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。尽管其经济价值与科研价值举足轻重，但目前针对海枣的基因组学资源仍较为稀缺，这严重阻碍了这一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长读长海枣基因组组装版本，其基因组总长为772.3 Mb，重叠群N50值达897.2 Kb；并依托该组装开展了针对性别决定区域与21个果实性状的全基因组关联分析（Genome-Wide Association Study，GWAS）。我们在R2R3-MYB转录因子（VIRESCENS）基因位点发现了果实颜色相关的GWAS信号，并鉴定出包含反转录转座子插入与起始密码子突变的功能等位基因。此外，我们还在多个连锁的蔗糖转化酶基因的缺失多态性区域，检测到与糖分组成相关的GWAS峰值。在其他作物物种中，MYB转录因子与蔗糖转化酶已被证实参与果实颜色与糖分组成的调控过程，这充分印证了平行进化在驯化物种进化分化进程中的关键作用。