Apple genome resequencing

Cultivated apple (Malus × domestica Borkh.), one of the most widely produced and agronomically important fruit crops in temperate regions, has been domesticated from M. sieversii in the Tian Shan Mountains since 4,000-10,000 years ago and dispersed from Central Asia to West Europe along the Silk Route, allowing hybridization and introgression from wild crabapples. Apple domestication is mainly related to two wild species: M. sieversii as the primary progenitor and M. sylvestris as a major secondary contributor. Centuries of human exploitation and selection have produced several thousand apple cultivars with diverse fruit sizes and flavors, the majority of which are maintained in germplasm repositories, leaving only a few dozen elite cultivars grown worldwide for fruit production. Unlike seed-propagated annual crops with intensive artificial selections and selfing peach with recent domestication bottlenecks, apple has a slow, weak, and complex domestication process with intensive wild-introgressions because of their lengthy juvenile phases, self-incompatibility and wide usage of vegetative propagation. Little information is available about genomic responses to the artificial selections in apple. In this study, we performed deep genome sequencing of 97 diverse apple accessions. The large amount of genomic variation resources has allowed us to gain new insights into apple evolution and domestication processes, which may help accelerate the usage of wild species in apple breeding practice.

栽培苹果（Malus × domestica Borkh.）是温带地区产量最高、农艺重要性最为显著的果树作物之一，其驯化始于距今4000至10000年前，由天山山脉的新疆野苹果（M. sieversii）驯化而来，并沿丝绸之路从中亚传播至西欧，期间与野生海棠果发生杂交与基因渐渗（introgression）。苹果的驯化主要涉及两个野生近缘种：新疆野苹果（M. sieversii）作为其首要祖先种，森林海棠（M. sylvestris）则为次要的核心基因贡献者。历经数百年的人类开发与人工选择，现已培育出数千个果型、风味各具特色的苹果栽培品种，其中绝大多数保存于种质资源库（germplasm repositories）中，全球范围内仅数十个优良栽培品种用于商业化果品生产。与经历高强度人工选择的种子繁殖一年生作物，以及近期遭遇驯化瓶颈的自交桃不同，苹果的驯化过程缓慢、温和且复杂，加之其幼年期漫长、自交不亲和（self-incompatibility）以及无性繁殖（vegetative propagation）的广泛应用，导致其存在频繁的野生种基因渐渗事件。目前关于苹果人工选择的基因组响应机制的相关研究仍较为匮乏。本研究对97份遗传背景多样的苹果种质居群（apple accessions）开展了深度基因组测序，依托海量基因组变异资源，为解析苹果演化与驯化历程提供了全新视角，有望加速野生种质资源在苹果育种实践中的应用。

搜集汇总

背景与挑战

背景概述

该数据集是苹果基因组重测序项目，包含97个多样化苹果种质的深度测序原始序列读取，使用Illumina HiSeq 2500平台生成。它旨在研究苹果的进化和驯化历史，为农业育种提供基因组变异资源，由康奈尔大学管理，涵盖117个样本和282个实验运行。