Domestication Process Research Articles

Saccharomyces cerevisiae wine strains show a wide range of competitive abilities and differential nutrient uptake behavior in co-culture with S. kudriavzevii

The wine industry has implemented complex starters with multiple yeast species as an efficient method to improve certain wine properties. Strains’ competitive fitness becomes essential for its use in such cases. In the present work, we studied this trait in 60 S. cerevisiae strains from different origins, co-inoculated with a S. kudriavzevii strain, and confirmed it to be associated with the strains' origin. To gather deeper knowledge about the characteristics of strains with highly competitive ability versus the rest, microfermentations using representative strains from each group were performed and the carbon and nitrogen sources uptake was analysed. Our results demonstrate that despite wine strains being the subclade with the highest competitive ability, they present a wide range of behaviors as well as nutrient uptake dynamics, which points to a heterogeneous nature of domestication processes. An interesting strategy was observed in the highly competitive strains (GRE and QA23), the nitrogen sources uptake in the competition was accelerated and the sugar fermentation was slowing despite the fermentation finish at the same time. Therefore, this competition study, using particular combinations of strains, expands the knowledge in the field of the usage of mixed starters in wine manufactured products.

Elephants as an animal model for self-domestication

Humans are unique in their sophisticated culture and societal structures, their complex languages, and their extensive tool use. According to the human self-domestication hypothesis, this unique set of traits may be the result of an evolutionary process of self-induced domestication, in which humans evolved to be less aggressive and more cooperative. However, the only other species that has been argued to be self-domesticated besides humans so far is bonobos, resulting in a narrow scope for investigating this theory limited to the primate order. Here, we propose an animal model for studying self-domestication: the elephant. First, we support our hypothesis with an extensive cross-species comparison, which suggests that elephants indeed exhibit many of the features associated with self-domestication (e.g., reduced aggression, increased prosociality, extended juvenile period, increased playfulness, socially regulated cortisol levels, and complex vocal behavior). Next, we present genetic evidence to reinforce our proposal, showing that genes positively selected in elephants are enriched in pathways associated with domestication traits and include several candidate genes previously associated with domestication. We also discuss several explanations for what may have triggered a self-domestication process in the elephant lineage. Our findings support the idea that elephants, like humans and bonobos, may be self-domesticated. Since the most recent common ancestor of humans and elephants is likely the most recent common ancestor of all placental mammals, our findings have important implications for convergent evolution beyond the primate taxa, and constitute an important advance toward understanding how and why self-domestication shaped humans' unique cultural niche.

Plant domestication shapes rhizosphere microbiome assembly and metabolic functions

BackgroundThe rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments.ResultsOur results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status.ConclusionsOur results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture.CBzZNC2FEDswGcHctbDosaVideo

The Domestication and Dispersal of Large-Fruiting Prunus spp.: A Metadata Analysis of Archaeobotanical Material

The Prunus genus contains many of the most economically significant arboreal crops, cultivated globally, today. Despite the economic significance of these domesticated species, the pre-cultivation ranges, processes of domestication, and routes of prehistoric dispersal for all of the economically significant species remain unresolved. Among the European plums, even the taxonomic classification has been heavily debated over the past several decades. In this manuscript, we compile archaeobotanical evidence for the most prominent large-fruiting members of Prunus, including peach, apricot, almonds, sloes, and the main plum types. By mapping out the chronology and geographic distributions of these species, we are able to discuss aspects of their domestication and dispersal more clearly, as well as identify gaps in the data and unanswered questions. We suggest that a clearer understanding of these processes will say a lot about ancient peoples, as the cultivation of delayed return crops is an indicator of a strong concept of land tenure and the specialization of these cultivation strategies seems to be tied to urbanism and reliable markets. Likewise, the evolution of domestication traits in long-generation perennials, especially within Rosaceae, represents awareness of grafting and cloning practices.

