The Puzzle of Rice Domestication

The origin of cultivated rice has puzzled plant biologists for decades. This is due, at least in part, to the complex evolutionary dynamics in rice cultivars and wild progenitors, particularly rapid adaptive differentiation and continuous gene flow within and between cultivated and wild rice. The long-standing controversy over single versus multiple and annual versus perennial origins of cultivated rice has been brought into shaper focus with the rapid accumulation of genetic and phylogenetic data. Molecular phylogenetic analyses revealed ancient genomic differentiation between rice cultivars, suggesting that they were domesticated from divergent wild populations. However, the recently cloned domestication gene sh4, responsible for the reduction of grain shattering from wild to cultivated rice, seems to have originated only once. Herein, we propose two models to reconcile apparently conflicting evidence regarding rice domestication. The snowoballing model considers a single origin of cultivated rice. In this model, a core of critical domestication alleles was fixed in the founding cultivar and then acted to increase the genetic diversity of cultivars through hybridization with wild populations. The combination model considers multiple origins of cultivated rice. In this model, Initial cultivars were domesticated from divergent wild populations and fixed different sets of domestication alleles. Subsequent crosses among these semi-domesticated cultivars resulted in the fixation of a similar set of critical domestication alleles in the contemporary cultivars. In both models, introgression has played an important role in rice domestication. Recent and future introgression of beneficial genes from the wild gene pool through conventional and molecular breeding programs can be viewed as the continuation of domestication.     

Microsatellites uncover extraordinary diversity in native American land races and wild populations of cultivated sunflower

The contemporary oilseed sunflower (Helianthus annuus L.) gene pool is a product of multiple breeding and domestication bottlenecks. Despite substantial phenotypic diversity, modest differences in molecular genetic diversity have been uncovered in anciently and recently domesticated sunflowers. The paucity of molecular marker polymorphisms in early analyses led to the hypothesis of a single domestication origin. Phylogenetic analyses were performed on 47 domesticated and wild germplasm accessions using 122 microsatellite loci distributed throughout the sunflower genome. Extraordinary allelic diversity was found in the Native American land races and wild populations, and progressively less allelic diversity was found in germplasm produced by successive cycles of domestication and breeding. Of 1,341 microsatellite alleles, 489 were unique to land races, exotic domesticates and wild populations, whereas only 15 were unique to elite inbred lines. The number of taxon-specific alleles was 35-fold greater among wild populations (26.27) than elite inbred lines (0.75). Microsatellite genotyping uncovered the possibility of multiple domestication origins. Land races domesticated by Native Americans of the southwestern US (Hopi and Havasupai) formed a clade independent of land races domesticated by Native Americans of the Great Plains and eastern US (Arikara and Seneca). Predictably, domestication and breeding have ratcheted genetic diversity down in sunflower. The contemporary oilseed sunflower gene pool, while not imperiled, could profit from an infusion of novel alleles from the reservoir of latent genetic diversity present in wild populations and Native American land races.     

Islands and streams: clusters and gene flow in wild barley populations from the Levant

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter‐mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analysing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication.     

Wild to crop introgression and genetic diversity in Lima bean (Phaseolus lunatus L.) in traditional Mayan milpas from Mexico

Despite the evolutionary, ecological and economic importance of introgression between a domesticated species and its wild relatives in centers of diversity and domestication, the role of traditional farmers in this process has received limited attention. In the Yucatan Peninsula, the region of Mexico that has the greatest amount of domesticated varieties of Lima bean, wild populations grow sympatrically with conspecific varieties, allowing the Mayan farmer to act directly on introgressed seed. We used 11 microsatellite loci to assess levels of introgression in three wild-domesticated complexes of Lima bean from the Yucatan Peninsula and analyze its impact on the genetic diversity of this crop. structure and InStruct analyses showed similar results. The Instruct analysis indicated that the complex with the lowest level of introgression was one where the farmer actively selected against wild plants and introgressed seed. In contrast, the complex with the highest level of introgression was one where the farmer has been consciously selecting a weedy morphotype for 15 years and has already incorporated it into his diet. Genetic diversity of the domesticated pool was higher in the complex with the higher level of introgression. This study showed that farmers have an important role in limiting or favoring the wild to crop introgression and influencing the levels of genetic diversity in their domesticated pool. Only when traditional farmers’ knowledge is taken into account can we correctly understand the dynamics, generation and maintenance of genetic diversity of the landraces in the centers of diversity and domestication.     

