Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei 430064, China.
Plant Physiol. 2019 May;180(1):435-452. doi: 10.1104/pp.18.01322. Epub 2019 Mar 13.
Knowledge of the genetic changes that occurred during the domestication and improvement of perennial trees at the RNA level is limited. Here, we used RNA sequencing analysis to compare representative sets of wild, landrace, and improved accessions of pear () to gain insight into the genetic changes associated with domestication and improvement. A close population relationship and similar nucleotide diversity was observed between the wild and landrace groups, whereas the improved group had substantially reduced nucleotide diversity. A total of 11.13 Mb of genome sequence was identified as bearing the signature of selective sweeps that occurred during pear domestication, whereas a distinct and smaller set of genomic regions (4.04 Mb) was identified as being associated with subsequent improvement efforts. The expression diversity of selected genes exhibited a 20.89% reduction from the wild group to the landrace group, but a 23.13% recovery was observed from the landrace to the improved group, showing a distinctly different pattern with variation of sequence diversity. Module-trait association analysis identified 16 distinct coexpression modules, six of which were highly associated with important fruit traits. The candidate trait-linked differentially expressed genes associated with stone cell formation, fruit size, and sugar content were identified in the selected regions, and many of these could also be mapped to the previously reported quantitative trait loci. Thus, our study reveals the specific pattern of domestication and improvement of perennial trees at the transcriptome level, and provides valuable genetic sources of fruit traits that could contribute to pear breeding and improvement.
有关多年生树木在驯化和改良过程中发生的 RNA 水平遗传变化的知识有限。在这里，我们使用 RNA 测序分析比较了梨的野生、地方品种和改良品种的代表群体，以深入了解与驯化和改良相关的遗传变化。野生和地方品种群体之间观察到密切的群体关系和相似的核苷酸多样性，而改良群体的核苷酸多样性则大大降低。总共鉴定出 11.13 Mb 的基因组序列，这些序列具有在梨驯化过程中发生的选择清除的特征，而一组明显较小的基因组区域（4.04 Mb）与随后的改良努力有关。从野生群体到地方品种群体，选择基因的表达多样性降低了 20.89%，但从地方品种到改良群体又恢复了 23.13%，表现出与序列多样性变化明显不同的模式。模块-性状关联分析鉴定出 16 个不同的共表达模块，其中 6 个与重要的果实性状高度相关。在选定区域中鉴定到与石细胞形成、果实大小和糖含量相关的候选性状相关的差异表达基因，其中许多基因也可以映射到先前报道的数量性状位点。因此，我们的研究揭示了多年生树木在转录组水平上的特定驯化和改良模式，并为果实性状提供了有价值的遗传资源，这些资源可能有助于梨的培育和改良。