The next era of crop domestication starts now

Current food systems are challenged by relying on a few input-intensive, staple crops. The prioritization of yield and the loss of diversity during the recent history of domestication has created contemporary crops and cropping systems that are ecologically unsustainable, vulnerable to climate change, nutrient poor, and socially inequitable. For decades, scientists have proposed diversity as a solution to address these challenges to global food security. Here, we outline the possibilities for a new era of crop domestication, focused on broadening the palette of crop diversity, that engages and benefits the three elements of domestication: crops, ecosystems, and humans. We explore how the suite of tools and technologies at hand can be applied to renew diversity in existing crops, improve underutilized crops, and domesticate new crops to bolster genetic, agroecosystem, and food system diversity. Implementing the new era of domestication requires that researchers, funders, and policymakers boldly invest in basic and translational research. Humans need more diverse food systems in the Anthropocene—the process of domestication can help build them.

Qualitative aspects of grunts vary with pigs' mental states

Studying human-animal interactions in domestic species and how they affect the establishment of a positive Human-Animal Relationship (HAR) may help us improve animal welfare and better understand the evolution of interspecific interactions associated with the domestication process. Understanding and describing the quality of an HAR requires information on several aspects of the animal biology and emotional states (social, spatial and postural behaviours, physiological and cognitive states). Growing evidence shows that acoustic features of animal vocalisations may be indicators of emotional states. Here, we tested the hypothesis that the quality of vocal expression may indicate the quality of HAR. At weaning, 30 piglets were positively handled by an experimenter who talked to and physically interacted with them three times a day, while 30 other piglets only received the contact necessary for proper husbandry. After two weeks, we recorded the behaviours and vocalisations produced in the presence of the static experimenter for five minutes. We repeated this test two weeks later, after a conditioning period during which human presence with additional positive contact was used as a reward for all piglets. We hypothesized this conditioning period would lead to a positive human-piglet relationship for all piglets. As expected, piglets that were positively handled at weaning expressed a higher attraction toward the experimenter, and, after the conditioning, piglets that were not positively handled at weaning expressed a similar level of attraction than the positively handled ones. Piglets positively handled at weaning generally produced shorter grunts than the other ones. However the latter expressed more flexibility in call structure when vocalising close to a human, with a decrease of grunt duration and an increase in pitch, frequency range and noisiness in their grunt. This differential effect of proximity between groups of piglets was attenuated after the conditioning during a standard reunion with a static human but remained over time when the human was providing additional positive contacts. Results suggest that first, changes in vocal structure are consistent with indicators of positive states in the presence of a human. Second, increasing familiarity and proximity between a human and a pig may induce changes in the acoustic structure of its grunts. Third, a human providing additional positive contacts triggers more changes in vocalisation structure than by their presence only. We show that vocalisation structure may allow us to assess the quality of human-pig relationship.

Restructuring plant types for developing tailor-made crops.

Plants have adapted to different environmental niches by fine-tuning the developmental factors working together to regulate traits. Variations in the developmental factors result in a wide range of quantitative variations in these traits that helped plants survive better. The major developmental pathways affecting plant architecture are also under the control of such pathways. Most notable are the CLAVATA-WUSCHEL pathway regulating shoot apical meristem fate, GID1-DELLA module influencing plant height and tillering, LAZY1-TAC1 module controlling branch/tiller angle and the TFL1-FT determining the floral fate in plants. Allelic variants of these key regulators selected during domestication shaped the crops the way we know them today. There is immense yield potential in the 'ideal plant architecture' of a crop. With the available genome-editing techniques, possibilities are not restricted to naturally occurring variations. Using a transient reprogramming system, one can screen the effect of several developmental gene expressions in novel ecosystems to identify the best targets. We can use the plant's fine-tuning mechanism for customizing crops to specific environments. The process of crop domestication can be accelerated with a proper understanding of these developmental pathways. It is time to step forward towards the next-generation molecular breeding for restructuring plant types in crops ensuring yield stability.

Domestication and microbiome succession may drive pathogen spillover.

