Transcriptome and Metabolite Insights into Domestication Process of Cultivated Barley in China

The domestication process of cultivated barley in China remains under debate because of the controversial origins of barley. Here, we analyzed transcriptomic and non-targeted metabolic data from 29 accessions together with public resequencing data from 124 accessions to explore the domestication process of cultivated barley in China (Cb-C). These analyses revealed that both Cb-C and Tibetan wild barley (Wb-T) were the descendants of wild barley from the Near East Fertile Crescent (Wb-NE), yielding little support for a local origin of Wb-T. Wb-T was more likely an intermediate in the domestication process from Wb-NE to Cb-C. Wb-T contributed more genetically to Cb-C than Wb-NE, and was domesticated into Cb-C about 3300 years ago. These results together seem to support that Wb-T may be a feralized or hybrid form of cultivated barley from the Near East Fertile Crescent or central Asia. Additionally, the metabolite analysis revealed divergent metabolites of alkaloids and phenylpropanoids and these metabolites were specifically targeted for selection in the evolutionary stages from Wb-NE to Wb-T and from Wb-T to Cb-C. The key missense SNPs in the genes HORVU6Hr1G027650 and HORVU4Hr1G072150 might be responsible for the divergence of metabolites of alkaloids and phenylpropanoids during domestication. Our findings allow for a better understanding of the domestication process of cultivated barley in China.

How to Tame

As our social worlds increasingly shift online, many of the technologies people encounter are mediated by algorithms. Algorithms have become deeply embedded into people's online lives, often working to tailor and personalize their routine encounters with the world. How does one domesticate, or make one's own, an algorithmic system? One of the goals as people adopt new technologies is to weave them into their everyday routines, establishing a pattern of use in order to make that technology their own. In this paper we focus on people's experiences domesticating the short-form video sharing application, TikTok. Through an interview study with 16 LGBTQ+ TikTok users, we explore how people's routine experiences with TikTok's For You Page algorithm influence and inform their domestication process. We first highlight people's motivations for adopting TikTok and the challenges they encounter in this initial acquisition phase of domestication. After adopting the platform, we discuss the challenges people experience across the final three phases of domestication: objectification, incorporation, and conversion. We find that though they enjoy TikTok, our participants feel that they are never fully able to domesticate TikTok. As they are never able to fully control their digital selves, and thus integrate it into their routine lives, TikTok is in constant misalignment with their personal moral economy. We discuss the implications of domesticating algorithmic systems, examining the questions of whose values shape the moral economy created by and through people's uses of algorithmic systems, and the impact of nostalgia on the domestication process.

Limited Genetic Diversity and High Differentiation in Angelica Dahurica Resulted by Domestication: Insights to Breeding and Conservation

Background： Angelica dahurica, belonging to the Apiaceae family, whose dry root is a famous traditional Chinese medicine named as “Bai zhi”. There are two cultivars (A. dahurica cv. ‘Hangbaizhi’ and A. dahurica cv. ‘Qibaizhi’), which have been domesticated for thousands of years. Long term artificial selection has led to great changes in root phenotypes of the two cultivars, and also decreased their adaptability to environment. We proposed hypothesis that the cultivars may lose some genetic diversity and highly differentiate from wild A. dahurica during the domestication process. However, few studies have been carried out on how domestication affects the genetic variation of this species. Here, we accessed the levels of genetic variation and differentiation within and between wild A. dahurica and its cultivars using 12 SSR markers. Results: The results revealed that the genetic diversity of the cultivars was much lower than that of wild A. dahurica, and A. dahurica cv. ‘Qibaizhi’ had lower genetic diversity compared to A. dahurica cv. ‘Hangbaizhi’. AMOVA analysis showed significant genetic differentiation between the wild and cultivated A. dahurica, and between A. dahurica cv. ‘Hangbaizhi’ and A. dahurica cv. ‘Qibaizhi’. The results of Bayesian, UPGMA, NJ and PcoA clustering analysis indicated that all 15 populations were assigned to two genetic clusters corresponding to the wild and cultivated resources. Bayesian clustering analysis further divided the cultivated resources into two sub-clusters corresponding to the two cultivars. Conclusions：Our study suggests that domestication process is likely the major factor resulting in the loss of genetic diversity in cultivated A. dahurica and significant genetic differentiation from the wild resources due to founder effect and/or artificially directional selections. This large-scale analysis of population genetics could provide valuable information for genetic resources conservation and breeding programs of Angelica dahurica.

