Domestication Process Research Articles

Comparative embryogenesis in ungulate domesticated species.

We compared embryogenesis of five species of domesticated even-toed and one odd-toed ungulate and used a phylogenetic framework to contextualize such comparison. Organ systems that occur relatively earlier in embryogenesis generally have more time to develop and therefore are found to be more mature at birth when compared to structures that appear later in development. We hypothesized that the less mature the animals' organs are at birth, the more they are susceptible to artificial selection. The horse had the most mature organs at birth, followed by cattle, reindeer, sheep/goat, and pig. This pattern of maturity could be observed almost during the entire development. Heterochronic shifts among species were observed only after fur starts to develop. Changes in the fur coloration are one of the first observable signs of domestication and the heterochrony of this trait may be related to the effects on neural crest-derived pigment cells by artificial selection. The six ungulate species also differ in the relative duration of their weaning period and the potential extent of its artificial shortening. We put all these traits in the context of their inherited evolutionary characteristics and artificial domestication process. Related to their altriciality, carnivoran domesticates, which also belong to Scrotifera, are less mature at birth than all domesticated ungulates. Although we detected clear character correlations to life history traits, it is impossible based on the present data, to trace specific exaptations to the domestication process. We hypothesize a deep time developmental penetration of adult characters into embryogenesis.

Diversity and Potential Function of the Bacterial Rhizobiome Associated to Physalis Ixocarpa Broth. in a Milpa System, in Michoacan, Mexico

Michoacan state has a long history in plant domestication’s. Physalis ixocarpa is a native plant that growth associated to maize crops from this region. Due to the domestication process includes the adaptation to environmental factors, we ask if (1) Does P. ixocarpa has the capacity of association with bacterial communities of the zone where it was domesticated? and (2) Does the rhizobiome of this plant can increase the potential functions in the soil? An experiment was established in a traditional milpa system. Samples of rhizobiome from corn, P. ixocarpa, P. philadelphica, and soil were sequenced using Next Generation Sequencing in the region 16S. The potential function, metabolic pathway reconstruction and participation of each bacteria genus was inferred using iVikodak platform. A total of 34 Phyla and 795 genera were identified. Purine metabolism’s was the principal function, where all rhizobiomes showed similar metabolic pathways. However, the difference among plant species is the participation of the distinct genera in the Purine metabolism. We conclude that the rhizobiome of P. ixocarpa maintains the capacity of bacterial association in the region and shows complementarity for the soil functions. Therefore, their utilization can be helpful in zones where the agricultural practices have degraded microbiological soil conditions.

Potential impact of Holocene climate changes on camel breeding practices of Neolithic pastoralists in the Central Asian drylands: A preliminary assessment

Archaeological findings from the Neolithic open-air location Ayakagytma ‘The Site’, situated in the south-eastern part of the Kyzyl-kum Desert in Uzbekistan, can potentially shed new light on the camel domestication process in the Central Asian drylands and help to connect it to regional changes of paleoclimate. Detailed analyses of composition and13C isotopic ratios of fatty acids performed on potsherds from an archaeological horizon of a Keltaminar culture dated at 3000–4000 cal BC combined with analogical analyses of modern camel and horse milk samples from Uzbekistan indicated a plausible possibility that camels were kept and milked by stockbreeders of Ayakagytma during this time period. The observed herding practices based almost exclusively on camel husbandry, as opposed to earlier more balanced herds of cattle, horses and camels, were probably an adaptation to climate transition from relatively humid to relatively dry, and the following changes in vegetation. Such climatic shift did not correspond with the general trend of Holocene moisture changes over the Westerlies-dominated Central Asia. However, it was in accordance with wet-to-dry climate transitions recorded in sediments of several lakes in the same region at around 4000 cal BP. The observed changes in Neolithic stockbreeding practices, as other inconsistencies in Holocene moisture evolution over a massive area of arid Central Asia, may have resulted from local manifestations of globally-forced climate changes and/or from local hydrographic alterations unrelated to paleoclimate.

