Development of pachytene FISH maps for six maize chromosomes and their integration with other maize maps for insights into genome structure variation.
Development of pachytene FISH maps for six maize chromosomes and their integration with other maize maps for insights into genome structure variation.
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DOI：
10.1007/s10577-012-9281-4
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发表时间：
2012-05
影响因子：
2.6
通讯作者：
Bass, Hank W.
中科院分区：
文献类型：
--
作者：
Figueroa, Debbie M.;Bass, Hank W.
关键词：
利用限制性片段长度多态性标记选择的高粱丙豆细菌人工染色体（BACs），建立了玉米1、3、4、5、6和8号染色体的完整细胞遗传学粗线素荧光原位杂交（FISH）图谱，其中19个核心仓标记和4个附加遗传框架位点。通过对燕麦玉米染色体附加系的转基因BAC FISH定位，我们发现沿粗线染色体的相对位点位置不随总臂长而变化，这表明4号和5号染色体上的被测位点在前期中期沿纤维均匀轴向收缩。此外，我们利用与9号染色体位点同源的高粱BACs，将9号染色体上的6个位点定位到1号和6号染色体上具有不同程度序列分化的重复共链区域。我们发现，即使第9号染色体的选择标记在合成区中没有对应的标记，成功的FISH定位也是可能的。总的来说，这29个FISH定位的基因座被用来为这6条玉米染色体创建迄今为止最广泛的粗线素FISH图谱。然后将fish定位的基因座合并到一个复合核型中，利用所有基因座在所有基因座上的相对标记位置，与重组结节预测的细胞遗传学、遗传连锁和基因组物理图谱进行直接比较分析。在所有成对图谱比较中观察到标记共线性，尽管在某些情况下标记分布模式差异很大。正如预期的那样，我们发现基于重组结节的预测最接近于细胞遗传学图谱的总体位置。细胞遗传学和连锁图谱的比较与先前的研究一致，表明遗传连锁图谱上的着丝粒周围异染色质区域的标记间距减少。事实上，与染色体数目或玉米自交系来源无关，在连锁图谱上，大多数位点比在细胞遗传学图谱上更靠近端粒，只有一些端粒位点不受影响。最后，有些令人惊讶的是，当我们将细胞遗传学FISH图谱与B73基因组物理图谱进行比较时，我们观察到位点的相对臂位之间存在相当大的差异，即使是与B73衍生的细胞遗传学图谱进行比较。这种变异在不同染色体臂之间更为明显，但在同一染色体臂内则不那么明显，与减数分裂纤维组织相比，排除了任何类型的依赖于近交系的线性脱氧核糖核酸的全局特征。该研究为整合玉米的细胞遗传学、连锁和物理图谱提供了新的联系，为分析玉米基因组结构提供了一种手段。本文的在线版本（doi:10.1007/s10577-012-9281-4）包含补充材料，授权用户可使用。
Integrated cytogenetic pachytene fluorescence in situ hybridization (FISH) maps were developed for chromosomes 1, 3, 4, 5, 6, and 8 of maize using restriction fragment length polymorphism marker-selected Sorghum propinquum bacterial artificial chromosomes (BACs) for 19 core bin markers and 4 additional genetic framework loci. Using transgenomic BAC FISH mapping on maize chromosome addition lines of oats, we found that the relative locus position along the pachytene chromosome did not change as a function of total arm length, indicative of uniform axial contraction along the fibers during mid-prophase for tested loci on chromosomes 4 and 5. Additionally, we cytogenetically FISH mapped six loci from chromosome 9 onto their duplicated syntenic regions on chromosomes 1 and 6, which have varying amounts of sequence divergence, using sorghum BACs homologous to the chromosome 9 loci. We found that successful FISH mapping was possible even when the chromosome 9 selective marker had no counterpart in the syntenic block. In total, these 29 FISH-mapped loci were used to create the most extensive pachytene FISH maps to date for these six maize chromosomes. The FISH-mapped loci were then merged into one composite karyotype for direct comparative analysis with the recombination nodule-predicted cytogenetic, genetic linkage, and genomic physical maps using the relative marker positions of the loci on all the maps. Marker colinearity was observed between all pair-wise map comparisons, although marker distribution patterns varied widely in some cases. As expected, we found that the recombination nodule-based predictions most closely resembled the cytogenetic map positions overall. Cytogenetic and linkage map comparisons agreed with previous studies showing a decrease in marker spacing in the peri-centromeric heterochromatin region on the genetic linkage maps. In fact, there was a general trend with most loci mapping closer towards the telomere on the linkage maps than on the cytogenetic maps, regardless of chromosome number or maize inbred line source, with just some of the telomeric loci exempted. Finally and somewhat surprisingly, we observed considerable variation between the relative arm positions of loci when comparing our cytogenetic FISH map to the B73 genomic physical maps, even where comparisons were to a B73-derived cytogenetic map. This variation is more evident between different chromosome arms, but less so within a given arm, ruling out any type of inbred-line dependent global features of linear deoxyribonucleic acid compared with the meiotic fiber organization. This study provides a means for analyzing the maize genome structure by producing new connections for integrating the cytogenetic, linkage, and physical maps of maize. The online version of this article (doi:10.1007/s10577-012-9281-4) contains supplementary material, which is available to authorized users.
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影响因子：
3.3
作者：
Falque, M;Décousset, L;Murigneux, A
通讯作者：
Murigneux, A
DOI：
10.1073/pnas.17.8.492
发表时间：
1931-01-01
影响因子：
11.1
作者：
Creighton, HB;McClintock, B
通讯作者：
McClintock, B
影响因子：
56.9
作者：
Buckler, Edward S.;Holland, James B.;McMullen, Michael D.
通讯作者：
McMullen, Michael D.
影响因子：
4
作者：
Figueroa, Debbie M.;Bass, Hank W.
通讯作者：
Bass, Hank W.
影响因子：
4.5
作者：
Baucom RS;Estill JC;Chaparro C;Upshaw N;Jogi A;Deragon JM;Westerman RP;Sanmiguel PJ;Bennetzen JL
通讯作者：
Bennetzen JL