Genetic Introgression Between Different Groups Reveals the Differential Process of Asian cultivated Rice

Genetic introgression plays an important role in the domestication of crops. The Asian cultivate rice consists of two major subspecies, they are indica and japonica. There are already many reports about existence of genetic introgression between the two subspecies. However, those studies often use few limited markers to characterize the genetic introgression that exists in some specific small populations. In this study we use the genome wide variation data of Asia cultivated rice to investigate their genetic introgression on the whole genome level. We detect a total of 13 significantly high introgression loci between the tropical japonica and indica population. Two different methods are used to identify the genetic introgression regions. For most of the detected introgression regions they generally get consistent results. Some previous known introgression genes are detected in the identified introgression loci, such as heat resistance gene TT1 and GLW7. The biological functions for these genetic introgression regions are annotated by the published QTL mapping results. We find that genetic introgression plays an important role in both the determination of the phenotype and the domestication process of different groups. Our study also provides useful information and resources for the study of rice gene function and domestication process.

Evaluation of Seed Dormancy, One of the Key Domestication Traits in Chickpea

Legume seed dormancy has been altered during the domestication process, resulting in non-dormant seeds with a testa that is readily permeable for water. Ultimately, this provides fast and uniform germination, in contrast to dormant seeds of the wild progenitor. To date, germination and seed dormancy were studied mostly in relation to two types of cultivated chickpea: kabuli and desi. We studied seed dormancy, from physiological and anatomical perspectives, in chickpea crops and compared cultivated chickpeas to the wild chickpea progenitor and set of recombinant inbred lines (RIL). There was significant difference in the macrosclereid length of parental genotypes. Cultivated chickpea (C. arietinum, ICC4958) had mean of 125 µm, while wild C. reticulatum (PI48977) had a mean of 165 µm. Histochemical staining of the seed coat also showed differences, mainly in terms of Sudan Red detection of lipidic substances. Imbibition and germination were tested and several germination coefficients were calculated. Cultivated chickpea seeds imbibed readily within 24 h, while the germination percentage of wild chickpea at various times was 36% (24 h), 46% (48 h), 60% (72 h) and reached 100% only after 20 days. RIL lines showed a broader distribution. This knowledge will ultimately lead to the identification of the underlying molecular mechanism of seed dormancy in chickpea, as well as allowing comparison to phylogenetically related legumes, such as pea, lentil and faba bean, and could be utilized in chickpea breeding programs.

Plant remains unearthed at the Donghulin site in Beijing: discussion on results of flotation

A number of charred plant seeds were recovered from the Donghulin site by means of flotation. The site is located in suburban Beijing and dates from 11,000 to 9000 BP. A total of 14 charred grains of foxtail millet have been collected and identified as of the domesticated species (Setaria italica) according to morphological analysis. One grain of broomcorn millet was also identified. These are the earliest domesticated millet grains recovered by flotation, providing crucial archaeological evidence for understanding the timing, locations, and processes of millet domestication. Moreover, the charred seeds of Setaria viridis provide important clues for exploring the wild ancestral plants of foxtail millet and the domestication process. The results of flotation at the Donghulin site are important for understanding the origins of dryland agriculture in North China, which was predominated by millet farming.

