f80364499b2a035a865f650f9dce408c pmc_10778555.pdf 67f63323dc321769c79172487c2adc91a99ee2a2 pmc_10778555.pdf d61c57d9fbe02361b9440e70a88d51c2034b57d017ff30753b9a4b17e1d60acf pmc_10778555.pdf Title: Variations in Casein Genes Are Associated with Milk Protein and Fat Contents in Sarda Goats (Capra hircus), with an Important Role of CSN1S2 for Milk Yield Subject: This work aimed to assess the variability of casein genes in a population of 153 bucks and 825 lactating does of the Sarda breed, and to perform association analysis between polymorphic sites and milk yield and composition traits. To genotype the casein genes, we chose an SNP panel including 44 SNPs mapping to the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3. Genotyping (made by KASP™ genotyping assay, based on competitive allele-specific PCR) revealed the high variability of the Sarda goat, and haplotype analysis revealed linkage disequilibrium (LD) between CSN1S1 and CSN2 genes, in addition to two LD blocks within the CSN1S2 and two LD blocks within the CSN3 gene, in bucks and does. Association analysis revealed that variability at all four casein genes was associated with milk protein content, total solids, and milk energy. The three Ca-sensitive casein genes were associated with lipid content, and CSN1S2 showed a unique pattern, with intron variants associated with milk yield, in addition to milk pH, NaCl, and SCS (Somatic Cell Score). This information might prove useful in selection schemes and in future investigations aiming to better understand the biology of lactation, and the direct link between genotype and phenotype. Keywords: casein gene cluster; sarda goat; capra hircus; dairy goat; milk traits; CSN1S1; CSN2; CSN1S2; CSN3 Author: Maria Luisa Dettori, Michele Pazzola, Antonia Noce, Vincenzo Landi and Giuseppe Massimo Vacca Creator: LaTeX with hyperref Producer: pdfTeX-1.40.25 CreationDate: Fri Dec 22 15:00:03 2023 CET ModDate: Fri Dec 22 15:04:45 2023 CET Custom Metadata: no Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 14 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 2400016 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- CPCWNO+VnURWPalladioL Type 1 Custom yes yes yes 10 0 JDWIZJ+EURM10 Type 1 Builtin yes yes yes 16 0 MOVRXS+URWPalladioL-Bold Type 1 Custom yes yes yes 21 0 GHGTFL+URWPalladioL-Roma Type 1 Custom yes yes yes 27 0 TNCYWX+URWPalladioL-Ital Type 1 Custom yes yes yes 32 0 RZKRHG+URWPalladioL-BoldItal Type 1 Custom yes yes yes 37 0 SZMRXJ+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 53 0 LLJJPJ+TimesNewRoman CID TrueType Identity-H yes yes yes 77 0 LLJHJA+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 83 0 LLJHJB+PalatinoLinotype CID TrueType Identity-H yes yes yes 86 0 LLJHKB+PalatinoLinotype TrueType WinAnsi yes yes no 92 0 LLJHKD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 95 0 YZIJXT+CMSY10 Type 1 Builtin yes yes yes 105 0 LLJHJA+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 120 0 LLJHJB+PalatinoLinotype CID TrueType Identity-H yes yes yes 123 0 LLJHKB+PalatinoLinotype TrueType WinAnsi yes yes no 129 0 LLJHKD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 132 0 LLJHJA+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 158 0 LLJHJB+PalatinoLinotype CID TrueType Identity-H yes yes yes 161 0 LLJHKB+PalatinoLinotype TrueType WinAnsi yes yes no 167 0 LLJHKD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 170 0 LLJIOO+PalatinoLinotype TrueType MacRoman yes yes no 173 0 LLJHJA+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 184 0 LLJHJB+PalatinoLinotype CID TrueType Identity-H yes yes yes 187 0 LLJHKB+PalatinoLinotype TrueType WinAnsi yes yes no 193 0 LLJHKD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 196 0 LLJIOO+PalatinoLinotype TrueType MacRoman yes yes no 199 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2024-09-01 08:22:00 CEST RepresentationInformation: pmc_10778555.