Whole-genome resequencing of wild and cultivated cannabis reveals the genetic structure and adaptive selection of important traits

BackgroundCannabis is an important industrial crop species whose fibre, seeds, flowers and leaves are widely used by humans. The study of cannabinoids extracted from plants has been popular research topic in recent years. China is one of the origins of cannabis and one of the few countries with wild cannabis plants. However, the genetic structure of Chinese cannabis and the degree of adaptive selection remain unclear.ResultsThe main morphological characteristics of wild cannabis in China were assessed. Based on whole-genome resequencing SNPs, Chinese cannabis could be divided into five groups in terms of geographical source and ecotype: wild accessions growing in the northwestern region; wild accessions growing in the northeastern region; cultivated accessions grown for fibre in the northeastern region; cultivated accessions grown for seed in northwestern region, and cultivated accessions in southwestern region. We further identified genes related to flowering time, seed germination, seed size, embryogenesis, growth, and stress responses selected during the process of cannabis domestication. The expression of flowering-related genes under long-day (LD) and short-day (SD) conditions showed that Chinese cultivated cannabis is adapted to different photoperiods through the regulation of Flowering locus T-like (FT-like) expression.ConclusionThis study clarifies the genetic structure of Chinese cannabis and offers valuable genomic resources for cannabis breeding.

Pistachio (Pistacia vera L.) Domestication and Dispersal Out of Central Asia

The pistachio (Pistacia vera L.) is commercially cultivated in semi-arid regions around the globe. Archaeobotanical, genetic, and linguistic data suggest that the pistachio was brought under cultivation somewhere within its wild range, spanning southern Central Asia, northern Iran, and northern Afghanistan. Historically, pistachio cultivation has primarily relied on grafting, suggesting that, as with many Eurasian tree crops, domestication resulted from genetically locking hybrids or favored individuals in place. Plant domestication and dispersal research has largely focused on weedy, highly adaptable, self-compatible annuals; in this discussion, we present a case study that involves a dioecious long-lived perennial—a domestication process that would have required a completely different traditional ecological knowledge system than that utilized for grain cultivation. We argue that the pistachio was brought under cultivation in southern Central Asia, spreading westward by at least 2000 years ago (maybe a few centuries earlier to the mountains of modern Syria) and moved eastward only at the end of the first millennium AD. The seeds remain rare in archaeological sites outside its native range, even into the mid-second millennium AD, and may not have been widely cultivated until the past few hundred years.

A single-nucleus transcriptomic atlas of the dog hippocampus reveals the potential relationship between specific cell types and domestication.

The process of domestication has led to dramatic differences in behavioral traits between domestic dogs and gray wolves. Whole-genome research found that a class of putative positively selected genes were related to various aspects of learning and memory, such as long-term potentiation and long-term depression. In this study, we constructed a single-nucleus transcriptomic atlas of the dog hippocampus to illustrate its cell types, cell lineage and molecular features. Using the transcriptomes of 105 057 nuclei from the hippocampus of a Beagle dog, we identified 26 cell clusters and a putative trajectory of oligodendrocyte development. Comparative analysis revealed a significant convergence between dog differentially expressed genes (DEGs) and putative positively selected genes (PSGs). Forty putative PSGs were DEGs in glutamatergic neurons, especially in Cluster 14, which is related to the regulation of nervous system development. In summary, this study provides a blueprint to understand the cellular mechanism of dog domestication.

Unraveling Origin, History, Genetics, and Strategies for Accelerated Domestication and Diversification of Food Legumes.

Domestication is a dynamic and ongoing process of transforming wild species into cultivated species by selecting desirable agricultural plant features to meet human needs such as taste, yield, storage, and cultivation practices. Human plant domestication began in the Fertile Crescent around 12,000 years ago and spread throughout the world, including China, Mesoamerica, the Andes and Near Oceania, Sub-Saharan Africa, and eastern North America. Indus valley civilizations have played a great role in the domestication of grain legumes. Crops, such as pigeon pea, black gram, green gram, lablab bean, moth bean, and horse gram, originated in the Indian subcontinent, and Neolithic archaeological records indicate that these crops were first domesticated by early civilizations in the region. The domestication and evolution of wild ancestors into today’s elite cultivars are important contributors to global food supply and agricultural crop improvement. In addition, food legumes contribute to food security by protecting human health and minimize climate change impacts. During the domestication process, legume crop species have undergone a severe genetic diversity loss, and only a very narrow range of variability is retained in the cultivars. Further reduction in genetic diversity occurred during seed dispersal and movement across the continents. In general, only a few traits, such as shattering resistance, seed dormancy loss, stem growth behavior, flowering–maturity period, and yield traits, have prominence in the domestication process across the species. Thus, identification and knowledge of domestication responsive loci were often useful in accelerating new species’ domestication. The genes and metabolic pathways responsible for the significant alterations that occurred as an outcome of domestication might aid in the quick domestication of novel crops. Further, recent advances in “omics” sciences, gene-editing technologies, and functional analysis will accelerate the domestication and crop improvement of new crop species without losing much genetic diversity. In this review, we have discussed about the origin, center of diversity, and seed movement of major food legumes, which will be useful in the exploration and utilization of genetic diversity in crop improvement. Further, we have discussed about the major genes/QTLs associated with the domestication syndrome in pulse crops and the future strategies to improve the food legume crops.

