Reggiana is an Italian autochthonous cattle breed reared mainly in the Emilia Romagna region (North of Italy), with a high density of farms in the province of Reggio Emilia, in the well-known worldwide Protected Designation of Origin Parmigiano-Reggiano cheese production area. Milk of this breed is almost exclusively utilized to produce a mono-breed Parmigiano-Reggiano cheese. Here, we took advantage from the phenotyping data collected in Reggiana cattle and investigated association of single nucleotide polymorphisms (SNPs) and haplotypes with several exterior traits and defects, including different grades of red coat colour, coat colour patterns, muzzle colour, stature, presence/absence and number of supernumerary nipples and length of nipples. DNA was extracted from blood and SNP genotyping was performed with the GeneSeek GGP Bovine 150k Array. PLINK v1.9 was used for quality checks. Haplotype estimation was carried out with SHAPEIT v.2. The final dataset comprises 1776 animals, 124,482 SNPs and 404,061 haplotypes. Single-SNPs and haplotype-based genome scans were performed with GEMMA v.0.98 via linear mixed models. Animals presented three main intensity of red of the coat colour (red, 83.7%; light-red 10.7%; dark-red, 5.6%). Association analysis for this trait pointed out two main significant regions on bovine chromosome (BTA) 5 and BTA13. Piedbaldism was observed in 4.3% cattle and associated with KIT gene markers (BTA6). The association study for muzzle colour reported that this trait is highly dependent on alleles at the MC1R gene (BTA18). Stature of the animals (in the range from 130 to 156 cm) was associated with SNPs in two regions harboring genes that have been already shown to affect this trait in several species: LCORL (BTA6) and PLAG1 (BTA14). A suggestive peak of association for the number of extra nipples was evidenced on BTA10. A suggestive peak of association on BTA8 was identified for the length of nipples. Overall, the identified genomic regions not only can be directly used in selection plans but also contribute to clarify the genetic mechanisms involved in determining exterior traits in cattle.
Samuele Bovo, G.S. (2021). Genome wide association studies for several morphological traits and defects in the Reggiana cattle breed [10.1080/1828051X.2021.1968170].
Genome wide association studies for several morphological traits and defects in the Reggiana cattle breed
Samuele Bovo;Giuseppina Schiavo;Hamed Kazemi;Giulia Moscatelli;Anisa Ribani;Mohamad Ballan;Stefania Dall’Olio;Luca Fontanesi
2021
Abstract
Reggiana is an Italian autochthonous cattle breed reared mainly in the Emilia Romagna region (North of Italy), with a high density of farms in the province of Reggio Emilia, in the well-known worldwide Protected Designation of Origin Parmigiano-Reggiano cheese production area. Milk of this breed is almost exclusively utilized to produce a mono-breed Parmigiano-Reggiano cheese. Here, we took advantage from the phenotyping data collected in Reggiana cattle and investigated association of single nucleotide polymorphisms (SNPs) and haplotypes with several exterior traits and defects, including different grades of red coat colour, coat colour patterns, muzzle colour, stature, presence/absence and number of supernumerary nipples and length of nipples. DNA was extracted from blood and SNP genotyping was performed with the GeneSeek GGP Bovine 150k Array. PLINK v1.9 was used for quality checks. Haplotype estimation was carried out with SHAPEIT v.2. The final dataset comprises 1776 animals, 124,482 SNPs and 404,061 haplotypes. Single-SNPs and haplotype-based genome scans were performed with GEMMA v.0.98 via linear mixed models. Animals presented three main intensity of red of the coat colour (red, 83.7%; light-red 10.7%; dark-red, 5.6%). Association analysis for this trait pointed out two main significant regions on bovine chromosome (BTA) 5 and BTA13. Piedbaldism was observed in 4.3% cattle and associated with KIT gene markers (BTA6). The association study for muzzle colour reported that this trait is highly dependent on alleles at the MC1R gene (BTA18). Stature of the animals (in the range from 130 to 156 cm) was associated with SNPs in two regions harboring genes that have been already shown to affect this trait in several species: LCORL (BTA6) and PLAG1 (BTA14). A suggestive peak of association for the number of extra nipples was evidenced on BTA10. A suggestive peak of association on BTA8 was identified for the length of nipples. Overall, the identified genomic regions not only can be directly used in selection plans but also contribute to clarify the genetic mechanisms involved in determining exterior traits in cattle.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
