Plant domestication: setting biological clocks

Through domestication of wild species, humans have induced large changes in the developmental and circadian clocks of plants. As a result of these changes, modern crops are more productive and adaptive to contrasting environments from the center of origin of their wild ancestors, albeit with low genetic variability and abiotic stress tolerance. Likewise, a complete restructuring of plant metabolic timekeeping probably occurred during crop domestication. Here, we highlight that contrasting timings among organs in wild relatives of crops allowed them to recognize environmental adversities faster. We further propose that connections among biological clocks, which were established during plant domestication, may represent a fundamental source of genetic variation to improve crop resilience and yield.     

Domestication and crop evolution of wheat andbarley: Genes,genomics, and future directions

Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of nextgeneration sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance(relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large,complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors,as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.     

四倍体野生稻快速驯化: 启动人类新农业文明

通过人工选择优良遗传变异,将野生植物驯化为栽培作物,以满足人类对食物的需求,是人类发展历史中的重要事件,推动了人类文明的持续发展。随着世界人口持续增加,耕地面积不断减少,灾害性天气频发,全球粮食安全问题日趋严峻。基于作物驯化的分子机理及重要农艺性状的遗传基础,结合高通量基因组测序和高效基因组编辑技术,从头驯化野生植物,...     

Plant microbiota modified by plant domestication

Human life became largely dependent on agricultural products after distinct crop-domestication events occurred around 10,000 years ago in different geographical sites. Domestication selected suitable plants for human agricultural practices with unexpected consequences on plant microbiota, which has notable effects on plant growth and health. Among other traits, domestication has changed root architecture, exudation, or defense responses that could have modified plant microbiota. Here we present the comparison of reported data on the microbiota from widely consumed cereals and legumes and their ancestors showing that different bacteria were found in domesticated and wild plant microbiomes in some cases. Considering the large variability in plant microbiota, adequate sampling efforts and function-based approaches are needed to further support differences between the microbiota from wild and domesticated plants. The study of wild plant microbiomes could provide a valuable resource of unexploited beneficial bacteria for crops.     

Mutualism breakdown in breadfruit domestication

During the process of plant domestication, below-ground communities are rarely considered. Some studies have attempted to understand the changes in root symbionts owing to domestication, but little is known about how it influences mycorrhizal response in domesticated crops. We hypothesized that selection for above-ground traits may also result in decreased mycorrhizal abundance in roots. Breadfruit (Artocarpus sp.) has a long domestication history, with a strong geographical movement of cultivars from west to east across the Melanesian and Polynesian islands. Our results clearly show a decrease in arbuscular mycorrhizas (AMs) along a domestication gradient from wild to recently derived cultivars. We showed that the vesicular and arbuscular colonization rate decreased significantly in more recently derived breadfruit cultivars. In addition, molecular analyses of breadfruit roots indicated that AM fungal species richness also responded along the domestication gradient. These results suggest that human-driven selection for plant cultivars can have unintended effects on below-ground mutualists, with potential impacts on the stress tolerance of crops and long-term food security.     

Shifts and disruptions in resource-use trait syndromes during the evolution of herbaceous crops

Trait-based ecology predicts that evolution in high-resource agricultural environments should select for suites of traits that enable fast resource acquisition and rapid canopy closure. However, crop breeding targets specific agronomic attributes rather than broad trait syndromes. Breeding for specific traits, together with evolution in high-resource environments, might lead to reduced phenotypic integration, according to predictions from the ecological literature. We provide the first comprehensive test of these hypotheses, based on a trait-screening programme of 30 herbaceous crops and their wild progenitors. During crop evolution plants became larger, which enabled them to compete more effectively for light, but they had poorly integrated phenotypes. In a subset of six herbaceous crop species investigated in greater depth, competitiveness for light increased during early plant domestication, whereas diminished phenotypic integration occurred later during crop improvement. Mass-specific leaf and root traits relevant to resource-use strategies (e.g. specific leaf area or tissue density of fine roots) changed during crop evolution, but in diverse and contrasting directions and magnitudes, depending on the crop species. Reductions in phenotypic integration and overinvestment in traits involved in competition for light may affect the chances of upgrading modern herbaceous crops to face current climatic and food security challenges.     