Molecular genetic variation of animals and plants under domestication

Domesticated plants and animals played crucial roles as models for evolutionary change by means of natural selection and for establishing the rules of inheritance, originally proposed by Charles Darwin and Gregor Mendel, respectively. Here, we review progress that has been made during the last 35 y in unraveling the molecular genetic variation underlying the stunning phenotypic diversity in crops and domesticated animals that inspired Mendel and Darwin. We notice that numerous domestication genes, crucial for the domestication process, have been identified in plants, whereas animal domestication appears to have a polygenic background with no obvious “domestication genes” involved. Although model organisms, such as Drosophila and Arabidopsis, have replaced domesticated species as models for basic research, the latter are still outstanding models for evolutionary research because phenotypic change in these species represents an evolutionary process over thousands of years. A consequence of this is that some alleles contributing to phenotypic diversity have evolved by accumulating multiple changes in the same gene. The continued molecular characterization of crops and farm animals with ever sharper tools is essential for future food security.

Leaf trait covariation and controls on leaf mass per area (LMA) following cotton domestication.

The process of domestication has driven dramatic shifts in plant functional traits, including leaf mass per area (LMA). It remains unclear whether domestication has produced concerted shifts in the lower-level anatomical traits that underpin LMA and how these traits in turn affect photosynthesis. In this study we investigated controls of LMA and leaf gas exchange by leaf anatomical properties at the cellular, tissue and whole-leaf levels, comparing 26 wild and 31 domesticated genotypes of cotton (Gossypium). As expected, domesticated plants expressed lower LMA, higher photosynthesis and higher stomatal conductance, suggesting a shift towards the 'faster' end of the leaf economics spectrum. At whole-leaf level, variation in LMA was predominantly determined by leaf density (LD) both in wild and domesticated genotypes. At tissue level, higher leaf volume per area (Vleaf) in domesticated genotypes was driven by a simultaneous increase in the volume of epidermal, mesophyll and vascular bundle tissue and airspace, while lower LD resulted from a lower volume of palisade tissue and vascular bundles (which are of high density), paired with a greater volume of epidermis and airspace, which are of low density. The volume of spongy mesophyll exerted direct control on photosynthesis in domesticated genotypes but only indirect control in wild genotypes. At cellular level, a shift to larger but less numerous cells with thinner cell walls underpinned a lower proportion of cell wall mass, and thus a reduction in LD. Taken together, cotton domestication has triggered synergistic shifts in the underlying determinants of LMA but also photosynthesis, at cell, tissue and whole-leaf levels, resulting in a marked shift in plant ecological strategy.

Allele-specific knockouts reveal a role for apontic-like in the evolutionary loss of larval melanin pigmentation in the domesticated silkworm, Bombyx mori.

The domesticated silkworm, Bombyx mori, and its wild progenitor, B. mandarina, are extensively studied as a model case of the evolutionary process of domestication. A conspicuous difference between these species is the dramatic reduction in melanin pigmentation in both larval and adult B. mori. Here we evaluate the efficiency of CRISPR/Cas9-targeted knockouts of pigment-related genes as a tool to understand their potential contributions to domestication-associated melanin pigmentation loss in B. mori. To demonstrate the efficacy of targeted knockouts in B. mandarina, we generated a homozygous CRISPR/Cas9-targeted knockout of yellow-y. In yellow-y knockout mutants, black body colour became lighter throughout the larval, pupal and adult stages, confirming a role for this gene in melanin pigment formation. Further, we performed allele-specific CRISPR/Cas9-targeted knockouts of the pigment-related transcription factor, apontic-like (apt-like) in B. mori × B. mandarina F1 hybrid individuals which exhibit B. mandarina-like larval pigmentation. Knockout of the B. mandarina allele of apt-like in F1 embryos results in white patches on the dorsal integument of larvae, whereas corresponding knockouts of the B. mori allele consistently exhibit normal F1 larval pigmentation. These results demonstrate a contribution of apt-like to the evolution of reduced melanin pigmentation in B. mori. Together, our results demonstrate the feasibility of CRISPR/Cas9-targeted knockouts as a tool for understanding the genetic basis of traits associated with B. mori domestication.

