Domestication Process Research Articles

Changes in microbial community structure and co-metabolism during the domestication of ofloxacin-degrading bacteria

BackgroundOfloxacin (OFL) is stable and difficult to degrade. It has been detected in water, soil, and plants throughout the world. This study domesticated OFL-contaminated livestock manure soil with simplified carbon sources to identify flora capable of effectively degrading OFL. The changes in the structural composition and diversity of the microbial community and the functional abundance of the soil flora were analyzed by metagenome sequencing technology. The Biolog-ECO microplate method was used to study the utilization of 31 different carbon sources by selected bacteria and to identify the best co-metabolized carbon source for degradation.ResultsAmino acid carbon sources were more likely to cause significant changes in community structures with increasing OFL concentrations during the acclimation stage. The abundance of Sphingobacterium decreased from 69.23% to 9.84%, while Alcaligenes increased from 0.27% to 62.79%, and Stenotrophomonas increased from 11.63% to 33.33%, becoming the dominant genus. The results suggested that Stenotrophomonas and Alcaligenes were potential candidate bacteria for the degradation of quinolone antibiotics, such as OFL. Compared with the first stage of acclimation, there was an 87% increase (the concentration was 30 mg·L−1) in the OFL degradation rate by functional flora obtained by gradient acclimation, and the functional abundance of the microbial community also increased and stabilized with the depth of the domestication process. The most significant changes in membrane transport were observed in the functional abundance of the microbial community, and it was found that itaconic acid, Tween 80, and L-aspartic acid could increase the biomass of the microbial community under OFL stress.ConclusionSignificant changes in the bacterial composition and functional abundance of the microbial community resulted from the addition of amino acid carbon sources, together with the OFL concentration. Functional flora resulting from domestication were better able to degrade OFL. The addition of a co-metabolic carbon source significantly enhanced the biomass of the functional flora. In this study, co-metabolism was performed by adding specific carbon sources, thus achieving metabolic diversity of functional flora and ultimately efficient biodegradation of OFL. This was an important discovery in the field of microbial remediation of environmental contamination.

One- and Two-Month-Old Dog Puppies Exhibit Behavioural Synchronization with Humans Independently of Familiarity

Behavioural synchronization is a widespread skill in social species as it helps increase group cohesion among individuals. Such a phenomenon is involved in social interactions between conspecifics as well as between individuals from different species. Most importantly, familiarity and affiliation between interacting partners influence the degree of behavioural synchronization they would exhibit with each other. For example, in human-dog dyads, the more a dog is affiliated with its human partner, the more it behaves in a synchronous way with them. However, little is known about the ontogeny of such a behaviour, especially from an interspecific perspective. The aim of the present study was thus to investigate the existence and modalities of activity synchrony, a type of behavioural synchronization, between humans and puppies. To do so, we observed 29 dog puppies interacting with two different humans (familiar and unfamiliar experimenters). Puppy movements and general activity in relation to the human ones were observed. Results evidenced that puppies did exhibit locomotor synchrony with humans, but familiarity did not affect its degree. It is the first time that activity synchrony with human walk is evidenced in puppies, highly suggesting that dogs' ability to behave in synchronization with humans seems to be genetically selected through the process of domestication, while the effect of familiarity on it might develop later during the individual ontogeny.

Comparative metabolic analysis of the adaptive Candida tropicalis to furfural stress response

The novel tolerant strain Candida tropicalis Y31-N (Y31-N) with the high tolerance against furfural was obtained by the continuous domestication processes from the parent strain Candida tropicalis Y-3 (Y-3). The xylitol yield was increased by more than 84.8% with the Y31-N, as well as the furfural consumption at about five-times rate than the Y-3. The Y31-N was able to control the cells membrane fluidity by regulating the composition of the fatty acids in cells, thus maintaining the integrity of cells membrane function to resist furfural stress, and could produce more ATP and NAD(P)H rapidly through the metabolic rearrangement to alleviate the furfural stress, compared to the Y-3. Moreover, several genes related to trehalose synthesis, GABA metabolism and NADPH production were verified to be essential for resistance to furfural by single-gene knockout. It provided a broader understanding of the mechanisms of furfural tolerance and prospective evidence for the further metabolic engineering.