驯化对作物微生物组多样性和群落结构的影响及作用途径

植物与共存微生物的相互作用对植物的生长、发育、健康等具有重大影响。人类驯化导致现代作物品种与其野生祖先在生理遗传特性、生长环境等方面存在明显差异, 这必然会影响作物与其微生物组的相互作用。理解驯化对作物微生物组的影响及其作用机理, 是充分应用微生物组进行作物改良或人工育种的重要理论基础。结合课题组前期研究基础, 该文综述了驯化对作物地下和地上部分细菌和真菌(尤其是益生菌和病原菌)群落组成和多样性影响的研究现状; 并结合驯化对作物植株形态、根系构型、根系分泌物等生理特征以及生长环境的影响, 分析了驯化塑造作物微生物组的作用途径, 提出了该领域值得重点关注的研究和发展方向。     

Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus)

The domestication syndrome comprises phenotypic changes that differentiate crops from their wild ancestors. We compared the genomic variation and phenotypic differentiation of the two putative domestication traits seed size and seed colour of the grain amaranth Amaranthus caudatus, which is an ancient crop of South America, and its two close wild relatives and putative ancestors A. hybridus and A. quitensis. Genotyping 119 accessions of the three species from the Andean region using genotyping by sequencing (GBS) resulted in 9485 SNPs that revealed a strong genetic differentiation of cultivated A. caudatus from its two relatives. A. quitensis and A. hybridus accessions did not cluster by their species assignment but formed mixed groups according to their geographic origin in Ecuador and Peru, respectively. A. caudatus had a higher genetic diversity than its close relatives and shared a high proportion of polymorphisms with their wild relatives consistent with the absence of a strong bottleneck or a high level of recent gene flow. Genome sizes and seed sizes were not significantly different between A. caudatus and its relatives, although a genetically distinct group of A. caudatus from Bolivia had significantly larger seeds. We conclude that despite a long history of human cultivation and selection for white grain colour, A. caudatus shows a weak genomic and phenotypic domestication syndrome and proposes that it is an incompletely domesticated crop species either because of weak selection or high levels of gene flow from its sympatric close undomesticated relatives that counteracted the fixation of key domestication traits.     

Preservation of plant genetic resources in the biotechnology era

Thousands of years ago humans began domesticating crops as a food source. Among the wild germplasm available, they selected those that were best adapted for cultivation and utilization. Although wild ancestors have continued to persist in regions where domestication took place, there is a permanent risk of loss of the genetic variability of cultivated plants and their wild relatives in response to changing environmental conditions and cultural practices. Recognizing this danger, plant ex situ genebank collections were created since the beginning of the last century. World-wide, more than 6 million accessions have been accumulated including the German ex situ genebank in Gatersleben, one of the four largest global collections, housing 150,000 accessions belonging to 890 genera and 3032 species. This review summarizes the ex situ plant genetic resources conservation behavior with a special emphasis on German activities. Strategies for maintenance and management of germplasm collections are reviewed, considering modern biotechnologies (in vitro and cryo preservation). General aspects on genetic diversity and integrity are discussed.     

Plant domestication disrupts biodiversity effects across major crop types

Plant diversity fosters productivity in natural ecosystems. Biodiversity effects might increase agricultural yields at no cost in additional inputs. However, the effects of diversity on crop assemblages are inconsistent, probably because crops and wild plants differ in a range of traits relevant to plant–plant interactions. We tested whether domestication has changed the potential of crop mixtures to over‐yield by comparing the performance and traits of major crop species and those of their wild progenitors under varying levels of diversity. We found stronger biodiversity effects in mixtures of wild progenitors, due to larger selection effects. Variation in selection effects was partly explained by within‐mixture differences in leaf size. Our results indicate that domestication might disrupt the ability of crops to benefit from diverse neighbourhoods via reduced trait variance. These results highlight potential limitations of current crop mixtures to over‐yield and the potential of breeding to re‐establish variance and increase mixture performance.     

