Genome biology, Год журнала: 2023, Номер 24(1)
Опубликована: Дек. 8, 2023
Many elite genes have been identified from the available cotton genomic data, providing various genetic resources for gene-driven breeding. However, backbone cultivar-driven breeding is most widely applied strategy. Revealing basis of strategy's restriction crucial transition
Язык: Английский
The Crop Journal, Год журнала: 2024, Номер 12(4), С. 1168 - 1175
Опубликована: Июнь 13, 2024
Wheat cultivar Zhongmai 895 was earlier found to carry YR86 in an 11.6 Mb recombination-suppressed region on chromosome 2AL when crossed with Yangmai 16. To fine-map the locus, we developed two large F2 populations from crosses Emai 580/Zhongmai and Avocet S/Zhongmai 895. Remarkably, both exhibited suppressed recombination same region. Collinearity analysis across Chinese Spring, Aikang 58, 10+ wheat genomes revealed a 4.1 chromosomal inversion spanning 708.5–712.6 Spring reference genome. Molecular markers were breakpoint used assess panel, revealing that 895, Jimai 22 shared common sequence named InvCS, whereas 16, 580, S InvAK58. The inverted configuration explained observed all three bi-parental populations. Normal 22/Zhongmai population, facilitating mapping of genetic interval 0.15 cM corresponding 710.27–712.56 falling within Thirty-three high-confidence genes annotated using genome, six identified as potential candidates for based genome transcriptome analyses. These results will accelerate map-based cloning its deployment breeding.
Язык: Английский
Процитировано
2
BMC Genomics, Год журнала: 2024, Номер 25(1)
Опубликована: Окт. 18, 2024
Mutton quality is closely related to genetic variants and gene expression alterations during growth development, resulting in differences nutritional values, flavor, odor. We first evaluated compared the composition of crude protein, fat, cholesterol, amino acid (AA), fatty (FA) longissimus dorsi muscle Guizhou black goats (GZB, n = 5) Yunshang (YBG, 6). The contents cholesterol FA odor GZB were significantly lower than that YBG, while concentrations umami acids intramuscular fat higher GZB. Furthermore, structural (SVs) genomes (n 30) YBG 11) explored. It was found some regions Chr 10/12/18 densely involved with a large number SVs YBG. By setting FST ≥ 0.25, we got 837 stratified SVs, which 25 (involved 12 genes, e.g., CORO1A, CLIC6, PCSK2, TMEM9) limited Functional enrichment analysis 14 protein-coding genes (e.g., ENPEP, LIPC, ABCA5, SLC6A15) revealed multiple terms pathways metabolisms AA, FA, cholesterol. 10) obtained by whole genome resequencing confirmed percentages 36.67 86.67% 96) PCR method. SVa SVd polymorphisms indicated moderate negative correlation HMGCS1 activity 17). This study comprehensively reveal potential mutton based on genomic compare between two goat breeds relationship. generated this provide data resource for deeper studies understand characteristics possible evolutionary outcomes better flavor extremely light
Язык: Английский
Процитировано
2
Molecular Ecology Resources, Год журнала: 2024, Номер unknown
Опубликована: Ноя. 26, 2024
The dimensions of phylogenetic research have expanded to encompass the study large-scale populations at microevolutionary level and comparisons between different species or taxonomic units macroevolutionary level. Traditional tools often struggle handle diverse complex data required for these evolutionary scales. In response this challenge, we introduce PhyloForge, a robust tool designed seamlessly integrate demands both micro- macroevolution, comprehensively utilising phylogenomic signals, such as genes, SNPs, structural variations, well mitochondrial chloroplast genomes. PhyloForge's innovation lies in its capability multiple enabling unified analysis multidimensional genomic data. This unique feature empowers researchers gain more comprehensive understanding aspects biological evolution. PhyloForge not only provides highly customisable experienced but also features an intuitively interface, facilitating effortless beginners. Extensive testing across various domains, including animals, plants fungi, attests broad applicability field phylogenetics. summary, has significant potential era genomics, offering new perspective toolset deeper evolution life. codes could be found GitHub (https://github.com/wangyayaya/PhyloForge/), program installed Conda (https://anaconda.org/wangxiaobei/phyloforge).
Язык: Английский
Процитировано
2
Life, Год журнала: 2023, Номер 13(6), С. 1360 - 1360
Опубликована: Июнь 9, 2023
A pangenome is a collection of the common and unique genomes that are present in given species. It combines genetic information all sampled, resulting large diverse range material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, not bound by physical constraints single genome, so it can capture more variability. Thanks introduction concept pangenome, possible use exceedingly detailed sequence data study evolutionary history two different species, or how populations within species differ genetically. In wake Human Pangenome Project, this review aims at discussing around human variation, which then framed pangenomic inform population genetics, phylogenetics, public health policy providing insights into basis diseases determining personalized treatments, targeting specific profile an individual. Moreover, technical limitations, ethical concerns, legal considerations discussed.
Язык: Английский
Процитировано
6
Genome biology, Год журнала: 2023, Номер 24(1)
Опубликована: Дек. 8, 2023
Many elite genes have been identified from the available cotton genomic data, providing various genetic resources for gene-driven breeding. However, backbone cultivar-driven breeding is most widely applied strategy. Revealing basis of strategy's restriction crucial transition
Язык: Английский
Процитировано
6