Transcriptome and Metabolite Insights into Domestication Process of Cultivated Barley in China.
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ABSTRACT:
SUBMITTER: Zhou Y
PROVIDER: S-EPMC8779797 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The importance of wild barley from Qinghai-Tibet Plateau in the origin and domestication of cultivated barley has long been underestimated. Population-based phylogenetic analyses were performed to study the origin and genetic diversity of Chinese domesticated barley, and address the possibility that the Tibetan region in China was an independent center of barley domestication. Wild barley (Hordeum vulgare ssp. spontaneum) populations from Southwest Asia, Central Asia, and Tibet along with domesticated barley from China were analyzed using two nuclear genes. Our results showed that Tibetan wild barley distinctly diverged from Southwest Asian (Near East) wild barley, that Central Asian wild barley is related to Southwest Asian wild barley, and that Chinese domesticated barley shares the same haplotypes with Tibetan wild barley. Phylogenetic analysis showed a close relationship between Chinese domesticated barley and the Tibetan wild barley, suggesting that Tibetan wild barley was the ancestor of Chinese domesticated barley. Our results favor the polyphyletic origin for cultivated barley.
| S-EPMC3643926 | biostudies-literature
Project description:The Near East Fertile Crescent is well recognized as a primary center of barley origin, diversity, and domestication. A large number of wild barleys have been collected from the Tibetan Plateau, which is characterized by an extreme environment. We used genome-wide diversity array technology markers to analyze the genotypic division between wild barley from the Near East and Tibet. Our results confirmed the existence of Tibetan wild barley and suggested that the split between the wild barleys in the Near East and those in Tibet occurred around 2.76 million years ago (Mya). To test the concept of polyphyletic domestication of barley, we characterized a set of worldwide cultivated barley. Some Chinese hulless and six-rowed barleys showed a close relationship with Tibetan wild barley but showed no common ancestor with other cultivated barley. Our data support the concept of polyphyletic domestication of cultivated barley and indicate that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. The current results may be highly significant in exploring the elite germplasm for barley breeding, especially against cold and drought stresses.
| S-EPMC3479512 | biostudies-literature
Project description:BackgroundCultivated barley (Hordeum vulgare) is widely used in animal feed, beverages, and foods and has become a model crop for molecular evolutionary studies. Few studies have examined the evolutionary fates of different types of genes in barley during the domestication process.ResultsThe rates of nonsynonymous substitution (Ka) to synonymous substitution (Ks) were calculated by comparing orthologous genes in different barley groups (wild vs. landrace and landrace vs. improved cultivar). The rates of evolution, properties, expression patterns, and diversity of positively selected genes (PSGs) and negatively selected genes (NSGs) were compared. PSGs evolved more rapidly, possessed fewer exons, and had lower GC content than NSGs; they were also shorter and had shorter intron, exon, and first exon lengths. Expression levels were lower, the tissue specificity of expression was higher, and codon usage bias was weaker for PSGs than for NSGs. Nucleotide diversity analysis revealed that PSGs have undergone a more severe genetic bottleneck than NSGs. Several candidate PSGs were involved in plant growth and development, which might make them as excellent targets for the molecular breeding of barley.ConclusionsOur comprehensive analysis of the evolutionary, structural, and functional divergence between PSGs and NSGs in barley provides new insight into the evolutionary trajectory of barley during domestication. Our findings also aid future functional studies of PSGs in barley.
| S-EPMC9158214 | biostudies-literature
Project description:Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.
| S-EPMC8003350 | biostudies-literature
Project description:The domestication of cultivated barley has been used as a model system for studying the origins and early spread of agrarian culture. Our previous results indicated that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. Here we reveal multiple origins of domesticated barley using transcriptome profiling of cultivated and wild-barley genotypes. Approximately 48-Gb of clean transcript sequences in 12 Hordeum spontaneum and 9 Hordeum vulgare accessions were generated. We reported 12,530 de novo assembled transcripts in all of the 21 samples. Population structure analysis showed that Tibetan hulless barley (qingke) might have existed in the early stage of domestication. Based on the large number of unique genomic regions showing the similarity between cultivated and wild-barley groups, we propose that the genomic origin of modern cultivated barley is derived from wild-barley genotypes in the Fertile Crescent (mainly in chromosomes 1H, 2H, and 3H) and Tibet (mainly in chromosomes 4H, 5H, 6H, and 7H). This study indicates that the domestication of barley may have occurred over time in geographically distinct regions.