Halloween and Valentine’s Day in Slovakia: new holidays or new opportunities for celebration?

This study deals with Halloween and Valentine’s Day in Slovakia from the perspective of the eventisation theory elaborated on by Winfried Gebhardt (2000), which reflects on internal as well as external changes in the field of holidays in modern societies and seeks to elucidate the cultural dimension of the processes of individualisation and pluralisation during the late-modernity period. The authors explore these two holidays as global phenomena with a focus on their holiday practice, i.e. on the ways of celebrating and spending holidays. At the same time, they analyse the historical and social processes related to the transformations of Europe’s and Slovakia’s holiday culture since the end of the 20th century. On this basis, they present research materials that clarify these processes of domestication as well as the ways of celebrating Halloween and Valentine’s Day in Slovakia. The empirical data form the basis for formulating findings on the ways of spending these two “new” holidays and their relationship to the process of eventisation of the holiday culture.

Variations in genetic diversity in cultivated Pistacia chinensis.

Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure of P. chinensis and to investigate the influence of intraspecific gene flow on the process of domestication and the diversification of varieties. We investigated the genetic structure of P. chinensis, as well as evolution and introgression in the subpopulations, through analysis of the plastid and nuclear genomes of 39P. chinensis individuals from across China. High levels of variation were detected in the P. chinensis plastome, and 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified. Phylogenetic analysis and population structure using the plastome dataset supported five clades of P. chinensis. Population structure analysis based on the nuclear SNPs showed two groups, clearly clustered together, and more than a third of the total individuals were classified as hybrids. Discordance between the plastid and nuclear genomes suggested that hybridization events may have occurred between highly divergent samples in the P. chinensis subclades. Most of the species in the P. chinensis subclade diverged between the late Miocene and the mid-Pliocene. The processes of domestication and cultivation have decreased the genetic diversity of P. chinensis. The extensive variability and structuring of the P. chinensis plastid together with the nuclear genomic variation detected in this study suggests that much unexploited genetic diversity is available for improvement in this recently domesticated species.

IDENTIFIKASI FITOPLANKTON PADA PERUT IKAN SELINCAH (Belontia hasselti) DARI RAWA MENTUKUL DI KABUPATEN BANGKA SELATAN

The Selincah fish (Belontia hasselti) is a local Indonesian fish that is widely consumed and has the potential to become ornamental fish. This fish must be domesticated to suppress its exploitation from natural catches. The domestication process requires biological information including eating habits. For this reason, in this study, the identification of phytoplankton contained in the stomach contents of the agile fish was carried out. Fish samples were obtained from Rawa Metukul, South Bangka Regency. The types of phytoplankton in the stomach and intestines of lively fish are the classes Bacillariophyceae, Chlorophyceae, Cyanophyceae, Chlorophyceae, Chrysophyceae, Chrysophyceae. The most dominant species were found in the Chlorophyceae class with an Index of preponderance value of 42.42%, while the Chrystophyceae class was found at least 2.99%.

Comparing Pears to Apples: Unlike Dogs, Cats Need Habituation before Lab Tests.

