Genetic analysis of wheat domestication and evolution under domestication

Wheat is undoubtedly one of the world's major food sources since the dawn of Near Eastern agriculture and up to the present day. Morphological, physiological, and genetic modifications involved in domestication and subsequent evolution under domestication were investigated in a tetraploid recombinant inbred line population, derived from a cross between durum wheat and its immediate progenitor wild emmer wheat. Experimental data were used to test previous assumptions regarding a protracted domestication process. The brittle rachis (Br) spike, thought to be a primary characteristic of domestication, was mapped to chromosome 2A as a single gene, suggesting, in light of previously reported Br loci (homoeologous group 3), a complex genetic model involved in spike brittleness. Twenty-seven quantitative trait loci (QTLs) conferring threshability and yield components (kernel size and number of kernels per spike) were mapped. The large number of QTLs detected in this and other studies suggests that following domestication, wheat evolutionary processes involved many genomic changes. The Br gene did not show either genetic (co-localization with QTLs) or phenotypic association with threshability or yield components, suggesting independence of the respective loci. It is argued here that changes in spike threshability and agronomic traits (e.g. yield and its components) are the outcome of plant evolution under domestication, rather than the result of a protracted domestication process. Revealing the genomic basis of wheat domestication and evolution under domestication, and clarifying their inter-relationships, will improve our understanding of wheat biology and contribute to further crop improvement.     

Agricultural Origins: Centers and Noncenters; A Near Eastern Reappraisal

Understanding the evolutionary history of crop plants is fundamental to our understanding of their respective adaptation profiles, which in turn, is a key element in securing future yield and quality improvement. Central topics in this field concern the mono- or polyphyletic origin of crop plants, and our ability to identify the geographic location where certain crop plants have originated. Understanding the geographical pattern of domestication may also assist in reconstructing the cultural processes underlying the Neolithic (agricultural) Revolution. Here we review prevailing views on the geographic pattern of Near Eastern plant domestication, and highlight the distinction between genetic domestication events and independent cultural events. A critical evaluation of the wealth of newly published geobotanical, genetic, and archaeological data provides strong support in favor of a specific core area in southeastern Turkey where most, if not all, founder Near Eastern crops were likely domesticated.     

Crop genomics: advances and applications

The completion of reference genome sequences for many important crops and the ability to perform high-throughput resequencing are providing opportunities for improving our understanding of the history of plant domestication and to accelerate crop improvement. Crop plant comparative genomics is being transformed by these data and a new generation of experimental and computational approaches. The future of crop improvement will be centred on comparisons of individual plant genomes, and some of the best opportunities may lie in using combinations of new genetic mapping strategies and evolutionary analyses to direct and optimize the discovery and use of genetic variation. Here we review such strategies and insights that are emerging.     

Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach

Crop evolution is a long‐term process involving selection by natural evolutionary forces and anthropogenic influences; however, the genetic mechanisms underlying the domestication and improvement of fruit crops have not been well studied to date. Here, we performed a population structure analysis in peach (Prunus persica) based on the genome‐wide resequencing of 418 accessions and confirmed the presence of an obvious domestication event during evolution. We identified 132 and 106 selective sweeps associated with domestication and improvement, respectively. Analysis of their tissue‐specific expression patterns indicated that the up‐regulation of selection genes during domestication occurred mostly in fruit and seeds as opposed to other organs. However, during the improvement stage, more up‐regulated selection genes were identified in leaves and seeds than in the other organs. Genome‐wide association studies (GWAS) using 4.24 million single nucleotide polymorphisms (SNPs) revealed 171 loci associated with 26 fruit domestication traits. Among these loci, three candidate genes were highly associated with fruit weight and the sorbitol and catechin content in fruit. We demonstrated that as the allele frequency of the SNPs associated with high polyphenol composition decreased during peach evolution, alleles associated with high sugar content increased significantly. This indicates that there is genetic potential for the breeding of more nutritious fruit with enhanced bioactive polyphenols without disturbing a harmonious sugar and acid balance by crossing with wild species. This study also describes the development of the genomic resources necessary for evolutionary research in peach and provides the large‐scale characterization of key agronomic traits in this crop species.     

