Nutrients, Journal Year: 2024, Volume and Issue: 16(11), P. 1603 - 1603
Published: May 24, 2024
Rice bean [
Language: Английский
Bioinformatics, Journal Year: 2023, Volume and Issue: 39(3)
Published: March 1, 2023
Abstract Summary Large-scale comparative genomic studies have provided important insights into species evolution and diversity, but also lead to a great challenge visualize. Quick catching or presenting key information hidden in the vast amount of data relationships among multiple genomes requires an efficient visualization tool. However, current tools for such remain inflexible layout and/or require advanced computation skills, especially genome-based synteny. Here, we developed easy-to-use flexible tool, NGenomeSyn [multiple (N) Genome Synteny], publication-ready syntenic whole genome local region features (e.g. repeats, structural variations, genes) across with high customization. provides easy way its users visualize large rich by simply adjusting options moving, scaling, rotation target genomes. Moreover, could be applied on non-genomic similar input formats. Availability implementation is freely available at GitHub (https://github.com/hewm2008/NGenomeSyn) Zenodo (https://doi.org/10.5281/zenodo.7645148).
Language: Английский
Citations
80
Poultry Science, Journal Year: 2025, Volume and Issue: 104(3), P. 104872 - 104872
Published: Feb. 1, 2025
Due to the monogamous mating system and late maturity of pigeons, their breeding cycle is longer compared that other poultry species, which has hindered optimization growth traits meat quality. While traditional methods are commonly used, they lack precision time-consuming. This study integrates phenotypic data from Tarim pigeons White King with genomic information, using genome-wide association analysis (GWAS) identify genetic markers associated key economic traits, thereby accelerating process. The results reveal significant correlations between body type characteristics (e.g., live weight chest depth) carcass supporting use as indirect selection criteria. GWAS identified several candidate genes, including PPARGC1A ADGRA3, linked muscle development metabolic regulation. To enhance efficiency, this developed a Liquid Phase Chip (LPC), designed high-throughput technology for identifying related traits. Although LPC not yet commercially available, 50 K pigeon could provide crucial theoretical support its future application. Ultimately, will serve an important tool efficiency in breeding, driving industry.
Language: Английский
Citations
1
Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)
Published: Feb. 20, 2025
Vigna radiata (L.) R. Wilczek var. (mungbean) is a pulse crop important for both the global protein security and sustainable production. Here, to facilitate genomics-assisted breeding programs in mungbean, we present high-quality reference genome originating from crop's centre of origin, India. In this study, significantly continuous assembly V. Indian cultivar, achieved through combination long-read PacBio HiFi sequencing Hi-C sequencing. The total assembled size ~596 Mb equating ~98% predicted complemented by contig N50 value 10.35 BUSCO score 98.5%. Around 502 anchored on 11 pseudochromosomes conforming chromosome count with distinctly identified telomeres centromeres. We 43,147 gene models which 39,144 coding genes were functionally annotated. was able resolve several gaps provides genomic resource accelerating mungbean programs.
Language: Английский
Citations
1
Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(10), P. 1933 - 1947
Published: Aug. 26, 2024
Closely related species often use the same genes to adapt similar environments. However, we know little about why such possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation climate presents a natural laboratory test these ideas, as even distantly must contend with stresses. Here, re-analyse genomic data from thousands of individuals 25 plant diverged lodgepole pine Arabidopsis (~300 Myr). We for genetic repeatability based on within-species associations between allele frequencies in variation 21 variables. Our results demonstrate significant statistical evidence deep time that not expected under randomness, identifying suite 108 gene families (orthogroups) functions repeatedly drive local adaptation climate. This set includes many orthogroups well-known abiotic stress response. Using co-expression networks quantify pleiotropy, find stronger exhibit greater network centrality broader expression tissues (higher pleiotropy), contrary 'cost complexity' theory. These may be important helping wild crop cope future change, representing candidates study.