Research on the socio-cognitive skills of different species often benefit from comparative experiments, however, the ecology of the species and development of the individuals may differently determine how they react to the same test situation. In this study, our aims were twofold: to observe and compare the spontaneous behaviour of companion cats and dogs in the same novel environment, and to habituate them (if needed) to the novel environment in the presence of their owners and an unfamiliar experimenter. The behaviour of 62 family cats, 31 experienced (which had the opportunity to meet strangers and explore unfamiliar places) and 31 inexperienced cats, and 27 family dogs was compared in an unfamiliar room. The subjects' behaviour was coded during the first five minutes in the presence of two passive persons, their owners, and an unfamiliar experimenter. Then, based on a set of rules, first the owner, and then the experimenter tried to initiate interactions with the subjects and the subjects' willingness to interact was evaluated. To pass the habituation test, subjects were expected to play with the experimenter or accept food from them. All dogs passed the test on the first occasion, while almost 60% of the cats failed. The cats' experience did not play a significant role, in fact, younger cats passed more easily. We found marked differences between dogs and cats in all behavioural variables; compared to dogs, cats spent more time crouching and close to their box, while less time exploring or close to the owner. We did not find a difference in the cats' behaviour based on their experience. Our results support the hypothesis that unlike dogs, cats need extensive habituation in a novel environment. This could partially be explained by the difference in the ecology and/or domestication process of the species, although developmental effects cannot be excluded. Our findings have fundamental consequences not only for the considerations of the testability of cats and on the interpretation of their data collected in the laboratory, but in a more general sense on developing comparative experiments.

Breeding toward improved ecological plant-microbiome interactions.

Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.

Genetic introgression between different groups reveals the differential process of Asian cultivated rice

The Asian cultivated rice consists of two major subspecies: indica and japonica. There are already many reports about the existence of genetic introgression between the two subspecies. They propose some possible introgression-related genes from the comparison of population parameters. This study uses 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 populations. Two different methods are used to identify the genetic introgression regions. For most of the detected introgression regions, they generally get consistent results. Some previously 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 a vital role in the determination of both 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 the domestication process.

Insights into the regulation of wild soybean tolerance to salt-alkaline stress.

Soybean is an important grain and oil crop. In China, there is a great contradiction between soybean supply and demand. China has around 100 million ha of salt-alkaline soil, and at least 10 million could be potentially developed for cultivated land. Therefore, it is an effective way to improve soybean production by breeding salt-alkaline-tolerant soybean cultivars. Compared with wild soybean, cultivated soybean has lost a large number of important genes related to environmental adaptation during the long-term domestication and improvement process. Therefore, it is greatly important to identify the salt-alkaline tolerant genes in wild soybean, and investigate the molecular basis of wild soybean tolerance to salt-alkaline stress. In this review, we summarized the current research regarding the salt-alkaline stress response in wild soybean. The genes involved in the ion balance and ROS scavenging in wild soybean were summarized. Meanwhile, we also introduce key protein kinases and transcription factors that were reported to mediate the salt-alkaline stress response in wild soybean. The findings summarized here will facilitate the molecular breeding of salt-alkaline tolerant soybean cultivars.

Diversity of Chemical Composition and Morphological Traits of Eight Iranian Wild Salvia Species during the First Step of Domestication

As one of the largest genera of the Lamiaceae family, Salvia has a wide distribution worldwide. Despite their great importance and medicinal use, most Salvia species are collected from their natural habitats, and some of them are endangered and vulnerable. This study aimed to evaluate the domestication process of eight Iranian native Salvia species. The studied species were cultivated and adapted to the cultivation area after two years, and then some of their important biochemical properties were investigated. According to some significant results, the root architecture was closely correlated with the climatic conditions of the species origins. The distribution of total dry matter varied widely among species; accordingly, S. sclarea and S. officinalis had 65.6% and 55.9% dry weights in their leaves, respectively. Moreover, S. nemorosa had a 24.3% dry weight in its flowers, while S. frigida (Jahrom), S. frigida (Targavar), S. virgata (Eghled), and S. macrosiphon had 44.6%, 43.3%, 46.0%, and 44.3% dry weights in their roots. The most potent antioxidant activity (IC50) was observed in the roots of S. macrosiphon (10.9 μg/mL) and S. sclarea (14.9 μg/mL), the stem of S. nemorosa (14.3 μg/mL), and the leaves of S. atropatana (14.0 μg/mL). Rosmarinic acid, a key phenolic substance in Salvia species, was present in the range of 0.24–0.47 mg/g dry weight. The essential oil content ranged from 0.35% in S. atropatana to 1.45% (w/w) in S. officinalis. β-caryophyllene, caryophyllene oxide, and germacrene D were the major ingredients of the essential oils. The cluster analysis based on the essential oil data revealed the most similarities between S. sclarea and S. macrosiphon, and a clear separation of S. virgate, S. syriaca, and S. officinalis from other species. Salvia spp. contain a wide variety of compounds of interest under cultivation, with S. sclarea having the greatest potential to profit from the production of medicinal compounds, such as phenolic compounds, flavonoids, and essential oils. Furthermore, S. officinalis, S. nemorosa, and S. sclarea are the best species for producing raw medicinal materials.

