•There is significant genotype × environment interaction.•There are different performances of eucalypt clones over time.•Temperature strongly influences the clustering of sites.•There are three ...mega-environments according to the latitude gradient formed over time.
The genetic gains from eucalypt breeding programs have decreased compared to previous decades while productivity reduced in recent years. This decrease is mainly attributed to climate change that, according to studies, has been limiting productivity and changing the adaptation of forest species. But other aspects can be listed, as pests and diseases and decreasing gains with the advance of breeding programs. The objective of this work is to investigate the genotype × site × age interaction in a multi-environment trial with eucalypt clones to verify the adaptability and stability of the genotypes and, finally, to identify mega-environments over time, as well as the influence of climate variables on the genotype performances. The trait diameter at breast height (DBH) of 11 Eucalyptus commercial clones at 11 sites (range from −0.84 to −24.23 latitude and from −39.60 to −52.59 longitude) and three evaluated ages (Age 1 – ranging from 13 to 17 months after planting; Age 2 – from 31 to 34 months; Age 3 – from 48 to 53 months old) was measured and analyzed by factor analytic multiplicative mixed (FAMM) model associated with the GGE biplot and multivariate regression tree using climate variables. A significant G × E interaction and genotypes with different performance across environments and ages were observed. There are clones with high adaptability to specific sites while others show good stability. The results clustered the sites into three mega-environments according to a latitude gradient, over time. The performance of Eucalyptus clones over time indicate precisely either roughly similar or extremely contrasting environments. Temperature affected the most the clustering of the studied sites followed by the latitudinal gradient, impacting productivity negatively, regardless of age. These results may help future studies on the development of selection strategies in tropical regions to address climate change and assist forest breeding programs to deal with the effect of climate change on eucalypt productivity.
General cognitive function is a prominent and relatively stable human trait that is associated with many important life outcomes. We combine cognitive and genetic data from the CHARGE and COGENT ...consortia, and UK Biobank (total N = 300,486; age 16-102) and find 148 genome-wide significant independent loci (P < 5 × 10
) associated with general cognitive function. Within the novel genetic loci are variants associated with neurodegenerative and neurodevelopmental disorders, physical and psychiatric illnesses, and brain structure. Gene-based analyses find 709 genes associated with general cognitive function. Expression levels across the cortex are associated with general cognitive function. Using polygenic scores, up to 4.3% of variance in general cognitive function is predicted in independent samples. We detect significant genetic overlap between general cognitive function, reaction time, and many health variables including eyesight, hypertension, and longevity. In conclusion we identify novel genetic loci and pathways contributing to the heritability of general cognitive function.
Animal temperament can be defined as a response to environmental or social stimuli. There are a number of temperament traits in cattle that contribute to their welfare, including their response to ...handling or milking, response to challenge such as human approach or intervention at calving, and response to conspecifics. In a number of these areas, the genetic basis of the trait has been studied. Heritabilities have been estimated and in some cases quantitative trait loci (QTL) have been identified. The variation is sometimes considerable and moderate heritabilities have been found for the major handling temperament traits, making them amenable to selection. Studies have also investigated the correlations between temperament and other traits, such as productivity and meat quality. Despite this, there are relatively few examples of temperament traits being used in selection programmes. Most often, animals are screened for aggression or excessive fear during handling or milking, with extreme animals being culled, or EBVs for temperament are estimated, but these traits are not commonly included routinely in selection indices, despite there being economic, welfare and human safety drivers for their. There may be a number of constraints and barriers. For some traits and breeds, there may be difficulties in collecting behavioral data on sufficiently large populations of animals to estimate genetic parameters. Most selection indices require estimates of economic values, and it is often difficult to assign an economic value to a temperament trait. The effects of selection primarily for productivity traits on temperament and welfare are discussed. Future opportunities include automated data collection methods and the wider use of genomic information in selection.
Greenhouse gases originating from the dairy sector, including methane (CH4), contribute to global warming. A possible strategy to reduce CH4 production is to use genetic selection. This requires ...genetic parameters for CH4 production and correlations with production traits. Data were available on 184 Holstein-Friesian cows. Methane production was measured in the milking robot during milking from December 2009 to April 2010. In total 2,456 observations for CH4 production were available. Milk yield (MY) and body weight (BW) were obtained at every milking from November 2008 to October 2010. In total 4,567 observations for milk yield and 4,570 observations for BW were available. Restricted maximum likelihood, using random regression models, was used to analyze the data. Heritability (standard error given in parentheses) for CH4 production ranged from 0.12 (0.16) to 0.45 (0.11), and genetic correlations with MY ranged from 0.49 (0.12) to 0.54 (0.26). The positive genetic correlation between CH4 production and milk yield indicates that care needs to be taken when genetically selecting for lower CH4 production, to avoid a decrease in MY at the animal level. However, this study shows that CH4 production is moderately heritable and therefore progress through genetic selection is possible.
