Background: Although several genetic linkage maps of the chicken genome have been published, the resolution of these maps is limited and does not allow the precise identification of recombination hotspots. The availability of more than 3.2 million SNPs in the chicken genome and the recent advances in high throughput genotyping techniques enabled us to increase marker density for the construction of a high-resolution linkage map of the chicken genome. This high-resolution linkage map allowed us to study recombination hotspots across the genome between two chicken populations: a purebred broiler line and a broiler x broiler cross. In total, 1,619 animals from the two different broiler populations were genotyped with 17,790 SNPs.
Results: The resulting linkage map comprises 13,340 SNPs. Although 360 polymorphic SNPs that had not been assigned to a known chromosome on chicken genome build WASHUC2 were included in this study, no new linkage groups were found. The resulting linkage map is composed of 31 linkage groups, with a total length of 3,054 cM for the sex-average map of the combined population. The sex-average linkage map of the purebred broiler line is 686 cM smaller than the linkage map of the broiler x broiler cross.
Conclusions: In this study, we present a linkage map of the chicken genome at a substantially higher resolution than previously published linkage maps. Regional differences in recombination hotspots between the two mapping populations were observed in several chromosomes near the telomere of the p arm; the sex-specific analysis revealed that these regional differences were mainly caused by female-specific recombination hotspots in the broiler x broiler cross.
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http://dx.doi.org/10.1186/1471-2156-11-11 | DOI Listing |
Nat Genet
January 2025
Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
Aberrant immune responses to viral pathogens contribute to pathogenesis, but our understanding of pathological immune responses caused by viruses within the human virome, especially at a population scale, remains limited. We analyzed whole-genome sequencing datasets of 6,321 Japanese individuals, including patients with autoimmune diseases (psoriasis vulgaris, rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), pulmonary alveolar proteinosis (PAP) or multiple sclerosis) and coronavirus disease 2019 (COVID-19), or healthy controls. We systematically quantified two constituents of the blood DNA virome, endogenous HHV-6 (eHHV-6) and anellovirus.
View Article and Find Full Text PDFSci Adv
January 2025
College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China.
Yellow seed coat color (SCC) is a valuable trait in , which is significantly correlated to high seed oil content (SOC) and low seed lignocellulose content (SLC). However, no dominant yellow SCC genes were identified in . In this study, a dominant yellow SCC N53-2 was verified, and then 58,981 eQTLs and 25 trans-eQTL hotspots were identified in a double haploid population derived from N53-2 and black SCC material Ken-C8.
View Article and Find Full Text PDFMol Biol Rep
January 2025
School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, 39564, USA.
Background: The gray snapper (Lutjanus griseus) is a marine reef fish commonly found in coastal and shelf waters of the tropical and subtropical western Atlantic Ocean. In this work, a draft reference genome was developed to support population genomic studies of gray snapper needed to assist with conservation and fisheries management efforts.
Methods And Results: Hybrid assembly of PacBio and Illumina sequencing reads yielded a 1,003,098,032 bp reference across 2039 scaffolds with N50 and L50 values of 1,691,591 bp and 163 scaffolds, respectively.
Alzheimers Dement
December 2024
University of Pennsylvania, Philadelphia, PA, USA.
Background: To date, Alzheimer's disease (AD) research has principally focused on neurons. In contrast, recent studies suggest that genetic mechanisms drive microglia towards prolonged inflammation in AD brains, exacerbating neurodegeneration. Indeed, many of the 70 disease-associated loci uncovered with genome-wide association studies (GWAS) reside near genes related to microglial function, such as TREM2.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
Background: Hispanic/Latino populations are underrepresented in Alzheimer Disease (AD) genetic studies. The Puerto Rican (PR) population, a three-way admixed (European, African, and Amerindian) population is the second-largest Hispanic group in the continental US. We performed a genome-wide association study (GWAS) in the PR population to identify novel AD susceptibility loci and characterize known AD genetic risk loci.
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