The use of artificial neural networks to diagnose mastitis in dairy cattle

The use of milk sample categorization for diagnosing mastitis using Kohonen's self-organizing feature map (SOFM) is reported. Milk trait data of 14 weeks of milking from commercial dairy cows in New Zealand was used to train and test a SOFM network. The SOFM network was useful in discriminating data patterns into four separate mastitis categories. Several other artificial neural networks were tested to predict the missing data from the recorded milk traits. A multi-layer perceptron (MLP) network proved to be most accurate (R² = 0.84, r = 0.92) when compared to other MLP (R² = 0.83, r = 0.92), Elman (R² = 0.80, r = 0.92), Jordan (R² = 0.81, r = 0.92) or linear regression (R² = 0.72, r = 0.85) methods. It is concluded that the SOFM can be used as a decision tool for the dairy farmer to reduce the incidence of mastitis in the dairy herd

Variation in bovine leptin gene affects milk fatty acid composition in New Zealand Holstein Friesian × Jersey dairy cows

Leptin is a protein hormone secreted from white adipose tissue. It regulates food/feed intake, body weight, immune function and reproduction. In our investigation, the polymerase chain reaction (PCR) amplification coupled with single-strand conformational polymorphism (SSCP) analysis was used to reveal variation in bovine leptin gene (LEP) in New Zealand (NZ) Holstein Friesian × Jersey (HF × J) dairy cows. Subsequent sequence analysis of a 430 bp amplicon spanning the entirety of exon 3 and part of the intron 2 region revealed three variant sequences (A₃, B₃ and C₃) containing a total of five nucleotide substitutions, all of which have been reported previously. Using general linear mixed-effect model analyses, the presence of variant A₃ (the most common variant) was associated with a decreased level of C15:1, C18:1 trans-11, C18:1 all trans, C18:2 trans-9, cis-12, C22:0 and C24:0 levels but increased levels of C12:1 and C13:0 iso (p<0.05). Variant B₃ was associated with reduced levels of C6:0, C8:0, C11:0, C13:0 and C20:0 but increased C17:0 iso and C24:0 levels (p<0.05). Variant C₃ was associated with decreased C17:0 iso levels but increased C20:0 (p<0.05) levels. In a genotype model, the A₃B₃ genotype was associated with increased levels of C22:0 and C24:0 but decreased C8:0, C10:0, C11:0, C13:0, C15:0 and grouped medium-chain fatty acid (MCFA) levels (p<0.05). Genotype A₃C₃ was found to be associated with decreased levels of C10:0, C11:0, C13:0 and grouped MCFA (p<0.05). This is the first report of findings of this kind in NZ HF × J cows, and they suggest that variation in exon 3 of bovine leptin gene could be explored as a means of decreasing the concentration of saturated fatty acids in milk

An association between lifespan and variation in insulin-like growth factor I receptor in sheep

Longevity in livestock is a valuable trait. When productive animals live longer, fewer replacement animals need to be raised. However, selection for longevity is not commonly the focus of breeding programs as direct selection for long-lived breeding stock is virtually impossible until late in the reproductive life of the animal. Additionally the underlying genetic factors or genes associated with longevity are either not known, or not well understood. In humans, there is evidence that IGF 1 receptor (IGF1R) is involved in longevity. Polymorphism in the IGF1R gene has been associated with longevity in a number of species. Recently, 3 alleles of ovine IGF1R were identified, but no analysis of the effect of IGF1R variation on sheep longevity has been reported. In this study, associations between ovine IGF1R variation, longevity and fertility were investigated. Polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) was used to type IGF1R variation in 1,716 New Zealand sheep belonging to 6 breeds and 36 flocks. Ovine IGF1R C was associated with age when adjusting for flock (present 5.5 ± 0.2 yr, absent 5.0 ± 0.1 yr, P = 0.02). A general linear mixed effects model suggested an association (P = 0.06) between age and genotype, when correcting for flock. Pairwise comparison (least significant difference) of specific genotypes revealed the difference to be between AA (5.0± 0.1 yr) and AC (5.6 ± 0.2 yr, P = 0.02). A weak negative Pearson correlation between fertility and longevity traits was observed (r = -0.25, P < 0.01). The finding of an association between variation in IGF1R and lifespan in sheep may be useful in prolonging the lifespan of sheep

Genetic diversity of selected genes that are potentially economically important in feral sheep of New Zealand

Background: Feral sheep are considered to be a source of genetic variation that has been lost from their domestic counterparts through selection. Methods: This study investigates variation in the genes KRTAP1-1, KRT33, ADRB3 and DQA2 in Merino-like feral sheep populations from New Zealand and its offshore islands. These genes have previously been shown to influence wool, lamb survival and animal health. Results: All the genes were polymorphic, but no new allele was identified in the feral populations. In some of these populations, allele frequencies differed from those observed in commercial Merino sheep and other breeds found in New Zealand. Heterozygosity levels were comparable to those observed in other studies on feral sheep. Our results suggest that some of the feral populations may have been either inbred or outbred over the duration of their apparent isolation. Conclusion: The variation described here allows us to draw some conclusions about the likely genetic origin of the populations and selective pressures that may have acted upon them, but they do not appear to be a source of new genetic material, at least for these four genes.This research was supported by the Brian Mason Scientific and Technical Trust

