Coconut palms (Cocos nucifera) are a combination of wild admixed populations and perennial crops with a worldwide distribution. Here we develop single nucleotide polymorphisms (SNPs) along the coconut genome based on Genotyping by Sequencing (GBS) for at least four different commercially important and widely cultivated coconut varieties and hybrids growing in northern South America. We present a comprehensive catalog of approximately 27K SNPs to conduct genetic diversity, population structure and linkage disequilibrium analysis. A relatively fast LD decay for the Atlantic accessions within ~250Kb was observed in comparison to the Pacific accessions ~ 1500 Kb. The complete SNPs sampling showed a strong population structure at K = 2, separating accessions from the Pacific and Atlantic coasts as it has been found in previous studies. At higher K values, one non-admixed group was observed for the Atlantic while further substructures emerged for the Pacific accessions, where three non-admixed groups were found. Population structure analysis also showed a great degree of admixture between the Atlantic and Pacific populations, and SNPs of the Pacific non-admixed genetic groups were mostly introgressed into the Atlantic individuals but the contrary was rarely observed. The results of principal component analysis and Neighbor-Joining Hierarchical Clustering were consistent with the results from Structure and provided a measure of genetic relationships among individual genotypes. The Pacific group has a lower genetic diversity and a higher rate of inbreeding than the Atlantic group. These results suggest that the Pacific coconuts of Colombia belong to the pre-Columbian population found on the Pacific coast of Panama and Peru. If it had been introduced after Columbus (as in Mexico), genetic diversity would have been higher than on the Atlantic coast.

中文翻译：

---

来自南美洲北部的椰子全基因组多样性揭示了哥伦比亚存在的基因型和强大的种群结构

椰子（Cocos nucifera）是野生混合种群和多年生作物的组合，分布在世界各地。在这里，我们通过基于测序的基因分型（GBS）沿着椰子基因组开发了沿椰子基因组的单核苷酸多态性（SNPs），用于在南美洲北部生长的至少四个不同的重要商业用途和广泛种植的椰子品种和杂种。我们提出了大约27K SNP的全面目录，以进行遗传多样性，种群结构和连锁不平衡分析。与〜1500 Kb的太平洋种质相比，大西洋品类在〜250Kb范围内观察到了相对快速的LD衰减。完整的SNP采样显示，在K = 2时，种群结构很强，如先前研究中所发现的，将太平洋和大西洋沿岸的种质分离开来。在较高的K值下，大西洋观察到一个非混合群，而太平洋种质又出现了进一步的亚结构，在那里发现了三个非混合群。种群结构分析还显示了大西洋和太平洋种群之间的高度融合，并且太平洋非混合遗传群体的SNP大多渗入了大西洋个体，但很少观察到相反的情况。主成分分析和Neighbor-Joining Hierarchical Clustering的结果与Structure的结果一致，并为个体基因型之间的遗传关系提供了度量。与大西洋集团相比，太平洋集团的遗传多样性较低，近交率更高。这些结果表明，哥伦比亚的太平洋椰子属于巴拿马和秘鲁的太平洋海岸上发现的哥伦布前种群。如果它是在哥伦布之后引入的（例如在墨西哥），则遗传多样性将比大西洋沿岸更高。