Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping.
Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping.
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DOI：
10.1186/1471-2164-9-287
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发表时间：
2008-06-16
期刊：
影响因子：
4.4
通讯作者：
Morillon, Raphael
中科院分区：
文献类型：
--
作者：
Luro, Francois L.;Costantino, Gilles;Terol, Javier;Argout, Xavier;Allario, Thierry;Wincker, Patrick;Talon, Manuel;Ollitrault, Patrick;Morillon, Raphael
在过去十年中，开发了大量微卫星标记用于基因分型以及鉴定亲缘关系密切的植物基因型。在柑橘中，先前开发的微卫星标记来自基因组文库，且通常位于非编码DNA序列中。为了在基因组图谱绘制项目和柑橘系统分析中优化这些EST - SSR作为遗传标记的使用，我们研究了它们与类型（二核苷酸或三核苷酸）相关的多态性以及它们在编码序列中的位置。
在来自克莱门氏柑橘EST文库的11000个单基因中，我们在1500个单基因（13.6%）中发现了至少一个微卫星序列（重复单元大小从2到6个核苷酸不等）。这些SSR中超过95%是二核苷酸或三核苷酸。如果三核苷酸微卫星在EST序列的所有部分都能遇到，那么二核苷酸微卫星则优先（50%）集中在5'端的前100个核苷酸内。我们通过用侧翼引物对10个柑橘属物种以及另外3个其他属的物种进行PCR扩增，评估了41个EST - SSR的多态性。超过90%的EST - SSR标记是多态的。此外，二核苷酸微卫星标记比三核苷酸标记更具多态性，这可能与其分布有关，它们更常位于5'非翻译区（UTR）。我们发现用EST - SSR标记评估的柑橘属物种及其近缘种之间的多样性关系与已确立的分类学和系统发育关系高度吻合。最后，研究了每种基因型以及所有两两组合的杂合性，以评估可作图标记的百分比。假定的柑橘种间杂种（酸橙柠檬或酸橙）观察到的值较高（>45%），而柑橘基本纯种（柑橘、柚子和香橼）的值较低（<30%）。在涉及种间杂种基因型的组合中观察到了对基因组作图最有利的组合。这些组合产生了更高水平的可作图标记（>70%），其中相当大比例适合用于同线性分析。
产生了41个新的EST - SSR标记，可用于柑橘遗传研究。无论SSR在EST中的位置如何，我们开发的EST - SSR标记在研究柑橘的遗传多样性和基因组作图方面都很有效。
During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from genomic libraries and more often located in non coding DNA sequences. To optimize the use of these EST-SSRs as genetic markers in genome mapping programs and citrus systematic analysis, we have investigated their polymorphism related to the type (di or trinucleotide) or their position in the coding sequences. Among 11000 unigenes from a Clementine EST library, we have found at least one microsatellite sequence (repeated units size ranged from 2 to 6 nucleotides) in 1500 unigenes (13.6%). More than 95% of these SSRs were di or trinucleotides. If trinucleotide microsatellites were encountered trough all part of EST sequences, dinucleotide microsatellites were preferentially (50%) concentrated in the 5' 100th nucleotides. We assessed the polymorphism of 41 EST-SSR, by PCR amplification droved with flanking primers among ten Citrus species plus 3 from other genera. More than 90% of EST-SSR markers were polymorphic. Furthermore, dinucleotide microsatellite markers were more polymorphic than trinucleotide ones, probably related to their distribution that was more often located in the 5' UnTranslated Region (UTR). We obtained a good agreement of diversity relationships between the citrus species and relatives assessed with EST-SSR markers with the established taxonomy and phylogeny. To end, the heterozygosity of each genotype and all dual combinations were studied to evaluate the percentage of mappable markers. Higher values (> 45%) were observed for putative Citrus inter-specific hybrids (lime lemon, or sour orange) than for Citrus basic true species (mandarin, pummelo and citron) (<30%). Most favorable combinations for genome mapping were observed in those involving interspecific hybrid genotypes. Those gave higher levels of mappable markers (>70%) with a significant proportion suitable for synteny analysis. Fourty one new EST-SSR markers were produced and were available for citrus genetic studies. Whatever the position of the SSR in the ESTs the EST-SSR markers we developed are powerful to investigate genetic diversity and genome mapping in citrus.
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影响因子：
5.4
作者：
Herrero, R;Asins, MJ;Navarro, L
通讯作者：
Navarro, L
影响因子：
2.4
作者：
Berube, Yanik;Zhuang, Jun;Ritland, Kermit
通讯作者：
Ritland, Kermit
影响因子：
5.4
作者：
CAI, Q;GUY, CL;MOORE, GA
通讯作者：
MOORE, GA
DOI：
10.21273/jashs.126.2.210
发表时间：
2001-03-01
影响因子：
1.9
作者：
Gulsen, O;Roose, ML
通讯作者：
Roose, ML
影响因子：
5.4
作者：
JARRELL, DC;ROOSE, ML;KUPPER, RS
通讯作者：
KUPPER, RS