Short Communication: Quantitative Trait Loci Affecting the Somatic Cell Score on Chromosomes 4 and 26 in Italian Holstein Cattle

Time- and population-dependent genetic patterns underlie bovine milk somatic cell count

The objective of this study was to determine whether genetic regulation of bovine milk somatic cell count (SCC) varied throughout the course of an individual lactation and to identify quantitative trait loci (QTL) that may differentiate populations of chronically mastitic and robustly healthy cows. Milk SCC has long been a proxy for clinical mastitis diagnosis in management and genetic improvement strategies to control the disease. Cows (n = 471) were genotyped on the Illumina BovineHD 777K BeadChip (Illumina Inc., San Diego, CA), and composite milk samples were collected for SCC at 0-1 d in milk (DIM), 3-5 DIM, 10-14 DIM, 90-110 DIM, and 210-230 DIM, with each time span representing key physiological transitions for the cow. Median lactation somatic cell score (SCS) and area under the SCS curve were calculated from farm test data. A total of 8 genome-wide associations were performed and 167 SNP spanning the genome were significantly associated (false discovery rate <0.05). Of these associated regions, 27 of 48 associated QTL were novel for clinical mastitis or SCC. The linkage disequilibrium block surrounding the associated QTL or a 1-Mb window in the absence of linkage disequilibrium was interrogated for candidate genes, and many of those identified were related to multiple arms of the immune system, including toll-like receptor signaling, macrophage activation, B-cell maturation, T-cell recruitment, and the complement pathway. These genes included EXOC4, BAMBI, ITSN2, IL34, FCN3, CD8A, and CD8B. In addition, we identified populations of robustly healthy (SCS ≤4 from 10-14 DIM until study end), chronically mastitic (SCS >4 from 10-14 DIM until study end), and average cows with fluctuating SCS, and calculated fixation indices to identify regions of the genome differentiating these 3 populations. A total of 12 SNP were identified that showed moderate allelic differentiation (Wright's F statistic, F_ST ≥ 0.4) between the "chronic," "healthy," and "average" populations of cows. Candidate genes in the region surrounding differentiated QTL were related to cell signaling and immune response, such as JAKMIP1 and MADCAM1. The wide range of significantly associated QTL spanning the genome and the diversity of gene functions reinforces that mastitis is a complex trait and suggests that selection based on lactation stage-specific SCS rather than a generalized score may lead to greater success in breeding mastitis-resistant cows.

A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds

Background

Identification of genomic regions that have been targets of selection may shed light on the genetic history of livestock populations and help to identify variation controlling commercially important phenotypes. The Azeri and Kuzestani buffalos are the most common indigenous Iranian breeds which have been subjected to divergent selection and are well adapted to completely different regions. Examining the genetic structure of these populations may identify genomic regions associated with adaptation to the different environments and production goals.

Results

A set of 385 water buffalo samples from Azeri (N = 262) and Khuzestani (N = 123) breeds were genotyped using the Axiom® Buffalo Genotyping 90 K Array. The unbiased fixation index method (F_ST) was used to detect signatures of selection. In total, 13 regions with outlier F_ST values (0.1%) were identified. Annotation of these regions using the UMD3.1 Bos taurus Genome Assembly was performed to find putative candidate genes and QTLs within the selected regions. Putative candidate genes identified include FBXO9, NDFIP1, ACTR3, ARHGAP26, SERPINF2, BOLA-DRB3, BOLA-DQB, CLN8, and MYOM2.

Conclusions

Candidate genes identified in regions potentially under selection were associated with physiological pathways including milk production, cytoskeleton organization, growth, metabolic function, apoptosis and domestication-related changes include immune and nervous system development. The QTL identified are involved in economically important traits in buffalo related to milk composition, udder structure, somatic cell count, meat quality, and carcass and body weight.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4759-x) contains supplementary material, which is available to authorized users.