Biogeographic bases for a shift in crop C : N : P stoichiometries during domestication

We lack both a theoretical framework and solid empirical data to understand domestication impacts on plant chemistry. We hypothesised that domestication increased leaf N and P to support high plant production rates, but biogeographic and climate patterns further influenced the magnitude and direction of changes in specific aspects of chemistry and stoichiometry. To test these hypotheses, we used a data set of leaf C, N and P from 21 herbaceous crops and their wild progenitors. Domestication increased leaf N and/or P for 57% of the crops. Moreover, the latitude of the domestication sites (negatively related to temperature) modulated the domestication effects on P (+), C (?), N : P (?) and C : P (?) ratios. Further results from a litter decomposition assay showed that domestication effects on litter chemistry affected the availability of soil N and P. Our findings draw attention to evolutionary effects of domestication legacies on plant and soil stoichiometry and related ecosystem services (e.g. plant yield and soil fertility).     

Seed traits and genes important for translational biology--highlights from recent discoveries

Seeds provide food, feed, fiber and fuel. They are also an important delivery system of genetic information, which is essential for the survival of wild species in ecosystems and the production of agricultural crops. In this review, seed traits and genes that are potentially important for agricultural applications are discussed. Over the long period of crop domestication, seed traits have been modified through intentional or unintentional selections. While most selections have led to seed traits favorable for agricultural consumption, such as larger seeds with higher nutritional value than the wild type, other manipulations in modern breeding sometimes led to negative traits, such as vivipary, precocious germination on the maternal plant or reduced seed vigor, as a side effect during the improvement of other characteristics. Greater effort is needed to overcome these problems that have emerged as a consequence of crop improvement. Seed biology researchers have characterized the function of many genes in the last decade, including those associated with seed domestication, which may be useful in addressing critical issues in modern agriculture, such as the prevention of vivipary and seed shattering or the enhancement of yields. Recent discoveries in seed biology research are highlighted in this review, with an emphasis on their potential for translational biology.     

Shaping polyploid wheat for success: Origins,domestication, and the genetic improvement of agronomic traits

Bread wheat (Triticum aestivum L., AABBDD, 2n = 6x = 42), which accounts for most of the cultivated wheat crop worldwide, is a typical allohexaploid with a genome derived from three diploid wild ancestors. Bread wheat arose and evolved via two sequential allopolyploidization events and was further polished through multiple steps of domestication. Today, cultivated allohexaploid bread wheat has numerous advantageous traits, including adaptive plasticity, favorable yield traits, and extended end-use quality, which have enabled its cultivation well beyond the ranges of its tetraploid and diploid progenitors to become a global staple food crop. In the past decade, rapid advances in wheat genomic research have considerably accelerated our understanding of the bases for the shaping of complex agronomic traits in this polyploid crop. Here, we summarize recent advances in characterizing major genetic factors underlying the origin, evolution, and improvement of polyploid wheats. We end with a brief discussion of the future prospects for the design of gene cloning strategies and modern wheat breeding.     

Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum

The domestication of diverse grain crops from wild grasses was a result of artificial selection for a suite of overlapping traits producing changes referred to in aggregate as ‘domestication syndrome’. Parallel phenotypic change can be accomplished by either selection on orthologous genes or selection on non‐orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many ‘classic’ domestication genes identified through quantitative trait locus mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization part of domestication targeted small and largely non‐overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.     