Emerging infectious diseases have posed growing medical, social and economic threats to humanity. The biological background of pathogen spillover or host switch, however, still has to be clarified. Disease ecology finds pathogen spillovers frequently but struggles to explain at the molecular level. Contrarily, molecular biological traits of host-pathogen relationships with specific molecular binding mechanisms predict few spillovers. Here we aim to provide a synthetic explanation by arguing that domestication, horizontal gene transfer even between superkingdoms as well as gradual exchange of microbiome (microbiome succession) are essential in the whole scenario. We present a new perspective at the molecular level which can explain the observations of frequent pathogen spillover events at the ecological level. This proposed rationale is described in detail, along with supporting evidence from the peer-reviewed literature and suggestions for testing hypothesis validity. We also highlight the importance of systematic monitoring of virulence genes across taxonomical categories and in the whole biosphere as it helps prevent future epidemics and pandemics. We conclude that that the processes of domestication, horizontal gene transfer and microbial succession might be important mechanisms behind the many spillover events driven and accelerated by climate change, biodiversity loss and globalization.

Eating smart: Free-ranging dogs follow an optimal foraging strategy while scavenging in groups

Foraging and acquiring of food is a delicate balance between managing the costs (both energy and social) and individual preferences. Previous research on solitarily foraging free-ranging dogs showed that they prioritise the nutritionally highest valued food, but do not ignore other less valuable food either, displaying typical scavenger behaviour. We conducted a similar experiment on 136 groups of dogs with the same set-up to see the change in foraging strategies, if any, under the influence of social cost like intra-group competition. We found multiple differences between the strategies of dogs foraging alone versus in groups with competition playing an implicit role in the dogs’ decision making when foraging in groups. Dogs continually assessed and evaluated the available resources in a “patch,” transitioning from random foraging to systematic foraging with time and more information. Dogs in groups used an, “eat first, sample afterwards” strategy whereas individual dogs sampled thoroughly before eating. Additionally, dogs in groups were quicker and more likely to respond to the experimental set-up and eat from it. The dogs adjusted their behaviour in terms of effort and time allocated according to the quality of the “patch.” Foraging in groups also provided benefits of reduced individual vigilance. The various decisions and choices made lend support to the optimal foraging theory wherein the dogs harvested the nutritionally richest patch possible with the least risk and cost involved but were willing to compromise if that was not possible. This underscores the cognitive, quick decision-making abilities and adaptable behaviour of these dogs, which is likely to have influenced the process of dog domestication.

Artificial Cultivation Changes Foliar Endophytic Fungal Community of the Ornamental Plant Lirianthe delavayi.

Many wild ornamental plant species have been introduced to improve the landscape of cities; however, until now, no study has been performed to explore the composition and function of foliar endophytes associated with cultivated rare plants in cities after their introduction. In this study, we collected the leaves of the healthy ornamental plant Lirianthe delavayi from wild and artificially cultivated habitats in Yunnan and compared their diversity, species composition, and functional predictions of their foliar endophytic fungal community based on high-throughput sequencing technology. In total, 3125 ASVs of fungi were obtained. The alpha diversity indices of wild L. delavayi populations are similar to those of cultivated samples; however, the species compositions of endophytic fungal ASVs were significantly varied in the two habitats. The dominant phylum is Ascomycota, accounting for more than 90% of foliar endophytes in both populations; relatively, artificial cultivation trends to increase the frequency of common phytopathogens of L. delavayi, such as Alternaria, Erysiphe. The relative abundance of 55 functional predictions is different between wild and cultivated L. delavayi leaves (p < 0.05); in particular, chromosome, purine metabolism, and peptidases are significantly increased in wild samples, while flagellar assembly, bacterial chemotaxis, and fatty acid metabolism are significantly enhanced in cultivated samples. Our results indicated that artificial cultivation can greatly change the foliar endophytic fungal community of L. delavayi, which is valuable for understanding the influence of the domestication process on the foliar fungal community associated with rare ornamental plants in urban environments.

