CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
Ethiopian Biodiversity Institute, P.O. Box 30726, Addis Ababa, Ethiopia.
BMC Plant Biol. 2022 Feb 14;22(1):69. doi: 10.1186/s12870-022-03449-4.
Coffea arabica L. is an economically important agricultural crop and the most popular beverage worldwide. As a perennial crop with recalcitrant seed, conservation of the genetic resources of coffee can be achieved through the complementary approach of in-situ and ex-situ field genebank. In Ethiopia, a large collection of C. arabica L. germplasm is preserved in field gene banks. Here, we report the whole-genome resequencing of 90 accessions from Choche germplasm bank representing garden and forest-based coffee production systems using Illumina sequencing technology.
The genome sequencing generated 6.41 billion paired-end reads, with a mean of 71.19 million reads per sample. More than 93% of the clean reads were mapped onto the C. arabica L. reference genome. A total of 11.08 million variants were identified, among which 9.74 million (87.9%) were SNPs (Single nucleotide polymorphisms) and 1.34 million (12.1%) were InDels. In all accessions, genomic variants were unevenly distributed across the coffee genome. The phylogenetic analysis using the SNP markers displayed distinct groups.
Resequencing of the coffee accessions has allowed identification of genetic markers, such as SNPs and InDels. The SNPs discovered in this study might contribute to the variation in important pathways of genes for important agronomic traits such as caffeine content, yield, disease, and pest in coffee. Moreover, the genome resequencing data and the genetic markers identified from 90 accessions provide insight into the genetic variation of the coffee germplasm and facilitate a broad range of genetic studies.
阿拉伯咖啡（Coffea arabica L.）是一种经济上重要的农业作物，也是全球最受欢迎的饮料。作为一种具有抗性种子的多年生作物，可以通过原位和异位田间基因库的互补方法来实现咖啡遗传资源的保存。在埃塞俄比亚，大量的阿拉伯咖啡种质资源被保存在田间基因库中。在这里，我们报告了使用 Illumina 测序技术对来自 Choche 种质库的 90 个埃塞俄比亚阿拉伯咖啡品系进行全基因组重测序的结果，这些品系代表了花园和森林咖啡生产系统。
基因组测序生成了 64.1 亿对末端读取序列，每个样本的平均读取量为 7119 万对。超过 93%的清洁读取序列被映射到阿拉伯咖啡参考基因组上。共鉴定出 1108 万个变异，其中 974 万个（87.9%）为单核苷酸多态性（SNP），134 万个（12.1%）为插入缺失（InDel）。在所有的品系中，基因组变异在咖啡基因组中分布不均匀。使用 SNP 标记进行的系统发育分析显示出不同的群体。
对咖啡品系进行重测序，允许鉴定出遗传标记，如 SNP 和 InDel。本研究中发现的 SNP 可能导致咖啡因含量、产量、疾病和害虫等重要农艺性状的基因的重要途径发生变异。此外，90 个品系的基因组重测序数据和鉴定的遗传标记为咖啡种质资源的遗传变异提供了深入的了解，并促进了广泛的遗传研究。
