Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops

How did the domestication of Fertile Crescent grain crops increase their yields?

The origins of agriculture, 10 000 years ago, led to profound changes in the biology of plants exploited as grain crops, through the process of domestication. This special case of evolution under cultivation led to domesticated cereals and pulses requiring humans for their dispersal, but the accompanying mechanisms causing higher productivity in these plants remain unknown. The classical view of crop domestication is narrow, focusing on reproductive and seed traits including the dispersal, dormancy and size of seeds, without considering whole-plant characteristics. However, the effects of initial domestication events can be inferred from consistent differences between traditional landraces and their wild progenitors.We studied how domestication increased the yields of Fertile Crescent cereals and pulses using a greenhouse experiment to compare landraces with wild progenitors. We grew eight crops: barley, einkorn and emmer wheat, oat, rye, chickpea, lentil and pea. In each case, comparison of multiple landraces with their wild progenitors enabled us to quantify the effects of domestication rather than subsequent crop diversification. To reveal the mechanisms underpinning domestication-linked yield increases, we measured traits beyond those classically associated with domestication, including the rate and duration of growth, reproductive allocation, plant size and also seed mass and number.Cereal and pulse crops had on average 50% higher yields than their wild progenitors, resulting from a 40% greater final plant size, 90% greater individual seed mass and 38% less chaff or pod material, although this varied between species. Cereal crops also had a higher seed number per spike compared with their wild ancestors. However, there were no differences in growth rate, total seed number, proportion of reproductive biomass or the duration of growth.The domestication of Fertile Crescent crops resulted in larger seed size leading to a larger plant size, and also a reduction in chaff, with no decrease in seed number per individual, which proved a powerful package of traits for increasing yield. We propose that the important steps in the domestication process should be reconsidered, and the domestication syndrome broadened to include a wider range of traits.

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives

We produced a unique large data set of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose, we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11 eudicots. All contigs were annotated using BLAST, prot4EST and Blast2GO. A strong originality of the data set is that each crop is associated with close relative species, which will permit whole-genome comparative evolutionary studies between crops and their wild-related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at http://arcad-bioinformatics.southgreen.fr/.

Whole-genome duplication as a key factor in crop domestication

Polyploidy is commonly thought to be associated with the domestication process because of its concurrence with agriculturally favourable traits and because it is widespread among the major plant crops(1-4). Furthermore, the genetic consequences of polyploidy(5-7) might have increased the adaptive plasticity of those plants, enabling successful domestication(6-8). Nevertheless, a detailed phylogenetic analysis regarding the association of polyploidy with the domestication process, and the temporal order of these distinct events, has been lacking(3). Here, we have gathered a comprehensive data set including dozens of genera, each containing one or more major crop species and for which sufficient sequence and chromosome number data exist. Using probabilistic inference of ploidy levels conducted within a phylogenetic framework, we have examined the incidence of polyploidization events within each genus. We found that domesticated plants have gone through more polyploidy events than their wild relatives, with monocots exhibiting the most profound difference: 54% of the crops are polyploids versus 40% of the wild species. We then examined whether the preponderance of polyploidy among crop species is the result of two, non-mutually-exclusive hypotheses: (1) polyploidy followed by domestication, and (2) domestication followed by polyploidy. We found support for the first hypothesis, whereby polyploid species were more likely to be domesticated than their wild relatives, suggesting that the genetic consequences of polyploidy have conferred genetic preconditions for successful domestication on many of these plants.

Plant Defense against Herbivorous Pests: Exploiting Resistance and Tolerance Traits for Sustainable Crop Protection

Interactions between plants and insect herbivores are important determinants of plant productivity in managed and natural vegetation. In response to attack, plants have evolved a range of defenses to reduce the threat of injury and loss of productivity. Crop losses from damage caused by arthropod pests can exceed 15% annually. Crop domestication and selection for improved yield and quality can alter the defensive capability of the crop, increasing reliance on artificial crop protection. Sustainable agriculture, however, depends on reduced chemical inputs. There is an urgent need, therefore, to identify plant defensive traits for crop improvement. Plant defense can be divided into resistance and tolerance strategies. Plant traits that confer herbivore resistance typically prevent or reduce herbivore damage through expression of traits that deter pests from settling, attaching to surfaces, feeding and reproducing, or that reduce palatability. Plant tolerance of herbivory involves expression of traits that limit the negative impact of herbivore damage on productivity and yield. Identifying the defensive traits expressed by plants to deter herbivores or limit herbivore damage, and understanding the underlying defense mechanisms, is crucial for crop scientists to exploit plant defensive traits in crop breeding. In this review, we assess the traits and mechanisms underpinning herbivore resistance and tolerance, and conclude that physical defense traits, plant vigor and herbivore-induced plant volatiles show considerable utility in pest control, along with mixed species crops. We highlight emerging approaches for accelerating the identification of plant defensive traits and facilitating their deployment to improve the future sustainability of crop protection.

Reciprocal genomic evolution in the ant-fungus agricultural symbiosis

The attine ant-fungus agricultural symbiosis evolved over tens of millions of years, producing complex societies with industrial-scale farming analogous to that of humans. Here we document reciprocal shifts in the genomes and transcriptomes of seven fungus-farming ant species and their fungal cultivars. We show that ant subsistence farming probably originated in the early Tertiary (55-60 MYA), followed by further transitions to the farming of fully domesticated cultivars and leaf-cutting, both arising earlier than previously estimated. Evolutionary modifications in the ants include unprecedented rates of genome-wide structural rearrangement, early loss of arginine biosynthesis and positive selection on chitinase pathways. Modifications of fungal cultivars include loss of a key ligninase domain, changes in chitin synthesis and a reduction in carbohydrate-degrading enzymes as the ants gradually transitioned to functional herbivory. In contrast to human farming, increasing dependence on a single cultivar lineage appears to have been essential to the origin of industrial-scale ant agriculture.

