Identification of candidate novel production variants on the Bos taurus chromosome X

Chromosome X is often excluded from bovine genetic studies due to complications caused by the sex specific nature of the chromosome. As chromosome X is the second largest cattle chromosome and makes up approximately 6% of the female genome, finding ways to include chromosome X in dairy genetic studies is important. Using female animals and treating chromosome X as an autosome, we performed X chromosome inclusive genome-wide association studies in the selective breeding environment of the New Zealand dairy industry, aiming to identify chromosome X variants associated with milk production traits. We report on the findings of these genome-wide association studies and their potential effect within the dairy industry. We identify missense mutations in the MOSPD1 and CCDC160 genes that are associated with decreased milk volume and protein production and increased fat production. Both of these mutations are exonic SNP that are more prevalent in the Jersey breed than in Holstein-Friesians. Of the 2 candidates proposed it is likely that only one is causal, though we have not been able to identify which is more likely.

High male specific contribution of the X-chromosome to individual global recombination rate in dairy cattle

Background

Meiotic recombination plays an important role in reproduction and evolution. The individual global recombination rate (GRR), measured as the number of crossovers (CO) per gametes, is a complex trait that has been shown to be heritable. The sex chromosomes play an important role in reproduction and fertility related traits. Therefore, variants present on the X-chromosome might have a high contribution to the genetic variation of GRR that is related to meiosis and to reproduction.

Results

We herein used genotyping data from 58,474 New Zealand dairy cattle to estimate the contribution of the X-chromosome to male and female GRR levels. Based on the pedigree-based relationships, we first estimated that the X-chromosome accounted for 30% of the total additive genetic variance for male GRR. This percentage was equal to 19.9% when the estimation relied on a SNP-BLUP approach assuming each SNP has a small contribution. We then carried out a haplotype-based association study to map X-linked QTL, and subsequently fine-mapped the identified QTL with imputed sequence variants. With this approach we identified three QTL with large effect accounting for 7.7% of the additive genetic variance of male GRR. The associated effects were equal to + 0.79, − 1.16 and + 1.18 CO for the alternate alleles. In females, the estimated contribution of the X-chromosome to GRR was null and no significant association with X-linked loci was found. Interestingly, two of the male GRR QTL were associated with candidate genes preferentially expressed in testis, in agreement with a male-specific effect. Finally, the most significant QTL was associated with PPP4R3C, further supporting the important role of protein phosphatase in double-strand break repair by homologous recombination.

Conclusions

Our study illustrates the important role the X-chromosome can have on traits such as individual recombination rate, associated with testis in males. We also show that contribution of the X-chromosome to such a trait might be sex dependent.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08328-8.

Heifers with positive genetic merit for fertility traits reach puberty earlier and have a greater pregnancy rate than heifers with negative genetic merit for fertility traits

This study investigated the hypothesis that dairy heifers divergent in genetic merit for fertility traits differ in the age of puberty and reproductive performance. New Zealand's fertility breeding value (FertBV) is the proportion of a sire's daughters expected to calve in the first 42 d of the seasonal calving period. We used the New Zealand national dairy database to identify and select Holstein-Friesian dams with either positive (POS, +5 FertBV, n = 1,334) or negative FertBV (NEG, -5% FertBV, n = 1,662) for insemination with semen from POS or NEG FertBV sires, respectively. The resulting POS and NEG heifers were predicted to have a difference in average FertBV of 10 percentage points. We enrolled 640 heifer calves (POS, n = 324; NEG, n = 316) at 9 d ± 5.4 d (± standard deviation; SD) for the POS calves and 8 d ± 4.4 d old for the NEG calves. Of these, 275 POS and 248 NEG heifers were DNA parent verified and retained for further study. The average FertBV was +5.0% (SD = 0.74) and -5.1% (SD = 1.36) for POS and NEG groups, respectively. Heifers were reared at 2 successive facilities as follows: (1) calf rearing (enrollment to ∼13 wk of age) and (2) grazier, after 13 wk until 22 mo of age. All heifers wore a collar with an activity sensor to monitor estrus events starting at 8 mo of age, and we collected weekly blood samples when individual heifers reached 190 kg of body weight (BW) to measure plasma progesterone concentrations. Puberty was characterized by plasma progesterone concentrations >1 ng/mL in at least 2 of 3 successive weeks. Date of puberty was defined when the first of these samples was >1 ng/mL. Heifers were seasonally bred for 98 d starting at ∼14 mo of age. Transrectal ultrasound was used to confirm pregnancy and combined with activity data to estimate breeding and pregnancy dates. We measured BW every 2 wk, and body condition and stature at 6, 9, 12, and 15 mo of age. The significant FertBV by day interaction for BW was such that the NEG heifers had increasingly greater BW with age. This difference was mirrored with the significant FertBV by month interaction for average daily gain, with the NEG heifers having a greater average daily gain between 9 and 18 mo of age. There was no difference in heifer stature between the POS and NEG heifers. The POS heifers were younger and lighter at puberty, and were at a lesser mature BW, compared with the NEG heifers. As a result, 94 ± 1.6% of the POS and 82 ± 3.2% of the NEG heifers had reached puberty at the start of breeding. The POS heifers were 20% and 11% more likely to be pregnant after 21 d and 42 d of breeding than NEG heifers (relative risk = 1.20, 95% confidence interval of 1.03-1.34; relative risk = 1.11, 95% confidence interval of 1.01-1.16). Results from this experiment support an association between extremes in genetic merit for fertility base on cow traits and heifer reproduction. Our results indicate that heifer puberty and pregnancy rates are affected by genetic merit for fertility traits, and these may be useful phenotypes for genetic selection.

