Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies
Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies
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DOI：
10.1007/s00438-011-0658-4
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发表时间：
2012-01-01
影响因子：
3.1
通讯作者：
Ollitrault, Patrick
中科院分区：
文献类型：
--
作者：
Garcia-Lor, Andres;Luro, Francois;Ollitrault, Patrick
与驯化历史相关的遗传分层是评估基因库内遗传关联研究相关性的关键参数。以往的分子和表型研究表明，栽培柑橘的多样性主要来自三个主要种之间的重组：C。medica（citron）、香橼C. reticulata（柑橘）和C.极大（柚）。然而，这些基本物种中的每一个对次生栽培物种（如C。sinensis（sweet橙子）、C.利蒙（lemon）、C. aurantium（sour橙子）、C. paradisi（葡萄柚）和最近的杂交种是未知的。我们的研究重点是：（1）插入-缺失（InDel）标记的发展及其与SSR标记在遗传多样性和系统发育研究中的比较;（2）分析基本分类群对次生种和现代栽培品种基因组的贡献;（3）描述柑橘基因库的组织结构，以评估如何在栽培柑橘基因库水平上进行遗传关联研究。InDel标记是较好的系统发育标记，用于追踪三个祖先物种的贡献，而SSR标记是更有用的种内多样性分析。柑桔基因库的大部分遗传组织与柑桔属植物间的分化有关。reticulata、网叶C. maxima和C.医学观察到高和广义LD，可能是由于基本物种和有限数量的种间重组之间的初始分化。这种结构排除了在属水平上的关联遗传研究，而不从种间杂种中开发额外的重组群体。关联遗传学研究也应该是负担得起的种内水平在一个结构不太像C。网状的。
Genetic stratification associated with domestication history is a key parameter for estimating the pertinence of genetic association study within a gene pool. Previous molecular and phenotypic studies have shown that most of the diversity of cultivated citrus results from recombination between three main species: C. medica (citron), C. reticulata (mandarin) and C. maxima (pummelo). However, the precise contribution of each of these basic species to the genomes of secondary cultivated species, such as C. sinensis (sweet orange), C. limon (lemon), C. aurantium (sour orange), C. paradisi (grapefruit) and recent hybrids is unknown. Our study focused on: (1) the development of insertion-deletion (InDel) markers and their comparison with SSR markers for use in genetic diversity and phylogenetic studies; (2) the analysis of the contributions of basic taxa to the genomes of secondary species and modern cultivars and (3) the description of the organisation of the Citrus gene pool, to evaluate how genetic association studies should be done at the cultivated Citrus gene pool level. InDel markers appear to be better phylogenetic markers for tracing the contributions of the three ancestral species, whereas SSR markers are more useful for intraspecific diversity analysis. Most of the genetic organisation of the Citrus gene pool is related to the differentiation between C. reticulata, C. maxima and C. medica. High and generalised LD was observed, probably due to the initial differentiation between the basic species and a limited number of interspecific recombinations. This structure precludes association genetic studies at the genus level without developing additional recombinant populations from interspecific hybrids. Association genetic studies should also be affordable at intraspecific level in a less structured pool such as C. reticulata.