Genomic variation in tomato, from wild ancestors to contemporary breeding accessions.
Genomic variation in tomato, from wild ancestors to contemporary breeding accessions.
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番茄的基因组变异，从野生祖先到当代育种品种。
DOI：
10.1186/s12864-015-1444-1
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发表时间：
2015-04-01
期刊：
影响因子：
4.4
通讯作者：
Cañizares J
中科院分区：
文献类型：
--
作者：
Blanca J;Montero-Pau J;Sauvage C;Bauchet G;Illa E;Díez MJ;Francis D;Causse M;van der Knaap E;Cañizares J
驯化改变了物种的基因组变异。量化这种变异可以深入了解驯化过程，促进育种者和种质中心使用的资源的管理，并使实验设计能够将性状与基因联系起来。我们描述并分析了包括 Solanum lycopersicum var. 在内的 1,008 个番茄种质的遗传多样性。番茄 (SLL)，S. lycopersicum var.使用 7,720 个 SNP 对 cerasiforme (SLC) 和 S. pimpinellifolium (SP) 进行基因分型。此外，我们探索了影响果实重量和形状的六个基因座的等位基因频率，以推断选择模式。我们的结果揭示了一种变异模式，强烈支持两步驯化过程、偶尔在野外杂交以及通过人类选择进行分化。这些解释与观察到的影响果实重量和形状的六个基因座的等位基因频率一致。在中美洲番茄驯化之前，厄瓜多尔安第斯地区和秘鲁北部的 SLC 中对果实重量进行了严格选择。影响果实形状的等位基因在 SLL 遗传亚群中进行了差异选择。我们的结果还阐明了 SLC 的生物学状态。真正的SLC在系统发育上位于SP和SLL之间，其果实形态多样。 SLC 和“樱桃番茄”不是同义词。基于形态学的术语“樱桃番茄”包括一些 SLC、当代品种以及 SP 和 SLL 之间的许多混合物。与老式组相比，当代 SLL 显示核苷酸多样性适度增加。这项研究广泛而详细地描述了番茄的基因组变异。番茄驯化似乎遵循两个步骤：第一次驯化在南美洲，第二次驯化在中美洲。果实重量和形状等位基因的分布支持 SLC 的驯化发生在安第斯地区。我们的结果还阐明了 SLC 作为番茄中真正的系统发育群的生物学地位。我们检测到厄瓜多尔和秘鲁的种质可能代表了一系列未经探索的变异，这些变异可能对作物改良感兴趣。本文的在线版本 (doi:10.1186/s12864-015-1444-1) 包含补充材料，可供授权用户使用。
Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection. Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and “cherry tomato” are not synonymous terms. The morphologically-based term “cherry tomato” included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups. This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement. The online version of this article (doi:10.1186/s12864-015-1444-1) contains supplementary material, which is available to authorized users.
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影响因子：
12.3
作者：
Knight R;Maxwell P;Birmingham A;Carnes J;Caporaso JG;Easton BC;Eaton M;Hamady M;Lindsay H;Liu Z;Lozupone C;McDonald D;Robeson M;Sammut R;Smit S;Wakefield MJ;Widmann J;Wikman S;Wilson S;Ying H;Huttley GA
通讯作者：
Huttley GA
影响因子：
30.8
作者：
Cong, Bin;Barrero, Luz S.;Tanksley, Steven D.
通讯作者：
Tanksley, Steven D.
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
5.4
作者：
MILLER, JC;TANKSLEY, SD
通讯作者：
TANKSLEY, SD
影响因子：
7.4
作者：
Munos, Stephane;Ranc, Nicolas;Causse, Mathilde
通讯作者：
Causse, Mathilde