Kompetitive Allele Specific PCR (KASP™) genotyping of 48 polymorphisms at different caprine loci in French Alpine and Saanen goat breeds and their association with milk composition

Abstract

Using a novel and fast genotyping method called Kompetitive Allele Specific PCR (KASP™), we carried out a pilot study on 48 single nucleotide polymorphisms (SNPs) belonging to 40 genes in French Alpine (n = 24) and Saanen (n = 25) goats reared in Romania. Furthermore, the associations of the 13 polymorphic genetic variants with milk production and composition were investigated. Thirty-five SNPs did not show polymorphism in the studied populations. Polymorphic SNPs were detected in the following genes: CAST, CLEC4E, DES, GHRHR, HSP90AA1, IL15RA, IL1RN, IL8, MITF, PPRC1, SOCS3, TNF and TNFSF13. The studied Alpine population was in Hardy-Weinberg disequilibrium at the g.62894878A>G locus (rs671391101) (P < 0.05). The results showed that four SNPs rs671391101 (GHRHR), rs640582069 (IL1RN) rs635583012 (SOCS3) and rs635969404 (IL15RA) out of the 13 polymorphic markers were significantly associated with milk production, protein, fat and lactose content in the Alpine breed. However, no significant effect was recorded in the Saanen population regarding milk yield or milk chemical composition. The current results provide new insights for the development of SNP marker-assisted selection technology in the goat industry and confirm the potential of using SNPs for the GHRHR, IL1RN, SOCS3, and IL15RA genes as candidate genes for selection, highlighting the direct implications of such genes for farm production outputs. The results from this study are relevant for future goat genomic studies and the inclusion of the associated traits into up-to-date selection schemes.

Influence of the Use of Milk Replacers and pH on the Texture Profiles of Raw and Cooked Meat of Suckling Kids

“…On average, the goat’s milk in this study had a higher content of fat and protein than those reported by other authors using comparable breeds [26,27,28,29,30,31,32]. However, the milk had similar lactose levels to those reported by several authors [26,28,30], but lower levels than those reported by others [29,31,33].…”

Introgression of Maize Lethal Necrosis Resistance Quantitative Trait Loci Into Susceptible Maize Populations and Validation of the Resistance Under Field Conditions in Naivasha, Kenya

“…DNA samples of poor quality were discarded and therefore, only samples with high DNA quality were retained and used in this study. Extracted genomic DNA samples were clearly labeled and stored at −20°C until further use ( Kusza et al, 2018 ). The 21 primers generated above were screened for polymorphism to MLN resistance using the 20 parent lines (one resistant donor and 19 susceptible lines) described earlier.…”

“…Data from Omega software were imported into KlusterCaller software (LGC Genomics, Queens Road, Teddington, Middlesex, TW11 0LY, United Kingdom) and cluster plots were normalized using ROX (passive reference dye) then called into X:X, X:Y, and Y:Y alleles depending on the corresponding genotype. Results were then exported onto Excel 2016 version, following 96-well plate format and calls were converted into specific alleles where X:X represented homozygous alleles for FAM, Y:Y represented homozygous alleles for HEX, and X:Y represented segregating (heterozygous) alleles (FAM/HEX; Graves et al, 2016 ; Kusza et al, 2018 ). The KASP analysis revealed that six of the SNP primers were polymorphic and could clearly discriminate between resistance alleles of donor parent (KS23-6) and the susceptibility alleles of the recipient parents ( Table 4 ).…”

Lipopolysaccharide triggers different transcriptional signatures in taurine and indicine cattle macrophages: Reactive oxygen species and potential outcomes to the development of immune response to infections

“…CeTF analysis of LPS treated MDMs displaying all DEGs associated to KeyTF for each bovine breed were plotted in the Cystoscape software and then overlapped by Diffany plugin [34] to highlight genes that were exclusive enriched for biological processed according to each bovine breed (Fig 4). Co-expression networks of Holstein and Gir LPS stimulated MDM revealed various genes detected in genome wide association studies that aim to improve genomic breeding indices (Fig 5 and S11 Table), e.g., milk production [64][65][66][67][68], clinical and subclinical mastitis [69][70][71][72], puberty [68,[73][74][75], feed efficiency [76], adaptation to ecologic conditions [77][78][79] and cellular and humoral immune responses [49,[80][81][82]. The biological process enrichment after co-expression analysis also stood out the importance of leukocyte migration and extracellular matrix organization, both controlled by chemokines and cytokines produced by macrophages in inflammation triggered by LPS in Gir and Holstein MDMs.…”