Domestication and genetic characteristics of pig – a review

Pigs are one of the main types of livestock kept by humans because of their high reproductive system and the ability to survive in all kinds of conditions. Modern pigs have gone through a long history of domestication processes, ranging from migration, selection, adaptation, and other natural events. Important records of pig origins have divided the domestic pig population into two main groups namely Asian and European breeds. These two groups clearly separated about 58,000 years ago. In particular it is recorded that the European wild boar was domesticated around the 4th century BC. European pigs then got new genes since the introduction of the Asian pig which is thought to have occurred at the end of the 18th century. Domestication of pigs affects the genetic diversity of these animals which in turn will disrupt the availability of pig germplasm. However, the need for superior breeds with high productivity values will be indispensable given the increasing food supply for the community both in terms of food quality and quantity. This fulfilment is actually not just for a moment but in a very long and sustainable period, and the latter can only be fulfilled if the genetic resources of pigs are maintained through good gene conservation programs.Keywords: Pig, genetic diversity, domestication, livestock genetic conservation

Low Temperature Rather Than Nitrogen Application Mainly Modulates the Floral Initiation of Different Ecotypes of Rapeseed (Brassica napus L.)

Rapeseed has formed three ecological types, namely winter, semi-winter, and spring during the long domestication process. Different ecotypes have different low-temperature requirements for floral initiation. Rapeseed growth has a large demand for nitrogen, and the amount of nitrogen application significantly impacts the number of flowering. Meanwhile, the time of floral imitation determined the quantity of floral bud, the final number of pods, and yield of rapeseed. Therefore, it is of great significance to understand the regulation of temperature and nitrogen on floral initiation. This experiment selected representative semi-winter and spring rapeseed varieties to study the leaf’s soluble sugar and protein concentration under different nitrogen supplies and the transcriptome reactions to vernalization for spring and semi-winter varieties rapeseed in transition to floral initiation. The results showed that the soluble sugar content and carbon-to-nitrogen ratio changed due to the different growth processes and nitrogen application rates. The increase of the sugar content to a peak could be regarded as the signal to start floral initiation. Reducing the nitrogen application rate increased the peak of sugar content, but the effect on the appearance time of the peak was not obvious. Under normal (20–25 °C) and low temperatures (10–15 °C), the floral initiation time of spring variety “1358” showed no difference, nor did expression of hub gene SOC1, which is involved in the flowering regulation network. The semi-winter variety “Zhongshuang No. 11” did not commence floral initiation under normal temperature because of the lacking of vernalization requirement. Low temperature promoted the floral initiation of semi-winter variety mainly through the FLC, SOC1, and LFY signaling pathways, and the gibberellin also played a positive factor in this process. In essence, the present study provides valuable information on the gene expression differences of vernalization-driven floral transition for spring and semi-winter ecotypes of rapeseed when the photoperiod is not an unlimited factor.

Structural Polymorphisms of Chromosome 3Am Containing Lr63 Leaf Rust Resistance Loci Reflect the Geographical Distribution of Triticum monococcum L. and Related Diploid Wheats

Wheat is one of the world’s crucial staple food crops. In turn, einkorn wheat (Triticum monococcum L.) is considered a wild relative of wheat (Triticum aestivum L.) and can be used as a source of agronomically important genes for breeding purposes. Cultivated T. monococcum subsp. monococcum originated from T. monococcum subsp. aegilopoides (syn. T. boeticum). For the better utilization of valuable genes from these species, it is crucial to discern the genetic diversity at their cytological and molecular levels. Here, we used a fluorescence in situ hybridization toolbox and molecular markers linked to the leaf rust resistance gene Lr63 (located on the short arm of the 3Am chromosome—3AmS) to track the polymorphisms between T. monococcum subsp. monococcum, T. boeticum and T. urartu (A-genome donor for hexaploid wheat) accessions, which were collected in different regions of Europe, Asia, and Africa. We distinguished three groups of accessions based on polymorphisms of cytomolecular and leaf rust resistance gene Lr63 markers. We observed that the cultivated forms of T. monococcum revealed additional marker signals, which are characteristic for genomic alternations induced by the domestication process. Based on the structural analysis of the 3AmS chromosome arm, we concluded that the polymorphisms were induced by geographical dispersion and could be related to adaptation to local environmental conditions.