Language: Английский
Citations
8
Nature Genetics, Journal Year: 2024, Volume and Issue: 56(5), P. 992 - 1005
Published: April 22, 2024
Language: Английский
Citations
7
Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14
Published: June 16, 2023
Underutilized pulses and their wild relatives are typically stress tolerant seeds packed with protein, fibers, minerals, vitamins, phytochemicals. The consumption of such nutritionally dense legumes together cereal-based food may promote global nutritional security. However, species deficient in a few or several desirable domestication traits thereby reducing agronomic value, requiring further genetic enhancement for developing productive, dense, climate resilient cultivars. This review article considers 13 underutilized focuses on germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential breeding transgenic manipulation, genetics tolerance traits. Recent progress has shown crop improvement security, example, basis stem determinacy fragrance moth bean rice bean, multiple abiotic horse gram tepary bruchid resistance lima low neurotoxin grass pea, photoperiod induced flowering anthocyanin accumulation adzuki have been investigated. Advances introgression to develop elite stocks pea β-ODAP (neurotoxin compound), Mungbean yellow mosaic India virus black using adaptation common genes from carried out. highlights wider programs introduce locally adapted de-domestication feralization evolution new variants these crops also highlighted.
Language: Английский
Citations
12
Theoretical and Applied Genetics, Journal Year: 2024, Volume and Issue: 137(5)
Published: April 8, 2024
Language: Английский
Citations
4
Horticulture Research, Journal Year: 2023, Volume and Issue: 10(4)
Published: Feb. 22, 2023
Garlic, an asexually propagated crop, is the second important bulb crop after onion and used as a vegetable medicinal plant. Abundant diverse garlic resources have been formed over thousands of years cultivation. However, genome variation, population structure genetic architecture agronomic traits were still not well elucidated. Here, 1 100 258 single nucleotide polymorphisms (SNPs) identified using genotyping-by-sequencing in 606 accessions collected from 43 countries. Population structure, principal component phylogenetic analysis showed that these divided into five subpopulations. Twenty traits, including above-ground growth bulb-related bolt-related two consecutive implemented genome-wide association study. In total, 542 SNPs associated with among which 188 repeatedly more than traits. One SNP (chr6: 1896135972) was ten These located within or near 858 genes, 56 transcription factors. Interestingly, one non-synonymous (Chr4: 166524085) ribosomal protein S5 Additionally, gene ontology enrichment candidate genes for genomic selection regions between complete-bolting non-bolting significantly enriched 'vegetative to reproductive phase transition meristem', 'shoot system development', 'reproductive process', etc. results provide valuable information reliable efficient achieve improvement superior varieties.
Language: Английский
Citations
10
Agronomy, Journal Year: 2023, Volume and Issue: 13(3), P. 811 - 811
Published: March 10, 2023
Novel germplasm resources are the key to crop breeding, with their genetic diversity and population structure analysis being highly significant for future faba bean breeding. We genotyped 410 global accessions using 130K targeted next-generation sequencing (TNGS) genotyping platform, resulting in a total of 38,111 high-quality SNP loci by high-standard filtering. found polymorphism information content (PIC) Nei’s gene were 0.0905–0.3750 0.0950–0.5000, averages 0.2471 0.3035, respectively. After evaluating PIC, on basis geographical origin (continent) structure-analysis-inferred subpopulations, we that from Asia (except China) Europe had rich diversity, while those winter sowing area China low. The divided into four subpopulations according clustering based (1972) distance neighbor-joining (NJ) method. However, same subpopulation contained materials different origins, thereby indicating flow or introgression occurred among accessions. Results NJ shared allele indicated three groups dissemination routes. results demonstrated relationships similar ecological environments geographic origins neighboring regions countries closer frequently within group, variation individuals was main source variation.
Language: Английский
Citations
10
Published: Jan. 1, 2025
Language: Английский
Citations
0