Impact of selection and breeding on the genetic diversity in Douglas-fir

Genetic changes following domestication of Douglas-fir were studied using isozyme data derived from two generations of seed orchards and their 49 wild progenitor populations. In addition, the breeding, production, and infusion populations used in the seed orchards were compared to their wild counterparts. Several parameters of gene diversity were measured (number of alleles per locus N _a, per cent of polymorphic loci PLP, and expected heterozygosity H, and population divergence D). These measures were similar or higher in the domesticated populations compared to their natural progenitors, indicating that early selection and breeding of a highly polymorphic species does not significantly reduce genetic variation. The two generations of seed orchards also did not differ, indicating that genetic variation may remain stable over future generations of forest plantations. Interestingly, compared to the natural populations, heterozygosity was higher in the seed orchards, probably due to pooling of widely distributed natural populations; however, rare localized or private alleles seemed to be less frequent in the domesticated populations. Differentiation values were not significant between the first generation orchards and the natural populations, but significant differences were observed between the second generation orchards and the wild progenitor populations, probably due to the interbreeding that forms the advanced generation seed orchards.     

Genetic Relationship in Cicer Sp. Expose Evidence for Geneflow between the Cultigen and Its Wild Progenitor

There is a debate concerning mono- or poly-phyletic origins of the Near Eastern crops. In parallel, some authors claim that domestication was not possible within the natural range of the wild progenitors due to wild alleles flow into the nascent crops. Here we address both, the mono- or poly-phyletic origins and the domestications within or without the natural range of the progenitor, debates in order to understand the relationship between domesticated chickpea (Cicer arietinum L.) and its wild progenitor (C. reticulatum Ladizinsky) with special emphasis on its domestication centre in southeastern Turkey. A set of 103 chickpea cultivars and landraces from the major growing regions alongside wild accessions (C. reticulatum, C. echinospermum P.H Davis and C. bijugum K.H. Rech) sampled across the natural distribution range in eastern Turkey were genotyped with 194 SNPs markers. The genetic affinities between and within the studied taxa were assessed. The analysis suggests a mono-phyletic origin of the cultigen, with several wild accession as likely members of the wild stock of the cultigen. Clear separation between the wild and domesticated germplasm was apparent, with negligible level of admixture. A single C. reticulatum accession shows morphological and allelic signatures of admixture, a likely result of introgression. No evidence of geneflow from the wild into domesticated germplasm was found. The traditional farming systems of southeaster Turkey are characterized by occurrence of sympatric wild progenitor—domesticated forms of chickpea (and likewise cereals and other grain legumes). Therefore, both the authentic crop landraces and the wild populations native to the area are a unique genetic resource. Our results grant support to the notion of domestication within the natural distribution range of the wild progenitor, suggesting that the Neolithic domesticators were fully capable of selecting the desired phenotypes even when facing rare wild-domesticated introgression events.     

