Genome-wide association mapping of date palm fruit traits

First author: Khaled M. Hazzouri; Affiliations: New York University Abu Dhabi (纽约大学阿布扎比分校): Abu Dhabi, United Arab Emirates

Corresponding author: Michael D. Purugganan 

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 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 genome-wide association studies (GWAS) 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 crops, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species.

海枣（Phoenix dactylifera）是中东和北非干旱地区的一种非常重要的水果作物。尽管海枣非常重要，但关于海枣树的基因组资源却很少，这严重限制了该多年生植物的演化基因组研究。本文中，作者基于三代长read测序技术报道了一个改良版的海枣基因组，大小约为772.3 Mb，Contig N50为897.2 Kb，并基于该组转版本进行了性别决定区域和21个水果性状的全基因组关联研究。作者通过GWAS鉴定到了一个控制果实颜色的R2R3-MYB转录因子VIRESCENS基因，并且鉴定到了功能性等位基因，包括一个反转录转座子插入和起始密码子突变。作者还发现在多个连锁的转化酶基因缺失多态性中存在与糖组成关联的GWAS峰值。 在其它作物的研究中，MYB转录因子和转化酶分别会参与果实颜色和糖组成，这表明平行演化在驯化物种的演化多样化中非常重要。

通讯：Michael D. Purugganan (https://as.nyu.edu/content/nyu-as/as/faculty/michael-purugganan.html)

个人简介：1985年，菲律宾大学，化学学士；1986年，哥伦比亚大学，化学硕士；1993年，佐治亚大学，植物学博士。

研究方向：植物适应性演化和生态基因组学；植物驯化遗传学；多细胞性和社会行为演化。

doi: https://doi.org/10.1038/s41467-019-12604-9

Journal: Nature Communications

Published date: October 15, 2019