| S-EPMC4169977 | biostudies-literature
Project description:Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyploidization and are cultivated worldwide. Although the overall genetic diversity between these two cultivated species has been studied with limited accessions, their population structure and genetic variations remain largely unknown.We resequence the genomes of 147 cotton accessions, including diverse wild relatives, landraces, and modern cultivars, and construct a comprehensive variation map to provide genomic insights into the divergence and dual domestication of these two important cultivated tetraploid cotton species. Phylogenetic analysis shows two divergent groups for G. hirsutum and G. barbadense, suggesting a dual domestication processes in tetraploid cottons. In spite of the strong genetic divergence, a small number of interspecific reciprocal introgression events are found between these species and the introgression pattern is significantly biased towards the gene flow from G. hirsutum into G. barbadense. We identify selective sweeps, some of which are associated with relatively highly expressed genes for fiber development and seed germination.We report a comprehensive analysis of the evolution and domestication history of allotetraploid cottons based on the whole genomic variation between G. hirsutum and G. barbadense and between wild accessions and modern cultivars. These results provide genomic bases for improving cotton production and for further evolution analysis of polyploid crops.
| S-EPMC5317056 | biostudies-literature
Project description:The cultivated cucumber (Cucumis sativus L.) was reported to have been developed from a wild cucumber (Cucumis hystrix Chakrav.), nevertheless, these two organisms exhibit noteworthy differences. For example, the wild cucumber is known for its high resistance to different biotic and abiotic stresses. Moreover, the leaves and fruits of the wild cucumber have a bitter taste compared to the cultivated cucumber. These differences could be attributed mainly to the differences in gene expression levels. In the present investigation, we analyzed the RNA-sequencing data to show the differentially expressed genes (DEGs) between the wild and cultivated cucumbers. The identified DEGs were further utilized for Gene Ontology (GO) and pathway enrichment analysis and for identification of transcription factors and regulators. In the results, several enriched GO terms in the biological process, cellular component, and molecular functions categories were identified and various enriched pathways, especially the biosynthesis pathways of secondary products were recognized. Plant-specific transcription factor families were differentially expressed between the wild and cultivated cucumbers. The results obtained provide preliminary evidence for the transcriptional differences between the wild and cultivated cucumbers which developed during the domestication process as a result of natural and/or artificial selection, and they formulate the basis for future genetic research and improvement of the cultivated cucumber.
| S-EPMC7020419 | biostudies-literature
Project description:Barley is used as a model cereal to decipher salt tolerance mechanisms due to its simpler genome than wheat and enhanced salt tolerance compared to rice and wheat. In the present study, RNA-Seq based transcriptomic profiles were compared between salt-tolerant wild (Hordeum spontaneum, genotype no. 395) genotype and salt-sensitive cultivated (H. vulgare, 'Mona' cultivar) subjected to salt stress (300 mM NaCl) and control (0 mM NaCl) conditions. Plant growth and physiological attributes were also evaluated in a separate experiment as a comparison. Wild barley was significantly less impacted by salt stress than cultivated barley in growth and physiology and hence was more stress-responsive functionally. A total of 6,048 differentially expressed genes (DEGs) including 3,025 up-regulated and 3,023 down-regulated DEGs were detected in the wild genotype in salt stress conditions. The transcripts of salt-stress-related genes were profoundly lower in the salt-sensitive than the tolerant barley having a total of 2,610 DEGs (580 up- and 2,030 down-regulated). GO enrichment analysis showed that the DEGs were mainly enriched in biological processes associated with stress defenses (e.g., cellular component, signaling network, ion transporter, regulatory proteins, reactive oxygen species (ROS) scavenging, hormone biosynthesis, osmotic homeostasis). Comparison of the candidate genes in the two genotypes showed that the tolerant genotype contains higher functional and effective salt-tolerance related genes with a higher level of transcripts than the sensitive one. In conclusion, the tolerant genotype consistently exhibited better tolerance to salt stress in physiological and functional attributes than did the sensitive one. These differences provide a comprehensive understanding of the evolved salt-tolerance mechanism in wild barley. The shared mechanisms between these two sub-species revealed at each functional level will provide more reliable insights into the basic mechanisms of salt tolerance in barley species.