Indications for Three Independent Domestication Events for the Tea Plant (Camellia sinensis (L.) O. Kuntze) and New Insights into the Origin of Tea Germplasm in China and India Revealed by Nuclear Microsatellites

Background

Tea is the world’s most popular non-alcoholic beverage. China and India are known to be the largest tea producing countries and recognized as the centers for the domestication of the tea plant (Camellia sinensis (L.) O. Kuntze). However, molecular studies on the origin, domestication and relationships of the main teas, China type, Assam type and Cambod type are lacking.

Methodology/Principal Findings

Twenty-three nuclear microsatellite markers were used to investigate the genetic diversity, relatedness, and domestication history of cultivated tea in both China and India. Based on a total of 392 samples, high levels of genetic diversity were observed for all tea types in both countries. The cultivars clustered into three distinct genetic groups (i.e. China tea, Chinese Assam tea and Indian Assam tea) based on STRUCTURE, PCoA and UPGMA analyses with significant pairwise genetic differentiation, corresponding well with their geographical distribution. A high proportion (30%) of the studied tea samples were shown to possess genetic admixtures of different tea types suggesting a hybrid origin for these samples, including the Cambod type.

Conclusions

We demonstrate that Chinese Assam tea is a distinct genetic lineage from Indian Assam tea, and that China tea sampled from India was likely introduced from China directly. Our results further indicate that China type tea, Chinese Assam type tea and Indian Assam type tea are likely the result of three independent domestication events from three separate regions across China and India. Our findings have important implications for the conservation of genetic stocks, as well as future breeding programs.

Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes

Grafting is an ancient agricultural practice that joins the root system (rootstock) of one plant to the shoot (scion) of another. It is most commonly employed in woody perennial crops to indirectly manipulate scion phenotype. While recent research has focused on scions, here we investigate rootstocks, the lesser-known half of the perennial crop equation. We review natural grafting, grafting in agriculture, rootstock diversity and domestication, and developing areas of rootstock research, including molecular interactions and rootstock microbiomes. With growing interest in perennial crops as valuable components of sustainable agriculture, rootstocks provide one mechanism by which to improve and expand woody perennial cultivation in a range of environmental conditions.

To Have and to Hold: Selection for Seed and Fruit Retention During Crop Domestication

Crop domestication provides a useful model system to characterize the molecular and developmental bases of morphological variation in plants. Among the most universal changes resulting from selection during crop domestication is the loss of seed and fruit dispersal mechanisms, which greatly facilitates harvesting efficiency. In this review, we consider the molecular genetic and developmental bases of the loss of seed shattering and fruit dispersal in six major crop plant families, three of which are primarily associated with seed crops (Poaceae, Brassicaceae, Fabaceae) and three of which are associated with fleshy-fruited crops (Solanaceae, Rosaceae, Rutaceae). We find that the developmental basis of the loss of seed/fruit dispersal is conserved in a number of independently domesticated crops, indicating the widespread occurrence of developmentally convergent evolution in response to human selection. With regard to the molecular genetic approaches used to characterize the basis of this trait, traditional biparental quantitative trait loci mapping remains the most commonly used strategy; however, recent advances in next-generation sequencing technologies are now providing new avenues to map and characterize loss of shattering/dispersal alleles. We anticipate that continued application of these approaches, together with candidate gene analyses informed by known shattering candidate genes from other crops, will lead to a rapid expansion of our understanding of this critical domestication trait.

Identification of candidate genes for dissecting complex branch number trait in chickpea

The present study exploited integrated genomics-assisted breeding strategy for genetic dissection of complex branch number quantitative trait in chickpea. Candidate gene-based association analysis in a branch number association panel was performed by utilizing the genotyping data of 401 SNP allelic variants mined from 27 known cloned branch number gene orthologs of chickpea. The genome-wide association study (GWAS) integrating both genome-wide GBS- (4556 SNPs) and candidate gene-based genotyping information of 4957 SNPs in a structured population of 60 sequenced desi and kabuli accessions (with 350-400 kb LD decay), detected 11 significant genomic loci (genes) associated (41% combined PVE) with branch number in chickpea. Of these, seven branch number-associated genes were further validated successfully in two inter (ICC 4958 × ICC 17160)- and intra (ICC 12299 × ICC 8261)-specific mapping populations. The axillary meristem and shoot apical meristem-specific expression, including differential up- and down-regulation (4-5 fold) of the validated seven branch number-associated genes especially in high branch number as compared to the low branch number-containing parental accessions and homozygous individuals of two aforesaid mapping populations was apparent. Collectively, this combinatorial genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in seven potential known/candidate genes [PIN1 (PIN-FORMED protein 1), TB1 (teosinte branched 1), BA1/LAX1 (BARREN STALK1/LIKE AUXIN1), GRAS8 (gibberellic acid insensitive/GAI, Repressor of ga13/RGA and Scarecrow8/SCR8), ERF (ethylene-responsive element-binding factor), MAX2 (more axillary growth 2) and lipase] governing chickpea branch number. The useful information generated from this study have potential to expedite marker-assisted genetic enhancement by developing high-yielding cultivars with more number of productive (pods and seeds) branches in chickpea.

