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Item Association of common and rare variants with Alzheimer's disease in more than 13,000 diverse individuals with whole-genome sequencing from the Alzheimer's Disease Sequencing Project.(Wiley Periodicals LLC on behalf of Alzheimer's Association, 2024-10-20) Lee W-P; Choi SH; Shea MG; Cheng P-L; Dombroski BA; Pitsillides AN; Heard-Costa NL; Wang H; Bulekova K; Kuzma AB; Leung YY; Farrell JJ; Lin H; Kunkle BW; Naj A; Blue EE; Nusetor F; Wang D; Boerwinkle E; Bush WS; Zhang X; De Jager PL; Dupuis J; Farrer LA; Fornage M; Martin E; Pericak-Vance M; Seshadri S; Wijsman EM; Wang L-S; Alzheimer's Disease Sequencing Project; Schellenberg GD; Destefano AL; Haines JL; Peloso GMINTRODUCTION Alzheimer's disease (AD) is a common disorder of the elderly that is both highly heritable and genetically heterogeneous. METHODS We investigated the association of AD with both common variants and aggregates of rare coding and non-coding variants in 13,371 individuals of diverse ancestry with whole genome sequencing (WGS) data. RESULTS Pooled-population analyses of all individuals identified genetic variants at apolipoprotein E (APOE) and BIN1 associated with AD (p < 5 × 10−8). Subgroup-specific analyses identified a haplotype on chromosome 14 including PSEN1 associated with AD in Hispanics, further supported by aggregate testing of rare coding and non-coding variants in the region. Common variants in LINC00320 were observed associated with AD in Black individuals (p = 1.9 × 10−9). Finally, we observed rare non-coding variants in the promoter of TOMM40 distinct of APOE in pooled-population analyses (p = 7.2 × 10−8). DISCUSSION We observed that complementary pooled-population and subgroup-specific analyses offered unique insights into the genetic architecture of AD. Highlights We determine the association of genetic variants with Alzheimer's disease (AD) using 13,371 individuals of diverse ancestry with whole genome sequencing (WGS) data. We identified genetic variants at apolipoprotein E (APOE), BIN1, PSEN1, and LINC00320 associated with AD. We observed rare non-coding variants in the promoter of TOMM40 distinct of APOE.Item Growth and Carcass Characteristics of Beef-Cross-Dairy-Breed Heifers and Steers Born to Different Dam Breeds.(MDPI (Basel, Switzerland), 2022-03-29) Williamson HR; Schreurs NM; Morris ST; Hickson RE; Ebrahimie EApproximately two thirds of the annual beef kill in New Zealand originates from the dairy industry. The recent increase in Jersey genetics in the dairy herd will inevitably result in an increase in Jersey genetics entering the beef herd from retention of dairy-origin calves for finishing. Limited literature is available on the effect of dam breed on the performance of beef-cross-dairy-breed progeny. The aim of this study was to investigate the effect of dam breed from dams with varying proportions of Friesian and Jersey genetics on growth traits and carcass characteristics of their 24-month-old beef-cross-dairy-breed heifer and steer progeny. Liveweights of 142 heifers and 203 steers from Friesian (F), Friesian-cross (FX), Friesian-Jersey (FJ) and Jersey-cross (JX) dams were recorded at birth, weaning, as yearlings and at slaughter. Carcass characteristics were also recorded. At each point measured, liveweight was greatest for calves born to F dams. Calves born to F dams took 93 days to reach a weaning weight of 100 kg, whereas those from FX, FJ and JX dams took 99, 101 and 102 days, respectively. Carcass weight was greatest for progeny of F dams (286 kg, compared with 279, 275 and 276 for progeny of FX, FJ and JX dams, respectively). The progeny of JX dams had yellower fat than all other dam breed groups and a greater incidence of excessively yellow fat (fat score ≥ 5).Item A Deletion in GDF7 is Associated with a Heritable Forebrain Commissural Malformation Concurrent with Ventriculomegaly and Interhemispheric Cysts in Cats(MDPI (Basel, Switzerland), 2020-06-19) Yu Y; Creighton EK; Buckley RM; Lyons LA; 99 Lives ConsortiumAn inherited neurologic syndrome in a family of mixed-breed Oriental cats has been characterized as forebrain commissural malformation, concurrent with ventriculomegaly and interhemispheric cysts. However, the genetic basis for this