Historical Evolution and Multidimensional Characterisation of the Butia Palm Landscape: A Comprehensive Conservation Approach

The Butia odorata palm grove in southeast Uruguay forms a particular landscape of the Pampa biome, which has been inhabited and transformed since the early Holocene. The forms and meanings of this contemporary landscape are the result of the historical interaction between culture and nature. The conservation of its natural and cultural heritage has been compromised by anthropic activities, leading to conservation proposals from different disciplinary perspectives that are partial and do not consider the landscape’s integrity. In this article, we propose a comprehensive approach, integrating the ecological, cultural and socioeconomic aspects through a historical look at the domestication process of this landscape. This approach is based on a transdisciplinary narrative aimed at generating a multidimensional and diachronic characterisation of the palm grove landscape on which to base a participatory definition of the most appropriate instrument for conservation through sustainable use.

Differential defensive and nutritional traits among cultivated tomato and its wild relatives shape their interactions with a specialist herbivore.

Cultivated tomato presented lower constitutive volatiles, reduced morphological and chemical defenses, and increased leaf nutritional quality that affect its resistance against the specialist herbivore Tuta absoluta compared to its wild relatives. Plant domestication process has selected desirable agronomic attributes that can both intentionally and unintentionally compromise other important traits, such as plant defense and nutritional value. However, the effect of domestication on defensive and nutritional traits of plant organs not exposed to selection and the consequent interactions with specialist herbivores are only partly known. Here, we hypothesized that the modern cultivated tomato has reduced levels of constitutive defense and increased levels of nutritional value compared with its wild relatives, and such differences affect the preference and performance of the South American tomato pinworm, Tuta absoluta-an insect pest that co-evolved with tomato. To test this hypothesis, we compared plant volatile emissions, leaf defensive (glandular and non-glandular trichome density, and total phenolic content), and nutritional traits (nitrogen content) among the cultivated tomato Solanum lycopersicum and its wild relatives S. pennellii and S. habrochaites. We also determined the attraction and ovipositional preference of female moths and larval performance on cultivated and wild tomatoes. Volatile emissions were qualitatively and quantitatively different among the cultivated and wild species. Glandular trichomes density and total phenolics were lower in S. lycopersicum. In contrast, this species had a greater non-glandular trichome density and leaf nitrogen content. Female moths were more attracted and consistently laid more eggs on the cultivated S. lycopersicum. Larvae fed on S. lycopersicum leaves had a better performance reaching shorter larval developmental times and increasing the pupal weight compared to those fed on wild tomatoes. Overall, our study documents that agronomic selection for increased yields has altered the defensive and nutritional traits in tomato plants, affecting their resistance to T. absoluta.

Crop domestication disrupts intercropping benefits: A case study from barley-faba bean mixture under contrasting P inputs.

How crop domestication mediates root functional traits and trait plasticity in response to neighboring plants is unclear, but it is important for selecting potential species to be grown together to facilitate P uptake. We grew two barley accessions representing a two-stage domestication process as a sole crop or mixed with faba bean under low and high P inputs. We analyzed six root functional traits associated with P acquisition and plant P uptake in five cropping treatments in two pot experiments. The spatial and temporal patterns of root acid phosphatase activity were characterized in situ with zymography at 7, 14, 21, and 28 days after sowing in a rhizobox. Under low P supply, wild barley had higher total root length (TRL), specific root length (SRL), and root branching intensity (RootBr) as well as higher activity of acid phosphatase (APase) in the rhizosphere, but lower root exudation of carboxylates and mycorrhizal colonization (MC), relative to domesticated barley. In response to neighboring faba bean, wild barley exhibited larger plasticity in all root morphological traits (TRL, SRL, and RootBr), while domesticated barley showed greater plasticity in root exudates of carboxylates and colonization by mycorrhiza. Wild barley with greater root morphology-related trait plasticity was a better match with faba bean than domesticated barley, indicated by higher P uptake benefits in wild barley/faba bean than domesticated barley/faba bean mixtures under low P supply. Our findings indicated that the domestication of barley disrupts the intercropping benefits with faba bean through the shifts of root morphological traits and their plasticity in barley. Such findings provide valuable information for barley genotype breeding and the selection of species combinations to enhance P uptake.