Crop wild relatives of the brinjal eggplant (Solanum melongena): Poorly represented in genebanks and many species at risk of extinction

PREMISE OF THE STUDY

Crop wild relatives (CWR) provide important traits for plant breeding, including pest, pathogen, and abiotic stress resistance. Therefore, their conservation and future availability are essential for food security. Despite this need, the world's genebanks are currently thought to conserve only a small fraction of the total diversity of CWR.

METHODS

We define the eggplant genepool using the results of recent taxonomic and phylogenetic studies. We identify the gaps in germplasm accessions for eggplant (Solanum melongena L.) CWR by comparing georeferenced herbarium records and germplasm accessions using a gap analysis methodology implementing species distribution models (SDM). Preliminary conservation assessments using IUCN criteria were done for all species and were combined with the gap analysis to pinpoint where under-collected and threatened CWR species coincide with high human disturbance and occur outside of protected areas.

KEY RESULTS

We show that many eggplant CWR are poorly represented in genebanks compared to their native ranges. Priority areas for future collecting are concentrated in Africa, especially along the Kenya-Tanzania border. Fourteen species of eggplant CWR are assessed as threatened or near-threatened; these are also concentrated in eastern Africa.

CONCLUSIONS

The knowledge base upon which conservation of wild relative germplasm depends must take into account both taxonomic and phylogenetic advances. Beyond traditional research focus on close relatives of crops, we emphasize the benefits of defining a broad CWR genepool, and the importance of assessing threats to wild species when targeting localities for future collection of CWR to improve crop breeding in the face of environmental change.

Global agricultural intensification during climate change: a role for genomics

Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.

Translational genomics for plant breeding with the genome sequence explosion

The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.

Evidence of a Strong Domestication Bottleneck in the Recently Cultivated New Zealand Endemic Root Crop, Arthropodium cirratum (Asparagaceae)

We use chloroplast DNA sequencing to examine aspects of the pre-European Māori cultivation of an endemic New Zealand root crop, Arthropodium cirratum (rengarenga). Researching the early stages of domestication is not possible for the majority of crops, because their cultivation began many thousands of years ago and/or they have been substantially altered by modern breeding methods. We found high levels of genetic variation and structuring characterised the natural distribution of A. cirratum, while the translocated populations only retained low levels of this diversity, indicating a strong bottleneck even at the early stages of this species’ cultivation. The high structuring detected at four chloroplast loci within the natural A. cirratum range enabled the putative source(s) of the translocated populations to be identified as most likely located in the eastern Bay of Plenty/East Cape region. The high structuring within A. cirratum also has implications for the conservation of genetic diversity within this species, which has undergone recent declines in both its natural and translocated ranges.

The Domestication Syndrome in Phoenix dactylifera Seeds: Toward the Identification of Wild Date Palm Populations

Investigating crop origins is a priority to understand the evolution of plants under domestication, develop strategies for conservation and valorization of agrobiodiversity and acquire fundamental knowledge for cultivar improvement. The date palm (Phoenix dactylifera L.) belongs to the genus Phoenix, which comprises 14 species morphologically very close, sometimes hardly distinguishable. It has been cultivated for millennia in the Middle East and in North Africa and constitutes the keystone of oasis agriculture. Yet, its origins remain poorly understood as no wild populations are identified. Uncultivated populations have been described but they might represent feral, i.e. formerly cultivated, abandoned forms rather than truly wild populations. In this context, this study based on morphometrics applied to 1625 Phoenix seeds aims to (1) differentiate Phoenix species and (2) depict the domestication syndrome observed in cultivated date palm seeds using other Phoenix species as a "wild" reference. This will help discriminate truly wild from feral forms, thus providing new insights into the evolutionary history of this species. Seed size was evaluated using four parameters: length, width, thickness and dorsal view surface. Seed shape was quantified using outline analyses based on the Elliptic Fourier Transform method. The size and shape of seeds allowed an accurate differentiation of Phoenix species. The cultivated date palm shows distinctive size and shape features, compared to other Phoenix species: seeds are longer and elongated. This morphological shift may be interpreted as a domestication syndrome, resulting from the long-term history of cultivation, selection and human-mediated dispersion. Based on seed attributes, some uncultivated date palms from Oman may be identified as wild. This opens new prospects regarding the possible existence and characterization of relict wild populations and consequently for the understanding of the date palm origins. Finally, we here describe a pipeline for the identification of the domestication syndrome in seeds that could be used in other crops.

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.

Using Ancient Traits to Convert Soil Health into Crop Yield: Impact of Selection on Maize Root and Rhizosphere Function

The effect of domestication and modern breeding on aboveground traits in maize (Zea mays) has been well-characterized, but the impact on root systems and the rhizosphere remain unclear. The transition from wild ecosystems to modern agriculture has focused on selecting traits that yielded the largest aboveground production with increasing levels of crop management and nutrient inputs. Root morphology, anatomy, and ecophysiological processes may have been affected by the substantial environmental and genetic shifts associated with this transition. As a result, root and rhizosphere traits that allow more efficient foraging and uptake in lower synthetic input environments might have been lost. The development of modern maize has led to a shift in microbiome community composition, but questions remain as to the dynamics and drivers of this change during maize evolution and its implications for resource acquisition and agroecosystem functioning under different management practices. Better understanding of how domestication and breeding affected root and rhizosphere microbial traits could inform breeding strategies, facilitate the sourcing of favorable alleles, and open new frontiers to improve resource use efficiency through greater integration of root development and ecophysiology with agroecosystem functioning.

