bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.03.24.644862

Genome-wide association studies reveal novel loci associated with carcass and body measures in goats (Capra hircus)

Zhang, L.·Duan, Y.·Zhao, S.·Yu, H.·Zhang, J.·Xu, N.·Zhao, Y.
View original source ↗Export metadata ↓

Abstract

Elucidating the genetic architecture of local goat populations is crucial for improving breeding strategies and conservation efforts. In southwestern China, there are numerous local goat resources, featuring rich phenotypic and genetic variations. Nevertheless, in-depth research on their production performance is scarce. Therefore, in this study, whole-genome 7x resequencing was performed on 776 individuals of six goat breeds (Dazu Black Goat, Yudong Black Goat, Banjiao Goat, Hechuan White Goat, Chuandong White Goat, and Youzhou Black Goat) in Chongqing to deeply investigate their population structure, genetic relationships, and heritability, and to identify significant genes related to growth traits and carcass traits. The mapping of significant genes for growth and carcass traits identified novel genetic loci, including a significant association at position 63,248,396 within ASIP on chromosome 13, which was linked to both traits, indicating a potential pleiotropic effect. Additional candidate genes for growth traits included CXCL14, PTGFR, and DPYD (body weight); CCSER1, HMCN1, and MYOM1 (body length); MALRD1 and ASIP (withers height); and MEIS2 and NLRC5 (chest circumference). For carcass traits, key candidate genes included ASIP, ATP5G1, COX3 and BCAR3. Functional enrichment analysis highlighted the calcium signaling pathway, glycan biosynthesis, and cytokine receptor interactions as key biological pathways influencing these traits. These findings provide novel insights into the genetic mechanisms underlying economically important traits in Chongqing local goats. The identification of ASIP as a pleiotropic gene, along with other newly discovered loci, offers valuable targets for genetic improvement and selective breeding programs, enhancing the productivity and sustainability of local goat populations.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Zhang, L., Duan, Y., Zhao, S., Yu, H., Zhang, J., Xu, N., Zhao, Y.. 2025-03-25. Genome-wide association studies reveal novel loci associated with carcass and body measures in goats (Capra hircus). https://doi.org/10.1101/2025.03.24.644862

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗
bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗
bioRxiv2026

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

Approximately 8% of the human genome is derived from ancient retroviral infections. The most recently integrated of these endogenous retroviruses is the HERV-K(HML-2) clade, whose expression has been associated with cancer, amyotrophic lateral sclerosis, and embryogenesis. Studies of HERV expression, particularly HML-2, have relied predominantly on short-read sequencing. However, the high similarity among HML-2 proviruses prevents many short reads from being assigned uniquely to individual loci. We therefore compared haplotype-resolved long-read genome assemblies from 292 donors to resolve variation in proviral structure and coding capacity. Several loci previously thought to be fixed were structurally polymorphic. Tandem arrays occurred at 13 loci and contained up to six proviral copies in a single array. At 8q11.23, we identified a previously undescribed full-length provirus in one haplotype. All 583 other haplotypes carried a solo-LTR. We found that standard reference genomes failed to represent the coding capacity retained in many individuals, whose proviruses contained intact open reading frames despite disruptive mutations in the reference sequences. Short-read genotypes left 32.5% of the tested donor-variant pairs unresolved at sites associated with viral reading frames. These findings show why HML-2 expression must be interpreted in the context of the structural and coding alleles each individual carries.

genomics↗