Browsing IJAFR, volume 58, 2019 by Title
Now showing items 6-9 of 9
Low-density genotype panel for both parentage verification and discovery in a multi-breed sheep populationThe generally low usage of artificial insemination and single-sire mating in sheep, compounded by mob lambing (and lambing outdoors), implies that parentage assignment in sheep is challenging. The objective here was to develop a low-density panel of single nucleotide polymorphisms (SNPs) for accurate parentage verification and discovery in sheep. Of particular interest was where SNP selection was limited to only a subset of chromosomes, thereby eliminating the ability to accurately impute genome-wide denser marker panels. Data used consisted of 10,933 candidate SNPs on 9,390 purebred sheep. These data consisted of 1,876 validated genotyped sire–offspring pairs and 2,784 validated genotyped dam–offspring pairs. The SNP panels developed consisted of 87 SNPs to 500 SNPs. Parentage verification and discovery were undertaken using 1) exclusion, based on the sharing of at least one allele between candidate parent–offspring pairs, and 2) a likelihood-based approach. Based on exclusion, allowing for one discordant offspring–parent genotype, a minimum of 350 SNPs was required when the goal was to unambiguously identify the true sire or dam from all possible candidates. Results suggest that, if selecting SNPs across the entire genome, a minimum of 250 carefully selected SNPs are required to ensure that the most likely selected parent (based on the likelihood approach) was, in fact, the true parent. If restricting the SNPs to just a subset of chromosomes, the recommendation is to use at least a 300-SNP panel from at least six chromosomes, with approximately an equal number of SNPs per chromosome.
Prediction of 24-hour milk yield and composition in dairy cows from a single part-day yield and sampleIrish Journal of Agricultural and Food Research | Volume 58: Issue 1 Prediction of 24-hour milk yield and composition in dairy cows from a single part-day yield and sample S. McParlandemail , B. Coughlan , B. Enright , M. O’Keeffe , R. O’Connor , L. Feeney and D.P. Berry DOI: https://doi.org/10.2478/ijafr-2019-0007 | Published online: 09 Aug 2019 PDF Abstract Article PDF References Recommendations Abstract The objective was to evaluate the accuracy of predicting 24-hour milk yield and composition from a single morning (AM) or evening (PM) milk weight and composition. A calibration dataset of 37,481 test-day records with both AM and PM yields and composition was used to generate the prediction equations; equations were validated using 4,644 test-day records. Prediction models were developed within stage of lactation and parity while accounting for the inter-milking time interval. The mean correlation between the predicted 24-hour yields and composition of milk, fat and protein and the respective actual values was 0.97 when based on just an AM milk yield and composition with a mean correlation of 0.95 when based on just a PM milk yield and composition. The regression of predicted 24-hour yield and composition on the respective actual values varied from 0.97 to 1.01 with the exception of 24-hour fat percentage predicted from a PM sample (1.06). A single AM sample is useful to predict 24-hour milk yield and composition when the milking interval is known.
Prevalence of QoI resistance and mtDNA diversity in the Irish Zymoseptoria tritici populationThe emergence and spread of Quinone outside Inhibitor (QoI) fungicide resistance in the Irish Zymoseptoria tritici population in the early 2000s had immediate impacts on the efficacy of the entire group of fungicides for the control of septoria tritici blotch. As a result, a dramatic reduction in the quantities applied to winter wheat occurred in the following seasons. Even in the absence of these fungicides, the frequency of the resistance allele, G143A in the pathogens mtDNA has remained exceptionally high (>97%), and as such, it can be anticipated that continued poor efficacy of current QoI fungicides will be observed. Amongst the isolates with G143A, differences in sensitivity to the QoI pyraclostrobin were observed in vitro. The addition of the alternative oxidase (AOX) inhibitor salicylhydroxamic acid increased sensitivity in these isolates, suggesting some continued impairment of respiration by the QoI fungicides, albeit weak. Interestingly, amongst those tested, the strains from a site with a high frequency of inserts in the MFS1 transporter gene known to enhance QoI efflux did not exhibit this increase in sensitivity. A total of 19 mtDNA haplotypes were detected amongst the 2017 strain collection. Phylogenetic analysis confirmed the suggestion of a common ancestry of all the haplotypes, even though three of the haplotypes contained at least one sensitive strain.
Sensory and ATP derivative-based indicators for assessing the freshness of Atlantic salmon (Salmo salar) and cod (Gadus morhua)Irish Journal of Agricultural and Food Research | Volume 58: Issue 1 Sensory and ATP derivative-based indicators for assessing the freshness of Atlantic salmon (Salmo salar) and cod (Gadus morhua) Colin Fogarty , Conor Smyth , Paul Whyte , Nigel Brunton and Declan Boltonemail DOI: https://doi.org/10.2478/ijafr-2019-0008 | Published online: 31 Oct 2019 PDF Abstract Article PDF References Recommendations Abstract To estimate the shelf life of fresh fish, the processor must know the period of time between catch/harvest and arrival at the processing plant. This information is not always available, necessitating the provision of methods to estimate the time since catch or harvest. The objectives of this study were therefore to develop and/or validate sensory and ATP derivative-based methods for rapidly assessing the freshness of fish. A quality index method (QIM; raw fish) and a quantitative descriptive analysis (QDA; cooked fish) were developed and validated (against bacterial count [total viable count (TVC)] and time) for salmon (Salmo salar) and cod (Gadus morhua). The production of inosine monophosphate (IMP), inosine and hypoxanthine (Hx) and associated ratios (IMP/Hx, K1-value or H-value) were also investigated for use as freshness markers. There was a linear relationship between QIM and TVC (R2 = 0.93 for salmon and R2 = 0.89 for cod), QIM and time (R2 = 0.96 for salmon and R2 = 0.98 for cod), QDA and TVC (R2 = 0.93 for salmon and R2 = 0.77 for cod) and QDA and time (R2 = 0.94 for salmon and R2 = 0.87 for cod), suggesting that the QIM and QDA schemes developed could be used to monitor/assess freshness. The H-value also increased linearly with TVC (R2 = 0.88 for salmon and R2 = 0.89 for cod) and time (R2 = 0.93 for salmon and R2 = 0.84 for cod). It was therefore concluded that both the QIM/QDA approach and monitoring ATP degradation, specifically expressed as the H-value, could be used as rapid methods to assess the freshness of salmon and cod arriving at the processing plant