Abstract
Objectives
We aimed to clarify the genetic overlaps underlying obesity-related traits, serum urate, and gout.
Methods
We conducted a comprehensive genome-wide cross-trait analysis to ...identify genetic correlation, pleiotropic loci, and causal relationships between obesity (the exposure variable), gout (the primary outcome) and serum urate (the secondary outcome). Summary statistics were collected from the hitherto largest genome-wide association studies conducted for BMI (N = 806 834), waist-to-hip ratio (WHR; N = 697 734), WHR adjusted for BMI (WHRadjBMI; N = 694 649), serum urate (N = 288 649), and gout (Ncases = 13 179 and Ncontrols = 750 634).
Results
Positive overall genetic correlations were observed for BMI (rg = 0.27, P = 6.62 × 10−7), WHR (rg = 0.22, P = 6.26 × 10−7) and WHRadjBMI (rg = 0.07, P = 6.08 × 10−3) with gout. Partitioning the whole genome into 1703 LD (linkage disequilibrium)-independent regions, a significant local signal at 4q22 was identified for BMI and gout. The global and local shared genetic basis was further strengthened by the multiple pleiotropic loci identified in the cross-phenotype association study, multiple shared gene–tissue pairs observed by Transcriptome-wide association studies, as well as causal relationships demonstrated by Mendelian randomization BMI–gout: OR (odds ratio) = 1.66, 95% CI = 1.45, 1.88; WHR–gout: OR = 1.57, 95% CI = 1.37, 1.81. Replacing the binary disease status of gout with its latent pathological measure, serum urate, a similar pattern of correlation, pleiotropy and causality was observed with even more pronounced magnitude and significance.
Conclusion
Our comprehensive genome-wide cross-trait analysis demonstrates a shared genetic basis and pleiotropic loci, as well as a causal relationship between obesity, serum urate, and gout, highlighting an intrinsic link underlying these complex traits.
Abstract
Using a cloned Eucalyptus urophylla × E. tereticornis family, the present study estimated clonal mean repeatability, inter-trait correlation, and clone-by-site interactions for height (H) ...and diameter at breast height (D) across 0.5–8 years of age as well as 8-year-old wood basic density (BD8), cellulose content (CC8), hemi-cellulose content (HC8), Klason lignin content (LC8), and lignin syringyl-to-guaiacyl ratio (S/G8). Clonal mean repeatability estimates were 0.40–0.91 for growth traits H and D over 0.5–8 years and 0.50–0.87 for wood properties at age 8 for three separate sites (except that of 0.01 for HC8 at Yanxi) and across sites, indicating moderate to high levels of genetic control of the traits investigated. H had high positive genetic correlation with D. Growth traits (H and/or D) showed generally positive genetic correlation with BD8 and CC8 while negative with HC8 and LC8. Significant genotype-by-environment (clone-by-site) interactions were observed for most traits, suggesting that clones should be matched to sites to increase genetic gain. Our results suggest that there is potential to use E. urophylla × E. tereticornis clones to increase yield with desirable wood properties in Southern China.
Genetic correlations between males and females are often thought to constrain the evolution of sexual dimorphism. However, sexually dimorphic traits and the underlying sexually dimorphic gene ...expression patterns are often rapidly evolving. We explore this apparent paradox by measuring the genetic correlation in gene expression between males and females (C
mf) across broad evolutionary timescales, using two RNA-sequencing data sets spanning multiple populations and multiple species. We find that unbiased genes have higher C
mf than sex-biased genes, consistent with intersexual genetic correlations constraining the evolution of sexual dimorphism. However, we found that highly sex-biased genes (both male and female biased) also had higher tissue specificity, and unbiased genes had greater expression breadth, suggesting that pleiotropy may constrain the breakdown of intersexual genetic correlations. Finally, we show that genes with high C
mf showed some degree of sex-specific changes in gene expression in males and females. Together, our results suggest that genetic correlations between males and females may be less important in constraining the evolution of sex-biased gene expression than pleiotropy. Sex-specific regulatory variation and tissue specificity may resolve the paradox of widespread sex bias within a largely shared genome.
