Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content

First author: Hue T.M.; Affiliations: The University of Queensland (昆士兰大学): St Lucia, Australia

Corresponding author: Robert J. Henry

Arabica coffee (Coffea arabica; 阿拉比卡咖啡) has a small gene pool limiting genetic improvement. Selection for caffeine content (咖啡因含量) within this gene pool would be assisted by identification of the genes controlling this important trait. Sequencing of DNA bulks from 18 genotypes with extreme high‐ or low‐caffeine content from a population of 232 genotypes was used to identify linked polymorphisms. To obtain a reference genome, a whole genome assembly of arabica coffee (variety K7) was achieved by sequencing using short read (Illumina) and long‐ ead (PacBio) technology. Assembly was performed using a range of assembly tools resulting in 76 409 scaffolds with a scaffold N50 of 54 544 bp and a total scaffold length of 1448 Mb. Validation of the genome assembly using different tools showed high completeness of the genome. More than 99% of transcriptome sequences mapped to the C. arabica draft genome, and 89% of BUSCOs were present. The assembled genome annotated using AUGUSTUS yielded 99 829 gene models. Using the draft arabica genome as reference in mapping and variant calling allowed the detection of 1444 nonsynonymous single nucleotide polymorphisms (SNPs) associated with caffeine content. Based on Kyoto Encyclopaedia of Genes and Genomes pathway‐ased analysis, 65 caffeine‐associated SNPs were discovered, among which 11 SNPs were associated with genes encoding enzymes involved in the conversion of substrates, which participate in the caffeine biosynthesis pathways. This analysis demonstrated the complex genetic control of this key trait in coffee.

阿拉比卡咖啡基因池较小，这个特性限制了其遗传改良的进程。对于控制咖啡因含量这个性状相关基因的鉴定将有助于在育种过程中对阿拉比卡咖啡进行人工选择。作者从总数为232个基因型的群体中选择了含有极高或者极低咖啡因含量这种极端表型的18个基因型，并进行了DNA混池测序以获取与咖啡因含量相关的多态性位点。作者通过结合二代和三代测序对阿拉比卡咖啡K7品种进行了基因组的de novo测序、组装，结果获得了76409个scaffold，N50长度为54544 bp，所有scaffold总长度为1448 Mb。作者利用多种软件对于基因组组装进行了验证，显示这个版本的组装十分完整。超过99%的转录组序列可以比对到基因组上，且89%的BUSCOs在基因组中存在。作者利用AUGUSTUS软件共预测了99829个基因模型。将这个基因组组装作为参考基因组，作者通过比对和变异检测共鉴定了1444个非同义SNP与咖啡因含量相关联。进一步基于KEGG通路分析，作者发现了65个与咖啡因含量相关的SNP，其中11个SNP与参与咖啡因生物合成通路上低物转换的酶相关。本文的研究揭示了咖啡中关于咖啡因含量性状复杂的遗传背景。

通讯：Robert J. Henry (http://www.uq.edu.au/about/director-qaafi)

个人简介：昆士兰大学，学士；麦考瑞大学，硕士；拉筹伯大学，博士。

研究方向：通过植物基因组测序捕获新的遗传资源用于作物产量提升。

doi: https://doi.org/10.1111/pbi.12912

Journal: Plant Biotechnology Journal

First Published date: 13 April, 2018

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