Validation of a single-nucleotide polymorphism panel for parentage testing of farmed red deer

Red deer behaviour prevents the accurate physical matching of dams to fawns and, therefore, breeders have to rely on DNA-based parentage testing. A panel consisting of 100 single nucleotide polymorphism markers, with an average minor allele frequency of 0.25, was able to resolve 92% of fawns to both parents. In comparison, an existing 12-marker microsatellite panel was able to resolve 68% of fawns to both parents. When excluding dam DNA information, the single nucleotide polymorphism panel matched 81% of the fawns to their sires and the microsatellite panel 71%.

Genetic variation in PLAG1 associates with early life body weight and peripubertal weight and growth in Bos taurus

Variation at the pleiomorphic adenoma gene 1 (PLAG1) locus has recently been implicated in the regulation of stature and weight in Bos taurus. Using a population of 942 outbred Holstein-Friesian dairy calves, we report confirmation of this effect, demonstrating strong association of early life body weight with PLAG1 genotype. Peripubertal body weight and growth rate were also significantly associated with PLAG1 genotype. Growth rate per kilogram of body weight, daily feed intake, gross feed efficiency and residual feed intake were not significantly associated with PLAG1 genotype. This study supports the status of PLAG1 as a key regulator of mammalian growth. Further, the data indicate the utility of PLAG1 polymorphisms for the selection of animals to achieve enhanced weight gain or conversely to aid the selection of animals with lower mature body weight and thus lower maintenance energy requirements.

A randomized, double-blind comparison of beclomethasone dipropionate extrafine aerosol and fluticasone propionate

BACKGROUND

Inhaled corticosteroids provide first-line treatment for asthma. An advance to improve potency was to produce new molecules with increased glucocorticoid receptor affinity (eg, fluticasone propionate [FP]). An alternative is to deliver more medication to both the large and small airway inflammation of asthma by using an extrafine aerosol (eg, beclomethasone dipropionate extrafine aerosol [BDP-extrafinel).

OBJECTIVE

To demonstrate clinical equivalence of BDP-extrafine (400 microg daily) and FP (400 microg daily) in symptomatic asthmatic patients over the course of 6 weeks.

METHODS

This was a double-blind, double-dummy, parallel-group, multicenter, 6-week study in adults with asthma taking conventional FP 100 to 250 microg daily or equivalent, and displaying signs/symptoms of active disease requiring additional therapy.

RESULTS

Eighty-eight patients were randomized to BDP-extrafine (and FP-placebo) and 84 to FP (and BDP-placebo). There were no significant differences between treatments with respect to symptom control, as evidenced by mean change from baseline in percentage days without asthma symptoms/nights without sleep disturbance observed at weeks 1 to 2, 3 to 4, or 5 to 6. Mean changes from baseline in AM PEFR at weeks 5 to 6 for BDP-extrafine (19.0) and FP (30.5) were equivalent (P = 0.022 for equivalence). There were significant (P < 0.001) within-treatment-group differences in mean change from baseline in AM PEFR at weeks 1 to 2 for both treatments. There was no difference in the incidence of patients reporting at least one adverse event during the study (BDP-extrafine 41%; FP 37%). Mean percentage change from baseline for AM plasma cortisol at week 6 was + 17.7% for BDP-extrafine and +4.2% for FP (P = 0.066 for difference).

CONCLUSIONS

BDP-extrafine and FP at doses of 400 microg daily provided equivalent asthma control in patients with symptomatic asthma and exhibited similar safety profiles.

