Development and Characterization of Novel EST-SSRs from Larix gmelinii and Their Cross-Species Transferability.
Development and Characterization of Novel EST-SSRs from Larix gmelinii and Their Cross-Species Transferability.
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落叶松新型 EST-SSR 的开发和表征及其跨物种可转移性
DOI：
10.3390/molecules200712469
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发表时间：
2015-07-09
期刊：
影响因子：
--
通讯作者：
Wei Z
中科院分区：
文献类型：
--
作者：
Zhang G;Sun Z;Zhou D;Xiong M;Wang X;Yang J;Wei Z
一套899 L。利用美国国家生物技术信息中心（NCBI）的gmelinii expression sequence tags（ESTs），探讨了落叶松SSR标记的可行性。根据BLASTX结果、基因本体（GO）分类和京都基因与基因组百科全书（KEGG）图谱，共鉴定出634个非冗余单基因，包括145个重叠群和489个单基因。约11.7%（74个）的单基因含有90个候选SSR，主要是三核苷酸（29个，32.2%）和二核苷酸（26个，28.9%）。开放阅读框（ORF，约54.4%）和5 '非翻译区（5'-UTR，31.2%）中的SSRs频率较高，而3 '非翻译区（3'-UTR，约14.4%）中的SSRs频率较低。在45个新的EST-SSR标记中，有9个在两个L. gmelinii种群。每个位点的等位基因数（Na）为2 ~ 4个，观察杂合度（Ho）为0.200-0.733，期望杂合度（He）为0.408-0.604。除Lg 41外，其余位点的近交系数均大于零。这9个EST-SSR标记大多数可用于近缘种L.日本山奈L. principis-rupprechtii和L. olgensis。这些新的EST-SSR标记将为落叶松比较基因组学、遗传资源保护和分子育种等方面的研究奠定基础。
A set of 899 L. gmelinii expression sequence tags (ESTs), available at the National Center of Biotechnology Information (NCBI), was employed to address the feasibility on development of simple sequence repeat (SSR) markers for Larch species. Totally, 634 non-redundant unigenes including 145 contigs and 489 singletons were finally identified and mainly involved in biosynthetic, metabolic processes and response to stress according to BLASTX results, gene ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) maps. Approximately 11.7% (74) unigenes contained 90 candidate SSRs, which were mainly trinucleotides (29, 32.2%) and dinucleotides (26, 28.9%). A relatively high frequency of SSRs was respectively found in the Open Reading Frame (ORF, about 54.4%) and 5′-untranslated region (5′-UTR, 31.2%), while a low frequency was observed in the 3′-untranslated region (3′-UTR, about 14.4%). Of the 45 novel EST-SSRs markers, nine were found to be polymorphic at two L. gmelinii populations. The number of alleles per locus (Na) ranged from two to four, and the observed (Ho) and expected (He) heterozygosity values were 0.200–0.733 and 0.408–0.604, respectively. The inbreeding coefficients (FIS) for all loci were more than zero except Lg41. Most of these 9EST-SSR markers were transferable to its related species L. kaempferi, L. principis-rupprechtii and L. olgensis. These novel EST-SSRs will be useful for further research on comparative genomics, genetic resources conservation and molecular breeding in larch trees.
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DOI：
10.3390/molecules19055777
发表时间：
2014-05-05
期刊：
Molecules (Basel, Switzerland)
影响因子：
--
作者：
Liu Z;Liu P;Luo D;Liu W;Wang Y
通讯作者：
Wang Y
影响因子：
3
作者：
Funda, Tomas;Chen, Charles C.;El-Kassaby, Yousry A.
通讯作者：
El-Kassaby, Yousry A.
影响因子：
4.9
作者：
Khasa, Damase P.;Jaramillo-Correa, Juan P.;Bousquet, Jean
通讯作者：
Bousquet, Jean
影响因子：
0.6
作者：
Kozyrenko, MM;Artyukova, EV;Zhuravlev, YN
通讯作者：
Zhuravlev, YN
影响因子：
2.6
作者：
Krutovsky, Konstantin V.;Tretyakova, Iraida N.;Vaganov, Eugene A.
通讯作者：
Vaganov, Eugene A.