Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
Mondi Forests, Tree Improvement Technology Programme, Trahar Technology Centre - TTC, Mountain Home Estate, Off Dennis Shepstone Dr., Hilton, 3245, South Africa.
New Phytol. 2022 Sep;235(5):1944-1956. doi: 10.1111/nph.18297. Epub 2022 Jul 2.
From its origins in Australia, Eucalyptus grandis has spread to every continent, except Antarctica, as a wood crop. It has been cultivated and bred for over 100 yr in places such as South Africa. Unlike most annual crops and fruit trees, domestication of E. grandis is still in its infancy, representing a unique opportunity to interrogate the genomic consequences of artificial selection early in the domestication process. To determine how a century of artificial selection has changed the genome of E. grandis, we generated single nucleotide polymorphism genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors. Breeding and wild populations appeared genetically distinct. We found genomic evidence of evolutionary processes known to have occurred in other plant domesticates, including interspecific introgression and intraspecific infusion from wild material. Furthermore, we found genomic regions with increased linkage disequilibrium and genetic differentiation, putatively representing early soft sweeps of selection. This is, to our knowledge, the first study of genomic signatures of domestication in a timber species looking beyond the first few generations of cultivation. Our findings highlight the importance of intra- and interspecific hybridization during early domestication.
从澳大利亚起源，按树已传播到除南极洲以外的各大洲，成为一种木材作物。它已经在南非等地被培育和种植了 100 多年。与大多数一年生作物和果树不同，按树的驯化仍处于初级阶段，这代表了一个独特的机会，可以在驯化过程的早期研究人工选择对基因组的影响。为了确定一个世纪的人工选择如何改变了按树的基因组，我们使用 EUChip60K 芯片为来自三个先进的南非育种计划的 1080 个个体生成了单核苷酸多态性基因型，并调查了相对于野生祖先的种群结构和全基因组分化模式。育种和野生种群在遗传上似乎是不同的。我们发现了与其他植物驯化种中已知发生的进化过程有关的基因组证据，包括种间渐渗和来自野生材料的种内渗透。此外，我们发现了具有增加的连锁不平衡和遗传分化的基因组区域，可能代表了早期选择的软筛选。据我们所知，这是对木材物种的驯化基因组特征的第一项研究，该研究超越了最初几代的种植。我们的研究结果强调了在早期驯化过程中种内和种间杂交的重要性。
