Bitocchi Elena, Rau Domenico, Benazzo Andrea, Bellucci Elisa, Goretti Daniela, Biagetti Eleonora, Panziera Alex, Laidò Giovanni, Rodriguez Monica, Gioia Tania, Attene Giovanna, McClean Phillip, Lee Rian K, Jackson Scott A, Bertorelle Giorgio, Papa Roberto
Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche Ancona, Italy.
Department of Agriculture, Università degli Studi di Sassari Sassari, Italy.
Front Plant Sci. 2017 Jan 6;7:2005. doi: 10.3389/fpls.2016.02005. eCollection 2016.
Crop species have been deeply affected by the domestication process, and there have been many efforts to identify selection signatures at the genome level. This knowledge will help geneticists to better understand the evolution of organisms, and at the same time, help breeders to implement successful breeding strategies. Here, we focused on domestication in the Mesoamerican gene pool of by sequencing 49 gene fragments from a sample of 45 wild and domesticated accessions, and as controls, two accessions each of the closely related species and . An excess of nonsynonymous mutations within the domesticated germplasm was found. Our data suggest that the cost of domestication alone cannot explain fully this finding. Indeed, the significantly higher frequency of polymorphisms in the coding regions observed only in the domesticated plants (compared to noncoding regions), the fact that these mutations were mostly nonsynonymous and appear to be recently derived mutations, and the investigations into the functions of their relative genes (responses to biotic and abiotic stresses), support a scenario that involves new functional mutations selected for adaptation during domestication. Moreover, consistent with this hypothesis, selection analysis and the possibility to compare data obtained for the same genes in different studies of varying sizes, data types, and methodologies allowed us to identify four genes that were strongly selected during domestication. Each selection candidate is involved in plant resistance/tolerance to abiotic stresses, such as heat, drought, and salinity. Overall, our study suggests that domestication acted to increase functional diversity at target loci, which probably controlled traits related to expansion and adaptation to new agro-ecological growing conditions.
作物物种受到驯化过程的深刻影响，人们已做出诸多努力在基因组水平上识别选择特征。这些知识将帮助遗传学家更好地理解生物体的进化，同时帮助育种者实施成功的育种策略。在此，我们聚焦于中美洲基因库中的驯化现象，对45份野生和驯化种质样本的49个基因片段进行测序，并以两个亲缘关系密切的物种（每个物种各两份种质）作为对照。我们发现驯化种质中存在过量的非同义突变。我们的数据表明，仅驯化成本无法完全解释这一发现。实际上，仅在驯化植物中观察到的编码区多态性频率显著更高（与非编码区相比），这些突变大多为非同义突变且似乎是近期产生的突变，以及对其相关基因功能（对生物和非生物胁迫的反应）的研究，都支持了一种在驯化过程中涉及为适应而选择新功能突变的情形。此外，与此假设一致，选择分析以及在不同规模、数据类型和方法的不同研究中比较同一基因数据的可能性，使我们能够识别出四个在驯化过程中受到强烈选择的基因。每个选择候选基因都与植物对非生物胁迫（如高温、干旱和盐度）的抗性/耐受性有关。总体而言，我们的研究表明驯化作用是增加目标位点的功能多样性，这些位点可能控制着与扩展及适应新农业生态生长条件相关的性状。