A simulation of the effect of inbreeding on crop domestication genetics with comments on the integration of archaeobotany and genetics: a reply to Honne and Heun

Archaeobotanical evidence for Near Eastern einkorn wheat, barley, and Chinese rice suggests that the fixation of key domestication traits such as non-shattering was slower than has often been assumed. This suggests a protracted period of pre-domestication cultivation, and therefore implies that both in time and in space the initial start of cultivation was separated from eventual domestication, when domesticated and wild populations would have become distinct gene pools. Archaeobotanical evidence increasingly suggests more pathways to cultivation than are represented by modern domesticated crop lines, including apparent early experiments with cultivation that did not lead to domestication, and early domesticates, such as two-grained einkorn and striate-emmeroid wheats, which went extinct in prehistory. This diverse range of early crops is hard to accommodate within a single centre of origin for all early Near Eastern cultivars, despite suggestions from genetic datasets that single origins from a single centre ought to be expected. This apparent discrepancy between archaeobotany and genetics highlights the need for modelling the expected genetic signature of different domestication scenarios, including multiple origins. A computer simulation of simple plant populations with 20 chromosomes was designed to explore potential differences between single and double origins of domesticated populations as they might appear in genomic datasets millennia later. Here we report a new simulation of a self-pollinating (2% outbreeding) plant compared to panmictic populations, and find that the general outcome is similar with multiple starts of cultivation drifting towards apparent monophyly in genome-wide phylogenetic analysis over hundreds of generations. This suggests that multiple origins of cultivation of a given species may be missed in some forms of modern genetic analysis, and it highlights the need for more complex modelling of population genetic processes associated with the origins of agriculture.     

The influence of host and non‐host companion plants on the behaviour of pest insects in field crops

Companion plants grown as ‘trap crops’ or ‘intercrops’ can be used to reduce insect infestations in field crops. The ways in which such reductions are achieved are being described currently using either a chemical approach, based on the ‘push‐pull strategy’, or a biological approach, based on the ‘appropriate/inappropriate landing theory’. The chemical approach suggests that insect numbers are reduced by chemicals from the intercrop ‘repelling’ insects from the main crop, and by chemicals from the trap‐crop ‘attracting’ insects away from the main crop. This approach is based on the assumptions that (1) plants release detectable amounts of volatile chemicals, and (2) insects ‘respond’ while still some distance away from the emitting plant. We discuss whether the above assumptions can be justified using the ‘appropriate/inappropriate landing theory’. Our tenet is that specialist insects respond only to the volatile chemicals released by their host plants and that these are released in such small quantities that, even with a heightened response to such chemicals, specialist insects can only detect them when a few metres from the emitting plant. We can find no robust evidence in the literature that plant chemicals ‘attract’ insects from more than 5 m and believe that ‘trap crops’ function simply as ‘interception barriers’. We can also find no evidence that insects are ‘repelled’ from landing on non‐host plants. Instead, we believe that ‘intercrops’ disrupt host‐plant finding by providing insects with a choice of host (appropriate) and non‐host (inappropriate) plant leaves on which to land, as our research has shown that, for intercropping to be effective, insects must land on the non‐host plants. Work is needed to determine whether non‐host plants are repellent (chemical approach) or ‘non‐stimulating’ (biological approach) to insects.     

作物驯化的遗传学研究及其在大豆育种中的应用

驯化遗传学是进化生物学研究的一个重要分支,对作物驯化历程进行深入探索,可以更好地认识人类早期农耕文明的产生和发展,了解物种的形成乃至生命的起源和进化,对指导人们利用野生资源来改良现有的栽培作物和培育新的有价值的品种也具有重要的意义。本文综述了作物驯化的遗传学研究内容和进展,以及重要作物大豆驯化起源的研究概况,探讨了目前作物驯化研究对大豆驯化遗传学及野生大豆资源综合利用的指导意义。     

作物驯化的遗传学研究及其在大豆育种中的应用

驯化遗传学是进化生物学研究的一个重要分支, 对作物驯化历程进行深入探索, 可以更好地认识人类早期农耕文明的产生和发展, 了解物种的形成乃至生命的起源和进化, 对指导人们利用野生资源来改良现有的栽培作物和培育新的有价值的品种也具有重要的意义。本文综述了作物驯化的遗传学研究内容和进展, 以及重要作物大豆驯化起源的研究概况, 探讨了目前作物驯化研究对大豆驯化遗传学及野生大豆资源综合利用的指导意义。     

