The Impact of Genetic Changes during Crop Domestication
The Impact of Genetic Changes during Crop Domestication
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DOI：
10.3390/agronomy8030026
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发表时间：
2018-03
期刊：
影响因子：
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通讯作者：
P. Smýkal;M. Nelson;J. Berger;E. V. von Wettberg
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文献类型：
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作者：
P. Smýkal;M. Nelson;J. Berger;E. V. von Wettberg
在过去的12，000年里，人类驯化了数百种植物和动物物种，作为食物，纤维，饲料和工具的来源，对人类社会和驯化物种的遗传结构产生了多方面的影响。作物驯化的结果是由人类偏好、种植实践和农业环境驱动的选择以及随后有效种群规模减少所产生的其他种群遗传过程所形成的。很明显，任何选择都会导致多样性的减少，有利于偏好的基因型，如不落粒的种子或增加的适口性。此外，农业实践大大减少了作物的有效种群规模，允许遗传漂变改变基因型频率。目前分子技术的进展，特别是基因组测序，提供了人类选择在作物驯化期间和之后作用于许多位点的证据。人口水平的分子分析也使我们能够澄清驯化过程本身的人口历史，这与扩大考古研究一起，可以阐明农作物的起源。驯化的植物物种被发现在160个分类科。大约有2500个物种经历了一定程度的驯化，250个物种被认为是完全驯化的。从野生物种到作物物种的进化轨迹是一个复杂的过程。考古记录表明，有一个时期的前驯化种植，而人类第一次开始故意种植野生林，具有良好的性状。后来，作物可能会多样化，因为它们生长在新的地区，有时超出了其野生亲戚的气候生态位。然而，在驯化过程中人类意向性的速度和水平仍然是一个积极讨论的话题。这些过程导致了所谓的驯化综合征，即人类在繁殖过程中对易于收获和生长优势的偏好可能产生的一组特征。这些性状包括种子和果实的传播能力降低，植物结构的变化，以及植物防御特性和适口性的变化。驯化意味着对现有的遗传变异进行选择性清除，以及通过突变或渐渗引入新的遗传变异。此外，在驯化过程中或在作物远离其起源中心的建立过程中的遗传瓶颈可能会进一步改变基因库。迄今为止，几百个基因和位点已被确定为目标的驯化和驯化后的分歧的经典遗传和关联作图。然而，只有少数这些已被表征，甚至更少的是野生型等位基因在自然种群中的作用。驯化后，只有有利的单倍型被保留在选定的基因周围，这就造成了一个遗传多样性极低的遗传谷。这些“选择性扫描”可以允许轻度有害的等位基因固定，并可能在培养的基因库中产生遗传负荷。虽然驯化的全种群基因组后果提供了几个预测作物的遗传多样性水平，我们的理解如何这种多样性对应于作物的营养方面还没有得到很好的理解。许多研究发现，现代栽培品种的关键微量营养素和维生素水平较低。我们怀疑，在驯化和驯化后的分歧，适口性和产量增加的选择加剧了许多作物的低营养水平，虽然相对较少的工作已经研究了这个问题。现代种质缺乏多样性可能会进一步限制我们为获得更高营养水平而进行育种的能力，尽管除了少数几种主食作物外，几乎没有人为此付出过努力。这是一个了解许多作物类群驯化的领域，可以为在快速变化的世界中培育更有营养的作物提供必要的见解。
Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world.