Altered expression of TaRSL4 gene by genome interplay shapes root hair length in allopolyploid wheat

Polyploidy is a major driving force in plant evolution and speciation. Phenotypic changes often arise with the formation, natural selection and domestication of polyploid plants. However, little is known about the consequence of hybridization and polyploidization on root hair development. Here, we report that root hair length of synthetic and natural allopolyploid wheats is significantly longer than those of their diploid progenitors, whereas no difference is observed between allohexaploid and allotetraploid wheats. The expression of wheat gene TaRSL4, an orthologue of AtRSL4 controlling the root hair development in Arabidopsis, was positively correlated with the root hair length in diploid and allotetraploid wheats. Moreover, transcript abundance of TaRSL4 homoeologue from A genome (TaRSL4-A) was much higher than those of other genomes in natural allopolyploid wheat. Notably, increased root hair length by overexpression of the TaRSL4-A in wheat led to enhanced shoot fresh biomass under nutrient-poor conditions. Our observations indicate that increased root hair length in allohexaploid wheat originated in the allotetraploid progenitors and altered expression of TaRSL4 gene by genome interplay shapes root hair length in allopolyploid wheat.

An Integrated Hypothesis on the Domestication of Bactris gasipaes

Peach palm (Bactris gasipaes Kunth) has had a central place in the livelihoods of people in the Americas since pre-Columbian times, notably for its edible fruits and multi-purpose wood. The botanical taxon includes both domesticated and wild varieties. Domesticated var gasipaes is believed to derive from one or more of the three wild types of var. chichagui identified today, although the exact dynamics and location of the domestication are still uncertain. Drawing on a combination of molecular and phenotypic diversity data, modeling of past climate suitability and existing literature, we present an integrated hypothesis about peach palm’s domestication. We support a single initial domestication event in south western Amazonia, giving rise to var. chichagui type 3, the putative incipient domesticate. We argue that subsequent dispersal by humans across western Amazonia, and possibly into Central America allowed for secondary domestication events through hybridization with resident wild populations, and differential human selection pressures, resulting in the diversity of present-day landraces. The high phenotypic diversity in the Ecuadorian and northern Peruvian Amazon suggest that human selection of different traits was particularly intense there. While acknowledging the need for further data collection, we believe that our results contribute new insights and tools to understand domestication and dispersal patterns of this important native staple, as well as to plan for its conservation.

De novo and comparative transcriptome analysis of cultivated and wild spinach

Spinach (Spinacia oleracea L.) is an economically important green leafy vegetable crop. In this study, we performed deep transcriptome sequencing for nine spinach accessions: three from cultivated S. oleracea, three from wild S. turkestanica and three from wild S. tetrandra. A total of approximately 100 million high-quality reads were generated, which were de novo assembled into 72,151 unigenes with a total length of 46.5 Mb. By comparing sequences of these unigenes against different protein databases, nearly 60% of them were annotated and 50% could be assigned with Gene Ontology terms. A total of 387 metabolic pathways were predicted from the assembled spinach unigenes. From the transcriptome sequencing data, we were able to identify a total of ~320,000 high-quality single nucleotide polymorphisms (SNPs). Phylogenetic analyses using SNPs as well as gene expression profiles indicated that S. turkestanica was more closely related to the cultivated S. oleracea than S. tetrandra. A large number of genes involved in responses to biotic and abiotic stresses were found to be differentially expressed between the cultivated and wild spinach. Finally, an interactive online database (http://www.spinachbase.org) was developed to allow the research community to efficiently retrieve, query, mine and analyze our transcriptome dataset.

Genomics and the Contrasting Dynamics of Annual and Perennial Domestication

Plant domestication modifies a wild species genetically for human use. Among thousands of domesticated plants, a major distinction is the difference between annual and perennial life cycles. The domestication of perennials is expected to follow different processes than annuals, with distinct genetic outcomes. Here we examine domestication from a population genetics perspective, with a focus on three issues: genetic bottlenecks during domestication, introgression as a source of local adaptation, and genetic load. These three issues have been studied nominally in major annual crops but even less extensively in perennials. Here we highlight lessons from annual plants, motivations to study these issues in perennial plants, and new approaches that may lead to further progress.

A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea

The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.

Independent mis-splicing mutations in TaPHS1 causing loss of preharvest sprouting (PHS) resistance during wheat domestication

Preharvest sprouting (PHS) is one of the major constraints of wheat production in areas where prolonged rainfall occurs during harvest. TaPHS1 is a gene that regulates PHS resistance on chromosome 3A of wheat, and two causal mutations in the positions +646 and +666 of the TaPHS1 coding region result in wheat PHS susceptibility. Three competitive allele-specific PCR (KASP) markers were developed based on the two mutations in the coding region and one in the promoter region and validated in 82 wheat cultivars with known genotypes. These markers can be used to transfer TaPHS1 in breeding through marker-assisted selection. Screening of 327 accessions of wheat A genome progenitors using the three KASP markers identified different haplotypes in both diploid and tetraploid wheats. Only one Triticum monococcum accession, however, carries both causal mutations in the TaPHS1 coding region and shows PHS susceptibility. Five of 249 common wheat landraces collected from the Fertile Crescent and surrounding areas carried the mutation (C) in the promoter (-222), and one landrace carries both the causal mutations in the TaPHS1 coding region, indicating that the mis-splicing (+646) mutation occurred during common wheat domestication. PHS assay of wheat progenitor accessions demonstrated that the wild-types were highly PHS-resistant, whereas the domesticated type showed increased PHS susceptibility. The mis-splicing TaPHS1 mutation for PHS susceptibility was involved in wheat domestication and might arise independently between T. monococcum and Triticum aestivum.

