瑞士雀巢研发中心Patrick Descombes等研究人员合作发现，异源多倍体阿拉比卡豆的基因组和群体基因组学揭示现代咖啡栽培品种的多样化历史。相关论文于2024年4月15日在线发表在《自然—遗传学》杂志上。

研究人员表示，阿拉比卡豆（Coffea arabica）是欧基尼奥伊德斯咖啡（Coffea eugenioides）和中果咖啡（Coffea canephora）的异源四倍体杂交种，是全球约60%咖啡产品的来源，其栽培品种经历了多次种群瓶颈。

研究人员展示了一个二倍体C. arabica品种及其二倍体祖先C.eugenioides和C. canephora的现代代表染色体组。这三个物种的二倍体亲本和后代亚基因组之间的基因组结构基本保持一致，没有明显的全局亚基因组优势。研究人员发现有证据表明，在35万-61万年前发生过一次创始多倍体事件，之后又经历了几次驯化前的瓶颈期，导致基因变异范围很窄。

野生品种和栽培品种祖先之间的分裂发生在距今约3.05万年前，随后是两个种群之间的迁移期。对现代品种（包括历史上与C. canephora杂交的品系）的分析突出了它们的育种历史和可能有助于抗病原体的基因位点，为未来基于基因组学的C. arabica育种奠定了基础。

附：英文原文

Title: The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Author: Salojrvi, Jarkko, Rambani, Aditi, Yu, Zhe, Guyot, Romain, Strickler, Susan, Lepelley, Maud, Wang, Cui, Rajaraman, Sitaram, Rastas, Pasi, Zheng, Chunfang, Muoz, Daniella Santos, Meidanis, Joo, Paschoal, Alexandre Rossi, Bawin, Yves, Krabbenhoft, Trevor J., Wang, Zhen Qin, Fleck, Steven J., Aussel, Rudy, Bellanger, Laurence, Charpagne, Aline, Fournier, Coralie, Kassam, Mohamed, Lefebvre, Gregory, Mtairon, Sylviane, Moine, Dborah, Rigoreau, Michel, Stolte, Jens, Hamon, Perla, Couturon, Emmanuel, Tranchant-Dubreuil, Christine, Mukherjee, Minakshi, Lan, Tianying, Engelhardt, Jan, Stadler, Peter, Correia De Lemos, Samara Mireza, Suzuki, Suzana Ivamoto, Sumirat, Ucu, Wai, Ching Man, Dauchot, Nicolas, Orozco-Arias, Simon, Garavito, Andrea, Kiwuka, Catherine, Musoli, Pascal, Nalukenge, Anne, Guichoux, Erwan, Reinout, Havinga, Smit, Martin, Carretero-Paulet, Lorenzo, Filho, Oliveiro Guerreiro, Braghini, Masako Toma, Padilha, Lilian, Sera, Gustavo Hiroshi, Ruttink, Tom, Henry, Robert, Marraccini, Pierre, Van de Peer, Yves, Andrade, Alan, Domingues, Douglas, Giuliano, Giovanni, Mueller, Lukas, Pereira, Luiz Filipe, Plaisance, Stephane, Poncet, Valerie, Rombauts, Stephane, Sankoff, David, Albert, Victor A., Crouzillat, Dominique, de Kochko, Alexandre, Descombes, Patrick

Issue&Volume: 2024-04-15

Abstract: Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

DOI: 10.1038/s41588-024-01695-w

Source: https://www.nature.com/articles/s41588-024-01695-w