Genomic breeding programs have been paramount in improving the rates of genetic progress of productive efficiency traits in livestock. Such improvement has been accompanied by the intensification of ...production systems, use of a wider range of precision technologies in routine management practices, and high-throughput phenotyping. Simultaneously, a greater public awareness of animal welfare has influenced livestock producers to place more emphasis on welfare relative to production traits. Therefore, management practices and breeding technologies in livestock have been developed in recent years to enhance animal welfare. In particular, genomic selection can be used to improve livestock social behavior, resilience to disease and other stress factors, and ease habituation to production system changes. The main requirements for including novel behavioral and welfare traits in genomic breeding schemes are: (1) to identify traits that represent the biological mechanisms of the industry breeding goals; (2) the availability of individual phenotypic records measured on a large number of animals (ideally with genomic information); (3) the derived traits are heritable, biologically meaningful, repeatable, and (ideally) not highly correlated with other traits already included in the selection indexes; and (4) genomic information is available for a large number of individuals (or genetically close individuals) with phenotypic records. In this review, we (1) describe a potential route for development of novel welfare indicator traits (using ideal phenotypes) for both genetic and genomic selection schemes; (2) summarize key indicator variables of livestock behavior and welfare, including a detailed assessment of thermal stress in livestock; (3) describe the primary statistical and bioinformatic methods available for large-scale data analyses of animal welfare; and (4) identify major advancements, challenges, and opportunities to generate high-throughput and large-scale datasets to enable genetic and genomic selection for improved welfare in livestock. A wide variety of novel welfare indicator traits can be derived from information captured by modern technology such as sensors, automatic feeding systems, milking robots, activity monitors, video cameras, and indirect biomarkers at the cellular and physiological levels. The development of novel traits coupled with genomic selection schemes for improved welfare in livestock can be feasible and optimized based on recently developed (or developing) technologies. Efficient implementation of genetic and genomic selection for improved animal welfare also requires the integration of a multitude of scientific fields such as cell and molecular biology, neuroscience, immunology, stress physiology, computer science, engineering, quantitative genomics, and bioinformatics.
Abstract
Genomic selection increases accuracy and decreases generation interval, speeding up genetic changes in the populations. However, intensive changes caused by selection can reduce the genetic ...variation and can strengthen undesirable genetic correlations. The purpose of this study was to investigate changes in genetic parameters for fitness traits related with prolificacy (FT1) and litter survival (FT2 and FT3), and for growth (GT1 and GT2) traits in pigs over time. The data set contained 21,269 (FT1), 23,246 (FT2), 23,246 (FT3), 150,492 (GT1), and 150,493 (GT2) phenotypic records obtained from 2009 to 2018. The pedigree file included 369,776 animals born between 2001 and 2018, of which 39,103 were genotyped. Genetic parameters were estimated with bivariate models (FT1-GT1, FT1-GT2, FT2-GT1, FT2-GT2, FT3-GT1, and FT3-GT2) using 3-yr sliding subsets. With a Bayesian implementation using the GIBBS3F90 program computations were performed as genomic analysis (GEN) or pedigree-based analysis (PED), that is, with or without genotypes, respectively. For GEN (PED), the changes in heritability from the first to the last year interval, that is, from 2009–2011 to 2015–2018 were 8.6 to 5.6 (7.9 to 8.8) for FT1, 7.8 to 7.2 (7.7 to 10.8) for FT2, 11.4 to 7.6 (10.1 to 7.5) for FT3, 35.1 to 16.5 (32.5 to 23.7) for GT1, and 35.9 to 16.5 (32.6 to 24.1) for GT2. Differences were also observed for genetic correlations as they changed from −0.31 to −0.58 (−0.28 to −0.73) for FT1-GT1, −0.32 to −0.50 (−0.29 to −0.74) for FT1-GT2, −0.27 to −0.45 (−0.30 to −0.65) for FT2-GT1, −0.28 to −0.45 (−0.32 to −0.66) for FT2-GT2, 0.14 to 0.17 (0.11 to 0.04) for FT3-GT1, and 0.14 to 0.18 (0.11 to 0.05) for FT3-GT2. Strong selection in pigs reduced heritabilities and emphasized the antagonistic genetic relationships between fitness and growth traits. With genotypes considered, heritability estimates were smaller and genetic correlations were greater than estimates with only pedigree and phenotypes. When selection is based on genomic information, genetic parameters estimated without this information can be biased because preselection is not accounted for by the model.