autosomal recessive syndrome in cats is unknown. Forty-three cats were genotyped on the Illumina Infinium Feline 63K iSelect DNA Array and used for analyses. Genome-wide association studies, including a sib-transmission disequilibrium test and a case-control association analysis, and homozygosity mapping, identified a critical region on cat chromosome A3. Short-read whole genome sequencing was completed for a cat trio segregating with the syndrome. A homozygous 7 bp deletion in growth differentiation factor 7 (GDF7) (c.221_227delGCCGCGC [p.Arg74Profs]) was identified in affected cats, by comparison to the 99 Lives Cat variant dataset, validated using Sanger sequencing and genotyped by fragment analyses. This variant was not identified in 192 unaffected cats in the 99 Lives dataset. The variant segregated concordantly in an extended pedigree. In mice, GDF7 mRNA is expressed within the roof plate when commissural axons initiate ventrally-directed growth. This finding emphasized the importance of GDF7 in the neurodevelopmental process in the mammalian brain. A genetic test can be developed for use by cat breeders to eradicate this variant.Item Sire Effects on Carcass of Beef-Cross-Dairy Cattle: A Case Study in New Zealand(MDPI (Basel, Switzerland), 2021-03) Martin N; Schreurs N; Morris S; Lopez-Villalobos N; McDade J; Hickson RThere is interest in increasing the carcass value of surplus calves born in the dairy industry that are reared for beef production in New Zealand. This experiment evaluated the carcass of Angus and Hereford sires via progeny testing of beef-cross-dairy offspring grown on hill country pasture. Weight and carcass traits were analyzed from 1015 animals and 1000 carcasses of 73 sires. The mean of the progeny group means was 567 kg for live weight at slaughter, 277 kg for carcass weight, 48.9% for dressing-out, 240.3 cm for carcass length, 73.6 cm2 for eye muscle area, 7.4 mm for rib fat depth, 0.91 for marble score, 3.05 for fat color score, 3.01 for meat color score, and 5.62 for ultimate pH. Sire affected (p < 0.05) carcass size and fat traits, but not fat color, meat color, or ultimate pH (p > 0.05). There was a 46 kg increase in carcass weight between the best and worst sires tested. Carcass fat traits were the most variable among sires. The use of genetically superior beef-breed sires over dairy-breed cows has the potential to increase carcass weights from surplus calves born in the dairy industry, while maintaining adequate fat levels and carcass quality.Item The future of molecular ecology in Aotearoa New Zealand: an early career perspective(Taylor and Francis Group on behalf of the Royal Society of New Zealand, 2022-07-14) Liggins L; Arranz V; Braid HE; Carmelet-Rescan D; Elleouet J; Egorova E; Gemmell MR; Hills SFK; Holland LP; Koot EM; Lischka A; Maxwell KH; McCartney LJ; Nguyen HTT; Noble C; Olmedo Rojas P; Parvizi E; Pearman WS; Sweatman JAN; Kaihoro TR; Walton K; Aguirre JD; Stewart LC; Moss SThe skills, insights, and genetic data gathered by molecular ecologists are pivotal to addressing many contemporary biodiversity, environmental, cultural, and societal challenges. Concurrently, the field of molecular ecology is being revolutionised by rapid technological development and diversification in the scope of its applications. Hence, it is timely to review the future opportunities of molecular ecological research in Aotearoa New Zealand, and to reconcile them with philosophies of open science and the implications for Indigenous data sovereignty and benefit sharing. Future molecular ecologists need to be interdisciplinary, equipped to embrace innovation, and informed about the broader societal relevance of their research, as well as advocates of best practice. Here, we present an ideal future for molecular ecology in Aotearoa, based on the perspectives of 23 early career researchers from tertiary institutions, Crown Research Institutes, research consultancies, and government agencies. Our article provides: a guide for molecular ecologists embarking on genetic research in Aotearoa, and a primer for individuals in a position to support early career molecular ecologists in Aotearoa. We outline our goals and highlight specific considerations–for molecular ecology and the scientific community in Aotearoa–based on our own experience and aspirations, and invite other researchers to join this dialogue.Item Developmental and epileptic encephalopathy: Personal utility of a genetic diagnosis for families(Wiley Periodicals LLC on behalf of International League Against Epilepsy, 2021-03) Jeffrey JS; Leathem J; King C; Mefford HC; Ross K; Sadleir LGObjectives Identifying genetic pathogenic variants improves clinical outcomes for children with developmental and epileptic encephalopathy (DEE) by directing therapy and enabling accurate reproductive and prognostic information for families. We aimed to explore the additional personal utility of receiving a genetic diagnosis for families. Methods Semi-structured interviews were conducted with fifteen families of children with a DEE who had received a genetic diagnosis. The interviews stimulated discussion focusing on the impact of receiving a genetic diagnosis for the family. Interview transcripts were analyzed using the six-step systematic process of interpretative phenomenological analysis (IPA). Results Three key themes were identified: “Importance of the label,” “Relief to end the diagnostic journey,” and “Factors that influence personal utility.” Families reported that receiving a genetic label improved their knowledge about the likely trajectory of the DEE, increased their hope for the future, and helped them communicate with others. The relief of finally having an answer for the cause of their child's DEE alleviated parental guilt and self-blame as well as helped families to process their grief and move forward. Delay in receipt of a genetic diagnosis diluted its psychological impact. Significance To date, the factors associated with the personal utility of a genetic diagnosis for DEEs have been under appreciated. This study demonstrates that identifying a genetic diagnosis for a child's DEE can be a psychological turning point for families. A genetic result has the potential to set these families on an adaptive path toward better quality of life through increased understanding, social connection, and support. Early access to genetic testing is important as it not only increases clinical utility, but also increases personal utility with early mitigation of family stress, trauma, and negative experiences.Item Genetics of alternative definitions of feed efficiency in grazing lactating dairy cows(NZSAP, 7/07/2016) Hurley, AM; Lopez-Villalobos, N; McParland, S; Lewis, E; Kennedy, E; O'Donovan, M; Burke, JL; Berry, DPThe objective of this study was to estimate genetic parameters for measures of energy conversion efficiency (ECE), energy balance (EB), net energy intake (NEI), net energy of lactation (NEL) and body weight (BW), within lactation stages in grazing dairy cows. Individual measurements of NEI (n=7,675) from 2,445 lactations on 1,245 grazing cows were available. Residual energy intake (REI) was defined as NEI minus predicted energy requirements; residual energy production (REP) was defined as net energy of lactation (NEL) minus predicted energy requirements. Energy conversion efficiency was defined as NEL divided by NEI; EB was defined as the difference between intake and energy required for maintenance plus lactation. Lactation was divided into three stages (8-90, 91-180, and >180 days in milk [DIM]). Genetic and phenotypic (co)variances for EB, NEL and BW were estimated using univariate and bivariate animal repeatability models. The models included the fixed effects of contemporary group (treatment and test-date), parity, DIM, as well as a random additive genetic effect of animal, a within-lactation stage random permanent environmental effect and an across-lactation permanent environmental effect. Heritability across-lactation stages varied from 0.13 (8-90 DIM) to 0.28 (91-180 DIM) for NEI, from 0.16 (8-90 DIM) to 0.33 (91-180 DIM) for NEL, from 0.04 (8-90 DIM) to 0.10 (91-180 and >180 DIM) for EB, from 0.03 (8-90 DIM) to 0.11 (>180 DIM) for REI, and from 0.04 (8-90 DIM) to 0.18 (>180 DIM) for ECE. A strong genetic association between REI and EB was evident when average BW change was close to zero. These genetic parameters from Holstein-Friesian dairy cows fed predominantly grazed grass imply that genetic improvement in selected efficiency traits is achievable.