Present and future management of asthma and COPD: proceedings from WONCA 1998

On 15 June 1998, a workshop on asthma and chronic obstructive pulmonary disease (COPD) was held at the WONCA conference in Dublin. Based on the current guidelines for diagnosis and treatment of asthma and COPD, new developments and present and future research projects were discussed. Based on these guidelines and the research findings, new developments were positioned. The final conclusion of this workshop was that there is a need to continue exchanging ideas at an international level. So an initiative to start a Scientific Group of Primary Care Research within the European Respiratory Society has been taken.

Genetic response from marker assisted selection in an outbred population for differing marker bracket sizes and with two identified quantitative trait loci

Effect of flanking quantitative trait loci (QTL)-marker bracket size on genetic response to marker assisted selection in an outbred population was studied by simulation of a nucleus breeding scheme. In addition, genetic response with marker assisted selection (MAS) from two quantitative trait loci on the same and different chromosome(s) was investigated. QTL that explained either 5% or 10% of phenotypic variance were simulated. A polygenic component was simulated in addition to the quantitative trait loci. In total, 35% of the phenotypic variance was due to genetic factors. The trait was measured on females only. Having smaller marker brackets flanking the QTL increased the genetic response from MAS selection. This was due to the greater ability to trace the QTL transmission from one generation to the next with the smaller flanking QTL-marker bracket, which increased the accuracy of estimation of the QTL allelic effects. Greater negative covariance between effects at both QTL was observed when two QTL were located on the same chromosome compared to different chromosomes. Genetic response with MAS was greater when the QTL were on the same chromosome in the early generations and greater when they were on different chromosomes in the later generations of MAS.

Recent asthma guidelines, what are the implications for patient management?

Recent publications in particular the British Thoracic Society guidelines for the management of adult asthma, recommend that bronchodilators should not be used more than once a day without anti-inflammatory treatment. There have not been any studies to determine what effect the implementation of these recommendations will have on our management of asthmatic patients. In this study 110 asthmatics who were using regular asthma treatment were identified. Thirty eight (34.5%) were using inhaled beta-agonists alone, of whom 11 (29%) required them more than once day for the relief of symptoms. Seventy two (65%) were using an inhaled anti-inflammatory agent plus an inhaled beta-agonist, of whom 38 (53%) were using their inhaled beta-agonist more than once per day. Forty-nine subjects (45%) therefore required a change in their management as their inhaled beta agonist use exceeded once a day. They were subsequently managed according to a treatment protocol based on current asthma guidelines and followed up over a three-month period. Twenty-eight of these (57%) required a change in their current therapy comprising of the addition of or an increased dose of their existing inhaled anti-inflammatory medication. Seventeen (34.6%) did not require a change in their current therapy, rather they required advice re: the proper use of their "preventitive" medication, or the introduction of a large volume spacer device. Four (8%) were on maximum therapy and no further intervention was possible. Forty-one (83.6%) reduced their inhaled beta agonist requirements to once or less per day within the study period.

Two-year follow up of the management of chronic or recurrent cough in children according to an asthma protocol

To test the hypothesis that many children with a chronic or recurring cough have asthma, 106 children with cough were treated according to an asthma protocol. At the end of 16 weeks, all but two of the children who completed this phase of the trial were free of cough. At a two-year follow up 97 children were reviewed: 71 were now diagnosed as having an asthmatic condition, 34 of whom required regular medication. The original histories of those who developed asthma were compared with those who had no further respiratory symptoms. The results suggest that many children with a chronic or recurring cough have a mild form of asthma, known as cough variant asthma, which is responsive to asthma therapy. Many will subsequently develop mild to moderately severe asthma. Those who subsequently develop an asthmatic condition are statistically more likely to have a family history of asthma or a personal history of atopy. The children are also more likely to have exercise-induced cough or nocturnal exacerbation of their cough. Managing a persistent or recurring cough according to an asthma protocol could mean that many asthmatic children will be diagnosed and treated earlier in the natural history of their illness.

Chronic or recurrent cough in children--a presentation of asthma?

Thirty-five children between the ages of one year and 11 years who presented with chronic or recurring cough over a two-year period were treated for asthma. They were given bronchodilator syrup for a trial period of one month. All the children improved symptomatically.It is suggested that any child with a persistent cough or recurring cough should be given bronchodilator syrup even in the absence of wheeze and particularly when there is a family history of asthma. This might result in the early diagnosis of unrecognized asthma and help to reduce the amount of unnecessary antibiotics and cough linctus that these children receive.