The Expression of Neogene TIGD3 that Derived from DNA Transposons in Colorectal Cancer Cell lines

DNA transposons are exposed to a molecular domestication process, which results in the formation of neogenes,which may play a role in human genetic instability. TIGD3 (Tigger-derived [TIGD] family of proteins) is one ofthese Neogene, and its role in the human genome is unknown.Aim: The expression of Neogene TIGD3 in colorectal cancer cell lines and its putative function in carcinogenesisare being investigated.Method: The protein expression of the TIGD3 gene was investigated using the western blot method in twelvecolorectal cancer cell lines (HCT116, SW48, LOVO, DLD1) that are microsatellite instable MSI, (SW480, SW620,HT29, LS123, COLO205, T84, SW403, SW1463) that are microsatellite stable MSS, and in healthy colon tissue as acontrol in our study.Results: The expression of the TIGD3 protein was found in all twelve colorectal cancer cell lines, with varyingdegrees of expression and numerous isoforms, which was not found in healthy colon tissue.Conclusion: There may be a link between colorectal cancer evolution or progression and TIGD3 gene expression.

Mutational load and deleterious mutations in goat genome from Kenya

Different domestication processes such as selection and effective population size are among other factors responsible for the accumulation of mutations in an animal. This study investigated the mutation load and accumulation of deleterious mutations in Kenyan goat populations using Single Nucleotide Polymorphism (SNP) data obtained from local (Galla = 12) and exotic (Saanen = 24, Alpine = 28, and Toggenburg = 30) goat genotypes. The SNP annotation was done on the ENSEMBLE goat (Capra hircus) using the Variant Effect Predictor (VEP). Sorting Intolerant from Tolerant (SIFT) was done on the annotated file using a score of > 0.01 to describe highly deleterious mutations. Biomart tool in the ENSEMBL goat C. hircus was used for Gene Ontology (GO) for the genes identified from highly deleterious mutations. The analysis disclosed no differences in mutation load among the studied genotypes. Overall, the synonymous mutations were in abundance compared to missense mutations, totaling 693 and 258 representing 1.01% and 0.37%, respectively. The calculated mutation load was similar (0.37) suggesting exposure of goats to similar domestication processes that are creating similar effects on the animal’s genome. Further analysis of the missense variants revealed 126 deleterious mutations and 132 tolerated mutations. A total of 111 genes were identified from the deleterious mutations and only 5 were among the highly deleterious mutations (SIFT score > 0.01) which include PROS1, EHBP1, LTN1, LRRN4, and FNDC3A. Gene Ontology describes these genes as responsible for different functions associated with animal reproduction, diseases, and memory. This study's results have confirmed the levels of mutation load and the presence of deleterious mutations in Kenyan goats. This can be used as a base to predict the future rate of mutation load to ensure better implementation of conservation programs to avoid an accumulation of deleterious mutations.

Morphogenetic diversity of the selected hatchery populations of an Indian major carp (Labeo rohita, Hamilton, 1822) in the Mymensingh region of Bangladesh

Environmental changes due to the domestication of wild population in hatchery conditions often lead to morphogenetic alterations in fish. Therefore, this study aimed to determine the genetic purity, demographic history, and population structure of Labeo rohita collected from three hatcheries in Bangladesh using a geometric morphometric approach in conjunction with mtDNA cyt b gene sequences and microsatellite markers. The geometric morphometric analysis revealed significant variation in centroid size (body size) among the different populations of L. rohita. However, MANCOVA and subsequent ANCOVA models showed no significant variation in body shape (relative wraps, RWs) among those populations. Both DNA-based techniques amplified all genotypes and revealed a high degree of genetic diversity across all populations. Clustering analyses based on the Neighbour-Joining (NJ) phylogenetic approach found that the hatchery populations have indisputably diverged from the wild populations. The study of haplotype networks, neutrality testing, and mismatch distributions revealed a complex population expansion pattern involving genetic introgression resulting from human translocation. This tendency is exacerbated further by anthropogenic factors, resulting in the loss of various alleles from hatchery populations. The unevenness of pair-wise FST and the hierarchical analysis of molecular variance of population structure showed a distinct variation between wild and hatchery populations. This genetic loss occurs due to improper domestication processes of the hatchery populations. Ignorance of appropriate hatchery procedures may lead to adverse selection by using poor seed leading to stock deterioration in the hatchery population. This study could help to establish appropriate breeding strategies and provide essential information for the genetic improvement program of L. rohita.