Genetic structure and relationships within and between cultivated and wild sorghum (<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench) in Kenya as revealed by microsatellite markers

Understanding the extent and partitioning of diversity within and among crop landraces and their wild/weedy relatives constitutes the first step in conserving and unlocking their genetic potential. This study aimed to characterize the genetic structure and relationships within and between cultivated and wild sorghum at country scale in Kenya, and to elucidate some of the underlying evolutionary mechanisms. We analyzed at total of 439 individuals comprising 329 cultivated and 110 wild sorghums using 24 microsatellite markers. We observed a total of 295 alleles across all loci and individuals, with 257 different alleles being detected in the cultivated sorghum gene pool and 238 alleles in the wild sorghum gene pool. We found that the wild sorghum gene pool harbored significantly more genetic diversity than its domesticated counterpart, a reflection that domestication of sorghum was accompanied by a genetic bottleneck. Overall, our study found close genetic proximity between cultivated sorghum and its wild progenitor, with the extent of crop-wild divergence varying among cultivation regions. The observed genetic proximity may have arisen primarily due to historical and/or contemporary gene flow between the two congeners, with differences in farmers’ practices explaining inter-regional gene flow differences. This suggests that deployment of transgenic sorghum in Kenya may lead to escape of transgenes into wild-weedy sorghum relatives. In both cultivated and wild sorghum, genetic diversity was found to be structured more along geographical level than agro-climatic level. This indicated that gene flow and genetic drift contributed to shaping the contemporary genetic structure in the two congeners. Spatial autocorrelation analysis revealed a strong spatial genetic structure in both cultivated and wild sorghums at the country scale, which could be explained by medium- to long-distance seed movement.     

Multiple domestication events explain the origin of Gossypium hirsutum landraces in Mexico

Several Mesoamerican crops constitute wild‐to‐domesticated complexes generated by multiple initial domestication events, and continuous gene flow among crop populations and between these populations and their wild relatives. It has been suggested that the domestication of cotton (Gossypium hirsutum) started in the northwest of the Yucatán Peninsula, from where it spread to other regions inside and outside of Mexico. We tested this hypothesis by assembling chloroplast genomes of 23 wild, landraces, and breeding lines (transgene‐introgressed and conventional). The phylogenetic analysis showed that the evolutionary history of cotton in Mexico involves multiple events of introgression and genetic divergence. From this, we conclude that Mexican landraces arose from multiple wild populations. Our results also revealed that their structural and functional chloroplast organizations had been preserved. However, genetic diversity decreases as a consequence of domestication, mainly in transgene‐introgressed (TI) individuals (π = 0.00020, 0.00001, 0.00016, 0, and 0, of wild, TI‐wild, landraces, TI‐landraces, and breeding lines, respectively). We identified homologous regions that differentiate wild from domesticated plants and indicate a relationship among the samples. A decrease in genetic diversity associated with transgene introgression in cotton was identified for the first time, and our outcomes are therefore relevant to both biosecurity and agrobiodiversity conservation.     

Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild‐to‐weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed‐shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.     

Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA

Background

Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity.

Methodology/Main Findings

Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ∼2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar.

Conclusions/Significance

These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection.     

Diversity and evolution of rice progenitors in Australia

In the thousands of years of rice domestication in Asia, many useful genes have been lost from the gene pool. Wild rice is a key source of diversity for domesticated rice. Genome sequencing has suggested that the wild rice populations in northern Australia may include novel taxa, within the AA genome group of close (interfertile) wild relatives of domesticated rice that have evolved independently due to geographic separation and been isolated from the loss of diversity associated with gene flow from the large populations of domesticated rice in Asia. Australian wild rice was collected from 27 sites from Townsville to the northern tip of Cape York. Whole chloroplast genome sequences and 4,555 nuclear gene sequences (more than 8 Mbp) were used to explore genetic relationships between these populations and other wild and domesticated rices. Analysis of the chloroplast and nuclear data showed very clear evidence of distinctness from other AA genome Oryza species with significant divergence between Australian populations. Phylogenetic analysis suggested the Australian populations represent the earliest‐branching AA genome lineages and may be critical resources for global rice food security. Nuclear genome analysis demonstrated that the diverse O. meridionalis populations were sister to all other AA genome taxa while the Australian O. rufipogon‐like populations were associated with the clade that included domesticated rice. Populations of apparent hybrids between the taxa were also identified suggesting ongoing dynamic evolution of wild rice in Australia. These introgressions model events similar to those likely to have been involved in the domestication of rice.     

