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10.1186/s12711-025-01012-x http://scihub22266oqcxt.onion/10.1186/s12711-025-01012-x C12551211!12551211 !41131485     free     free     free Deprecated: Implicit conversion from float 231.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 231.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 231.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 231.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 231.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 231.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 231.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 231.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 265.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 265.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 265.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Warning: imagejpeg(C:\Inetpub\vhosts\kidney.de\httpdocs\phplern\41131485 .jpg): Failed to open stream: No such file or directory in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 117       Genet+Sel+Evol 2025 ; 57 (1 ): 61 Nephropedia Template TP {{tp|p=41131485 |t=2025. Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes |pdf=|usr=}}{{41131485 }} gab.com Text Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes JO: Genet Sel Evol http://www.kidney.de/pget.php?&tw=1&pmid=41131485 #FOAvip BACKGROUND: The current cattle reference genome assembly, a pseudo-linear sequence produced using sequences from a single Hereford cow, represents a limitation when performing genetic studies, especially when investigating the whole spectrum of genetic variations within the species. Detecting structural variations (SVs) poses significant challenges when relying solely on conventional methods of sequencing read mapping to the current bovine genome assembly. RESULTS: In this study, we used long-reads (LR) and bioinformatic tools to construct a comprehensive bovine pangenome, using as a backbone the Hereford ARS-UCD1.2 reference genome assembly, and incorporating genetic diversity of 64 good quality de novo genome assemblies representing 14 French dairy and beef cattle breeds. Using a combination of complementary approaches, we explored the pangenome graph and identified 2.563 Gb of sequences common to all samples, and cumulated 0.295 Gb of variable sequences. Notably, we discovered 0.159 Gb of novel sequences not present in the current reference genome assembly. Our analysis also revealed 109,275 SVs, of which 84,612 were bi-allelic. These included 27,171 insertions and 24,592 deletions, while the remaining 32,849 SVs corresponded to alternate allele sequences defined as sequence substitutions between the reference genome and the sample sequence. Genome-wide association studies using SNPs and a panel of 221 SVs, shared between the pangenome and the EuroGMD chip, revealed well-known QTLs across the genome for the Holstein, Montbéliarde and Normande breeds. Among those, a QTL on chromosome 11 presents an SV with a highly significant effect on stature in the Holstein breed. This SV is a 6.2 kb deletion affecting the 5'UTR, first exon and part of the first intron of the MATN3 gene, suggesting a potential regulatory and coding effect. CONCLUSIONS: Our study provides new insights into the genetic diversity of 14 French dairy and beef breeds and highlights the utility of pangenome graphs in capturing structural variation. The identified SV associated with stature highlights the importance of integrating SVs into GWAS for a more comprehensive understanding of complex traits. Twit Text FOAVip Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes ????Genet Sel Evol http://www.kidney.de/pget.php?&tw=1&pmid=41131485 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=41131485 #FOAvip English Wikipedia <ref>{{Cite pmid|41131485 }}</ref> Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes #MMPMID41131485 Sorin V ; Naji MM ; Birbes C ; Grohs C ; Escouflaire C ; Fritz S ; Eché C ; Marcuzzo C ; Suin A ; Donnadieu C ; Gaspin C ; Iampietro C ; Milan D ; Drouilhet L ; Tosser-Klopp G ; Boichard D ; Klopp C ; Sanchez MP ; Boussaha M Genet Sel Evol 2025[Oct]; 57 (1 ): 61 PMID41131485 show ga BACKGROUND: The current cattle reference genome assembly, a pseudo-linear sequence produced using sequences from a single Hereford cow, represents a limitation when performing genetic studies, especially when investigating the whole spectrum of genetic variations within the species. Detecting structural variations (SVs) poses significant challenges when relying solely on conventional methods of sequencing read mapping to the current bovine genome assembly. RESULTS: In this study, we used long-reads (LR) and bioinformatic tools to construct a comprehensive bovine pangenome, using as a backbone the Hereford ARS-UCD1.2 reference genome assembly, and incorporating genetic diversity of 64 good quality de novo genome assemblies representing 14 French dairy and beef cattle breeds. Using a combination of complementary approaches, we explored the pangenome graph and identified 2.563 Gb of sequences common to all samples, and cumulated 0.295 Gb of variable sequences. Notably, we discovered 0.159 Gb of novel sequences not present in the current reference genome assembly. Our analysis also revealed 109,275 SVs, of which 84,612 were bi-allelic. These included 27,171 insertions and 24,592 deletions, while the remaining 32,849 SVs corresponded to alternate allele sequences defined as sequence substitutions between the reference genome and the sample sequence. Genome-wide association studies using SNPs and a panel of 221 SVs, shared between the pangenome and the EuroGMD chip, revealed well-known QTLs across the genome for the Holstein, Montbéliarde and Normande breeds. Among those, a QTL on chromosome 11 presents an SV with a highly significant effect on stature in the Holstein breed. This SV is a 6.2 kb deletion affecting the 5'UTR, first exon and part of the first intron of the MATN3 gene, suggesting a potential regulatory and coding effect. CONCLUSIONS: Our study provides new insights into the genetic diversity of 14 French dairy and beef breeds and highlights the utility of pangenome graphs in capturing structural variation. The identified SV associated with stature highlights the importance of integrating SVs into GWAS for a more comprehensive understanding of complex traits. |*Genome [MESH] |*Genomic Structural Variation [MESH] |Animals [MESH] |Cattle/genetics [MESH] |France [MESH] |Genetic Variation [MESH] |Genome-Wide Association Study [MESH] |Phenotype [MESH] |Polymorphism, Single Nucleotide [MESH]Application of a French cattle pangenome, from structural variant disc(epmc).pdf DeepDyve Pubget Overpricing