•Sunburn is one of the most important damage in apple fruit production all over the world.•Physiological and metabolical disorders are triggered by sun radiation exposure.•New strategies for early ...detection in field have been developed.•Genomic and transcriptomic information will useful to understand the molecular mechanisms involved.
Climate change negatively influences many human activities and one of the most affected is agriculture. In the apple industry, water availability, elevated temperatures and altered phenology will transform fruit production in traditional growing regions. Extended periods of intense solar radiation and high temperatures during the growing season cause problems in fruit quality increasing losses and reducing sustainability and profitability. Photooxidative and heat stress stimulate sunburn development on apple fruit in the field growing under increasingly stressful conditions. In particular, apples growing in semi-arid conditions are frequently exposed to high solar irradiance and elevated temperature during the growing season that promote the development of sun-related skin disorders. Furthermore, regions that have traditionally not faced sunburn pressure may begin to experience losses in this area. Apple cultivars differ in their susceptibility to sun damage, which is evidenced, in part, by the timing of symptom development and severity. Some studies attribute genotypic variation to physiological and morphological differences while others do to antioxidant-related metabolic differences between them. Here, we discuss the physiological and molecular progress and gaps in knowledge of sunburn damage and the development of sunburn resistance in apple fruit. This information will help develop stronger sunburn mitigation strategies and enhance breeding efforts to address challenges associated with sunburn in apple production.
Genomic selection increases accuracy and decreases generation interval, accelerating genetic changes in populations. Assumptions of genetic improvement must be addressed to quantify the magnitude and ...direction of change. Genetic trends of US dairy cattle breeds were examined to determine the genetic gain since the implementation of genomic evaluations in 2009. Inbreeding levels and generation intervals were also investigated. Breeds included Ayrshire, Brown Swiss, Guernsey, Holstein (HO), and Jersey (JE), which were characterized by the evaluation breed the animal received. Mean genomic predicted breeding values (PBV¯) were analyzed per year to calculate genetic trends for bulls and cows. The data set contained 154,008 bulls and 33,022,242 cows born since 1975. Breakpoints were estimated using linear regression, and nonlinear regression was used to fit the piecewise model for the small sample number in some years. Generation intervals and inbreeding levels were also investigated since 1975. Milk, fat, and protein yields, somatic cell score, productive life, daughter pregnancy rate, and livability PBV¯ were documented. In 2017, 100% of bulls in this data set were genotyped. The percentage of genotyped cows has increased 23 percentage points since 2010. Overall, production traits have increased steadily over time, as expected. The HO and JE breeds have benefited most from genomics, with up to 192% increase in genetic gain since 2009. Due to the low number of observations, trends for Ayrshire, Brown Swiss, and Guernsey are difficult to infer from. Trends in fertility are most substantial; particularly, most breeds are trending downwards and daughter pregnancy rate for JE has been decreasing steadily since 1975 for bulls and cows. Levels of genomic inbreeding are increasing in HO bulls and cows. In 2017, genomic inbreeding levels were 12.7% for bulls and 7.9% for cows. A suggestion to control this is to include the genomic inbreeding coefficient with a negative weight to the selection index of bulls with high future genomic inbreeding levels. For sires of bulls, the current generation intervals are 2.2 yr in HO, 3.2 in JE, 4.4 in Brown Swiss, 5.1 in Ayrshire, and 4.3 in Guernsey. The number of colored breed bulls in the United States is currently at an extremely low level, and this number will only increase with a market incentive or additional breed association involvement. Increased education and extension could be beneficial to increase knowledge about inbreeding levels, use of genomics and genetic improvement, and genetic diversity in the genomic selection era.
•Reproductive traits showed a low correlation with carcass traits.•The results of this study are encouraging for using the probability of precocious calving as selection criteria in Nelore ...breed.•Selection to increase growth should increase carcass yield and scrotal circumference.•The inclusion of subcutaneous backfat or rump fat thickness in selection indexes would increase the carcass grade.