Quantitative trait locus analysis of the early domestication of sunflower

Genetic analyses of the domestication syndrome have revealed that domestication-related traits typically have a very similar genetic architecture across most crops, being conditioned by a small number of quantitative trait loci (QTL), each with a relatively large effect on the phenotype. To date, the domestication of sunflower (Helianthus annuus L.) stands as the only counterexample to this pattern. In previous work involving a cross between wild sunflower (also H. annuus) and a highly improved oilseed cultivar, we found that domestication-related traits in sunflower are controlled by numerous QTL, typically of small effect. To provide insight into the minimum genetic changes required to transform the weedy common sunflower into a useful crop plant, we mapped QTL underlying domestication-related traits in a cross between a wild sunflower and a primitive Native American landrace that has not been the target of modern breeding programs. Consistent with the results of the previous study, our data indicate that the domestication of sunflower was driven by selection on a large number of loci, most of which had small to moderate phenotypic effects. Unlike the results of the previous study, however, nearly all of the QTL identified herein had phenotypic effects in the expected direction, with the domesticated allele producing a more crop-like phenotype and the wild allele producing a more wild-like phenotype. Taken together, these results are consistent with the hypothesis that selection during the post-domestication era has resulted in the introduction of apparently maladaptive alleles into the modern sunflower gene pool.     

Growing larger with domestication: a matter of physiology,morphology or allocation?

• Domestication might affect plant size. We investigated whether herbaceous crops are larger than their wild progenitors, and the traits that influence size variation.
• We grew six crop plants and their wild progenitors under common garden conditions. We measured the aboveground biomass gain by individual plants during the vegetative stage. We then tested whether photosynthesis rate, biomass allocation to leaves, leaf size and specific leaf area (SLA) accounted for variations in whole‐plant photosynthesis, and ultimately in aboveground biomass.
• Despite variations among crops, domestication generally increased the aboveground biomass (average effect +1.38, Cohen's d effect size). Domesticated plants invested less in leaves and more in stems than their wild progenitors. Photosynthesis rates remained similar after domestication. Variations in whole‐plant C gains could not be explained by changes in leaf photosynthesis. Leaves were larger after domestication, which provided the main contribution to increases in leaf area per plant and plant‐level C gain, and ultimately to larger aboveground biomass.
• In general, cultivated plants have become larger since domestication. In our six crops, this occurred despite lower investment in leaves, comparable leaf‐level photosynthesis and similar biomass costs of leaf area (i.e. SLA) than their wild progenitors. Increased leaf size was the main driver of increases in aboveground size. Thus, we suggest that large seeds, which are also typical of crops, might produce individuals with larger organs (i.e. leaves) via cascading effects throughout ontogeny. Larger leaves would then scale into larger whole plants, which might partly explain the increases in size that accompanied domestication.

     

Polyploidy and the evolution of domesticated plants

Polyploidy and domestication are common features of plant evolution. A number of selective advantages conferred by polyploidy appear relevant to domestication. Surprisingly, the correlation between the two has not previously been examined. Anderson (Plants, man and life. University of California Press, Berkeley, CA, 1969) asserted that we do not yet know exactly what percentage of cultivated plants and weeds are polyploid, but it must be high. Heiser (Seeds to civilization, the story of food, 2d ed., W. H. Freeman, San Francisco, CA, 1981) stated that a large number of the major food crops are polyploids, giving wheat, sugar cane, potatoes, sweet potatoes, and bananas as examples. In this study, the distribution of polyploidy in 244 crop species was compared to the estimates of polyploidy in their respective higher categories. The proportion of polyploidy in crop plants was considered in relation to taxonomic origin, habitat, and reproductive strategies of the crops. The study showed that the crop species were a random selection as far as ploidy level is concerned and that domestication did not appear to have favored polyploid over diploid genomes or vice versa. Vegetative, seed, and tree crops were statistically homogenous in their polyploid composition. The distribution of polyploidy in annual and perennial crops did not differ statistically. The data imply that polyploid genomic constitution neither facilitated nor hindered the ability of wild species for domestication.     