Evolutionarily advanced ant farmers rear polyploid fungal crops

Innovative evolutionary developments are often related to gene or genome duplications. The crop fungi of attine fungus-growing ants are suspected to have enhanced genetic variation reminiscent of polyploidy, but this has never been quantified with cytological data and genetic markers. We estimated the number of nuclei per fungal cell for 42 symbionts reared by 14 species of Panamanian fungus-growing ants. This showed that domesticated symbionts of higher attine ants are polykaryotic with 7-17 nuclei per cell, whereas nonspecialized crops of lower attines are dikaryotic similar to most free-living basidiomycete fungi. We then investigated how putative higher genetic diversity is distributed across polykaryotic mycelia, using microsatellite loci and evaluating models assuming that all nuclei are either heterogeneously haploid or homogeneously polyploid. Genetic variation in the polykaryotic symbionts of the basal higher attine genera Trachymyrmex and Sericomyrmex was only slightly enhanced, but the evolutionarily derived crop fungi of Atta and Acromyrmex leaf-cutting ants had much higher genetic variation. Our opposite ploidy models indicated that the symbionts of Trachymyrmex and Sericomyrmex are likely to be lowly and facultatively polyploid (just over two haplotypes on average), whereas Atta and Acromyrmex symbionts are highly and obligatorily polyploid (ca. 5-7 haplotypes on average). This stepwise transition appears analogous to ploidy variation in plants and fungi domesticated by humans and in fungi domesticated by termites and plants, where gene or genome duplications were typically associated with selection for higher productivity, but allopolyploid chimerism was incompatible with sexual reproduction.

A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea

A combinatorial approach of candidate gene-based association analysis and genome-wide association study (GWAS) integrated with QTL mapping, differential gene expression profiling and molecular haplotyping was deployed in the present study for quantitative dissection of complex flowering time trait in chickpea. Candidate gene-based association mapping in a flowering time association panel (92 diverse desi and kabuli accessions) was performed by employing the genotyping information of 5724 SNPs discovered from 82 known flowering chickpea gene orthologs of Arabidopsis and legumes as well as 832 gene-encoding transcripts that are differentially expressed during flower development in chickpea. GWAS using both genome-wide GBS- and candidate gene-based genotyping data of 30,129 SNPs in a structured population of 92 sequenced accessions (with 200-250 kb LD decay) detected eight maximum effect genomic SNP loci (genes) associated (34% combined PVE) with flowering time. Six flowering time-associated major genomic loci harbouring five robust QTLs mapped on a high-resolution intra-specific genetic linkage map were validated (11.6-27.3% PVE at 5.4-11.7 LOD) further by traditional QTL mapping. The flower-specific expression, including differential up- and down-regulation (>three folds) of eight flowering time-associated genes (including six genes validated by QTL mapping) especially in early flowering than late flowering contrasting chickpea accessions/mapping individuals during flower development was evident. The gene haplotype-based LD mapping discovered diverse novel natural allelic variants and haplotypes in eight genes with high trait association potential (41% combined PVE) for flowering time differentiation in cultivated and wild chickpea. Taken together, eight potential known/candidate flowering time-regulating genes [efl1 (early flowering 1), FLD (Flowering locus D), GI (GIGANTEA), Myb (Myeloblastosis), SFH3 (SEC14-like 3), bZIP (basic-leucine zipper), bHLH (basic helix-loop-helix) and SBP (SQUAMOSA promoter binding protein)], including novel markers, QTLs, alleles and haplotypes delineated by aforesaid genome-wide integrated approach have potential for marker-assisted genetic improvement and unravelling the domestication pattern of flowering time in chickpea.

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.

The genomics of microbial domestication in the fermented food environment

Shortly after the agricultural revolution, the domestication of bacteria, yeasts, and molds, played an essential role in enhancing the stability, quality, flavor, and texture of food products. These domestication events were probably the result of human food production practices that entailed the continual recycling of isolated microbial communities in the presence of abundant agricultural food sources. We suggest that within these novel agrarian food niches the metabolic requirements of those microbes became regular and predictable resulting in rapid genomic specialization through such mechanisms as pseudogenization, genome decay, interspecific hybridization, gene duplication, and horizontal gene transfer. The ultimate result was domesticated strains of microorganisms with enhanced fermentative capacities.

Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations

BACKGROUND AND AIMS

Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species.

METHODS

Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite.

KEY RESULTS

Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species.

CONCLUSIONS

This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool.