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2024-07-12 02:35:31 CEST Size: 2400016 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 416 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: section.1 Item: Title: Materials and Methods Destination: section.2 Children: Item: Title: Animals and Sampling Destination: subsection.2.1 Item: Title: Phenotyping Destination: subsection.2.2 Item: Title: Genotyping Destination: subsection.2.3 Item: Title: Bioinformatic and Statistical Analysis Destination: subsection.2.4 Item: Title: Results Destination: section.3 Children: Item: Title: Genotyping Destination: subsection.3.1 Item: Title: Descriptive Statistics and Association Analysis Destination: subsection.3.2 Item: Title: LD Analysis Destination: subsection.3.3 Item: Title: Discussion Destination: section.4 Children: Item: Title: Association Analysis The Outstanding Role of CSN1S2 Destination: subsection.4.1 Item: Title: CSN1S1 and CSN2 Genes Are Associated with Milk Protein and Fat Content Destination: subsection.4.2 Item: Title: CSN3 Variation Is Associated with Protein Content Destination: subsection.4.3 Item: Title: Conclusions Destination: section.5 Item: Title: References Destination: appendix.A. Info: Title: Variations in Casein Genes Are Associated with Milk Protein and Fat Contents in Sarda Goats (Capra hircus), with an Important Role of CSN1S2 for Milk Yield Author: Maria Luisa Dettori, Michele Pazzola, Antonia Noce, Vincenzo Landi and Giuseppe Massimo Vacca Subject: This work aimed to assess the variability of casein genes in a population of 153 bucks and 825 lactating does of the Sarda breed, and to perform association analysis between polymorphic sites and milk yield and composition traits. To genotype the casein genes, we chose an SNP panel including 44 SNPs mapping to the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3. Genotyping (made by KASP™ genotyping assay, based on competitive allele-specific PCR) revealed the high variability of the Sarda goat, and haplotype analysis revealed linkage disequilibrium (LD) between CSN1S1 and CSN2 genes, in addition to two LD blocks within the CSN1S2 and two LD blocks within the CSN3 gene, in bucks and does. Association analysis revealed that variability at all four casein genes was associated with milk protein content, total solids, and milk energy. The three Ca-sensitive casein genes were associated with lipid content, and CSN1S2 showed a unique pattern, with intron variants associated with milk yield, in addition to milk pH, NaCl, and SCS (Somatic Cell Score). This information might prove useful in selection schemes and in future investigations aiming to better understand the biology of lactation, and the direct link between genotype and phenotype. Keywords: casein gene cluster; sarda goat; capra hircus; dairy goat; milk traits; CSN1S1; CSN2; CSN1S2; CSN3 Creator: LaTeX with hyperref Producer: pdfTeX-1.40.25 CreationDate: Fri Dec 22 15:00:03 CET 2023 ModDate: Fri Dec 22 15:04:45 CET 2023 ID: 0x9cf95819e1cf9db170a70f5df3e3b60b, 0x9cf95819e1cf9db170a70f5df3e3b60b Filters: FilterPipeline: FlateDecode Fonts: Type1: Font: BaseFont: TNCYWX+URWPalladioL-Ital FontSubset: true FirstChar: 40 LastChar: 151 FontDescriptor: FontName: TNCYWX+URWPalladioL-Ital Flags: Symbolic FontBBox: -170, -305, 1010, 941 FontFile: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: JDWIZJ+EURM10 FontSubset: true FirstChar: 11 LastChar: 22 FontDescriptor: FontName: JDWIZJ+EURM10 Flags: Symbolic FontBBox: -32, -243, 1060, 720 FontFile: true ToUnicode: true Font: BaseFont: RZKRHG+URWPalladioL-BoldItal FontSubset: true FirstChar: 49 LastChar: 117 FontDescriptor: FontName: RZKRHG+URWPalladioL-BoldItal Flags: Symbolic FontBBox: -170, -300, 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