Ovine FABP₄ variation and its association with flystrike susceptibility

Flystrike is a major cost and a welfare issue for the New Zealand sheep industry. There are several factors that can predispose sheep to flystrike, such as having fleecerot, a urine-stained breech, and “dags” (an accumulation of fecal matter in the wool of the breech). The FABP₄ gene (FABP₄) has been associated with variation in ovine fleecerot resistance, with a strong genetic correlation existing between fleecerot and flystrike occurrence. In this study, blood samples were collected from sheep with and without flystrike for DNA typing. PCR-SSCP analyses were used to genotype two regions of ovine FABP₄. Sheep with the A₁ variant of FABP₄ were found to be less likely (odds ratio 0.689, P = 0.014) to have flystrike than those without A₁. The likelihood of flystrike occurrence decreased as copy number of A₁ increased (odds ratio 0.695, P = 0.006). This suggests that FABP₄ might be a candidate gene for flystrike resilience in sheep, although further research is required to verify this association

The complexity of the ovine and caprine keratin-associated protein genes

Sheep (Ovis aries) and goats (Capra hircus) have, for more than a millennia, been a source of fibres for human use, be it for use in clothing and furnishings, for insulation, for decorative and ceremonial purposes, or for combinations thereof. While use of these natural fibres has in some respects been superseded by the use of synthetic and plant-based fibres, increased accounting for the carbon and water footprint of these fibres is creating a re-emergence of interest in fibres derived from sheep and goats. The keratin-associated proteins (KAPs) are structural components of wool and hair fibres, where they form a matrix that cross-links with the keratin intermediate filaments (KIFs), the other main structural component of the fibres. Since the first report of a complete KAP protein sequence in the late 1960s, considerable effort has been made to identify the KAP proteins and their genes in mammals, and to ascertain how these genes and proteins control fibre growth and characteristics. This effort is ongoing, with more and more being understood about the structure and function of the genes. This review consolidates that knowledge and suggests future directions for research to further our understanding

Variation in the fatty acid synthase gene (FASN) and its association with milk traits in Gannan yaks

Fatty acid synthase (FASN) is an enzyme involved in the synthesis of fatty acids (FA) and plays a central role in de novo lipogenesis in mammals. This study was conducted to ascertain the relative level of expression of the FASN gene (FASN) in tissues from the yak (Bos grunniens), and to search for variation in two regions of yak FASN using polymerase chain reaction single-stranded conformational polymorphism (PCR-SSCP) analyses; it also ascertains whether that variation is associated with yak milk traits. The gene was found to be expressed in twelve tissues, with the highest expression detected in the mammary gland, followed by subcutaneous fat tissue. Two regions of the gene were analyzed in 290 Gannan yaks: A region spanning exon 24-intron 24 and a region spanning exon 34. These regions both produced two PCR-SSCP patterns, which, upon sequencing, represented different DNA sequences. This sequence variation resulted from the presence of three nucleotide substitutions: c.4296+38C/T (intron 24), c.5884A/G, and c.5903G/A, both located in exon 34. The exon 34 substitutions would result in the amino acid substitutions p.Thr1962Ala and p.Gly1968Glu if expressed. Four haplotypes spanning from the exon 24-intron 24 region to exon 34 were identified. Of these, two were common (A₁-A₂ and B₁-A₂), and two were rare (A₁-B₂ and B₁-B₂) in the yaks investigated. The presence of A₁-A₂ was associated with an increase in milk fat content (p = 0.050) and total milk solid content (p = 0.037), while diplotype A₁-A₂/B₁-A₂ had a higher milk fat content (p = 0.038) than the other diplotypes. This study suggests that further characterization of the FASN gene might provide for an improved understanding of milk traits in yaks

Characterization of footrot bacteria Dichelobacter nodosus using PCR amplification and DNA sequence analysis

Dichelobacter nodosus is an essential causative agent of footrot in ruminants, particularly in sheep, goats and cattle. In this study, more than 100 footrot samples were collected from 4 different farming regions in New Zealand (NZ). Selective media were chosen and isolation and routine growth conditions were optimized for NZ D. nodosus serotypes. Approximately 1000 primary plates were anaerobically subcultured several times and examined with Gram staining in order to detect single colonies of D. nodosus. Both the variable region and a part of the conserved region of fimbrial subunit gene (fimA) were amplified from bacterial DNA using polymerase chain reaction (PCR). On the basis of PCR and DNA sequencing, 6 new D. nodosus isolates were identified and characterized from NZ. These sequences of D. nodosus fimA gene from NZ were genetically different from previously reported strains in the GenBank (NCBI) and commercial vaccine strains

Role of bovine MHC genes in resistance to mastitis

In this research we have used the MHC typing technologies we have developed forsheep, in dairy cattle. We have identified eleven alleles at the Bovine DQA2 locus to date,including two new sequences (Accession Numbers AF 388177 and AF388178). Thesegregation of these alleles has been assessed in large progeny groups derived from eight sires,covering two dairy breeds (Holstein-Friesian and Jersey). Preliminary evaluation revealsstatistically significant differences in mean somatic cell count for the progeny groups and a linkbetween particular alleles and increased or decreased somatic cell count in some sirelines

A celebration of wool biology

Opening address of the conferenc