Parallel reductions in phenolic constituents resulting from the domestication of eggplant

Crop domestication is often accompanied by changes in metabolite compositions that alter traits such as flavor, color, or other beneficial properties. Fruits of eggplants (Solanum melongena L.) and related species are abundant and diverse in pharmacologically interesting phenolic compounds, particularly hydroxycinnamic acid (HCA) conjugates such as the antioxidant caffeoylquinic acids (CQA) and HCA-polyamine amides (HCAA). To understand metabolite variability through the lens of natural and artificial selection, HPLC-DAD was used to generate phenolic profiles for 32 compounds in fruits from 93 accessions representing 9 Solanum species. Profiles were used for identification of species-level and infraspecific chemical patterns across both genetic distance and landscape. Sampling of plant lines included the undomesticated progenitor of eggplant and Asian landraces with a genetic background associated with three Asian regions near proposed separate centers of domestication to test whether chemical changes were convergent despite different origins. Results showed ten compounds were unique to species, and ten other compounds varied significantly in abundance among species. Five CQAs and three HCA-polyamine conjugates were more abundant in wild (undomesticated) versus domesticated eggplant, indicating that artificial selection may have led to reduced phenolic levels. No chemical abundance patterns were associated with site-origin. However, one genetically distinct lineage of geographically-restricted SE Asian eggplants (S. melongena subsp. ovigerum) had a higher HCAA content and diversity than other lineages, which is suggested to be related to artificial selection for small, firm fruit. Overall, patterns show that fruit size, palatability and texture were preferentially selected over health-beneficial phytochemical content during domestication of several nightshade crops.

Genomic basis of the differences between cider and dessert apple varieties

Unraveling the genomic processes at play during variety diversification is of fundamental interest for understanding evolution, but also of applied interest in crop science. It can indeed provide knowledge on the genetic bases of traits for crop improvement and germplasm diversity management. Apple is one of the most important fruit crops in temperate regions, having both great economic and cultural values. Sweet dessert apples are used for direct consumption, while bitter cider apples are used to produce cider. Several important traits are known to differentiate the two variety types, in particular fruit size, biennial versus annual fruit bearing, and bitterness, caused by a higher content in polyphenols. Here, we used an Illumina 8k SNP chip on two core collections, of 48 dessert and 48 cider apples, respectively, for identifying genomic regions responsible for the differences between cider and dessert apples. The genome-wide level of genetic differentiation between cider and dessert apples was low, although 17 candidate regions showed signatures of divergent selection, displaying either outlier F_ST values or significant association with phenotypic traits (bitter versus sweet fruits). These candidate regions encompassed 420 genes involved in a variety of functions and metabolic pathways, including several colocalizations with QTLs for polyphenol compounds.

Domestication in Murtilla (Ugni molinae) Reduced Defensive Flavonol Levels but Increased Resistance Against a Native Herbivorous Insect

Plant domestication can have negative consequences for defensive traits against herbivores, potentially reducing the levels of chemical defenses in plants and consequently their resistance against herbivores. We characterized and quantified the defensive flavonols from multiple cultivated ecotypes with wild ancestors of murtilla, Ugni molinae Turcz, an endemic plant from Chile, at different times of the year, and examined their effects on a native insect herbivore, Chilesia rudis Butler (Lepidoptera: Arctiidae). We hypothesized that domestication results in a decrease in flavonol levels in U. molinae plants, and that this negatively affected C. rudis performance and preference. Ethanolic extracts were made from leaves, stems, and fruit of murtilla plants for flavonol analysis. Flavonols identified were kaempferol, quercetin, rutin, and quercetin 3-D-β-glucoside, the last two being the most abundant. More interestingly, we showed differences in flavonol composition between wild and cultivated U. molinae that persisted for most of the year. Relative amounts of all four flavonols were higher in wild U. molinae leaves; however, no differences were found in the stem and fruit between wild and cultivated plants. In choice and no-choice assays, C. rudis larvae gained more mass on, and consumed more leaf material of, wild as compared with cultivated U. molinae plants. Moreover, when applied to leaves, larvae ate more leaf material with increasing concentrations of each flavonol compound. Our study demonstrates that domestication in U. molinae reduced the amount of flavonols in leaves as well as the performance and preference of C. rudis, indicating that these compounds stimulate feeding of C. rudis.

Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement

Background

Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten maize transcriptomes were sequenced to analyze AS changes and signatures of selection in maize domestication and improvement.

Results

In maize and teosinte, 13,593 highly conserved genes, including 12,030 multiexonic genes, were detected. By identifying AS isoforms from mutliexonic genes, we found that AS types were not significantly different between maize and teosinte. In addition, the two main AS types (intron retention and alternative acceptor) contributed to more than 60% of the AS events in the two species, but the average unique AS events per each alternatively spliced gene in maize (4.12) was higher than that in teosinte (2.26). Moreover, 94 genes generating 98 retained introns with transposable element (TE) sequences were detected in maize, which is far more than 9 retained introns with TEs detected in teosinte. This indicates that TE insertion might be an important mechanism for intron retention in maize. Additionally, the AS levels of 3864 genes were significantly different between maize and teosinte. Of these, 151 AS level-altered genes that are involved in transcriptional regulation and in stress responses are located in regions that have been targets of selection during maize improvement. These genes were inferred to be putatively improved genes.

Conclusions

We suggest that both maize and teosinte share similar AS mechanisms, but more genes have increased AS complexity during domestication from teosinte to maize. Importantly, a subset of AS level-increased genes that encode transcription factors and stress-responsive proteins may have been selected during maize improvement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1582-5) contains supplementary material, which is available to authorized users.