The seed sector development in low-income countries: Lessons from the Malawi seed sector policy process

IntroductionExternal conditionalities have shaped public policy development in borrowing nations. This has been through top-down policy support programs, an example being the policy reforms under the structural adjustment program. Under the seed sector reforms Malawi committed to the Southern Africa Development Community and the Common Market for Eastern and Southern Africa harmonized seed regulations technical agreements.MethodsTo contribute to the debate, we analyzed the Malawi seed sector policy process by investigating three questions: What were the leading events? Who were the stakeholders involved, and their roles? Which factors influenced the policy process? Qualitative tools were employed based on policy process theory using the Kaleidoscope Model. We used stakeholder inception, planning, feedback workshops, and key informant interviews (N = 17). This data was complemented by grey literature as secondary information. Snowball sampling was used to identify key informant interview participants based on the saturation principle. Narrative analysis focusing on content, structure, and dialogic context was used.ResultsOur results show a strong external influence on the seed sector policy process. This began after independence when development partners supported the establishment of the public agricultural research system to improve production for food security and export. Failure to achieve the earlier objectives resulted in economic reforms aimed at private sector-led seed sector development based on market-oriented policies. The increase in the private sector's role called for adopting and enacting regulatory policies and legislation that used policy transfer theory. International financial institutions, multinational companies, and regional economic communities led this process. Our evidence suggests that the civil society community in Malawi contested the policies for not recognizing farmers' rights. This affected the domestication process of the harmonized seed regulations technical agreements.DiscussionTherefore, we recommend critical consideration and embracing of existing domestic social, political, and technical conditions to support economic policy reforms. This would help reduce unintended consequences and improve inclusivity. Governments may need to play an interlocutory role for the various actors in the policy domain during the domestication process.

The city from the point of view of children: social inequalities in representing and using urban public spaces

This paper was written under the research project CRiCity: “Children and their Right to the City: Tackling urban inequity through the participatory design of child-friendly cities” developed in Lisbon and Porto and funded by the Portuguese Foundation for Science and Technology (FCT) through national funds (PTDC/SOC-SOC/30415/2017). We focus on two case-studies developed in Porto. Our aim is to present some of the findings of the focus groups and drawing activities developed with children in two institutions. During this research, it was evident that children from middle and high classes are more subjected to institutionalization, domestication and hyper-protection processes than those from lower social classes. Also, we conclude that the phenomena of insularization and specialization contributes to aggravating restrictions on public spaces by producing forms of socio-spatial segregation depending not only on age, but also on class and social status.

A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes.

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, from which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, and 14,707 multiallelic variations with precise breakpoints were discovered. The SV spectrum is characterized by an excess of derived insertions compared to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep breeds worldwide. A novel 168-bp insertion in the 5' untranslated region (5' UTR) of HOXB13 is found at high frequency in long-tailed sheep. Further genome-wide association study and gene expression analyses suggest that this mutation is causative for the long-tail trait. In summary, we have developed a panel of high-quality de novo assemblies and present a catalog of structural variations in sheep. Our data capture abundant candidate functional variations that were previously unexplored and provide a fundamental resource for understanding trait biology in sheep.

