Data from: Phylogenetic relationships, breeding implications, and cultivation history of Hawaiian taro (Colocasia esculenta) through genome-wide SNP genotyping

Taro, Colocasia esculenta, is one of the world’s oldest root crops and of
particular economic and cultural significance in Hawai‘i, where
historically more than 150 different landraces were grown. We developed a
genome-wide set of more than 2400 high-quality single nucleotide
polymorphism (SNP) markers from 70 taro accessions of Hawaiian, South
Pacific, Palauan, and mainland Asian origins, with several objectives: (a)
uncover the phylogenetic relationships between Hawaiian and other Pacific
landraces, (b) shed light on the history of taro cultivation in Hawai‘i,
and (c) develop a tool to discriminate among Hawaiian and other taros. We
found that almost all existing Hawaiian landraces fall into five
monophyletic groups that are largely consistent with the traditional
Hawaiian classification based on morphological characters, e.g., leaf
shape and petiole color. Genetic diversity was low within these clades but
considerably higher between them. Population structure analyses further
indicated that the diversification of taro in Hawai‘i most likely occurred
by a combination of frequent somatic mutation and occasional
hybridization. Unexpectedly, the South Pacific accessions were found
nested within the clades mainly composed of Hawaiian accessions, rather
than paraphyletic to them. This suggests that the origin of clades
identified here preceded the colonization of Hawai‘i, and that early
Polynesian settlers brought taro landraces from different clades with
them. In the absence of a sequenced genome, this marker set provides a
valuable resource towards obtaining a genetic linkage map, and to study
the genetic basis of phenotypic traits of interest to taro breeding such
as disease resistance.

芋（Taro，学名：Colocasia esculenta）是全球最古老的块根作物之一，在夏威夷地区兼具重要的经济与文化价值，历史上当地曾种植超过150种不同的地方品种（landraces）。本研究针对源自夏威夷、南太平洋、帕劳及亚洲大陆的70份芋种质资源（accessions），开发了一套覆盖全基因组的2400余个高质量单核苷酸多态性（single nucleotide polymorphism, SNP）标记，研究目标如下：(a) 解析夏威夷与其他太平洋地区芋地方品种间的系统发育关系（phylogenetic relationships）；(b) 厘清夏威夷地区芋的栽培历史；(c) 开发可区分夏威夷芋及其他芋类种质的分子工具。研究结果显示，现存的夏威夷芋地方品种几乎均可划归为5个单系群（monophyletic groups），该聚类结果与基于叶片形态、叶柄颜色等性状建立的夏威夷传统分类体系基本一致。这些进化支（clades）内部的遗传多样性水平较低，而支系间的遗传多样性则显著更高。群体结构分析（population structure analyses）进一步表明，夏威夷地区芋的物种多样化过程极有可能是频繁体细胞突变（somatic mutation）与偶发杂交（hybridization）共同作用的结果。出乎意料的是，南太平洋芋种质材料并未与以夏威夷种质为主的进化支形成并系群（paraphyletic group），而是嵌套于这些进化支内部。该发现暗示，本研究鉴定出的进化支起源早于夏威夷群岛的人类殖民历史，早期波利尼西亚定居者携带着来自不同进化支的芋地方品种迁徙至此。在尚未完成芋全基因组测序的前提下，这套标记资源可为构建芋遗传连锁图谱（genetic linkage map），以及解析芋育种中关注的抗病性（disease resistance）等目标表型性状（phenotypic traits）的遗传基础提供极具价值的研究工具。