutant in maize. Proc. Natl. Acad. Sci. USA, 76(5):p.2369-2371.
48. Dooner, H.K., unpublished.
49. Dooner, H.K. & Belachew, A., 1989. Transposition pattern of the maize element Ac from the bz-m2(Ac) allele. Genetics, 122: p. 447-457.
50. Dooner, H.K., English, J., Ralston, E., 1986. A single genetic unit specifies two transposition functions in the maize element activator. Science, 234: p. 210-211.
51. Dooner, H. K. & Martine-Ferez, I. M., 1997. Recombination occurs uniformly within the bronze gene, a meitotic recombination hotspot in the maize genome. Plant Cell, 9: p.1633-1646.
2. Salvador, R. J., Maize. in The Encyclopedia of Mexico: History Culture and Society (ed. Wemer, Michael S.), 1997. Fitzroy Dearborn Publishers,
3. Maguire, M. P., 1966. The relationship of crossing over to chromosome synapsis in a short paracentric inversion. Genetics, 53(6): p.1071-1077.
4. Smith, H. H., 1967. Relative biological effectiveness of different type of ionizing radiations: cytogenetics effects in maize. Radiat Res Suppl., 7: p. 190-195.
5. Coe, E.., 1968. Heritable repression due to paramutation in maize. Science, 162(856): p. 925.
6. Maguire, M. P., 1968. Chromosome pairing in altered constitutions and models of synapsis and crossing-over. Genet Res, 12(1): p. 21-27.
7. Ghidoni, A., 1968. Transmission and phenotypic effect of a duplicate chromosome segment in maize. Mol. Gen Genet, 101(4): p. 317-332.
8. Mottinger, J.P., 1970. The effects of X-rays on the bronze and shrunken loci in maize. Genetics, 64: p. 259-271.
9. Thomas, C.A., 1971. The genetic organization of chromosome. Annu. Rev. Genet., 5: p. 237-256.
10. Ralston, E.J., English, J. & Dooner, H. K., 1989. Chromosome-Breaking Structure in Maize Involving a Fractured Ac Element. Proc. Natl. Acad. Sci. USA, 86: p. 9451-9455.
11. Gierl, A., Saedler, H. & Peterson, P. A., 1989. Maize transposable elements. An. Rev. Genet.. 23: p. 71-85.
12. Das, O., Levi-Minzi, Simona., Koury, Michelle, Benner, M., Messing, J, 1990.A somatic gene rearrangement contributing to genetic diversity in maize. Proc. Natl. Acad. Sci. USA, 87(20): p. 7809-7813.
13. Arumuganathan, K.E., E. D., 1991. Nuclear DNA content of some important plant species. Plant Mol. Bio. Rep., 9: p. 208-218.
14. Robbins, T.P., Walker, E. L., Kermicle, J. L., Alleman, M. & Dellaporta, S. L., 1991. Meiotic instability of the R-r complex arising from displaced intragenic exchange and intrachromosomal. Genetics, 129: p. 271-283.
15. Dooner, H.K. & Belachew., A, 1991, Chromosome breakage by pairs of closely linked transposable elements of the Ac-Ds family in maize. Genetics,. 129: p. 855-862.
16. Barnes, T.M., Kohara, Y., Coulson, A. & Hekimi, S.,1995. Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans,. Genetics, 141 : p. 159-179.
17. Ananiev, E.V., Phillips, R. L. & Rines, H. W., 1998. Complex structure of knob DNA on maize chromosome 9: Retrotransposon invasion into heterochromatin,. Genetics, 149.: p. 2025-2037.
18. Eyre-Walker, A., Gaut, R. L., Hilton, H., Feldman, D. L. & Gaut, B. S., 1998. Investigation of the bottleneck leading to the domestication of maize. Proc. Natl. Acad. Sci. USA, 95: p.4441-4446.
19. Wade, P.A., Gegonne, A., Jones, P. L., Ballestar, E., Aubry, F. & Wolffe, A. P., 1999. Mi-2 complex couples DNA methulation to chromatin remodelling and histone deacetylation,. Nature Genetics., 23: p. 62-6.
20. Gaut, B.S., Le Thierry d'Ennequin, M., Peek, A. S. & Sawkins, M. C., 2000. Maize as a model for the evolution of plant nuclear genomes. Proc. Natl. Acad. Sci. USA, 97: p. 7008-7015.
21. Gaut, B.S., 2001. Patterns of chromosomal duplication in maize and their implication for comparative maps of the grasses. Gen. Research., 11: p. 55-66.
22. Martinez-Perez, E., and Moore, G, 2004. Promiscuous maize chromosomes. Science, 303: p. 49-50.
23. Pawlowski W. P. et al, 2004. Coordination of meiotic recombination, pairing, and synapsis by PHS1. Science, 303: p. 89-92.
24. Fang, Z., Cone, K., Sanchez-Villeda, H., Polacco, M., McMullen, M.,Schroeder, S., Gardiner, J., Ddavis, G., Havermann, S., Yim, Y., Vroh Bi I. and Coe, E., 2003. iMap: a database-driven utility to integrate and access the genetic and physical maps of maize. Bioinformatics, Vol. 19(no.16): p. 2105-2111.
25. Maize Genetics and Genomics Database Team,., Map Data In MaizeGDB. http://www.maizegdb.org/map.php.
26. Lee, M., Sharopova, N., Beavis, W., Grant, D., Katt, M., Blair, D., and Hallauer, A., 2002. Expanding the genetic map of maize with the intermated B73×Mo17 (IBM) population. Plant Mol. Biol., Vol. 48: p.453-461.