Domestication of Bileh Fish Rasbora sp. Origin of Aceh Waters Through Different Feed Therapy

Domestication is the process of taming fish from the wild to the aquaculture environment. There are 3 stages of the domestication process, namely: taming/adapting to the aquaculture environment, seeking fish to grow, and seeking fish to reproduce. Bileh fish can already be adapted to aquaculture containers, which is the first stage of the domestication process. However, information on suitable feed for fish growth is still limited. The aim of this study was to determine the effect of different feeding on the growth of bileh fish reared in controlled containers. The research method was experimental and used a completely randomized design (CRD), which consisted of 4 treatments (P) with 3 replications. The treatments given were artificial feed (P1), artemia (P2), rotifer (P3) and daphnia (P4). The research phase included preparation of containers, collection of bileh fish, experimental feed, maintenance, and data collection. Parameters taken and evaluated included: specific growth rate (SGR), absolute length growth (ALG), and survival rate (SR). The data were processed and analyzed with statistics (Anova). The results of statistical analysis showed that feed treatment had a significant effect on SGR (P<0.05), but had no significant effect on ALG and SR (P>0.05). The best treatment was P1 (artificial feeding) with an SGR value of 0.91%/day, ALG of 1.03 cm and SR of 100%.

Genetic changes in the genus Vitis and the domestication of vine.

The genus Vitis belongs to the Vitaceae family and is divided into two subgenera: Muscadinia and Vitis, the main difference between these subgenera being the number of chromosomes. There are many hypotheses about the origin of the genus, which have been formed with archaeological studies and lately with molecular analyses. Even though there is no consensus on the place of origin, these studies have shown that grapes have been used by man since ancient times, starting later on its domestication. Most studies point to the Near East and Greece as the beginning of domestication, current research suggests it took place in parallel in different sites, but in all cases Vitis vinifera (L.) subsp. sylvestris [Vitis vinifera (L.) subsp. sylvestris (Gmelin) Hagi] seems to be the species chosen by our ancestors to give rise to the now known Vitis vinifera (L.) subsp. vinifera [=sativa (Hegi)= caucasica (Vavilov)]. Its evolution and expansion into other territories followed the formation of new empires and their expansion, and this is where the historical importance of this crop lies. In this process, plants with hermaphrodite flowers were preferentially selected, with firmer, sweeter, larger fruits of different colors, thus favoring the selection of genes associated with these traits, also resulting in a change in seed morphology. Currently, genetic improvement programs have made use of wild species for the introgression of disease resistance genes and tolerance to diverse soil and climate environments. In addition, the mapping of genes of interest, both linked to agronomic and fruit quality traits, has allowed the use of molecular markers for assisted selection. Information on the domestication process and genetic resources help to understand the gene pool available for the development of cultivars that respond to producer and consumer requirements.

Selection signature analysis reveals RDH5 performed key function in vision during sheep domestication process.

As one of the most successful domesticated animals in the Neolithic age, sheep gradually migrated all over the world with human activities. During the domestication process, remarkable changes have taken place in morphology, physiology, and behavior, resulting in different breeds with different characters via artificial and natural selection. However, the genetic background responsible for these phenotypic variations remains largely unclear. Here, we used whole genome resequencing technology to compare and analyze the genome differences between Asiatic mouflon wild sheep (Ovis orientalis) and Hu sheep (Ovis aries). A total of 755 genes were positively selected in the process of domestication and selection, and the genes related to sensory perception had directional evolution in the autosomal region, such as OPRL1, LEF1, TAS1R3, ATF6, VSX2, MYO1A, RDH5, and some novel genes. A missense mutation of c.T722C/p.M241T in exon 4 of RDH5 existing in sheep were found, and the T allele was completely fixed in Hu sheep. In addition, the mutation with the C allele reduced the retinol dehydrogenase activity encoding by RDH5, which can impair retinoic acid metabolism and further influenced the visual cycle. Overall, our results showed significant enrichment for positively selected genes involved in sensory perception development during sheep domestication; RDH5 and its variants may be related to the retinal degeneration in sheep. We infer that the wild sheep ancestors with weaker visual sensitivity were weeded out by humans, and the mutation was selective, swept by the dual pressures of natural and artificial selection.

Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population.

As one of the world's top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica (CSA) remain unclear. We newly generated 94 Camellia sinensis (C. sinensis) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies.