John C McEwan | AgResearch Limited (original) (raw)
Papers by John C McEwan
BMC Genomics, Aug 3, 2007
Animal Feed Science and Technology, 2019
Animal Genetics, Apr 7, 2019
Genetics Selection Evolution, Apr 26, 2006
Animal Genetics, Jul 30, 2018
bioRxiv (Cold Spring Harbor Laboratory), Sep 23, 2015
Orphanet Journal of Rare Diseases, Sep 2, 2015
G3 Genes|Genomes|Genetics, 2021
Events of inbreeding are inevitable in critically endangered species. Reduced population sizes an... more Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition,...
Scientific Reports, 2017
Meckel syndrome (MKS) is an inherited autosomal recessive hepatorenal fibrocystic syndrome, cause... more Meckel syndrome (MKS) is an inherited autosomal recessive hepatorenal fibrocystic syndrome, caused by mutations in TMEM67, characterized by occipital encephalocoele, renal cysts, hepatic fibrosis, and polydactyly. Here we describe an ovine model of MKS, with kidney and liver abnormalities, without polydactyly or occipital encephalocoele. Homozygous missense p.(Ile681Asn; Ile687Ser) mutations identified in ovine TMEM67 were pathogenic in zebrafish phenotype rescue assays. Meckelin protein was expressed in affected and unaffected kidney epithelial cells by immunoblotting, and in primary cilia of lamb kidney cyst epithelial cells by immunofluorescence. In contrast to primary cilia of relatively consistent length and morphology in unaffected kidney cells, those of affected cyst-lining cells displayed a range of short and extremely long cilia, as well as abnormal morphologies, such as bulbous regions along the axoneme. Putative cilia fragments were also consistently located within the cy...
Journal of Animal Science, 2017
Evidence exists from a range of species on the impact of karyotype abnormalities on reproductive ... more Evidence exists from a range of species on the impact of karyotype abnormalities on reproductive performance. Despite this, cytogenetic analyses of cattle, especially females, are not routinely undertaken. Genome-wide single nucleotide polymorphism (SNP) genotype data are now, however, routinely being generated in many species globally at a relatively low cost. The objective of the present study was to evaluate the potential of routinely available SNP genotype data to identify sex-chromosome aberrations using X chromosome monosomy 59,X0 as a case study for illustration. A single 2.5-yr old Holstein-Friesian heifer was detected with a mean allelic intensity of SNP on the X chromosome almost 17 standard deviations less than the mean of other genotyped females ( = 103,326). Following cytogenetic analysis (10 replicates by karyotyping and a further 140 by FISH), the female was deduced to be a non-mosaic 59,X0. The female had never produced a calf and, although gross examination revealed no physical abnormalities, she was smaller in size than expected based on her breed and age. Given the age of the animal at slaughter, the uterus and uterine tubes appeared immature and inactive. The oviduct appeared normal while the single ovary present contained a markedly reduced number of follicles. There was, however, some evidence of prior ovulation and formation of corpora lutea. The approach proposed in the present study to identify allosome aneuploidy from routinely available genotype data can be used to screen for such abnormalities at no additional cost to the breeder or producer.
Animal, 2015
Measuring and mitigating methane (CH4) emissions from livestock is of increasing importance for t... more Measuring and mitigating methane (CH4) emissions from livestock is of increasing importance for the environment and for policy making. Potentially, the most sustainable way of reducing enteric CH4emission from ruminants is through the estimation of genomic breeding values to facilitate genetic selection. There is potential for adopting genetic selection and in the future genomic selection, for reduced CH4emissions from ruminants. From this review it has been observed that both CH4emissions and production (g/day) are a heritable and repeatable trait. CH4emissions are strongly related to feed intake both in the short term (minutes to several hours) and over the medium term (days). When measured over the medium term, CH4yield (MY, g CH4/kg dry matter intake) is a heritable and repeatable trait albeit with less genetic variation than for CH4emissions. CH4emissions of individual animals are moderately repeatable across diets, and across feeding levels, when measured in respiration chambe...
Animals
In this study, we analysed the effect of human-mediated selection on the gene pool of wild and fa... more In this study, we analysed the effect of human-mediated selection on the gene pool of wild and farmed red deer populations based on genotyping-by-sequencing data. The farmed red deer sample covered populations spread across seven countries and two continents (France, Germany, Hungary, Latvia, New Zealand, Poland, and Slovakia). The Slovak and Spain wild red deer populations (the latter one in a large game estate) were used as control outgroups. The gene flow intensity, relationship and admixture among populations were tested by the Bayesian approach and discriminant analysis of principal components (DAPC). The highest gene diversity (He = 0.19) and the lowest genomic inbreeding (FHOM = 0.04) found in Slovak wild population confirmed our hypothesis that artificial selection accompanied by bottlenecks has led to the increase in overall genomic homozygosity. The Bayesian approach and DAPC consistently identified three separate genetic groups. As expected, the farmed populations were cl...
Background Rumen microbes break down complex dietary carbohydrates into energy sources for the ho... more Background Rumen microbes break down complex dietary carbohydrates into energy sources for the host and are increasingly shown to be a key aspect of animal performance. Host genotypes can be combined with microbial DNA sequencing to predict performance traits or traits related to environmental impact, such as enteric methane emissions. Metagenome profiles were generated from 3,139 rumen samples, collected from 1,200 dual purpose ewes, using Restriction Enzyme-Reduced Representation Sequencing (RE-RRS). Phenotypes were available for methane (CH4) and carbon dioxide (CO2) emissions, the ratio of CH4 to CH4 plus CO2 (CH4Ratio), feed efficiency (Residual Feed Intake: RFI), liveweight at the time of methane collection (LW), liveweight at 8 months (LW8), fleece weight at 12 months (FW12) and parasite resistance measured by faecal egg count (FEC1). We estimated the proportion of phenotypic variance explained by host genetics and the rumen microbiome, as well as prediction accuracies for ea...
Frontiers in Genetics
Enteric methane emissions from ruminants account for ∼35% of New Zealand’s greenhouse gas emissio... more Enteric methane emissions from ruminants account for ∼35% of New Zealand’s greenhouse gas emissions. This poses a significant threat to the pastoral sector. Breeding has been shown to successfully lower methane emissions, and genomic prediction for lowered methane emissions has been introduced at the national level. The long-term genetic impacts of including low methane in ruminant breeding programs, however, are unknown. The success of the New Zealand sheep industry is currently heavily reliant on the prolificacy, fecundity and survival of adult ewes. The objective of this study was to determine genetic and phenotypic correlations between adult maternal ewe traits (live weight, body condition score, number of lambs born, litter survival to weaning, pregnancy scanning and fleece weight), faecal andNematodirusegg counts and measures of methane in respiration chambers. More than 9,000 records for methane from over 2,200 sheep measured in respiration chambers were collected over 10 yea...
Introduction Methane is a waste product generated by methanogenic archaea in the rumen of the hos... more Introduction Methane is a waste product generated by methanogenic archaea in the rumen of the host. In New Zealand, methane emitted by ruminants accounts for ~31% of anthropogenic greenhouse gas (GHG) emissions. Mitigation strategies to lower ruminant methane production are an important aspect of the national strategy to reduce GHG emissions. It has been shown that methane varies both with the genetics of the individual ruminant host and with the microbial populations present in the rumen. Current research is focussed on diet, vaccination, chemical inhibition, and genetic selection of lower emitting animals. The mitigation of methane production by genetic selection has been shown to be effective by divergently selecting for high and low methane emitting sheep (PinaresPatino et al. 2011; 2013). This approach is attractive as breeding is cumulative and sustainable. The many thousands of methane measures required for a commercial breeding program, however, would be prohibitively diffic...
Background Producing animal protein while reducing the animal’s impact on the environment, e.g., ... more Background Producing animal protein while reducing the animal’s impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible. Results Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (...
Frontiers in Genetics
There is simultaneous interest in improving the feed efficiency of ruminant livestock and reducin... more There is simultaneous interest in improving the feed efficiency of ruminant livestock and reducing methane (CH4) emissions. The relationship (genetic and phenotypic) between feed efficiency (characterized as residual feed intake: RFI) and greenhouse gases [methane (CH4) and carbon dioxide (CO2)] traits in New Zealand (NZ) maternal sheep has not previously been investigated, nor has their relationship with detailed estimates of body composition. To investigate these relationships in NZ maternal sheep, a feed intake facility was established at AgResearch Invermay, Mosgiel, NZ in 2015, comprising automated feeders that record individual feeding events. Individual measures of feed intake, feeding behavior (length and duration of eating events), and gas emissions (estimated using portable accumulation chambers) were generated on 986 growing maternal ewe lambs sourced from three pedigree recorded flocks registered in the Sheep Improvement Limited database (www.sil.co.nz). Additional data ...
BMC Genomics, Aug 3, 2007
Animal Feed Science and Technology, 2019
Animal Genetics, Apr 7, 2019
Genetics Selection Evolution, Apr 26, 2006
Animal Genetics, Jul 30, 2018
bioRxiv (Cold Spring Harbor Laboratory), Sep 23, 2015
Orphanet Journal of Rare Diseases, Sep 2, 2015
G3 Genes|Genomes|Genetics, 2021
Events of inbreeding are inevitable in critically endangered species. Reduced population sizes an... more Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition,...
Scientific Reports, 2017
Meckel syndrome (MKS) is an inherited autosomal recessive hepatorenal fibrocystic syndrome, cause... more Meckel syndrome (MKS) is an inherited autosomal recessive hepatorenal fibrocystic syndrome, caused by mutations in TMEM67, characterized by occipital encephalocoele, renal cysts, hepatic fibrosis, and polydactyly. Here we describe an ovine model of MKS, with kidney and liver abnormalities, without polydactyly or occipital encephalocoele. Homozygous missense p.(Ile681Asn; Ile687Ser) mutations identified in ovine TMEM67 were pathogenic in zebrafish phenotype rescue assays. Meckelin protein was expressed in affected and unaffected kidney epithelial cells by immunoblotting, and in primary cilia of lamb kidney cyst epithelial cells by immunofluorescence. In contrast to primary cilia of relatively consistent length and morphology in unaffected kidney cells, those of affected cyst-lining cells displayed a range of short and extremely long cilia, as well as abnormal morphologies, such as bulbous regions along the axoneme. Putative cilia fragments were also consistently located within the cy...
Journal of Animal Science, 2017
Evidence exists from a range of species on the impact of karyotype abnormalities on reproductive ... more Evidence exists from a range of species on the impact of karyotype abnormalities on reproductive performance. Despite this, cytogenetic analyses of cattle, especially females, are not routinely undertaken. Genome-wide single nucleotide polymorphism (SNP) genotype data are now, however, routinely being generated in many species globally at a relatively low cost. The objective of the present study was to evaluate the potential of routinely available SNP genotype data to identify sex-chromosome aberrations using X chromosome monosomy 59,X0 as a case study for illustration. A single 2.5-yr old Holstein-Friesian heifer was detected with a mean allelic intensity of SNP on the X chromosome almost 17 standard deviations less than the mean of other genotyped females ( = 103,326). Following cytogenetic analysis (10 replicates by karyotyping and a further 140 by FISH), the female was deduced to be a non-mosaic 59,X0. The female had never produced a calf and, although gross examination revealed no physical abnormalities, she was smaller in size than expected based on her breed and age. Given the age of the animal at slaughter, the uterus and uterine tubes appeared immature and inactive. The oviduct appeared normal while the single ovary present contained a markedly reduced number of follicles. There was, however, some evidence of prior ovulation and formation of corpora lutea. The approach proposed in the present study to identify allosome aneuploidy from routinely available genotype data can be used to screen for such abnormalities at no additional cost to the breeder or producer.
Animal, 2015
Measuring and mitigating methane (CH4) emissions from livestock is of increasing importance for t... more Measuring and mitigating methane (CH4) emissions from livestock is of increasing importance for the environment and for policy making. Potentially, the most sustainable way of reducing enteric CH4emission from ruminants is through the estimation of genomic breeding values to facilitate genetic selection. There is potential for adopting genetic selection and in the future genomic selection, for reduced CH4emissions from ruminants. From this review it has been observed that both CH4emissions and production (g/day) are a heritable and repeatable trait. CH4emissions are strongly related to feed intake both in the short term (minutes to several hours) and over the medium term (days). When measured over the medium term, CH4yield (MY, g CH4/kg dry matter intake) is a heritable and repeatable trait albeit with less genetic variation than for CH4emissions. CH4emissions of individual animals are moderately repeatable across diets, and across feeding levels, when measured in respiration chambe...
Animals
In this study, we analysed the effect of human-mediated selection on the gene pool of wild and fa... more In this study, we analysed the effect of human-mediated selection on the gene pool of wild and farmed red deer populations based on genotyping-by-sequencing data. The farmed red deer sample covered populations spread across seven countries and two continents (France, Germany, Hungary, Latvia, New Zealand, Poland, and Slovakia). The Slovak and Spain wild red deer populations (the latter one in a large game estate) were used as control outgroups. The gene flow intensity, relationship and admixture among populations were tested by the Bayesian approach and discriminant analysis of principal components (DAPC). The highest gene diversity (He = 0.19) and the lowest genomic inbreeding (FHOM = 0.04) found in Slovak wild population confirmed our hypothesis that artificial selection accompanied by bottlenecks has led to the increase in overall genomic homozygosity. The Bayesian approach and DAPC consistently identified three separate genetic groups. As expected, the farmed populations were cl...
Background Rumen microbes break down complex dietary carbohydrates into energy sources for the ho... more Background Rumen microbes break down complex dietary carbohydrates into energy sources for the host and are increasingly shown to be a key aspect of animal performance. Host genotypes can be combined with microbial DNA sequencing to predict performance traits or traits related to environmental impact, such as enteric methane emissions. Metagenome profiles were generated from 3,139 rumen samples, collected from 1,200 dual purpose ewes, using Restriction Enzyme-Reduced Representation Sequencing (RE-RRS). Phenotypes were available for methane (CH4) and carbon dioxide (CO2) emissions, the ratio of CH4 to CH4 plus CO2 (CH4Ratio), feed efficiency (Residual Feed Intake: RFI), liveweight at the time of methane collection (LW), liveweight at 8 months (LW8), fleece weight at 12 months (FW12) and parasite resistance measured by faecal egg count (FEC1). We estimated the proportion of phenotypic variance explained by host genetics and the rumen microbiome, as well as prediction accuracies for ea...
Frontiers in Genetics
Enteric methane emissions from ruminants account for ∼35% of New Zealand’s greenhouse gas emissio... more Enteric methane emissions from ruminants account for ∼35% of New Zealand’s greenhouse gas emissions. This poses a significant threat to the pastoral sector. Breeding has been shown to successfully lower methane emissions, and genomic prediction for lowered methane emissions has been introduced at the national level. The long-term genetic impacts of including low methane in ruminant breeding programs, however, are unknown. The success of the New Zealand sheep industry is currently heavily reliant on the prolificacy, fecundity and survival of adult ewes. The objective of this study was to determine genetic and phenotypic correlations between adult maternal ewe traits (live weight, body condition score, number of lambs born, litter survival to weaning, pregnancy scanning and fleece weight), faecal andNematodirusegg counts and measures of methane in respiration chambers. More than 9,000 records for methane from over 2,200 sheep measured in respiration chambers were collected over 10 yea...
Introduction Methane is a waste product generated by methanogenic archaea in the rumen of the hos... more Introduction Methane is a waste product generated by methanogenic archaea in the rumen of the host. In New Zealand, methane emitted by ruminants accounts for ~31% of anthropogenic greenhouse gas (GHG) emissions. Mitigation strategies to lower ruminant methane production are an important aspect of the national strategy to reduce GHG emissions. It has been shown that methane varies both with the genetics of the individual ruminant host and with the microbial populations present in the rumen. Current research is focussed on diet, vaccination, chemical inhibition, and genetic selection of lower emitting animals. The mitigation of methane production by genetic selection has been shown to be effective by divergently selecting for high and low methane emitting sheep (PinaresPatino et al. 2011; 2013). This approach is attractive as breeding is cumulative and sustainable. The many thousands of methane measures required for a commercial breeding program, however, would be prohibitively diffic...
Background Producing animal protein while reducing the animal’s impact on the environment, e.g., ... more Background Producing animal protein while reducing the animal’s impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible. Results Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (...
Frontiers in Genetics
There is simultaneous interest in improving the feed efficiency of ruminant livestock and reducin... more There is simultaneous interest in improving the feed efficiency of ruminant livestock and reducing methane (CH4) emissions. The relationship (genetic and phenotypic) between feed efficiency (characterized as residual feed intake: RFI) and greenhouse gases [methane (CH4) and carbon dioxide (CO2)] traits in New Zealand (NZ) maternal sheep has not previously been investigated, nor has their relationship with detailed estimates of body composition. To investigate these relationships in NZ maternal sheep, a feed intake facility was established at AgResearch Invermay, Mosgiel, NZ in 2015, comprising automated feeders that record individual feeding events. Individual measures of feed intake, feeding behavior (length and duration of eating events), and gas emissions (estimated using portable accumulation chambers) were generated on 986 growing maternal ewe lambs sourced from three pedigree recorded flocks registered in the Sheep Improvement Limited database (www.sil.co.nz). Additional data ...