{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T13:35:54Z","timestamp":1765546554947,"version":"3.40.5"},"reference-count":44,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2020,3,12]],"date-time":"2020-03-12T00:00:00Z","timestamp":1583971200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of Food and Agriculture, US Department of Agriculture National Research Support Program-8","award":["CA-D*-ASC-7233-RR"],"award-info":[{"award-number":["CA-D*-ASC-7233-RR"]}]},{"name":"Multi-State Research Project NC-1170","award":["CA-D*-ASC-6414-RR"],"award-info":[{"award-number":["CA-D*-ASC-6414-RR"]}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Animal Genetics"],"published-print":{"date-parts":[[2020,6]]},"abstract":"<jats:title>Summary<\/jats:title><jats:p>An embryonic lethal mutation in chicken named <jats:italic>cleft primary palate <\/jats:italic>(<jats:italic>cpp<\/jats:italic>) is inherited in an autosomal recessive mode and results in a severely truncated upper beak. In this study, genotyping and sequencing techniques were employed to advance our genetic and genomic knowledge of the mutation\u2019s chromosomal location, candidate region and possible causative element using a congenic inbred line. Herein, the candidate region for the <jats:italic>cpp<\/jats:italic> developmental mutation was established as a ca. 5.1\u00a0Mb region of chicken chromosome 11 (GGA 11) through the use of a 600K Affymetrix SNP array. The SNPs identified from this array linked to <jats:italic>cpp<\/jats:italic> were used to genotype individuals from the congenic inbred line over several generations and thereby fine\u2010map the causative region resulting in an approximately 200\u00a0kb size reduction. This candidate region (4.9\u00a0Mb) was sequenced via capture array in a cohort of 24 individuals, including carriers, mutants and their wild type (wt) siblings. Interestingly, the GGA 11 region for <jats:italic>cpp<\/jats:italic> encompasses the predicted centromere location and is thus unlikely to be highly disrupted by further recombination. Here we report on the variation unique to the <jats:italic>cpp<\/jats:italic> mutation, i.e. single\u2010nucleotide variants and insertions or deletions. Although the candidate region contains several genes of interest with regard to the <jats:italic>cpp<\/jats:italic> phenotype, only one <jats:italic>cpp<\/jats:italic>\u2010linked variant was predicted to have a significant physiological effect by causing a frameshift mutation in <jats:italic>ESRP2<\/jats:italic>, which has a role in tissue\u2010specific splicing during development.<\/jats:p>","DOI":"10.1111\/age.12927","type":"journal-article","created":{"date-parts":[[2020,3,12]],"date-time":"2020-03-12T07:50:10Z","timestamp":1583999410000},"page":"423-429","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Mapping of the chicken <i>cleft primary palate<\/i> mutation on chromosome 11 and sequencing of the 4.9\u00a0Mb linked region"],"prefix":"10.1111","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9109-7773","authenticated-orcid":false,"given":"I. A.","family":"Youngworth","sequence":"first","affiliation":[{"name":"Department of Genetics Stanford University Stanford CA 94305 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9901-3597","authenticated-orcid":false,"given":"M. E.","family":"Delany","sequence":"additional","affiliation":[{"name":"Department of Animal Science University of California Davis Davis CA 95616 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2020,3,12]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.jhered.a107511"},{"key":"e_1_2_7_3_1","first-page":"29","article-title":"Inbred lines as genetic resources of chickens","volume":"4","author":"Abplanalp H","year":"1992","journal-title":"Poultry Science Review"},{"key":"e_1_2_7_4_1","unstructured":"AndrewsS.(2010)FastQC: a quality control tool for high throughput sequence data.http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.3021305"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.08954"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/ajmg.a.33727"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.4141805"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.4161\/fly.19695"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2012.00035"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/ejo\/26.1.7"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mod.2004.05.018"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.06536-11"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1002\/aja.1001950404"},{"key":"e_1_2_7_17_1","unstructured":"Broad Institute. 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