Oueslati Amel, Salhi-Hannachi Amel, Luro François, Vignes Hélène, Mournet Pierre, Ollitrault Patrick
Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis (FST), Université de Tunis El Manar, Tunis, Tunisia.
AGAP Research Unit, Centre de coopération Internationale en Recherche Agronomique pour le Développement Petit-Bourg, Guadeloupe, France.
PLoS One. 2017 Oct 5;12(10):e0185618. doi: 10.1371/journal.pone.0185618. eCollection 2017.
The mandarin horticultural group is an important component of world citrus production for the fresh fruit market. This group formerly classified as C. reticulata is highly polymorphic and recent molecular studies have suggested that numerous cultivated mandarins were introgressed by C. maxima (the pummelos). C. maxima and C. reticulata are also the ancestors of sweet and sour oranges, grapefruit, and therefore of all the "small citrus" modern varieties (mandarins, tangors, tangelos) derived from sexual hybridization between these horticultural groups. Recently, NGS technologies have greatly modified how plant evolution and genomic structure are analyzed, moving from phylogenetics to phylogenomics. The objective of this work was to develop a workflow for phylogenomic inference from Genotyping By Sequencing (GBS) data and to analyze the interspecific admixture along the nine citrus chromosomes for horticultural groups and recent varieties resulting from the combination of the C. reticulata and C. maxima gene pools. A GBS library was established from 55 citrus varieties, using the ApekI restriction enzyme and selective PCR to improve the read depth. Diagnostic polymorphisms (DPs) of C. reticulata/C. maxima differentiation were identified and used to decipher the phylogenomic structure of the 55 varieties. The GBS approach was powerful and revealed 30,289 SNPs and 8,794 Indels with 12.6% of missing data. 11,133 DPs were selected covering the nine chromosomes with a higher density in genic regions. GBS combined with the detection of DPs was powerful for deciphering the "phylogenomic karyotypes" of cultivars derived from admixture of the two ancestral species after a limited number of interspecific recombinations. All the mandarins, mandarin hybrids, tangelos and tangors analyzed displayed introgression of C. maxima in different parts of the genome. C. reticulata/C. maxima admixture should be a major component of the high phenotypic variability of this germplasm opening up the way for association studies based on phylogenomics.
宽皮柑橘园艺群体是世界鲜食柑橘生产的重要组成部分。该群体以前被归类为柑桔，具有高度多态性，最近的分子研究表明，许多栽培柑桔是柚（C. maxima）渗入的结果。柚和柑桔也是甜橙、酸橙、葡萄柚的祖先，因此也是所有通过这些园艺群体间有性杂交衍生出的“小型柑橘”现代品种（柑桔、橘橙、橘柚）的祖先。最近，新一代测序（NGS）技术极大地改变了植物进化和基因组结构的分析方式，从系统发育学转向了系统基因组学。这项工作的目的是开发一种从简化基因组测序（GBS）数据进行系统基因组推断的工作流程，并分析九个柑橘染色体上园艺群体以及柑桔和柚基因库组合产生的现代品种的种间混合情况。使用ApekI限制性内切酶和选择性PCR建立了一个包含55个柑橘品种的GBS文库，以提高测序深度。鉴定了柑桔/柚分化的诊断性多态性（DPs），并用于解读这55个品种系统基因组结构。GBS方法功能强大，揭示了30289个单核苷酸多态性（SNPs）和8794个插入缺失（Indels），缺失数据占12.6%。选择了11133个DPs覆盖九条染色体，在基因区域密度更高。GBS结合DPs检测对于解读两个祖先物种在有限数量的种间重组后混合产生的品种的“系统基因组核型”很有效。所有分析的柑桔、柑桔杂种、橘柚和橘橙在基因组的不同部分都显示出柚的渗入。柑桔/柚混合应该是这种种质高表型变异性的一个主要组成部分，为基于系统基因组学的关联研究开辟了道路。