Genetic mapping of a new race specific resistance allele effective to Puccinia hordei at the Rph9/Rph12locus on chromosome 5HL in barley

Background

Tea is one of the most popular beverages in the world. Many species in the Thea section of the Camellia genus can be processed for drinking and have been domesticated. However, few investigations have focused on the genetic consequence of domestication and geographic origin of landraces on tea plants using credible wild and planted populations of a single species. Here, C. taliensis provides us with a unique opportunity to explore these issues.

Results

Fourteen nuclear microsatellite loci were employed to determine the genetic diversity and domestication origin of C. taliensis, which were represented by 587 individuals from 25 wild, planted and recently domesticated populations. C. taliensis showed a moderate high level of overall genetic diversity. The greater reduction of genetic diversity and stronger genetic drift were detected in the wild group than in the recently domesticated group, indicating the loss of genetic diversity of wild populations due to overexploitation and habitat fragmentation. Instead of the endangered wild trees, recently domesticated individuals were used to compare with the planted trees for detecting the genetic consequence of domestication. A little and non-significant reduction in genetic diversity was found during domestication. The long life cycle, selection for leaf traits and gene flow between populations will delay the emergence of bottleneck in planted trees. Both phylogenetic and assignment analyses suggested that planted trees may have been domesticated from the adjacent central forest of western Yunnan and dispersed artificially to distant places.

Conclusions

This study contributes to the knowledge about levels and distribution of genetic diversity of C. taliensis and provides new insights into genetic consequence of domestication and geographic origin of planted trees of this species. As an endemic tea source plant, wild, planted and recently domesticated C. taliensis trees should all be protected for their unique genetic characteristics, which are valuable for tea breeding.     

Tagging the signatures of domestication in common bean (Phaseolus vulgaris) by means of pooled DNA samples

BACKGROUND AND AIMS: The main aim of this study was to use an amplified fragment length polymorphism (AFLP)-based, large-scale screening of the whole genome of Phaseolus vulgaris to determine the effects of selection on the structure of the genetic diversity in wild and domesticated populations. METHODS: Using pooled DNA samples, seven each of wild and domesticated populations of P. vulgaris were studied using 2506 AFLP markers (on average, one every 250 kb). About 10 % of the markers were also analysed on individual genotypes and were used to infer allelic frequencies empirically from bulk data. In both data sets, tests were made to determine the departure from neutral expectation for each marker using an F(ST)-based method. KEY RESULTS: The most important outcome is that a large fraction of the genome of the common bean (16 %; P < 0.01) appears to have been subjected to effects of selection during domestication. Markers obtained in individual genotypes were also mapped and classified according to their proximities to known genes and quantitative trait loci (QTLs) of the domestication syndrome. Most of the markers that were found to be potentially under the effects of selection were located in the proximity of previously mapped genes and QTLs related to the domestication syndrome. CONCLUSIONS: Overall, the results indicate that in P. vulgaris a large portion of the genome appears to have been subjected to the effects of selection, probably because of linkage to the loci selected during domestication. As most of the markers that are under the effects of selection are linked to known loci related to the domestication syndrome, it is concluded that population genomics approaches are very efficient in detecting QTLs. A method based on bulk DNA samples is presented that is effective in pre-screening for a large number of markers to determine selection signatures.     

A draft genome of sweet cherry (Prunus avium L.) reveals genome‐wide and local effects of domestication

Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety “Big Star*” and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome‐wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.     

Genetics and phylogenetics of rice domestication

With genetically divergent cultivars and ecologically distinct wild progenitors, rice has posed a great challenge to the genetic and phylogenetic studies of the origin and evolution of crop species. A growing body of phylogenetic evidence suggested that the diverged genomic backgrounds of indica and japonica rice cultivars were derived independently from genetically distinct wild populations. However, a domestication gene, sh4, which was responsible for the reduction of grain shattering, seems to have originated only once, and it is now fixed in both cultivars. Two models have been proposed to reconcile these data. Whereas the 'combination model' emphasizes the importance of early introgression between independently domesticated cultivars, the 'snowballing model' emphasizes the importance of introgression from local populations of wild species into an ancestral domesticated population. In either case, the domestication of rice was a dynamic process.     

