The bracteatus pineapple genome and domestication of clonally propagated crops

First author: Li-Yu Chen; Affiliations: Fujian Agriculture and Forestry University (福建农林大学): Fuzhou, China

Corresponding author: Ray Ming 

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a ‘one-step operation’. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars ‘Smooth Cayenne’ and ‘Queen’ exhibited ancient and recent admixture, while ‘Singapore Spanish’ supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.

来自南美、无性繁殖作物菠萝的驯化被认为是“one-step operation”。作者对红苞凤梨Ananas comosus var. bracteatus CB5进行了全基因组测序，组装了513Mb的基因组序列，挂载到25个染色体上，共预测了29412个蛋白编码基因。通过比较CB5、F153以及MD2的基因组，作者鉴定了基因组上有关纤维合成、颜色形成、糖分积累以及果实成熟相关的区域。作者还对89个菠萝个体进行了重测序。菠萝栽培种无刺卡因类和皇后类中存在古老与近代的混合，而西班牙Spanish类则符合“one-step operation”驯化。作者鉴定了25个选择性清除区域，包括一个强烈的清除区域包含一对串联重复的菠萝蛋白酶抑制因子。四个自交不亲和性候选基因在F153中连锁，但在自交亲和的CB5中不具功能。本文的研究支持了有性重组和“one-step operation”方式在无性系作物的驯化历史中共同存在。这项工作将为其他无性繁殖作物有性和无性驯化轨迹的探索提供参考。

通讯：明瑞光（http://net.fafu.edu.cn/hist/13/f8/c6013a136184/page.htm）

个人简介：1991-1995年，美国夏威夷大学，植物遗传育种博士；1995-1998年，美国德州农工大学，博士后。

研究方向：植物性染色体的起源与进化；被子植物性别决定基因网络；木瓜与甘蔗基因组结构与功能；甘蔗生物产量超亲遗传的分子机理。

doi: https://doi.org/10.1038/s41588-019-0506-8

Journal: Nature Genetics

Published date: September 30, 2019