Variation in the fruit development gene POINTED TIP regulates protuberance of tomato fruit tip

The domestication of tomato has led to striking variations in fruit morphology. Here, we show a genome-wide association study (GWAS) to understand the development of the fruit tip and describe a POINTED TIP (PT) gene that encodes a C2H2-type zinc finger transcription factor. A single nucleotide polymorphism is found to change a histidine (H) to an arginine (R) in the C2H2 domain of PT and the two alleles are referred to as PTH and PTR. Knocking out PTH leads to development of pointed tip fruit. PTH functions to suppress pointed tip formation by downregulating the transcription of FRUTFULL 2 (FUL2), which alters the auxin transport. Our evolutionary analysis and previous studies by others suggest that the PTR allele likely hitch-hiked along with other selected loci during the domestication process. This study uncovers variation in PT and molecular mechanism underlying fruit tip development in tomato.

Characterisation and pre-selection of Acca sellowiana genotypes by multivariate analysis

Feijoa (Acca sellowiana) is a native Brazilian fruit with a peculiar flavour, a considerable amount of bioactive compounds and antioxidant activity. Even though this fruit tree is currently cultivated in several countries around the world, in Brazil, the process of domestication is underway, and the selection and breeding of new genotypes that are more productive and with better fruit quality is necessary. The objective of this work was to evaluate phenotypic diversity among and within progeny and to study the correlations among the quality variables of Feijoa fruit, seeking to select individuals with superior characteristics using principal component analysis. The parents who formed the progeny (families) were selected from a participatory breeding programme. We observed that individuals 47 and 93 had a combination of desirable fruit characteristics for selection, and individuals 15, 910, 98 and 410 should be selected for future crossings, as they had a high total fruit mass and soluble solid content or the highest percentage of pulp and rounded fruit shape. Larger fruit, in general, had a lower percentage of pulp. Principal component analysis is a viable tool in the pre-selection of new genotypes and potential progenitors for Feijoa breeding programmes.

Genetic diversity of modern lines of hybrid pigs based on variations in mitochondrial DNA sequence

Genetic diversity of modern lines of hybrid pigs based on variations in mitochondrial DNA sequence

Comparative Analysis of Environment-Responsive Alternative Splicing in the Inflorescences of Cultivated and Wild Tomato Species

Cultivated tomato (Solanum lycopersicum) is bred for fruit production in optimized environments, in contrast to harsh environments where their ancestral relatives thrive. The process of domestication and breeding has profound impacts on the phenotypic plasticity of plant development and the stress response. Notably, the alternative splicing (AS) of precursor message RNA (pre-mRNA), which is one of the major factors contributing to transcriptome complexity, is responsive to developmental cues and environmental change. To determine a possible association between AS events and phenotypic plasticity, we investigated environment-responsive AS events in the inflorescences of cultivated tomato and its ancestral relatives S. pimpinellifolium. Despite that similar AS frequencies were detected in the cultivated tomato variety Moneymaker and two S. pimpinellifolium accessions under the same growth conditions, 528 genes including splicing factors showed differential splicing in the inflorescences of plants grown in open fields and plastic greenhouses in the Moneymaker variety. In contrast, the two S. pimpinellifolium accessions, LA1589 and LA1781, had 298 and 268 genes showing differential splicing, respectively. Moreover, seven heat responsive genes showed opposite expression patterns in response to changing growth conditions between Moneymaker and its ancestral relatives. Accordingly, there were eight differentially expressed splice variants from genes involved in heat response in Moneymaker. Our results reveal distinctive features of AS events in the inflorescences between cultivated tomato and its ancestral relatives, and show that AS regulation in response to environmental changes is genotype dependent.