中华猕猴桃和美味猕猴桃自然居群遗传结构及其种间杂交渐渗

 利用9对SSR引物对中华猕猴桃（Actinidia chinensis）和美味猕猴桃（A. deliciosa）两近缘种的5个同域分布复合体和各自1个非同域分布居群进行了遗传多样性、居群遗传结构的分析以及种间杂交渐渗的探讨。结果表明：1）两物种共有等位基因比例高达81.13%,物种特有等位基因较少（中华猕猴桃：13.27%,美味猕猴桃：5.61%）,但共享等位基因表型频率在两近缘种间存在差异,而且与各同域复合体中两物种样本的交错程度或间距存在关联;2）两种猕猴桃均具有极高遗传多样性,美味猕猴桃的遗传多样性（H_o＝0 .749, PIC＝0.818）都略高于中华猕猴桃（H_o＝0.686,PIC＝0.799）;3）两猕 猴桃物种均具有较低的Nei’s居群遗传分化度,但AMOVA分析结果揭示种内异域居群间（F_ST=0.091 5）和同域复合体种间（F_ST=0.111 5）均存在一定程度的遗传分化;中华猕猴桃居群遗传分化（G_ST=0.086; F_ST=0.212 1）高于美味猕猴桃（G_ST= 0.080;F_ST=0.142 0）;4）同域分布复合体两物种间的遗传分化（G_ST=0.020）低于物种内异域居群间的遗传分化（中华猕猴桃：G_ST=0.086; 美味猕猴桃：G_ST=0.080）,同域复合体物种间的基因流（N_m＝7.89 -29.75）远远高于 同种异域居群间（中华猕猴桃：N_m =2.663; 美味猕猴桃：N_m=2.880）; 5）居群UPGMA聚类揭示在同一地域的居群优先聚类,个体聚类结果显示多数个体聚在各自居群组内,但各地理居群并不按地理距离的远近聚类,这与Mantel相关性检测所揭示的居群间遗传距离与地理距离没有显著性相关的结果一致。进一步分析表明两种猕猴桃的遗传多样性和居群遗传结构不仅受其广域分布、远交、晚期分化等生活史特性的影响,同时还与猕猴桃的染色体基数高 (x=29)、倍性复杂和种间杂交等因素密切相关,其中两种猕猴桃的共享祖先多态性和同域分布种间杂交基因渗透对两猕猴桃的居群遗传结构产生了重要影响。     

Chloroplast DNA variation confirms a single origin of domesticated sunflower (Helianthus annuus L.)

Although sunflower was long thought to be the product of a single domestication in what is now the east-central United States, recent archaeological and genetic evidence have suggested the possibility of an independent origin of domestication, perhaps in Mexico. We therefore used hypervariable chloroplast simple-sequence repeat markers to search for evidence of a possible Mexican origin of domestication. This work resulted in the identification of 45 chloroplast haplotypes from 26 populations across the range of wild sunflower as well as 3 haplotypes from 15 domesticated lines, representing both primitive and improved cultivars. The 3 domesticated haplotypes were characterized by 1 primary haplotype (found at a frequency of 6.7% in the wild) as well as 2 rare haplotypes, which are most likely the products of mutation or introgression. One of these rare haplotypes was not observed in the wild, bringing the total number of haplotypes identified to 46. A principal coordinate analysis revealed the presence of 3 major haplotype clusters, one of which contained the primary domesticated haplotype, the 2 rare domesticated variants, as well as haplotypes found across much of the range of wild sunflower. The Mexican haplotypes, on the other hand, fell well outside of this cluster. Although our data do not provide insight into the specific location of sunflower domestication, the relative rarity of the primary domesticated haplotype in the wild, combined with the dissimilarity between this haplotype and those found in the Mexican populations surveyed, provides further evidence that the extant domesticated sunflowers are the product of a single domestication event somewhere outside of Mexico.     