Global investigation of the co‐evolution of MIRNA genes and microRNA targets during soybean domestication

Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome‐wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evolutionary patterns during soybean domestication: MIRs and miRNA targets with high expression and duplication status, and with greater numbers of partners, exhibit lower nucleotide divergence than their counterparts without these characteristics, suggesting that expression level, duplication status, and miRNA–target interaction are essential for evolution of MIRs and miRNA targets. Further investigation revealed that miRNA–target pairs that are subjected to strong purifying selection have greater similarities than those that exhibited genetic diversity. Moreover, mediated by domestication and improvement, the similarities of a large number of miRNA–target pairs in cultivated soybean populations were increased compared to those in wild soybeans, whereas a small number of miRNA–target pairs exhibited decreased similarity, which may be associated with the adoption of particular domestication traits. Taken together, our results shed light on the co‐evolution of MIRs and miRNA targets during soybean domestication.     

Molecular insights into the evolution of crop plants

The domestication and improvement of crop plants have long fascinated evolutionary biologists, geneticists, and anthropologists. In recent years, the development of increasingly powerful molecular and statistical tools has reinvigorated this now fast-paced field of research. In this paper, we provide an overview of how such tools have been applied to the study of crop evolution. We also highlight lessons that have been learned in light of a few long-standing and interrelated hypotheses concerning the origins of crop plants and the nature of the genetic changes underlying their evolution. We conclude by discussing compelling evolutionary genomic approaches that make possible the efficient and unbiased identification of genes controlling crop-related traits and provide further insight into the actual timing of selection on particular genomic regions.     

Proposal for Teaching Evolutionary Biology: A bridge between research and educational practice

We present quantitative results for the doctoral thesis of the first-named author of this article. The objective was to recommend and test a teaching proposal for core knowledge of evolutionary biology in secondary education. The focus of the study is ‘Problem cores in teaching’. The ‘Weaving evolutionary thinking’ teaching unit, designed for and tested in this study, entailed: selecting basic evolutionary knowledge from the model of evolution through variation and natural selection; designing a coordinated set of activities, teaching resources and evaluation tools; leading a process of teacher training; and building bridges between: the teaching model, research into the teaching of evolutionary biology, our own teaching experience and that of the secondary school teacher who participated in the project. The data collected through questionnaires show significant differences in favour of the experimental group, which means that the proposal may be favourably assessed in the context of Mexican education, in terms of feasibility, relevance and the pedagogical transformation of knowledge.     

Crop domestication and the disruption of species interactions

The process of crop domestication involves artificial selection for beneficial traits in plants, such as yield, standard development times for ease of harvest, and pest and disease resistance. This process has greatly improved crop performance and can allow farmers to produce viable harvests in previously un-profitable circumstances. However, there is growing evidence that domestication may impact species interactions perhaps through the amplification of effects across spatial scales and so have a pervasive influence on the functioning and sustainability of agro-ecosystems. This can occur directly, through unintentional alteration to crop traits that disrupt the host-finding ability of natural enemies; or indirectly through alterations to within-plant nutritional quality that impacts herbivore size and density and then ramifies throughout food chains. At the field level, the low variability in traits between individual plants means that particular weed and invertebrate communities are associated with each crop type. At the landscape level, the use of one or a few varieties across wide spatial scales, planted and harvested relatively synchronously, further reduces diversity. This process acting across multiple spatial scales represents a considerable selection pressure that may result in feedback-loops which favour the occurrence of particular traits within the community (e.g. resistance to pesticides). In order to properly balance the ‘pros and cons’ of the widespread adoption of new varieties, for the future, we must consider how particular traits influence interactions within the wider ecological community, and how these effects amplify across spatial scales. Here we argue that the process of domestication (with the primary goal of yield increases) and the widespread use of a few varieties has led to potentially detrimental impacts on species interactions, and suggest possible strategies for mitigating some of these negative impacts in the future.     

