scholarly journals Genome features of common vetch ( Vicia sativa ) in natural habitats

Plant Direct ◽  
2021 ◽  
Vol 5 (10) ◽  
Author(s):  
Kenta Shirasawa ◽  
Shunichi Kosugi ◽  
Kazuhiro Sasaki ◽  
Andrea Ghelfi ◽  
Koei Okazaki ◽  
...  
Keyword(s):  
Vicia Sativa ◽  
Common Vetch ◽  
Natural Habitats ◽  
Genome Features

scholarly journals Genome features of common vetch (Vicia sativa) in natural habitats

2021 ◽  
Author(s):  
Kenta Shirasawa ◽  
Shunichi Kosugi ◽  
Kazuhiro Sasaki ◽  
Andrea Ghelfi ◽  
Koei Okazaki ◽  
...  
Keyword(s):  
De Novo ◽  
Population Level ◽  
Wild Plants ◽  
Wild Plant ◽  
Vicia Sativa ◽  
Natural Environments ◽  
Common Vetch ◽  
Natural Habitats ◽  
Crop Species ◽  
The Common

AbstractWild plants are often tolerant to biotic and abiotic stresses in their natural environments, whereas domesticated plants such as crops frequently lack such resilience. This difference is thought to be due to the high levels of genome heterozygosity in wild plant populations and the low levels of heterozygosity in domesticated crop species. In this study, common vetch (Vicia sativa) was used as a model to examine this hypothesis. The common vetch genome (2n = 14) was estimated as 1.8 Gb in size. Genome sequencing produced a reference assembly that spanned 1.5 Gb, from which 31,146 genes were predicted. Using this sequence as a reference, 24,118 single nucleotide polymorphisms were discovered in 1,243 plants from 12 natural common vetch populations in Japan. Common vetch genomes exhibited high heterozygosity at the population level, with lower levels of heterozygosity observed at specific genome regions. Such patterns of heterozygosity are thought to be essential for adaptation to different environments. These findings suggest that high heterozygosity at the population level would be required for wild plants to survive under natural conditions while allowing important gene loci to be fixed to adapt the conditions. The resources generated in this study will provide insights into de novo domestication of wild plants and agricultural enhancement.HighlightSequence analysis of the common vetch (Vicia sativa) genome and SNP genotyping across natural populations revealed nucleotide diversity levels associated with native population environments.

scholarly journals Genome survey sequencing of common vetch (Vicia sativa L.) and genetic diversity analysis of Chinese germplasm with genomic SSR markers

2021 ◽  
Author(s):  
Lin Ma ◽  
Xiao Wang ◽  
Min Yan ◽  
Fang Liu ◽  
Shuxing Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Gc Content ◽  
Vicia Sativa ◽  
Whole Genome ◽  
Common Vetch ◽  
High Genetic Diversity ◽  
Genome Survey ◽  
Genome Features ◽  
High Quality Sequence

Abstract Background Common vetch (Vicia sativa L.) is an annual legume with excellent suitability in cold and dry regions. Despite its great applied potential, the genomic information regarding common vetch currently remains unavailable. Methods and results In the present study, the whole genome survey of common vetch was performed using the next-generation sequencing (NGS). A total of 79.84 Gbp high quality sequence data were obtained and assembled into 3,754,145 scaffolds with an N50 length of 3556 bp. According to the K-mer analyses, the genome size, heterozygosity rate and GC content of common vetch genome were estimated to be 1568 Mbp, 0.4345 and 35%, respectively. In addition, a total of 76,810 putative simple sequence repeats (SSRs) were identified. Among them, dinucleotide was the most abundant SSR type (44.94%), followed by Tri- (35.82%), Tetra- (13.22%), Penta- (4.47%) and Hexanucleotide (1.54%). Furthermore, a total of 58,175 SSR primer pairs were designed and ten of them were validated in Chinese common vetch. Further analysis showed that Chinese common vetch harbored high genetic diversity and could be clustered into two main subgroups. Conclusion This is the first report about the genome features of common vetch, and the information will help to design whole genome sequencing strategies. The newly identified SSRs in this study provide basic molecular markers for germplasm characterization, genetic diversity and QTL mapping studies for common vetch.

scholarly journals Genome Survey Sequencing of Common Vetch (Vicia Sativa L.) and Genetic Diversity Analysis of Chinese Germplasm with Genomic SSR Markers