27. Sharopova, N., McMullen, M.D., Schultz, I., Schroeder, S., Sanchez-Villeda,H.,Gardiner, J., Bergstrom, D., Houchins, K., Melia-Hancock, S., Musket, T., et al. 2002. Development and mapping of SSR markers for maize. Plant Mol. Biol., Vol.48: p. 463-481.
28. Cone, K., McMullen,M., Vroh Bi,I., Davis,G, Yim,Y., Gardiner, J., Polacco,M.,Sanchez-Villeda, H., Fang,Z., Schroeder, S. et al, 2002. Genetic, physical and informatics resoumes for maize: On the road to an integrated map. Plant Physiol., Vol. 130: p. 1598-1605.
29. Vroh Bi, I. et.al., 2004 manuscript in preparation.
30. Sodedund, C., Humphray, D., and French,L., 2000. Contigs built with fingerprints, markers and FPC V4.7. Genome Research, Vol. 10: p. 1772-1787.
31. Davis, G., McMullen,M., Baysdorfer, C.,Musket,T., Grant, D., Staebell,M.S.,Xu,G., Polacco,M., Koster, L., Melia-Hancock,S. et al, 1999. A maize map standard with sequenced core markers, grass genome reference points, and 932 ESTs in a 1736-locus map. Genetics, Vol. 152: p.1137-1172.
32. Sharopova, N., McMullen, M.D., Schultz, I., Schroeder, S., Sanchez-Villeda, H.,Gardiner, J., Bergstrom, D., Houchins, K., Melia-Hancock, S., Musket, T., et al, 2002. Development and mapping of SSR markers for maize. Plant Mol. Biol.,
Vol. 48: p. 463-481.
33. Yim, Y., Davis,G, Duru,N., Musket,T., McMullen,M., Soderlund,C., Polacco,M. Gardiner, J., Cone,K. and Coe,E., 2002. Characterization of maize BAC libraries and anchoring of the physical map to the genetic map using high density BAC filter hybridization. Plant Physiol., Vol. 130: p.1686-1696.
34. Arabidopsis-Genome-Initiative, 2000. Analysis of the genome sequence of the flowedng plant arabidopsis thaliana. Nature Genetics, 408: p. 796-815.
35. Yu, J., Hu, S., et al, 2002. A draft sequence of the rice genome (Oryza sativa L.ssp. indica). Science, 296: p. 79-92.
36. Goff, S.A., Ricke, D. et al, 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296: p. 92-100.
37. Feng, Q., Zhang, Y., et al, 2002. Sequence and analysis of rice chromosome 4. Nature, 420: p. 316-320.
38. Sasaki, T., Matsumoto, T. et al, 2002. The genome sequence and structure of rice chromosome 1. Nature, 420(312-316).
39. Bennetzen, J.L., Schrick, K., Springer, P. S., Brown, W. E., SanMiguel, P., 1994. Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome, 37: p.565-576.
40. SanMiguel, P., Alexander Tikhonov, Young-Kwan Jin, Natasha Motchoulskaia, Dmitrii Zakharov, Admasu Melake-Berhan, Patricia Springer, Keith J. Edwards, Michael Lee, Zoya Avramova, Jeffrey L. 1996. Bennetzen, Nested Retrotransposons in the intergenic regions of maize Genome. Science, 274(5288): p.765-768.
41. Vicient, C.M., Jaaskelainen, M. J., Kalendar, R. & Schulman, A. H., 2001. Active retrotransposons are a common feature of grass genome. Plant Physiology, 125: p. 1283-92.
42. Meyers, B., "Tingey, SV., Morgante, M., 2001. Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Research, 11: p. 1660.
43. Tikhonow, A.P., SaMiguel, P.J., Nakajima, Y., Georenstein, N.M., Bennetsen,J.L. & Avramova, Z., 1999. Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc. Natl. Acad. Sci. USA, 96: p. 7409-7414.
44. Civardi, L., Xia, Y., Edwards, KJ., Schnable, PS., Nikolau, BJ., 1994. The relationship between genetic and physical distances in the cloned a1-sh2 interval of th Zea Mays L. genome. Proc. Natl. Acad. Sci. USA, 91(17): p. 8268-8272.
45. Yao, H., Zhou, Q., Li, Jin., Smith, H., Yandeau, M., Nikolau, BJ., Schnable, PS.,2002. Molecular characterization of meiotic recombination across the 140-kb multigenic al-sh2 interval. Proc. Natl. Acad. Sci. USA, 99(9): p. 6157-6162.
46. Dooner, H.K. & Nelson, OE, 1977. Controlling element-induced alterations in UDPglucose: Flavonoid glucosyltransferase, the enzyme specified by the bronze locus in maize. Proc. Natl. Acad. Sci. USA, 74(12): p.5623-5627.
47. Dooner, H. K. & Nelson OE.,1979.Heterogeneous flavonoid glucosyltransferases in purple derivatives from a controlling element-suppressed bronze mutant in maize. Proc. Natl. Acad. Sci. USA, 76(5):p.2369-2371.
48. Dooner, H.K., unpublished.
49. Dooner, H.K. & Belachew, A., 1989. Transposition pattern of the maize element Ac from the bz-m2(Ac) allele. Genetics, 122: p. 447-457.
50. Dooner, H.K., English, J., Ralston, E., 1986. A single genetic unit specifies two transposition functions in the maize element activator. Science, 234: p. 210-211.
51. Dooner, H. K. & Martine-Ferez, I. M., 1997. Recombination occurs uniformly within the bronze gene, a meitotic recombination hotspot in the maize genome. Plant Cell, 9: p.1633-1646.