Grey wolf genomic history reveals a dual ancestry of dogs

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

Adaptation and biocultural conservation of traditional agroforestry systems in the Tehuacán Valley: access to resources and livelihoods strategies

Traditional agroforestry systems (TAFS) are important areas for conserving biodiversity, ecosystems benefits and biocultural heritage, outstandingly local knowledge, management techniques, and domestication processes. These systems have adapted to environmental, social, technological, and cultural changes throughout history. However, contemporary drastic socio-environmental changes as climate variability, economic inequality, migration, among others, have caused a productive crisis, with several consequences as productive land abandonment, threaten the sustainability of TAFS and vulnerating livelihoods. In such context, the question arises of what kind of adaptations are needed to face these changes, and how access to water and land, should be managed to improve adaptation of TAFS? The study analyzes TAFS in the Tehuacán Valley, a region with high biological and cultural diversity and early signs of agriculture in Mexico, where TAFS have remained active until present. The study analyzes the capacity of TAFS to conserve biodiversity and sustain local livelihoods, despite socio-environmental threats. It is based on a political ecology approach, which proposes that socio-ecological systems degradation is linked to unequal access to land and natural resources. Looking for an integral study of adaptations of TAFS to socio-environmental changes, this study combines qualitative and historical research methodology with quantitative methods evaluating plant diversity and spatial analysis. The study findings show that differentiated access to resources, water, land, and forest, is a key factor that limits adaptation of TAFS, impacting livelihood strategies, changing management patterns, and constraining social capacities for coping with socio-environmental changes. TAFS have significantly higher species richness than forests but lower diversity. The main contribution of the study is the methodological approach looking for an integral analysis of natural resources management and biocultural conservation in agroecosystems, and the identification of the unequal access to resources, as a keystone to understand and act for improving adaptive strategies of TAFS to socio-environmental changes.

A stepwise route to domesticate rice by controlling seed shattering and panicle shape

Asian rice (Oryza sativa L.) is consumed by more than half of the world's population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (Oryza rufipogon Griff.) acquired non-seed-shattering behavior, allowing humans to increase grain yield. Previous studies argued that a reduction in seed shattering triggered by the sh4 mutation led to increased yield during rice domestication, but our experiments using wild introgression lines show that the domesticated sh4 allele alone is insufficient for shattering loss in O. rufipogon. The interruption of abscission layer formation requires both sh4 and qSH3 mutations, demonstrating that the selection of shattering loss in wild rice was not as simple as previously suggested. Here we identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we further demonstrated that seed shattering alone did not significantly impact yield; rather, yield increases were observed with closed panicle formation controlled by SPR3 and further augmented by nonshattering, conferred by integration of sh4 and qSH3 alleles. Complementary manipulation of panicle shape and seed shattering results in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which together led to the loss of shattering.

Metabolomic Analysis Identifies Differences Between Wild and Domesticated Chili Pepper Fruits During Development (Capsicum annuum L.).

Capsicum spp. members are a rich source of specialized compounds due to their secondary metabolism. Some metabolic pathways have suffered modifications during the domestication process and improvement of agricultural traits. Here, we compared non-targeted LC–MS profiles from several areas: wild accessions (C. annuum L. var. glabriusculum), domesticated cultivars (C. annuum L.), and the F1 progeny of a domesticated, and a wild accession cross (in both directions) throughout seven stages of fruit development of chili pepper fruits. The main detected differences were in glycerophospholipid metabolism, flavone and flavonol biosynthesis, sphingolipid metabolism, and cutin biosynthesis. The domesticated group exhibited a higher abundance in 12′-apo-β-carotenal, among others capsorubin, and β-tocopherol. Palmitic acid and derivates, terpenoids, and quercitrin were prevalent in the wild accessions. F1 progeny showed a higher abundance of capsaicin, glycol stearate, and soyacerebroside I. This work supports evidence of the side-affectation of trait selection over the metabolism of chili pepper fruit development. Furthermore, it was also observed that there was a possible heterosis effect over the secondary metabolism in the F1 progeny.