Genotypic to expression profiling of bovine calcium channel, voltage-dependent, alpha-2/delta subunit 1 gene, and their association with bovine mastitis among Frieswal (HFX Sahiwal) crossbred cattle of Indian origin

Calcium channel, voltage-dependent, alpha-2/delta subunit 1 (CACNA2D1) gene is considered to be an important noncytokine candidate gene influencing mastitis. Scanty of reports are available until today regarding the role play of CACNA2D1 gene on the susceptibility of bovine mastitis. We interrogated the CACNA2D1 G519663A [A>G] SNP by PCR-RFLP among two hundreds Frieswal (HF X Sahiwal) crossbred cattle of Indian origin. Genotypic frequency of AA (51.5, n=101) was comparatively higher than AG (35, n=70) and GG (14.5, n=29). Association of Somatic cell score (SCS) with genotypes revealed that, GG genotypes showing lesser count (less susceptible to mastitis) compare to AA and AG. Relative expression of CACNA2D1 transcript (in milk samples) was significantly higher among GG than AG and AA. Further we have also isolated blood sample from the all groups and PBMCs were cultured from each blood sample as per the standard protocol. They were treated with Calcium channel blocker and the expression level of the CACNA2D1 gene was evaluated by Real Time PCR. Results show that expression level decline in each genotypic group after treatment and expression level of GG are again significantly higher than AA and AG. Thus, it may be concluded that GG genotypic animals are favorable for selecting disease resistant breeds.

Polymorphisms of the ATP1A1 gene associated with mastitis in dairy cattle

Mastitis affects the concentrations of potassium and sodium in milk. Since sodium-potassium adenosine triphosphatase (Na(+), K(+)-ATPase) is critical for maintaining the homeostasis of these two ions, and is involved in cell apoptosis and pathogenesis, we presumed that polymorphism of the ATP1A1 gene, which encodes the bovine Na(+), K(+)-ATPase α1 subunit could be associated with mastitis. The ATP1A1 gene was analyzed in 320 Holstein cows using PCR low ionic strength single-strand conformation polymorphism (PCR-LIS-SSCP) and DNA sequencing methods. A C/A SNP was identified at nucleotide position -15,739 in exon 17 of the ATP1A1 gene, but it did not induce any change in amino acids. We examined a possible association of polymorphism of the ATP1A1 gene with somatic cell score and 305-day milk yields. Individuals with genotype CC in ATP1A1 had significantly lower somatic cell scores and 305-day milk yields than those with genotype CA. We also examined changes in Na(+), K(+)-ATPase activity of red cell membranes. The Na(+), K(+)-ATPase activity was significantly higher in dairy cows with genotype CC compared to the other two genotypes, and the Na(+), K(+)-ATPase activity of the resistant group was significantly higher than that of the susceptible group in dairy cows. We conclude that this polymorphism has potential as a marker for mastitis resistance in dairy cattle.

Gene polymorphisms: the keys for marker assisted selection and unraveling core regulatory pathways for mastitis resistance

One of the most frequent mammary diseases impacting lactating animals is mastitis, an inflammation of the mammary gland most commonly caused by bacterial infection. The severity of mastitis is greatly influenced by the invading organism and the subsequent immune response which must recognize the foreign organism, recruit immune cells, eliminate the invading pathogen, and resolve the inflammatory response. The speed, strength, and duration of this response and subsequent disease susceptibility are critically tied to the genetic background of an animal. However, the genetic contribution has been difficult to identify due to the complex interactions that must occur for effective disease resistance. Recent studies have utilized polymorphisms to better define the genes and chromosomal regions that contribute to mastitis resistance. This review will examine these studies with primary emphasis in bovine systems, as the most work regarding mastitis has been conducted in this species.

Single nucleotide polymorphism of CACNA2D1 gene and its association with milk somatic cell score in cattle

The objective of the present study was to identify polymorphisms of the CACNA2D1 gene, and to analyze associations between these polymorphisms and mastitis in several cattle breeds. Through PCR-RFLP methods and DNA sequencing, an allelic variant corresponding to the A→G mutations and Aspartic (Asp) to Glycine (Gly) amino acid replacement at positions 526745 in the exon 25 of bovine CACNA2D1 gene could be detected. Two alleles, A and G, and three genotypes, AA, AG and GG were defined. Genetic character in the studied populations indicated that the A526745G loci of CACNA2D1 gene was moderate polymorphism and fitted with Hardy-Weinberg equilibrium (P > 0.05). The effects of CACNA2D1 polymorphisms on somatic cell score (SCS) were analyzed and significant association was found between A526745G and SCS. The mean of genotype GG was significantly lower than those of genotype AG and AA (P = 0.0469). Information provided in this research could be useful in further studies to determine the role of CACNA2D1 gene in the mastitis resistance.