| S-EPMC9047362 | biostudies-literature
Project description:MALDI mass spectrometry imaging was performed to localize metabolites during the first seven days of the barley germination. Up to 100 mass signals were detected of which 85 signals were identified as 48 different metabolites with highly tissue-specific localizations. Oligosaccharides were observed in the endosperm and in parts of the developed embryo. Lipids in the endosperm co-localized in dependency on their fatty acid compositions with changes in the distributions of diacyl phosphatidylcholines during germination. 26 potentially antifungal hordatines were detected in the embryo with tissue-specific localizations of their glycosylated, hydroxylated, and O-methylated derivates. In order to reveal spatio-temporal patterns in local metabolite compositions, multiple MSI data sets from a time series were analyzed in one batch. This requires a new preprocessing strategy to achieve comparability between data sets as well as a new strategy for unsupervised clustering. The resulting spatial segmentation for each time point sample is visualized in an interactive cluster map and enables simultaneous interactive exploration of all time points. Using this new analysis approach and visualization tool germination-dependent developments of metabolite patterns with single MS position accuracy were discovered. This is the first study that presents metabolite profiling of a cereals' germination process over time by MALDI MSI with the identification of a large number of peaks of agronomically and industrially important compounds such as oligosaccharides, lipids and antifungal agents. Their detailed localization as well as the MS cluster analyses for on-tissue metabolite profile mapping revealed important information for the understanding of the germination process, which is of high scientific interest.
| S-EPMC4777520 | biostudies-literature
Project description:BackgroundUnderstanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses.ResultsThe root transcriptomes of widely differing cultivated and wild carrots were sequenced. A method accounting for sequencing errors was introduced to optimize SNP (single nucleotide polymorphism) discovery. 11,369 SNPs were identified. Of these, 622 (out of 1000 tested SNPs) were validated and used to genotype a large set of cultivated carrot, wild carrot and other wild Daucus carota subspecies, primarily of European origin. Phylogenetic analysis indicated that eastern carrot may originate from Western Asia and western carrot may be selected from eastern carrot. Different wild D. carota subspecies may have contributed to the domestication of cultivated carrot. Genetic diversity was significantly reduced in western cultivars, probably through bottlenecks and selection. However, a high proportion of genetic diversity (more than 85% of the genetic diversity in wild populations) is currently retained in western cultivars. Model simulation indicated high and asymmetric gene flow from wild to cultivated carrots, spontaneously and/or by introgression breeding. Nevertheless, high genetic differentiation exists between cultivated and wild carrots (Fst = 0.295) showing the strong effects of selection. Expression patterns differed radically for some genes between cultivated and wild carrot roots which may be related to changes in root traits. The up-regulation of water-channel-protein gene expression in cultivars might be involved in changing water content and transport in roots. The activated expression of carotenoid-binding-protein genes in cultivars could be related to the high carotenoid accumulation in roots. The silencing of allergen-protein-like genes in cultivated carrot roots suggested strong human selection to reduce allergy. These results suggest that regulatory changes of gene expressions may have played a predominant role in domestication.ConclusionsWestern carrots may originate from eastern carrots. The reduction in genetic diversity in western cultivars due to domestication bottleneck/selection may have been offset by introgression from wild carrot. Differential gene expression patterns between cultivated and wild carrot roots may be a signature of strong selection for favorable cultivation traits.
| S-EPMC4213543 | biostudies-literature