Inbreeding can cause an important bias in the estimates of quantitative genetic parameters, which in turn can affect the estimated potential for a selection response in species that are simultaneous ...hermaphrodite with partial self-fertilization. In the present study, the biases caused by self-fertilization on heritability (h2) estimates for productive traits were assessed at different ages in the tropical hermaphrodite pectinid Argopecten nucleus. Self-fertilization rates were estimated in both oocytes and adults, as the percentage of zygotes formed from unfertilized oocytes and by paternity analysis using microsatellite genetic markers, respectively. Fifty sexually mature individuals were individually spawned and genotyped using microsatellite markers. The sperm of one individual used as a male was used to fertilize the oocytes of 4 other individuals, generating 10 half-sibling families (HS) and 40 full-siblings families (FS). At the age of 3.5 months, the total weight, and the length, height, and width of the shell of 60 animals per FS family were individually measured. At the age of 9 months, the same measurements were repeated in the same individuals, which were then euthanized to weigh the soft tissues. In addition, the fecundity was estimated in each individual (number of oocytes produced), and a paternity analysis was performed. No significant differences were found in the average inbreeding rates estimated in oocytes and adults. However, no significant correlation was observed in the estimates of family self-fertilization rates when using both methods. The individuals derived from crossbreeding showed higher average values for productive traits than those produced by selfing, although interactions between the genotype and the depth of culture were observed in both groups. The h2 estimates using statistical models that consider self-fertilization in adults (models II and III) were lower than those observed when self-fertilization rates were estimated in oocytes, or not included in the model. However, the genetic correlations between the traits were similar using both methods for estimating self-fertilization rates. The present results suggest that self-fertilization results in inbreeding depression and induces an overestimation of the h2 for productive traits, but it does not affect estimates of genetic correlations or genotype by environment interactions.
•First report of inbreeding depression in A. nucleus.•Spontaneous development of unfertilized oocytes does not predict inbreeding in adults.•Selfing affects h2 estimations but not the GEI or genetic correlations among traits.•The accuracy of h2 estimations can be improved by inclusion of individual inbreeding.
Growth is one of the most important traits of commercial fishes. Bighead carp are intensively cultured in China and some Asian countries; however, the genetic basis of growth is less understood. In ...this study, we calculated the heritability of growth-related traits in a mixed population of 840 bighead carp and estimated growth-related QTL in a family of bighead carp using bulked segregation analysis of resequencing data. High phenotypic (0.70–0.95) and genetic (0.77–0.97) correlations were found between all growth-related traits. Estimated heritability of 0.20 ± 0.11, 0.28 ± 0.14, 0.32 ± 0.16, 0.14 ± 0.11 and 0.12 ± 0.09 were obtained for body weight, body height, head length, total length, and body length in bighead carp with seven month old. In the BSA analysis for progeny with extreme segregated body weight of a single family, three regions located in LG01, LG11 and LG22, respectively with a total length of 17.84 Mb which were obtained according to correlation thresholds. Annotation of genes within this region yielded 120 and 61 nonsynonymous and code-shifting mutations, respectively, by comparing SNPs and InDel between the two growth difference groups. Finally, 14 candidate genes, including T-box transcription factor 3, transcription factor E2F2, paired box gene 9, and fibroblast growth factor 6b were identified. Association analysis and mRNA levels revealed that paired box gene 9 and fibroblast growth factor 6b were significantly associated with growth-related traits in extreme growth samples. These results provide insights into the genetic mechanisms underlying the regulation of growth and development in the bighead carp.
•Calculated the heritability of growth traits in a mixed population of 840 bighead carp.•A region of 17.84 MB was located by BSA analysis between groups of weight extremes.•181 genes with genotypic differences were annotated and 14 candidate genes were identified.•Pax9 and lrp6 were significantly associated with growth by mRNA expression and SNP association analysis.
Genetic parameters of sperm abnormality traits were evaluated in HF crossbred bulls using Bayesian univariate, bivariate and random regression models. Data from 161 bulls on 1,527 ejaculates ...collected from 2010 to 2020 at BAIF (Bharatiya Agro Industries Foundation) was utilized for this study. Four sperm abnormality traits viz. total abnormalities (A), head abnormality (HA), mid-piece abnormality (MA) and tail abnormality (TA) were included in the analysis. Gibbs sampling was done to implement a Bayesian framework. Means for A, HA, MA and TA were 10.77%, 2.99%. 2.61% and 5.10% respectively. Heritability and repeatability estimates obtained from univariateanalysis were below 0.1. Genetic correlations obtained for the total abnormalities with semen production traits like ejaculate volume, sperm concentration, initial sperm motility, post-thaw motility and the total number of spermatozoa were negative. Heritability and repeatability estimates were higher in the case of random regression models where the values tend to increase with the age of the bulls. Heritability ranged from 0.025 (3 years) to 0.139 (10 years) for total abnormality estimates. In general, the estimates of genetic parameters for abnormality were low and found to increase with age.
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