Peach (Prunus persica) is one of the most important fruit crops globally, but its cultivation can be hindered by large tree size. ‘Zhongyoutao 14’ (CN14) is a temperature-sensitive semi-dwarf (TSSD) cultivar which might be useful as breeding stock. The genome of CN14 was sequenced and assembled de novo using single-molecule real-time sequencing and chromosome conformation capture assembly. A high-quality genome was assembled and annotated, with 228.82 Mb mapped to eight chromosomes. Eighty-six re-sequenced F₁ individuals and 334 previously re-sequenced accessions were used to identify candidate genes controlling TSSD and flower type and size. An aquaporin tonoplast intrinsic protein (PpTIP2) was a strong candidate gene for control of TSSD. Sequence variations in the upstream regulatory region of PpTIP2 correlated with different transcriptional activity at different temperatures. PpB3-1, a candidate gene for flower type (SH) and flower size, contributed to petal development and promoted petal enlargement. The locus of another 12 agronomic traits was identified through genome-wide association study. Most of these loci exhibited consistent and precise association signals, except for flesh texture and flesh adhesion. A 6015-bp insertion in exon 3 and a 26-bp insertion upstream of PpMYB25 were associated with fruit hairless. Along with a 70.5-Kb gap at the F-M locus in CN14, another two new alleles were identified in peach accessions. Our findings will not only promote genomic research and agronomic breeding in peach but also provide a foundation for the peach pan-genome.

中文翻译：

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桃花半矮化栽培品种的从头染色体水平基因组确定水通道蛋白 PpTIP2 负责温度敏感的半矮化性状和 PpB3-1 负责花类型和大小

桃（Prunus persica）是全球最重要的水果作物之一，但其种植可能会受到大树的阻碍。'中油桃14'（CN14）是温敏半矮化（TSSD）品种，可用作种畜。使用单分子实时测序和染色体构象捕获组装对 CN14 的基因组进行了测序和从头组装。组装和注释了一个高质量的基因组，其中 228.82 Mb 映射到八个染色体。86 个重新测序的 F ₁个体和 334 个先前重新测序的种质用于鉴定控制TSSD和花类型和大小的候选基因。一种水通道蛋白液泡内源蛋白（PpTIP2) 是控制TSSD的强有力的候选基因。PpTIP2上游调控区的序列变异与不同温度下的不同转录活性相关。PpB3-1是花型 ( SH ) 和花大小的候选基因，有助于花瓣发育并促进花瓣扩大。通过全基因组关联研究确定了另外 12 个农艺性状的基因座。这些基因座中的大多数都表现出一致和精确的关联信号，除了肉质地和肉粘附。外显子 3 中的 6015 bp 插入和PpMYB25上游的 26 bp 插入与果实无毛有关。除了FM上的 70.5-Kb 间隙位点 CN14 中，另外两个新的等位基因在桃种质中被鉴定。我们的研究结果不仅将促进桃的基因组研究和农艺育种，而且为桃泛基因组的研究奠定了基础。