2021 ◽  
Author(s):  
lin ma ◽  
Xiao Wang ◽  
Min Yan ◽  
Fang Liu ◽  
Xuemin Wang
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Gc Content ◽  
Vicia Sativa ◽  
Whole Genome ◽  
Common Vetch ◽  
High Genetic Diversity ◽  
Genome Survey ◽  
Genome Features ◽  
High Quality Sequence

Abstract Common vetch (Vicia sativa L.) is an annual legume with excellent suitability in cold and dry regions. Despite its great applied potential, the genomic information regarding common vetch currently remains unavailable. In the present study, the whole genome survey of common vetch was performed using the next-generation sequencing (NGS). A total of 79.84 Gbp high quality sequence data were obtained and assembled into 3,754,145 scaffolds with an N50 length of 3,556 bp. According to the K-mer analyses, the genome size, heterozygosity rate and GC content of common vetch genome were estimated to be 1,568 Mbp, 0.4345% and 35%, respectively. In addition, a total of 76,810 putative simple sequence repeats (SSRs) were identified. Among them, dinucleotide was the most abundant SSR type (44.94%), followed by Tri- (35.82%), Tetra- (13.22%), Penta- (4.47%) and Hexanucleotide (1.54%). Furthermore, a total of 58,175 SSR primer pairs were designed and ten of them were validated in Chinese common vetch. Further analysis showed that Chinese common vetch harbored high genetic diversity and could be clustered into two main subgroups. This is the first report about the genome features of common vetch, and the information will help to design whole genome sequencing strategies. The newly identified SSRs in this study provide basic molecular markers for germplasm characterization, genetic diversity and QTL mapping studies for common vetch.

Scanning electron microscopy observations of pollen morphology in common vetch (Vicia sativa) subspecies

2021 ◽  
pp. 1-14
Author(s):  
Rui Dong ◽  
Zhongjie Lu ◽  
Zhengyu Yang ◽  
Yanrong Wang ◽  
Chao Chen
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Pollen Morphology ◽  
Polar View ◽  
Polar Axis ◽  
Vicia Sativa ◽  
Common Vetch ◽  
Plant Phylogeny ◽  
Axis Length ◽  
Scanning Electron

Abstract Common vetch (Vicia sativa) is an important forage and green manure crop that is widely cultivated around the world. However, the large number of subspecies and accessions of common vetch has made taxonomic research on this species difficult. Pollen morphology data can provide important evidence in the study of plant phylogeny. Therefore, in this research, light microscopy and scanning electron microscopy were used to observe seven morphological traits of pollens from 22 common vetch accessions, and residual maximum likelihood and pattern analysis was conducted. The results showed that the pollen grains of the 22 accessions were all monad pollen and the polar view revealed three-lobed circular and triangular shapes, while the equatorial view mainly revealed an oblate shape; only one accession showed an oblate spherical shape. All accessions were 3-zonocolporate and the colpus length extended close to the poles. The polar axis length was (19.39 ± 0.97)–(42.12 ± 0.76) μm and the equatorial axis length was (35.97 ± 1.27)–(45.25 ± 0.81) μm. We found that qualitative traits of pollen shape, aperture polar view and ornamentation were highly stable. Among them, polar axis length, equatorial axis length and colpus length and width had significant differences among the accessions. The ratios of the equatorial and polar axes had significant differences among the subspecies. This trait information could be used for the classification and identification of common vetch accessions and subspecies.

scholarly journals Search for Resistant Genotypes to Cuscuta campestris Infection in Two Legume Species, Vicia sativa and Vicia ervilia

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 738
Author(s):  
Eva María Córdoba ◽  
Mónica Fernández-Aparicio ◽  
Clara Isabel González-Verdejo ◽  
Carmela López-Grau ◽  
María del Valle Muñoz-Muñoz ◽  
...  
Keyword(s):  
Agricultural Production ◽  
Host Plants ◽  
Resistance Breeding ◽  
Parasitic Plants ◽  
Vicia Sativa ◽  
Common Vetch ◽  
Germplasm Collections ◽  
Bitter Vetch ◽  
Cuscuta Campestris ◽  
Resistant Genotypes

