Gomez Céline, Dussert Stéphane, Hamon Perla, Hamon Serge, Kochko Alexandre de, Poncet Valérie
UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier CEDEX 5, France.
BMC Evol Biol. 2009 Jul 16;9:167. doi: 10.1186/1471-2148-9-167.
Among Coffea species, C. canephora has the widest natural distribution area in tropical African forests. It represents a good model for analyzing the geographical distribution of diversity in relation to locations proposed as part of the "refuge theory". In this study, we used both microsatellite (simple sequence repeat, SSR) and restriction fragment length polymorphism (RFLP) markers to investigate the genetic variation pattern of C. canephora in the Guineo-Congolean distribution zone.
Both markers were first compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among wild C. canephora genotypes. As expected, SSR markers were found to have a higher genetic distance detection capacity than RFLP. Nevertheless, similarity matrices showed significant correlations when Mantel's test was carried out (r = 0.66, p < 0.0001). Finally, both markers were equally effective for group discrimination and phylogenetic studies, but SSR markers tended to outperform RFLP markers in discriminating the source of an individual among diversity groups and in putative hybrid detection. Five well defined genetic groups, one in the Upper Guinean forests, the four others in the Lower Guinean forests, were identified, corresponding to geographical patterning in the individuals.
Our data suggested that the Dahomey Gap, a biogeographical barrier, played a role in wild C. canephora differentiation. Climatic variations during the Pleistocene and/or Holocene probably caused the subgroup differentiation in the Congolese zone through the presence of a mosaic of putative refugia. Recent hybridization between C. canephora diversity groups, both for spontaneous individuals and cultivars, was further characterised according to their geographic dissemination or breeding history as a consequence of human activities.
在咖啡属物种中，卡内弗拉咖啡在热带非洲森林中的自然分布区域最广。它是分析与“避难所理论”中所提出地点相关的多样性地理分布的良好模型。在本研究中，我们使用微卫星（简单序列重复，SSR）和限制性片段长度多态性（RFLP）标记来研究卡内弗拉咖啡在几内亚-刚果分布区的遗传变异模式。
在对野生卡内弗拉咖啡基因型的遗传多样性和关系进行研究时，首先比较了这两种标记的信息含量和效率。正如预期的那样，发现SSR标记比RFLP具有更高的遗传距离检测能力。然而，进行Mantel检验时相似性矩阵显示出显著相关性（r = 0.66，p < 0.0001）。最后，两种标记在群体区分和系统发育研究中同样有效，但在区分多样性群体中的个体来源和推定杂种检测方面，SSR标记往往优于RFLP标记。确定了五个明确的遗传群体，一个在上几内亚森林，另外四个在下几内亚森林，这与个体中的地理格局相对应。
我们的数据表明，作为生物地理屏障的达荷美峡口在野生卡内弗拉咖啡的分化中起了作用。更新世和/或全新世期间的气候变化可能通过存在推定避难所的镶嵌体导致了刚果地区的亚组分化。由于人类活动，根据其地理传播或育种历史，进一步表征了卡内弗拉咖啡多样性群体之间近期的杂交情况，包括自发个体和栽培品种。
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