Domestication-associated PHYTOCHROME C is a flowering time repressor and a key factor determining Setaria as a short-day plant.

Phytochromes play vital roles in the regulation of flowering time, but little is known in Panicoideae species, especially the C4 model Setaria. Here, genomic variations of PHYTOCHROME C (PHYC) between wild and cultivated Setaria gene pools were analysed and three SiphyC mutants were identified. The function of SiPHYC was verified by CRISPR-Cas9 approach and transcriptome sequencing. Furthermore, efficiency of indoor cultivation of SiphyC mutants were systematically evaluated. An extreme purified selection of PHYC was detected in wild to cultivated domestication process of Setaria. SiphyC mutants and knockout transgenic plants showed an early heading date and a loss of response to short-day photoperiod. Furthermore, variable expression of SiFTa, SiMADS14 and SiMADS15 might be responsible for promoting flowering of SiphyC mutants. Moreover, SiphyC mutant was four times that of the indoor plot ratio of wild-type and produced over 200 seeds within 45 d per individual. Our results suggest that domestication-associated SiPHYC repressed flowering and determined Setaria as a short-day plant, and SiphyC mutants possess the potential for creating efficient indoor cultivation system suitable for research on Setaria as a model, and either for maize or sorghum as well.

Phenotypical and gene co-expression network analyses of seed shattering in divergent sorghum (Sorghum spp.)

Sorghum [Sorghum bicolor (L.) Moench], a multipurpose C4 crop, is also a model species of the Poaceae family for plant research. During the process of domestication, the modification of seed dispersal mode is considered a key event, as the loss of seed shattering caused a significant increase in yield. In order to understand the seed shattering process in sorghum, we further studied eight previously identified divergent sorghum germplasm with different shattering degrees. We described their phenotypes in great detail, analyzed the histology of abscission zone, and conducted a gene co-expression analysis. We observed that the abscission layer of the most strong-shattering varieties began to differentiate before the 5–10 cm panicles development stage and was completely formed at flag leaf unfolding. The protective cells on the pedicels were also fully lignified by flowering. Through the weighted gene correlation network analysis (WGCNA), we mined for candidate genes involved in the abscission process at the heading stage. We found that these genes were mainly associated with such biological processes as hormone signal transmission (SORBI_3003G361300, SORBI_3006G216500, SORBI_3009G027800, SORBI_3007G077200), cell wall modification and degradation (SORBI_3002G205500, SORBI_3004G013800, SORBI_3010G022400, SORBI_3003G251800, SORBI_3003G254700, SORBI_3003G410800, SORBI_3009G162700, SORBI_3001G406700, SORBI_3004G042700, SORBI_3004G244600, SORBI_3001G099100), and lignin synthesis (SORBI_3004G220700, SORBI_3004G062500, SORBI_3010G214900, SORBI_3009G181800). Our study has provided candidate genes required for shedding for further study. We believe that function characterization of these genes may provide insight into our understanding of seed shattering process.

Population transcriptomic analysis identifies the comprehensive lncRNAs landscape of spike in wheat (Triticum aestivum L.)