Genomic screening for artificial selection during domestication and improvement in maize

BACKGROUND: Artificial selection results in phenotypic evolution. Maize (Zea mays L. ssp. mays) was domesticated from its wild progenitor teosinte (Zea mays subspecies parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties. The landraces provided the genetic material for modern plant breeders to select improved varieties and inbred lines by enhancing traits controlling agricultural productivity and performance. Artificial selection during domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. SCOPE: This review is a summary of research on the identification and characterization by population genetics approaches of genes affected by artificial selection in maize. CONCLUSIONS: Analysis of DNA sequence diversity at a large number of genes in a sample of teosintes and maize inbred lines indicated that approx. 2 % of maize genes exhibit evidence of artificial selection. The remaining genes give evidence of a population bottleneck associated with domestication and crop improvement. In a second study to efficiently identify selected genes, the genes with zero sequence diversity in maize inbreds were chosen as potential targets of selection and sequenced in diverse maize landraces and teosintes, resulting in about half of candidate genes exhibiting evidence for artificial selection. Extended gene sequencing demonstrated a low false-positive rate in the approach. The selected genes have functions consistent with agronomic selection for plant growth, nutritional quality and maturity. Large-scale screening for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown. These approaches should also be applicable to other domesticated species if specific demographic conditions during domestication exist.     

Introgression and the fate of domesticated genes in a wild mammal population

When domesticated species are not reproductively isolated from their wild relatives, the opportunity arises for artificially selected variants to be re‐introduced into the wild. However, the evolutionary consequences of introgression of domesticated genes back into the wild are poorly understood. By combining high‐throughput genotyping with 25 years of long‐term ecological field data, we describe the occurrence and consequences of admixture between a primitive sheep breed, the free‐living Soay sheep of St Kilda, and more modern breeds. Utilizing data from a 50 K ovine SNP chip, together with forward simulations of demographic scenarios, we show that admixture occurred between Soay sheep and a more modern breed, consistent with historical accounts, approximately 150 years ago. Haplotype‐sharing analyses with other breeds revealed that polymorphisms in coat colour and pattern in Soay sheep arose as a result of introgression of genetic variants favoured by artificial selection. Because the haplotypes carrying the causative mutations are known to be under natural selection in free‐living Soay sheep, the admixture event created an opportunity to observe the outcome of a ‘natural laboratory’ experiment where ancestral and domesticated genes competed with each other. The haplotype carrying the domesticated light coat colour allele was favoured by natural selection, while the haplotype associated with the domesticated self coat pattern allele was associated with decreased survival. Therefore, we demonstrate that introgression of domesticated alleles into wild populations can provide a novel source of variation capable of generating rapid evolutionary changes.     

Inference of domestication history and differentiation between early‐ and late‐flowering varieties in pearl millet

Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa. Farmers usually grow varieties with different cycle lengths and complementary functions in Sahelian agrosystems. Both the level of genetic differentiation of these varieties and the domestication history of pearl millet have been poorly studied. We investigated the neutral genetic diversity and population genetic structure of early‐ and late‐flowering domesticated and wild pearl millet populations using 18 microsatellite loci and 8 nucleotide sequences. Strikingly, early‐ and late‐flowering domesticated varieties were not differentiated over their whole distribution area, despite a clear difference in their isolation‐by‐distance pattern. Conversely, our data brought evidence for two well‐differentiated genetic pools in wild pearl millet, allowing us to test scenarios with different numbers and origins of domestication using approximate Bayesian computation (ABC). The ABC analysis showed the likely existence of asymmetric migration between wild and domesticated populations. The model choice procedure indicated that a single domestication from the eastern wild populations was the more likely scenario to explain the polymorphism patterns observed in cultivated pearl millet.