Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies.
Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies.
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杂交蔷薇的基因组和转录组测序为育种、花性状改良和分类学研究提供微卫星标记
DOI：
10.1186/s12870-018-1322-5
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发表时间：
2018-06-15
影响因子：
5.3
通讯作者：
Zhang Z
中科院分区：
文献类型：
--
作者：
Qi W;Chen X;Fang P;Shi S;Li J;Liu X;Cao X;Zhao N;Hao H;Li Y;Han Y;Zhang Z
背景：月季是一种观赏、食用和药用价值很高的植物，但其分子标记资源相对有限，尤其是花特异性标记。在这项研究中，我们进行了现代玫瑰基因组和花转录组测序。我们获得了全面的核苷酸信息，从许多潜在的简单重复序列（SSR）标记被确定，但被发现有很高的扩增失败率和PCR产物redundancy.Results：我们采用了一种过滤策略与组装的基因组序列进行BLAST分析，并确定了124,591个基因组和2,292个EST标记与独特的退火位点。这些标志物具有更大的可靠性比过滤前获得的。针对转录组序列的额外BLAST分析发现了与4100个转录物相关的5225个基因组SSR，其中2138个与针对非冗余数据库注释的功能基因相关。超过90%的这些新开发的分子标记是多态性的，基于PCR使用SSR的子集来分析四倍体现代玫瑰品种，二倍体蔷薇属物种和草莓加入。通过聚类分析（基于这些结果）确定的蔷薇属物种之间的关系与现代玫瑰育种史一致，而草莓被隔离在一个单独的集群，作为expected.Conclusions：我们的研究结果为玫瑰花性状的改良，育种和分类提供了有价值的分子遗传工具。重要的是，我们描述了一种可重复的器官特异性策略，用于植物中的分子标记开发和选择，该策略可应用于其他作物。
Background:Rosa hybrida is a valuable ornamental, food and medicinal crop worldwide, but with relatively limited molecular marker resources, especially for flower-specific markers. In this study, we performed genomic and floral transcriptomic sequencing of modern rose. We obtained comprehensive nucleotide information, from which numerous potential simple sequence repeat (SSR) markers were identified but were found to have high rates of amplification failure and PCR product redundancy.Results:We applied a filtering strategy for BLAST analysis with the assembled genomic sequence and identified 124,591 genomic and 2,292 EST markers with unique annealing sites. These markers had much greater reliability than those obtained before filtering. Additional BLAST analysis against the transcriptomic sequences uncovered 5225 genomic SSRs associated with 4100 transcripts, 2138 of which were associated with functional genes that were annotated against the non-redundant database. More than 90% of these newly developed molecular markers were polymorphic, based on PCR using a subset of SSRs to analyze tetraploid modern rose accessions, diploid Rosa species and one strawberry accession. The relationships among Rosa species determined by cluster analysis (based on these results) were in agreement with modern rose breeding history, whereas strawberry was isolated in a separate cluster, as expected.Conclusions:Our results provide valuable molecular-genetic tools for rose flower trait improvement, breeding and taxonomy. Importantly, we describe a reproducible organ-specific strategy for molecular marker development and selection in plants, which can be applied to other crops.
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使用 RNA-Seq 组装具有超过 13,000 个全长表达基因的玫瑰转录组，并开发玫瑰 (Rosa L.) 的 WagRhSNP 68k Axiom SNP 阵列。
影响因子：
5.6
作者：
Koning-Boucoiran CF;Esselink GD;Vukosavljev M;van 't Westende WP;Gitonga VW;Krens FA;Voorrips RE;van de Weg WE;Schulz D;Debener T;Maliepaard C;Arens P;Smulders MJ
通讯作者：
Smulders MJ
影响因子：
5.4
作者：
Martin, M;Piola, F;Heizmann, P
通讯作者：
Heizmann, P
影响因子：
10.7
作者：
Kumar, Sudhir;Stecher, Glen;Tamura, Koichiro
通讯作者：
Tamura, Koichiro
影响因子：
30.8
作者：
通讯作者：
--
通过大白菜（Brassica rapa L. ssp pekinensis）深度转录组测序对 EST-SSR 进行表征和开发
影响因子：
2.9
作者：
Ding Q;Li J;Wang F;Zhang Y;Li H;Zhang J;Gao J
通讯作者：
Gao J