BackgroundLong noncoding RNAs (lncRNAs) are emerging as the important regulators involving in growth and development as well as stress response in plants. However, current lncRNA studies were mainly performed at the individual level and the significance of it is not well understood in wheat.ResultsIn this study, the lncRNA landscape of wheat spike was characterized through analysing a total of 186 spike RNA-seq datasets from 93 wheat genotypes. A total of 35,913 lncRNAs as well as 1,619 lncRNA-mRNA pairs comprised of 443 lncRNAs and 464 mRNAs were obtained. Compared to coding genes, these lncRNAs displayed rather low conservation among wheat and other gramineous species. Based on re-sequencing data, the genetic variations of these lncRNA were investigated and obvious genetic bottleneck were found on them during wheat domestication process. Furthermore, 122 lncRNAs were found to act as ceRNA to regulate endogenous competition. Finally, association and co-localization analysis of the candidate lncRNA-mRNA pairs identified 170 lncRNAs and 167 target mRNAs significantly associated with spike-related traits, including lncRNA.127690.1/TraesCS2A02G518500.1 (PMEI) and lncRNA.104854.1/TraesCS6A02G050300.1 (ATG5) associated with heading date and spike length, respectively.ConclusionsThis study reported the lncRNA landscape of wheat spike through the population transcriptome analysis, which not only contribute to better understand the wheat evolution from the perspective of lncRNA, but also lay the foundation for revealing roles of lncRNA playing in spike development.

Perspective on the present state and future usefulness of marama bean (Tylosema esculentum)

AbstractRecent focus on indigenous knowledge of plant species that have long been consumed by mankind, but not having a prominent place in organized agriculture, has raised the profile of what steps are needed to bring such potentially useful plant species into formal agriculture practice. Many of these orphan plants have been cultivated, albeit usually without much improvement. Tylosema esculentum (marama bean) is unusual; in that, it has not been grown as a crop but only collected from wild stands. The nutritious seeds have been consumed, and other potentially useful products from the marama seeds and tubers have been identified. The marama bean grows under inhospitable environments, particularly hot arid conditions, and, if domesticated, could be grown in environments where there are no high‐yielding alternatives. The perspective of this article is to view the current status of the marama bean domestication and the possible pathways to bring this plant into wider agricultural use. The scientific basis for an improved crop yield needs to be coupled with the identification of possible added value characteristics for growers. These include acceptability as a food, possible industrial use, the development and distribution of improved seed, and the recruitment of growers to plant marama as a crop. The authors' international collaboration has already made advances in some of these areas. We discuss the current ongoing developments and existing gaps in moving this plant into formal agriculture, along with a plan for the future developments necessary for marama to provide food security under climate change, particularly in Africa. Even as the process of domestication of marama bean is proceeding, its unusual and potentially useful characteristics will greatly benefit the improvement of other legume crops needed to provide adequate nutrition to about 35% of the world population living in semi‐arid to arid regions of the developing world.

HOME GARDENS IN LATIN AMERICA: WILD FOODS IN THE MESOAMERICAN EKUARO OF P'URÉPECHAS, MEXICO AND THE ANDEAN CHAKRA OF KICHWAS, ECUADOR

Agroforestry systems comprise important spaces for biodiversity involving traditional ecological knowledge in their management. In Latin America, within Mesoamerican region as well as Andean exists a prominent kind of agroforestry system called home gardens, distinguished by the presence of domesticated plants and animals, coexisting with wild foods. In this paper, we addressed a comparative view on home gardens between p’urhépecha ekuaro and kichwa chakra to document qualitatively the relationship between diversity of wild food and food sovereignty in Mesoamerica and Andean regions, within a context of cultural change, and to contribute to the discussion of wild-domesticated continuum related to plants in different home gardens. The ethnographic research shows three main elements: 1) that the diversity of forms of lives domesticated and wild that coexist in the home gardens form part of a food sovereignty system; 2) cultural change does not just affect home gardens in negative ways; 3) wild foods are in a very complex process of domestication in which it is difficult to define the lines between wild and domesticated. Wild food studies have to consider a broad approach to how wild food relates to human cultures.