Barley: a translational model for adaptation to climate change

Barley (Hordeum vulgare ssp. vulgare) is an excellent model for understanding agricultural responses to climate change. Its initial domestication over 10 millennia ago and subsequent wide migration provide striking evidence of adaptation to different environments, agro-ecologies and uses. A bottleneck in the selection of modern varieties has resulted in a reduction in total genetic diversity and a loss of specific alleles relevant to climate-smart agriculture. However, extensive and well-curated collections of landraces, wild barley accessions (H. vulgare ssp. spontaneum) and other Hordeum species exist and are important new allele sources. A wide range of genomic and analytical tools have entered the public domain for exploring and capturing this variation, and specialized populations, mutant stocks and transgenics facilitate the connection between genetic diversity and heritable phenotypes. These lay the biological, technological and informational foundations for developing climate-resilient crops tailored to specific environments that are supported by extensive environmental and geographical databases, new methods for climate modelling and trait/environment association analyses, and decentralized participatory improvement methods. Case studies of important climate-related traits and their constituent genes - including examples that are indicative of the complexities involved in designing appropriate responses - are presented, and key developments for the future highlighted.

Variation in susceptibility to Wheat dwarf virus among wild and domesticated wheat

We investigated the variation in plant response in host-pathogen interactions between wild (Aegilops spp., Triticum spp.) and domesticated wheat (Triticum spp.) and Wheat dwarf virus (WDV). The distribution of WDV and its wild host species overlaps in Western Asia in the Fertile Crescent, suggesting a coevolutionary relationship. Bread wheat originates from a natural hybridization between wild emmer wheat (carrying the A and B genomes) and the wild D genome donor Aegilops tauschii, followed by polyploidization and domestication. We studied whether the strong selection during these evolutionary processes, leading to genetic bottlenecks, may have resulted in a loss of resistance in domesticated wheat. In addition, we investigated whether putative fluctuations in intensity of selection imposed on the host-pathogen interactions have resulted in a variation in susceptibility to WDV. To test our hypotheses we evaluated eighteen wild and domesticated wheat taxa, directly or indirectly involved in wheat evolution, for traits associated with WDV disease such as leaf chlorosis, different growth traits and WDV content. The plants were exposed to viruliferous leafhoppers (Psammotettix alienus) in a greenhouse trial and evaluated at two time points. We found three different plant response patterns: i) continuous reduction in growth over time, ii) weak response at an early stage of plant development but a much stronger response at a later stage, and iii) remission of symptoms over time. Variation in susceptibility may be explained by differences in the intensity of natural selection, shaping the coevolutionary interaction between WDV and the wild relatives. However, genetic bottlenecks during wheat evolution have not had a strong impact on WDV resistance. Further, this study indicates that the variation in susceptibility may be associated with the genome type and that the ancestor Ae. tauschii may be useful as genetic resource for the improvement of WDV resistance in wheat.

The evolution of halophytes, glycophytes and crops, and its implications for food security under saline conditions

The effective development of salt tolerant crops requires an understanding that the evolution of halophytes, glycophytes and our major grain crops has involved significantly different processes. Halophytes (and other edaphic endemics) generally arose through colonization of habitats in severe disequilibrium by pre-adapted individuals, rather than by gradual adaptation from populations of 'glycophytes'. Glycophytes, by contrast, occur in low sodium ecosystems, where sodium was and is the major limiting nutrient in herbivore diets, suggesting that their evolution reflects the fact that low sodium individuals experienced lower herbivory and had higher fitness. For domestication/evolution of crop plants, the selective pressure was human imposed and involved humans co-opting functions of defense and reproductive security. Unintended consequences of this included loss of tolerance to various stresses and loss of the genetic variability needed to correct that. Understanding, combining and manipulating all three modes of evolution are now critical to the development of salt tolerant crops, particularly those that will offer food security in countries with few economic resources and limited infrastructure. Such efforts will require exploiting the genetic structures of recently evolved halophytes, the genetic variability of model plants, and endemic halophytes and 'minor' crops that already exist.

Correlated genetic effects on reproduction define a domestication syndrome in a forest tree

Compared to natural selection, domestication implies a dramatic change in traits linked to fitness. A number of traits conferring fitness in the wild might be detrimental under domestication, and domesticated species typically differ from their ancestors in a set of traits known as the domestication syndrome. Specifically, trade-offs between growth and reproduction are well established across the tree of life. According to allocation theory, selection for growth rate is expected to indirectly alter life-history reproductive traits, diverting resources from reproduction to growth. Here we tested this hypothesis by examining the genetic change and correlated responses of reproductive traits as a result of selection for timber yield in the tree Pinus pinaster. Phenotypic selection was carried out in a natural population, and progenies from selected trees were compared with those of control trees in a common garden experiment. According to expectations, we detected a genetic change in important life-history traits due to selection. Specifically, threshold sizes for reproduction were much higher and reproductive investment relative to size significantly lower in the selected progenies just after a single artificial selection event. Our study helps to define the domestication syndrome in exploited forest trees and shows that changes affecting developmental pathways are relevant in domestication processes of long-lived plants.

Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato

A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.

Structure and function of the bacterial root microbiota in wild and domesticated barley

The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare). Bacterial families Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae dominate the barley root-enriched microbiota. Host genotype has a small, but significant, effect on the diversity of root-associated bacterial communities, possibly representing a footprint of barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the barley root-associated microbiota. Strikingly, protein families assigned to these same traits showed evidence of positive selection. Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface.