This study was carried out to estimate the heritability and genetic correlations between adjusted weights at 210 (W210) and 450 (W450) days of age, scrotal circumference adjusted at 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC), probability of precocious calving (PPC), stayability (STAY), ribeye area (REA), subcutaneous backfat thickness (BF), and rump fat (RF) traits. The covariance components and genetic parameters for all traits but PPC and STAY were estimated considering a linear animal model, for the remaining traits a threshold animal model was used. The single-step genomic BLUP (ssGBLUP) procedure was used for all traits, and the correlation estimates were obtained by two-traits analysis. The heritability estimated by single-trait analysis were 0.21 ± 0.01, 0.43 ± 0.01, 0.47 ± 0.02, 0.52 ± 0.02, 0.11 ± 0.01, 0.12 (0.07–0.16), 0.37 (0.26–0.38), 0.33 ± 0.02, 0.17 ± 0.01 and 0.33 ± 0.02 for W210, W450, SC365, SC450, AFC, PPC, STAY, REA, BF and RF, respectively. Growth traits (W210 and W450) showed high (0.95) genetic correlation with one another, moderate (0.30 to 0.66) with REA and scrotal circumferences, and low (−0.07 to 0.20) with female reproductive traits (AFC, PPC, and STAY) and fat carcass indicator traits (BF and RF). Female reproductive traits displayed moderate (−0.29 to 0.52) genetic correlations with male reproductive traits, and varied from low to moderate (−0.02 to 0.35) with carcass traits. Additionally, carcass traits exhibited low to moderate (−0.02 to 0.48) genetic correlations with all traits, except for the genetic correlation between BF and RF (0.73). Hence, higher genetic gains by direct selection would be obtained for W450, SC365, SC450, STAY, REA, and RF. Selection to increase growth traits might increase carcass yield and scrotal circumference, and it would not affect carcass fat content, precocity, and cow longevity indicator traits. The results of this study encourage the use of PPC in Nelore cattle since the selection for such trait would improve the productivity and longevity of the cows. The inclusion of carcass quality indicator traits such as BF or RF in selection indices would increase the genetic gain for carcass grade, but it will require further studies to estimate the economic value of these traits.
Cancer is traditionally labeled a “cellular growth problem.” However, it is fundamentally an issue of macroevolution where new systems emerge from tissue by breaking various constraints. To study ...this process, we used experimental platforms to “watch evolution in action” by comparing the profiles of karyotypes, transcriptomes, and cellular phenotypes longitudinally before, during, and after key phase transitions. This effort, alongside critical rethinking of current gene-based genomic and evolutionary theory, led to the development of the Genome Architecture Theory. Following a brief historical review, we present four case studies and their takeaways to describe the pattern of genome-based cancer evolution. Our discoveries include 1. The importance of non-clonal chromosome aberrations or NCCAs; 2. Two-phased cancer evolution, comprising a punctuated phase and a gradual phase, dominated by karyotype changes and gene mutation/epigenetic alterations, respectively; 3. How the karyotype codes system inheritance, which organizes gene interactions and provides the genomic basis for physiological regulatory networks; and 4. Stress-induced genome chaos, which creates genomic information by reorganizing chromosomes for macroevolution. Together, these case studies redefine the relationship between cellular macro- and microevolution: macroevolution does not equal microevolution + time. Furthermore, we incorporate genome chaos and gene mutation in a general model: genome reorganization creates new karyotype coding, then diverse cancer gene mutations can promote the dominance of tumor cell populations. Finally, we call for validation of the Genome Architecture Theory of cancer and organismal evolution, as well as the systematic study of genomic information flow in evolutionary processes.
Human DNA Repair Genes Wood, Richard D.; Mitchell, Michael; Sgouros, John ...
Science (American Association for the Advancement of Science),
02/2001, Volume:
291, Issue:
5507
Journal Article
Peer reviewed
Cellular DNA is subjected to continual attack, both by reactive species inside cells and by environmental agents. Toxic and mutagenic consequences are minimized by distinct pathways of repair, and ...130 known human DNA repair genes are described here. Notable features presently include four enzymes that can remove uracil from DNA, seven recombination genes related to RAD51, and many recently discovered DNA polymerases that bypass damage, but only one system to remove the main DNA lesions induced by ultraviolet light. More human DNA repair genes will be found by comparison with model organisms and as common folds in three-dimensional protein structures are determined. Modulation of DNA repair should lead to clinical applications including improvement of radiotherapy and treatment with anticancer drugs and an advanced understanding of the cellular aging process.
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