Analysis of the first Taraxacum kok-saghyz transcriptome reveals potential rubber yield related SNPs.
Analysis of the first Taraxacum kok-saghyz transcriptome reveals potential rubber yield related SNPs.
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对第一个塔拉萨克姆·萨格里兹转录组的分析揭示了潜在的橡胶产量相关的SNP。
DOI：
10.1038/s41598-017-09034-2
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发表时间：
2017-08-30
影响因子：
4.6
通讯作者：
Cornish K
中科院分区：
文献类型：
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作者：
Luo Z;Iaffaldano BJ;Zhuang X;Fresnedo-Ramírez J;Cornish K
蒲公英（Taraxacumkok-saghyz，TK）是一种具有高分子量橡胶、短育种周期和适应环境多样性的潜在替代作物。然而，橡胶产量和农艺相关性状的改进仍然需要在它成为商业上可行的作物之前。从来自具有高和低橡胶产量的基因型的根池开发基于RNA-Seq的转录组。从头组装了总共55，532个长度超过200 bp的转录物。在已知的50个橡胶生物合成相关基因中，有49个与472个转录本具有显著的同源性。158个转录本在高橡胶和低橡胶基因型之间显著差异表达。21，036个SNPs在高橡胶TK基因型和低橡胶TK基因型中存在差异。其中，在39个转录本中发现了50个SNP，与公开检索的49个橡胶生物合成相关基因高度同源。117个SNPs位于36个差异表达基因序列中。这一全面的TK转录组学参考，以及包括与橡胶相关基因同源物和差异表达基因相关的推定外显子标记在内的大量SNP，为橡胶相关性状的进一步遗传解剖、比较基因组学和TK育种的标记辅助选择提供了坚实的基础。
Taraxacum kok-saghyz (TK) is a potential alternative crop for natural rubber (NR) production, due to its high molecular weight rubber, short breeding cycle, and diverse environmental adaptation. However, improvements in rubber yield and agronomically relevant traits are still required before it can become a commercially-viable crop. An RNA-Seq based transcriptome was developed from a pool of roots from genotypes with high and low rubber yield. A total of 55,532 transcripts with lengths over 200 bp were de novo assembled. As many as 472 transcripts were significantly homologous to 49 out of 50 known plant putative rubber biosynthesis related genes. 158 transcripts were significantly differentially expressed between high rubber and low rubber genotypes. 21,036 SNPs were different in high and low rubber TK genotypes. Among these, 50 SNPs were found within 39 transcripts highly homologous to 49 publically-searched rubber biosynthesis related genes. 117 SNPs were located within 36 of the differentially expressed gene sequences. This comprehensive TK transcriptomic reference, and large set of SNPs including putative exonic markers associated with rubber related gene homologues and differentially expressed genes, provides a solid foundation for further genetic dissection of rubber related traits, comparative genomics and marker-assisted selection for the breeding of TK.
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影响因子：
4.6
作者：
Arias M;Hernandez M;Remondegui N;Huvenaars K;van Dijk P;Ritter E
通讯作者：
Ritter E
DOI：
10.13057/biodiv/d170262
发表时间：
2016-01-01
期刊：
Biodiversitas: Journal of Biological Diversity
影响因子：
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作者：
Cornish, K.;Kopicky, S. L.;Streeter, J. G.
通讯作者：
Streeter, J. G.
影响因子：
7.4
作者：
FUJIHARA, S;YAMAGUCHI, M
通讯作者：
YAMAGUCHI, M
影响因子：
5.8
作者：
Conesa, A;Götz, S;Robles, M
通讯作者：
Robles, M
影响因子：
14.8
作者：
通讯作者：
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