The Taming of Psidium guajava: Natural and Cultural History of a Neotropical Fruit

Guava (Psidium guajava L., Myrtaceae) is a Neotropical fruit that is widely consumed around the world. However, its evolutionary history and domestication process are unknown. Here we examine available ecological, taxonomic, genetic, archeological, and historical evidence about guava. Guava needs full sunlight, warm temperatures, and well-distributed rainfall throughout the year to grow, but tolerates drought. Zoochory and anthropochory are the main forms of dispersal. Guava’s phylogenetic relationships with other species of the genus Psidium are unclear. A group of six species that share several morphological characteristics are tentatively accepted as the Psidium guajava complex. DNA analyses are limited to the characterization of crop genetic diversity within localities and do not account for possible evolutionary and domestication scenarios. A significant amount of archeological information exists, with a greater number and older records in South America than in Mesoamerica, where there are also numerous historical records. From this information, we propose that: (1) the guava ancestor may have originated during the Middle or Late Miocene, and the savannas and semi-deciduous forests of South America formed during the Late Pleistocene would have been the most appropriate ecosystems for its growth, (2) the megafauna were important dispersers for guava, (3) dispersal by humans during the Holocene expanded guava’s geographic range, including to the southwestern Amazonian lowlands, (4) where its domestication may have started, and (5) with the European conquest of the Neotropics, accompanied by their domestic animals, new contact routes between previously remote guava populations were established. These proposals could direct future research on the evolutionary and domestication process of guava.

The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns

Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well-understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and nine wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a global reduction of diversity during the domestication process, although several genes also showed patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyzes revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totaling 2,449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that the combined and intricated effects of the domestication and improvement processes do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome. Overall, these analyzes pave the way toward the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.

Fruit Quality Characters of Myrtle (Myrtus communis L.) Selections: Review of a Domestication Process

Interest in myrtle (Myrtus communis L.) by food, cosmetics, and pharmaceutic industries generated the integration of biomasses harvested from wild populations as raw materials with yields of cultivated orchards. The domestication process is reviewed considering shoot, fruit, and leaf biometric characters of selections obtained in three steps of the program. The first step started in Sardinia (Italy) in 1995 by the analysis of wild germplasm variability. Seventy accessions were the object of the first studied population of mother plants. Agamic propagation tests, as well quality evaluations of fruit and leaves, were integrated into the first step. In the second step, a field of comparison of forty-two agamically propagated cultivars functional to biomass production and to food uses was planted and evaluated for phenotypic characters. In the third step, a new population of twenty selections was obtained by open cross-pollination of some of the cultivars and further phenotypic selection in seedling population. In this review, the three populations are compared for biometric shoot, leaves and fruit characters, in order to verify the pressure of domestication process on these traits. Wild populations showed high variability only partially used during the first step, while the hybridization may create new variability for use in the genetic improvement of myrtle.

Evolution under domestication of correlated characters in populations of Stenocereus stellatus (Pfeiff.) Riccob., under different forms of management in central Mexico: genetic diversity, damage, and defense mechanisms

Across the process of domestication, human selection produces changes in target attributes as well as changes that are not necessarily desired by humans due to pleiotropic or linked genes. In this paper we addressed, correlated changes between genetic diversity, damage level, defense mechanisms (resistance and tolerance), and fitness due to the domestication process of Stenocereus pruinosus (Otto ex Pfeiff.) Buxbaum and Stenocereus stellatus (Pfeiff.) Riccobono, an endemic columnar cactus of south-central Mexico. One hundred eighty individuals of S. stellatus from wild, in situ managed, and cultivated populations of Valle de Tehuacán and Mixteca Baja, Puebla, were sampled, and attributes including damage level, defense mechanisms and fitness (number of fruits) were measured. The DNA of 176 individuals was extracted to amplify and analyze five microsatellites in order to estimate genetic diversity and structure. As expected, cultivated populations showed a significantly higher damage level, as well as lower resistance and genetic diversity. Depending on the form of management, correlations between genetic diversity and the rest of the attributes exhibited different patterns. In wild populations, genetic diversity was positively correlated with damage and negatively with resistance; in situ managed populations exhibited the opposite pattern, and in cultivated populations, no correlations were found between these attributes. We propose a hypothetic model of human selection to explain the variation in these correlations. No differences in genetic diversity and tolerance were detected between regions; however, the populations of Valle de Tehuacán exhibited more damage and more resistance. In both regions, populations showed a positive correlation between fitness and resistance and a negative correlation between damage and resistance, suggesting the existence of a defense mechanism to ensure fitness. Also, non-regional differentiation suggests an eventual gene flow due to pollinators, human movement of branches, or a common ancestry before the domestication process.