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A small number of bacterial families dominate the root-enriched barley microbiota

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The host genotype determines the profile of a subset of community members

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Functions relevant for host interactions are enriched in root-associated taxa

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Genes mediating host, bacteria, and phage interactions show signs of positive selection

Crop domestication and its impact on naturally selected trophic interactions

Crop domestication is the process of artificially selecting plants to increase their suitability to human requirements: taste, yield, storage, and cultivation practices. There is increasing evidence that crop domestication can profoundly alter interactions among plants, herbivores, and their natural enemies. Overall, little is known about how these interactions are affected by domestication in the geographical ranges where these crops originate, where they are sympatric with the ancestral plant and share the associated arthropod community. In general, domestication consistently has reduced chemical resistance against herbivorous insects, improving herbivore and natural enemy performance on crop plants. More studies are needed to understand how changes in morphology and resistance-related traits arising from domestication may interact with environmental variation to affect species interactions across multiple scales in agroecosystems and natural ecosystems.

Watermelon origin solved with molecular phylogenetics including Linnaean material: another example of museomics

Type specimens are permanently preserved biological specimens that fix the usage of species names. This method became widespread from 1935 onwards and is now obligatory. We used DNA sequencing of types and more recent collections of wild and cultivated melons to reconstruct the evolutionary history of the genus Citrullus and the correct names for its species. We discovered that the type specimen of the name Citrullus lanatus, prepared by a Linnaean collector in South Africa in 1773, is not the species now thought of as watermelon. Instead, it is a representative of another species that is sister to C. ecirrhosus, a tendril-less South African endemic. The closest relative of the watermelon instead is a West African species. Our nuclear and plastid data furthermore reveal that there are seven species of Citrullus, not four as assumed. Our study implies that sweet watermelon originates from West, not southern Africa as previously believed, and that the South African citron melon has been independently domesticated. These findings affect and explain numerous studies on the origin of these two crops that led to contradictory results because of the erroneous merging of several distinct species.

The impact of domestication on resistance to two generalist herbivores across 29 independent domestication events

The domestication of crops is among the most important innovations in human history. Here, we test the hypothesis that cultivation and artificial selection for increased productivity of crops reduced plant defenses against herbivores. We compared the performance of two economically important generalist herbivores - the leaf-chewing beet armyworm (Spodoptera exigua) and the phloem-feeding green peach aphid (Myzus persicae) - across 29 crop species and their closely related wild relatives. We also measured putative morphological and chemical defensive traits and correlated them with herbivore performance. We show that, on average, domestication significantly reduced resistance to S. exigua, but not M. persicae, and that most independent domestication events did not cause differences in resistance to either herbivore. In addition, we found that multiple plant traits predicted resistance to S. exigua and M. persicae, and that domestication frequently altered the strength and direction of correlations between these traits and herbivore performance. Our results show that domestication can alter plant defenses, but does not cause strong allocation tradeoffs as predicted by plant defense theory. These results have important implications for understanding the evolutionary ecology of species interactions and for the search for potential resistance traits to be targeted in crop breeding.

Doubling down on genomes: polyploidy and crop plants

Polyploidy, or whole genome multiplication, is ubiquitous among angiosperms. Many crop species are relatively recent allopolyploids, resulting from interspecific hybridization and polyploidy. Thus, an appreciation of the evolutionary consequences of (allo)polyploidy is central to our understanding of crop plant domestication, agricultural improvement, and the evolution of angiosperms in general. Indeed, many recent insights into plant biology have been gleaned from polyploid crops, including, but not limited to wheat, tobacco, sugarcane, apple, and cotton. A multitude of evolutionary processes affect polyploid genomes, including rapid and substantial genome reorganization, transgressive gene expression alterations, gene fractionation, gene conversion, genome downsizing, and sub- and neofunctionalization of duplicate genes. Often these genomic changes are accompanied by heterosis, robustness, and the improvement of crop yield, relative to closely related diploids. Historically, however, the genome-wide analysis of polyploid crops has lagged behind those of diploid crops and other model organisms. This lag is partly due to the difficulties in genome assembly, resulting from the genomic complexities induced by combining two or more evolutionarily diverged genomes into a single nucleus and by the significant size of polyploid genomes. In this review, we explore the role of polyploidy in angiosperm evolution, the domestication process and crop improvement. We focus on the potential of modern technologies, particularly next-generation sequencing, to inform us on the patterns and processes governing polyploid crop improvement and phenotypic change subsequent to domestication.

Genetic diversity in Malus ×domestica (Rosaceae) through time in response to domestication

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PREMISE OF THE STUDY

Patterns of genetic diversity in domesticated plants are affected by geographic region of origin and cultivation, intentional artificial selection, and unintentional genetic bottlenecks. While bottlenecks are mainly associated with the initial domestication process, they can also affect diversity during crop improvement. Here, we investigate the impact of the improvement process on the genetic diversity of domesticated apple in comparison with other perennial and annual fruit crops.•

METHODS

Apple cultivars that were developed at various times (ranging from the 13th through the 20th century) and 11 of the 15 apple cultivars that are used for 90% of the apple production in the United States were surveyed for genetic diversity based on either 9 or 19 simple sequence repeats (SSRs). Diversity was compared using standard metrics and model-based approaches based on expected heterozygosity (He) at equilibrium. Improvement bottleneck data for fruit crops were also collected from the literature.•

KEY RESULTS

Domesticated apples showed no significant reduction in genetic diversity through time across the last eight centuries. Diversity was generally high, with an average He > 0.7 for apples from all centuries. However, diversity of the apples currently used for the bulk of commercial production was lower.•

CONCLUSIONS

The improvement bottleneck in domesticated apples appears to be mild or nonexistent, in contrast to improvement bottlenecks in many annual and perennial fruit crops, as documented from the literature survey. The low diversity of the subset of cultivars used for commercial production, however, indicates that an improvement bottleneck may be in progress for this perennial crop.