Gut evolution in early Cambrian trilobites and the origin of predation on infaunal macroinvertebrates: evidence from muscle scars in Mesolenellus

Trilobites are particularly common Cambrian fossils, but their trophic impact on the rapidly evolving marine ecosystems of that time is difficult to assess, due to uncertainties on how diverse their feeding habits truly were. Gut anatomy might help to constrain inferences on trilobite feeding ecology, but preservation of digestive organs is exceedingly rare. Muscle scars on the glabella, known as ‘frontal auxiliary impressions’ (FAIs), have been interpreted as evidence of the evolution of a pouch‐like organ with powerful extrinsic muscles (i.e. a crop) in some trilobites. Here we describe FAIs in Mesolenellus hyperboreus from Cambrian Stage 4 strata of North Greenland, which represents the oldest example of such structures and their first report in the Suborder Olenellina. Mesolenellus FAIs suggest that the crop in trilobites was clearly differentiated from the rest of the digestive tract, and essentially located under a hypertrophied glabellar frontal lobe. Reviews of the digestive anatomy of trilobite sister‐taxa and the glabellar morphology of the oldest‐known trilobites suggest that the gut of the trilobite ancestor was an essentially simple tract (i.e. no well‐differentiated crop) flanked laterally by numerous midgut glands. A crop first evolved in the Cambrian in groups like olenelloids and (later) paradoxidoids. Using ichnological evidence, we hypothesize that the emergence of olenelloids yields evidence for the evolution of predatory inclinations in a group of arthropods originally dominated by surface‐deposit‐feeders. By allowing the exploitation of a rapidly developing food source, infaunal animals, the diversification of feeding strategies in trilobites might partially explain their unparalleled evolutionary success.     

The influence of genetics on future crop production strategies: from traits to genes, and genes to traits

This paper discusses how a genetical approach to plant physiology can contribute to research underpinning the production of new crop varieties. It highlights the interactions between genetics and plant breeding and how the current advances in genetics and the new science of genomics can contribute to our understanding of the genetical control of key agronomic traits ‐ the process of ‘translating’ traits to identified and mapped genes. Advances in genomics, such as the sequencing of whole genomes and expressed sequence tags, are producing information on genes and gene structures, but without knowing their function. A great deal more biology will be necessary to translate gene structure to function ‐ the process of translating genes to traits. Combining these ‘forward’ and ‘reverse’ genetic approaches will allow us to get comprehensive knowledge of the biology of agronomic traits at the physiological, biochemical and molecular levels, so that the ‘circuitry’ of our crop plants can be elucidated. This will enable plant breeders to manipulate crop phenotype using marker‐assisted breeding or genetic engineering approaches with a precision not previously possible.     

Plant domestication slows pest evolution

Agricultural practices such as breeding resistant varieties and pesticide use can cause rapid evolution of pest species, but it remains unknown how plant domestication itself impacts pest contemporary evolution. Using experimental evolution on a comparative phylogenetic scale, we compared the evolutionary dynamics of a globally important economic pest – the green peach aphid (Myzus persicae) – growing on 34 plant taxa, represented by 17 crop species and their wild relatives. Domestication slowed aphid evolution by 13.5%, maintained 10.4% greater aphid genotypic diversity and 5.6% higher genotypic richness. The direction of evolution (i.e. which genotypes increased in frequency) differed among independent domestication events but was correlated with specific plant traits. Individual‐based simulation models suggested that domestication affects aphid evolution directly by reducing the strength of selection and indirectly by increasing aphid density and thus weakening genetic drift. Our results suggest that phenotypic changes during domestication can alter pest evolutionary dynamics.     

Recombination systems and plant domestication

Speculations on the role of recombination systems in plant domestication are presented. It is suggested that those colonizing species which had more open, or at least more flexible, recombination systems were, in a sense, pre-adapted to domestication. Such systems allow the rapid switching of variability between the potential and free states, an ability which is argued to have been of great importance during the domestication process. Species which were never domesticated, or were abandoned later, are suggested to have had inappropriate recombination systems which did not allow the storage and/or release of sufficient variability. A review of the ecology of recombination systems in disturbed habitats and a comparison of some aspects of the recombination systems in crop progenitors with those in non-cultivated colonizing species provides some evidence both for and against the hypothesis.