The dodders (Cuscuta spp.) are parasitic plants that feed on the stems of their host plants. Cuscuta campestris is one of the most damaging parasitic plants for the worldwide agricultural production of broad-leaved crops. Its control is limited or non-existent, therefore resistance breeding is the best alternative both economically and environmentally. Common vetch (Vicia sativa) and bitter vetch (Vicia ervilia) are highly susceptible to C. campestris, but no resistant genotypes have been identified. Thus, the aim of this study was to identify in V. sativa and V.ervilia germplasm collections genotypes resistant to C. campestris infection for use in combating this parasitic plant. Three greenhouse screening were conducted to: (1) identify resistant responses in a collection of 154 accessions of bitter vetch and a collection of 135 accessions of common vetch genotypes against infection of C. campestris; (2) confirm the resistant response identified in common vetch accessions; and (3) characterize the effect of C. campestris infection on biomass of V. sativa resistant and susceptible accessions. Most common vetch and bitter vetch genotypes tested were susceptible to C. campestris. However, the V. sativa genotype Vs.1 exhibited high resistance. The resistant phenotype was characterized by a delay in the development of C. campestris posthaustorial growth and a darkening resembling a hypersensitive-like response at the penetration site. The resistant mechanism was effective in limiting the growth of C. campestris as the ratio of parasite/host shoot dry biomass was more significantly reduced than the rest of the accessions. To the best or our knowledge, this is the first identification of Cuscuta resistance in V. sativa genotypes.

Rhizobium changzhiense sp. nov., isolated from effective nodules of Vicia sativa L. in North China

2021 ◽  
Author(s):  
Junjie Zhang ◽  
Shanshan Peng ◽  
Mitchell Andrews ◽  
Chunzeng Liu ◽  
Yimin Shang ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Vicia Sativa ◽  
Common Vetch ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Rhizobial Species ◽  
Distinct Lineage ◽  
Type Strains

Three fast-growing rhizobial strains isolated from effective nodules of common vetch (Vicia sativa L.) were characterized using a polyphasic approach. All three strains were assigned to the genus Rhizobium on the basis of the results of 16S rRNA gene sequence analysis. Phylogenetic analysis based on concatenated atpD-recA genes separated the strains into a distinct lineage represented by WYCCWR 11279T, which showed average nucleotide identity values of 95.40 and 93.61 % with the most similar phylogenetic type strains of Rhizobium sophorae CCBAU 03386T and Rhizobium laguerreae FB TT, respectively. The digital DNA–DNA hybridization relatedness values between WYCCWR 11279T and the closest related type strains were less than 70 %. Therefore, a novel rhizobial species is proposed, Rhizobium changzhiense sp. nov., and strain WYCCWR 11279T (=HAMBI 3709T=LMG 31534T) is designated as the type strain for the novel species.

scholarly journals Identification of novel drought-responsive miRNA regulatory network of drought stress response in common vetch (Vicia sativa)

2021 ◽  
Vol 16 (1) ◽  
pp. 1111-1121
Author(s):  
Yongqun Zhu ◽  
Qiuxu Liu ◽  
Wenzhi Xu ◽  
Li Yao ◽  
Xie Wang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Stress Response ◽  
Protein Transport ◽  
Target Genes ◽  
Comparison Group ◽  
Stress Factors ◽  
Leguminous Plant ◽  
Vicia Sativa ◽  
Common Vetch ◽  
Drought Treatment

Abstract Drought is among the most important natural disasters with severe effects on animals and plants. MicroRNAs are a class of noncoding RNAs that play a crucial role in plant growth, development, and response to stress factors, including drought. However, the microRNAs in drought responses in common vetch (Vicia sativa), an annual herbaceous leguminous plant commonly used for forage by including it in mixed seeding during winter and spring, have not been characterized. To explore the microRNAs’ response to drought in common vetch, we sequenced 10 small RNA (sRNA) libraries by the next-generation sequencing technology. We obtained 379 known miRNAs belonging to 38 families and 47 novel miRNAs. The two groups had varying numbers of differentially expressed miRNAs: 85 in the comparison group D5 vs C5 and 38 in the comparison group D3 vs C3. Combined analysis of mRNA and miRNA in the same samples under drought treatment identified 318 different target genes of 123 miRNAs. Functional annotation of the target genes revealed that the miRNAs regulate drought-responsive genes, such as leucine-rich repeat receptor-like kinase-encoding genes (LRR-RLKs), ABC transporter G family member 1 (ABCG1), and MAG2-interacting protein 2 (MIP2). The genes were involved in various pathways, including cell wall biosynthesis, reactive oxygen removal, and protein transport. The findings in this study provide new insights into the miRNA-mediated regulatory networks of drought stress response in common vetch.

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