{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T14:20:41Z","timestamp":1789395641829,"version":"build-2803163510"},"reference-count":26,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Xinjiang ARS program","award":["XJARS-09-202602"],"award-info":[{"award-number":["XJARS-09-202602"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Vet. Sci.","Veterinary Sciences"],"abstract":"<jats:p>Litter size is an economically important reproductive trait in dairy goats, but its genetic improvement remains challenging because of its complex genetic architecture and the influence of multiple environmental factors. This study aimed to identify genomic loci associated with litter size-related traits and to evaluate the potential of an intergenic variant near the candidate gene CTNND2 as a molecular marker in Saanen dairy goats. A total of 341 does with reproductive records were analyzed using a genome-wide association study (GWAS), followed by candidate SNP genotyping and association analysis. A shared association signal for litter size and live-born kid number was identified on chromosome 20, leading to the selection of the intergenic SNP CM048886.1:g.61357858G&gt;A located near CTNND2 for further evaluation. Three genotypes (GG, AG, and AA) were detected, and the locus exhibited moderate genetic diversity (PIC = 0.27) while conforming to Hardy\u2013Weinberg equilibrium. Association analysis revealed nominal associations between the SNP and both litter size (p = 0.0445) and live-born kid number (p = 0.0448), whereas no significant association was observed with average kid birth weight (p = 0.125). Goats carrying the A allele showed numerically higher litter size and live-born kid number than those carrying the G allele. These findings identify CM048886.1:g.61357858G&gt;A, an intergenic variant near CTNND2, as a promising candidate marker for litter size-related traits in Saanen dairy goats and provide a foundation for future validation studies and the development of molecular breeding strategies to improve reproductive performance.<\/jats:p>","DOI":"10.3390\/vetsci13090961","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T13:05:26Z","timestamp":1789391126000},"page":"961","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-Wide Association Screening and Candidate SNP Analysis Identify an Intergenic Variant Near CTNND2 Associated with Litter Size Traits in Saanen Dairy Goats"],"prefix":"10.3390","volume":"13","author":[{"given":"Jianqing","family":"Zhao","sequence":"first","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Shuhao","family":"Guo","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Uygur Autonomous Region Academy of Animal Sciences, Urumqi 830011, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Jianwu","family":"Li","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Uygur Autonomous Region Academy of Animal Sciences, Urumqi 830011, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Wenjie","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Uygur Autonomous Region Academy of Animal Sciences, Urumqi 830011, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Yuqi","family":"Ma","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Uygur Autonomous Region Academy of Animal Sciences, Urumqi 830011, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Weiming","family":"Gao","sequence":"additional","affiliation":[{"name":"Xinjiang Uygur Autonomous Region Academy of Animal Sciences, Urumqi 830011, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.5713\/ajas.19.0253","article-title":"Current status of global dairy goat production: An overview","volume":"32","author":"Miller","year":"2019","journal-title":"Asian-Australas. J. Anim. Sci."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Chen, W., Han, Y., Chen, Y., Liu, X., Liang, H., Wang, C., and Khan, M.Z. (2025). Potential candidate genes associated with litter size in goats: A review. Animals, 15.","DOI":"10.3390\/ani15010082"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Mahmoudi, P., Rashidi, A., Nazari-Ghadikolaei, A., Rostamzadeh, J., Razmkabir, M., and Huson, H.J. (2022). Genome-wide association study reveals novel candidate genes for litter size in Markhoz goats. Front. Vet. Sci., 9.","DOI":"10.3389\/fvets.2022.1045589"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1007\/s11250-011-0034-8","article-title":"Genetic and phenotypic parameter estimates for reproduction traits in indigenous Arsi-Bale goats","volume":"44","author":"Kebede","year":"2012","journal-title":"Trop. Anim. Health Prod."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"3443","DOI":"10.2527\/jas.2011-3872","article-title":"Genetic parameters for body weight, reproduction, and parasite resistance traits in the Creole goat","volume":"89","author":"Gunia","year":"2011","journal-title":"J. Anim. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1080\/1828051X.2020.1869601","article-title":"Genetic analysis of litter size and number of kids born alive across parities in Spanish goat breeds using a random regression model","volume":"20","author":"Ziadi","year":"2021","journal-title":"Ital. J. Anim. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Fang, X., Gu, B., Chen, M., Sun, R., Zhang, J., Zhao, L., and Zhao, Y. (2023). Genome-wide association study of the reproductive traits of the Dazu Black Goat (Capra hircus) using whole-genome resequencing. Genes, 14.","DOI":"10.3390\/genes14101960"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Sun, X., Niu, Q., Jiang, J., Wang, G., Zhou, P., Li, J., Chen, C., Liu, L., Xu, L., and Ren, H. (2023). Identifying candidate genes for litter size and three morphological traits in Youzhou Dark goats based on genome-wide SNP markers. Genes, 14.","DOI":"10.3390\/genes14061183"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1083\/jcb.144.3.519","article-title":"Delta-catenin, an adhesive junction-associated protein which promotes cell scattering","volume":"144","author":"Lu","year":"1999","journal-title":"J. Cell Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1007\/s00439-016-1705-3","article-title":"Genetic alterations of delta-catenin\/NPRAP\/Neurojungin (CTNND2): Functional implications in complex human diseases","volume":"135","author":"Lu","year":"2016","journal-title":"Hum. Genet."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1542","DOI":"10.1038\/onc.2014.89","article-title":"Delta-catenin, a Wnt\/beta-catenin modulator, reveals inducible mutagenesis promoting cancer cell survival adaptation and metabolic reprogramming","volume":"34","author":"Nopparat","year":"2015","journal-title":"Oncogene"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1530\/REP-14-0685","article-title":"The role of WNT signaling in adult ovarian folliculogenesis","volume":"150","year":"2015","journal-title":"Reproduction"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1210\/er.2014-1020","article-title":"Intraovarian control of early folliculogenesis","volume":"36","author":"Hsueh","year":"2015","journal-title":"Endocr. Rev."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"139192","DOI":"10.1016\/j.ijbiomac.2024.139192","article-title":"Whole genome and transcriptome analyses in dairy goats identify genetic markers associated with high milk yield","volume":"292","author":"Zhao","year":"2025","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: A tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Patterson, N., Price, A.L., and Reich, D. (2006). Population structure and eigenanalysis. PLoS Genet., 2.","DOI":"10.1371\/journal.pgen.0020190"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/ng.2310","article-title":"Genome-wide efficient mixed-model analysis for association studies","volume":"44","author":"Zhou","year":"2012","journal-title":"Nat. Genet."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"4833","DOI":"10.1093\/bioinformatics\/btaa610","article-title":"Rapid epistatic mixed-model association studies by controlling multiple polygenic effects","volume":"36","author":"Wang","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"731","DOI":"10.21105\/joss.00731","article-title":"qqman: An R package for visualizing GWAS results using Q-Q and Manhattan plots","volume":"3","author":"Turner","year":"2018","journal-title":"J. Open Source Softw."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3321","DOI":"10.1073\/pnas.70.12.3321","article-title":"Analysis of gene diversity in subdivided populations","volume":"70","author":"Nei","year":"1973","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_21","first-page":"314","article-title":"Construction of a genetic linkage map in man using restriction fragment length polymorphisms","volume":"32","author":"Botstein","year":"1980","journal-title":"Am. J. Hum. Genet."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"An, X., Ma, T., Hou, J., Fang, F., Han, P., Yan, Y., Zhao, H., Song, Y., Wang, J., and Cao, B. (2013). Association analysis between variants in KISS1 gene and litter size in goats. BMC Genet., 14.","DOI":"10.1186\/1471-2156-14-63"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s11259-011-9476-8","article-title":"Polymorphism of GDF9 gene and its association with litter size in goats","volume":"35","author":"Chu","year":"2011","journal-title":"Vet. Res. Commun."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1111\/rda.13196","article-title":"Polymorphism of GDF9 and BMPR1B genes and their association with litter size in Markhoz goats","volume":"53","author":"Shokrollahi","year":"2018","journal-title":"Reprod. Domest. Anim."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"309","DOI":"10.5194\/aab-65-309-2022","article-title":"Meta-analysis of association between c.963A>G single-nucleotide polymorphism on BMP15 gene and litter size in goats","volume":"65","author":"Zergani","year":"2022","journal-title":"Arch. Anim. Breed."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"107632","DOI":"10.1016\/j.anireprosci.2024.107632","article-title":"Genetic insights into litter size in goats: A meta-analysis of KISS1 and BMP15 SNP variants","volume":"271","author":"Gholizadeh","year":"2024","journal-title":"Anim. Reprod. Sci."}],"container-title":["Veterinary Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-7381\/13\/9\/961\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T13:47:29Z","timestamp":1789393649000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-7381\/13\/9\/961"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,14]]},"references-count":26,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["vetsci13090961"],"URL":"https:\/\/doi.org\/10.3390\/vetsci13090961","relation":{},"ISSN":["2306-7381"],"issn-type":[{"value":"2306-7381","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,14]]}}}