Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization
Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization
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DOI：
10.1104/pp.103.034538
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发表时间：
2004-04-01
期刊：
影响因子：
7.4
通讯作者：
Coe, EH
中科院分区：
文献类型：
--
作者：
Gardiner, J;Schroeder, S;Coe, EH
我们的目标是构建一个强大的物理图谱玉米（Zea mays）综合集成的遗传图谱。我们已经使用二维24 × 24 overgo合并策略将玉米表达的序列标记（EST）单基因锚到高密度过滤器上的165，888个细菌人工染色体（BAC）。一套70，716个玉米EST公共序列为10，723个EST单基因组装体的衍生奠定了基础。从这些集合中，应用10，642个40 bp的overgo序列作为杂交探针。获得了9，371个overgo探针的BAC地址，成功率为88%。超过96%的成功overgo探针鉴定了两个或更多个BAC，而5%鉴定了50个以上的BAC。大多数BAC（79%）与一个或两个overgos杂交。少数BAC与8个或更多的overgos杂交，表明这些BAC必须是基因丰富的。大约5，670个重叠群鉴定了组装在一个重叠群内的BAC，表明这些探针具有高度的基因座特异性。BAC重叠群中总共2，050 Mb中的总共1，795 Mb（Mb; 87%）与一个或多个overgos相关，overgos作为单核苷酸多态性开发的序列标记位点。覆盖密度范围从小于每兆赫兹一次覆盖到大于每兆赫兹20次覆盖。大多数重叠群（52%）被overgos击中，每兆碱基包含3到9个overgos。对约1，022 Mb基因锚定BAC重叠群的分析表明，总共13，900个overgo-contig位点中有9，003个是基因锚定的。我们的研究结果表明，overgos是一个强大的方法，用于产生基因特异性杂交探针，促进组装的综合遗传和物理图谱的玉米。
Our goal is to construct a robust physical map for maize (Zea mays) comprehensively integrated with the genetic map. We have used a two-dimensional 24 X 24 overgo pooling strategy to anchor maize expressed sequence tagged (EST) unigenes to 165,888 bacterial artificial chromosomes (BACs) on high-density filters. A set of 70,716 public maize ESTs seeded derivation of 10,723 EST unigene assemblies. From these assemblies, 10,642 overgo sequences of 40 bp were applied as hybridization probes. BAC addresses were obtained for 9,371 overgo probes, representing an 88% success rate. More than 96% of the successful overgo probes identified two or more BACs, while 5% identified more than 50 BACs. The majority of BACs identified (79%) were hybridized with one or two overgos. A small number of BACs hybridized with eight or more overgos, suggesting that these BACs must be gene rich. Approximately 5,670 overgos identified BACs assembled within one contig, indicating that these probes are highly locus specific. A total of 1,795 megabases (Mb; 87%) of the total 2,050 Mb in BAC contigs were associated with one or more overgos, which are serving as sequence-tagged sites for single nucleotide polymorphism development. Overgo density ranged from less than one overgo per megabase to greater than 20 overgos per megabase. The majority of contigs (52%) hit by overgos contained three to nine overgos per megabase. Analysis of approximately 1,022 Mb of genetically anchored BAC contigs indicates that 9,003 of the total 13,900 overgo-contig sites are genetically anchored. Our results indicate overgos are a powerful approach for generating gene-specific hybridization probes that are facilitating the assembly of an integrated genetic and physical map for maize.