Data from: Genome-wide association mapping of date palm fruit traits

Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial crop species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform GWAS mapping of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor (VIRESCENS) gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crop species, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species.

海枣（Phoenix dactylifera）是中东与北非干旱地区的重要果树作物。尽管其具有重要的经济价值，但目前针对海枣的基因组学资源仍较为匮乏，极大阻碍了这类多年生作物的进化基因组学研究。本研究报道了一个优化后的海枣长读长基因组组装结果，其组装总长度为772.3 Mb，重叠群（contig）N50达到897.2 Kb；研究利用该组装结果对性别决定区域以及21个果实性状开展了全基因组关联分析（Genome-Wide Association Study, GWAS）定位。我们在R2R3-MYB转录因子（VIRESCENS）基因处发现了与果实颜色相关的GWAS信号，并鉴定出两类功能性等位基因：一类携带反转录转座子插入突变，另一类存在起始密码子变异。此外，我们还发现了与糖分组成相关的GWAS峰值位点，该区域覆盖多个连锁的转化酶基因的缺失多态性。MYB转录因子与转化酶在其他作物中也被证实与果实颜色及糖分组成相关，这表明平行进化在驯化物种的演化分化过程中发挥着重要作用。