2012年第11期《遗传》封面说明

作物的驯化是人类从开始种植和储存的野生作物中选择优良性状,使之形态特征适应于农业生产方向进化的过程,因此,大部分种子作物驯化后在落粒性、种子休眠和植株形态等方面都出现了相似的变化。水稻是研究谷类作物驯化的良好模式生物。稻属包含2种栽培稻,分别为亚洲栽培稻(Oryza sativa L.)和非洲栽培稻(O. glaberrima Steud.),其中亚洲栽培稻遍布全世界,包含两个主要亚种,粳稻亚种(O. sativa L. ssp. japonica)和籼稻亚种(O. sativa L. ssp. indica)。稻属丰富的近缘种和广泛的地域分布非常有利于研究确定现代栽培稻的驯化地域。此外,水稻基因组较小、具高质量精细图谱,加上功能基因研究上的进展,也为深入开展水稻驯化进程研究奠定了基础。详见本期第XX-XX页区树俊,汪鸿儒,储成才“亚洲栽培稻主要驯化性状研究进展”,对水稻关键驯化性状研究进行的比较全面的综述。封面图中央是选取23株AA基因组的亚洲栽培稻及其近缘野生稻,利用水稻驯化过程中受到选择的控制稻壳颜色基因Bh4上下游各50 kb中的SNP位点所构建的进化树;图外从左下至右下沿顺时针方向,反映的是水稻驯化过程中稻壳颜色、谷粒形状、穗型的变化趋势。 区树俊,汪鸿儒,储成才（绘图：区树俊）     

Heritability and genetic correlations of fear-related behaviour in Red Junglefowl--possible implications for early domestication

Domesticated species differ from their wild ancestors in a number of traits, generally referred to as the domesticated phenotype. Reduced fear of humans is assumed to have been an early prerequisite for the successful domestication of virtually all species. We hypothesized that fear of humans is linked to other domestication related traits. For three generations, we selected Red Junglefowl (ancestors of domestic chickens) solely on the reaction in a standardized Fear of Human-test. In this, the birds were exposed for a gradually approaching human, and their behaviour was continuously scored. This generated three groups of animals, high (H), low (L) and intermediate (I) fearful birds. The birds in each generation were additionally tested in a battery of behaviour tests, measuring aspects of fearfulness, exploration, and sociality. The results demonstrate that the variation in fear response of Red Junglefowl towards humans has a significant genetic component and is genetically correlated to behavioural responses in other contexts, of which some are associated with fearfulness and others with exploration. Hence, selection of Red Junglefowl on low fear for humans can be expected to lead to a correlated change of other behavioural traits over generations. It is therefore likely that domestication may have caused an initial suite of behavioural modifications, even without selection on anything besides tameness.     

Domestication of plants in the Americas: insights from Mendelian and molecular genetics

BACKGROUND: Plant domestication occurred independently in four different regions of the Americas. In general, different species were domesticated in each area, though a few species were domesticated independently in more than one area. The changes resulting from human selection conform to the familiar domestication syndrome, though different traits making up this syndrome, for example loss of dispersal, are achieved by different routes in crops belonging to different families. GENETIC AND MOLECULAR ANALYSES OF DOMESTICATION: Understanding of the genetic control of elements of the domestication syndrome is improving as a result of the development of saturated linkage maps for major crops, identification and mapping of quantitative trait loci, cloning and sequencing of genes or parts of genes, and discoveries of widespread orthologies in genes and linkage groups within and between families. As the modes of action of the genes involved in domestication and the metabolic pathways leading to particular phenotypes become better understood, it should be possible to determine whether similar phenotypes have similar underlying genetic controls, or whether human selection in genetically related but independently domesticated taxa has fixed different mutants with similar phenotypic effects. CONCLUSIONS: Such studies will permit more critical analysis of possible examples of multiple domestications and of the origin(s) and spread of distinctive variants within crops. They also offer the possibility of improving existing crops, not only major food staples but also minor crops that are potential export crops for developing countries or alternative crops for marginal areas.