So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Despite many challenges faced by animal producers, including environmental problems, diseases, economic pressure, and feed availability, it is still predicted that animal production in developing countries will continue to sustain the future growth of the world's meat production. In these areas, livestock performance is generally lower than those obtained in Western Europe and North America. Although many factors can be involved, climatic factors are among the first and crucial limiting factors of the development of animal production in warm regions. In addition, global warming will further accentuate heat stress-related problems. The objective of this paper was to review the effective strategies to alleviate heat stress in the context of tropical livestock production systems. These strategies can be classified into three groups: those increasing feed intake or decreasing metabolic heat production, those enhancing heat-loss capacities, and those involving genetic selection for heat tolerance. Under heat stress, improved production should be possible through modifications of diet composition that either promotes a higher intake or compensates the low feed consumption. In addition, altering feeding management such as a change in feeding time and/or frequency, are efficient tools to avoid excessive heat load and improve survival rate, especially in poultry. Methods to enhance heat exchange between the environment and the animal and those changing the environment to prevent or limit heat stress can be used to improve performance under hot climatic conditions. Although differences in thermal tolerance exist between livestock species (ruminants > monogastrics), there are also large differences between breeds of a species and within each breed. Consequently, the opportunity may exist to improve thermal tolerance of the animals using genetic tools. However, further research is required to quantify the genetic antagonism between adaptation and production traits to evaluate the potential selection response. With the development of molecular biotechnologies, new opportunities are available to characterize gene expression and identify key cellular responses to heat stress. These new tools will enable scientists to improve the accuracy and the efficiency of selection for heat tolerance. Epigenetic regulation of gene expression and thermal imprinting of the genome could also be an efficient method to improve thermal tolerance. Such techniques (e.g. perinatal heat acclimation) are currently being experimented in chicken.

Adaptation to hot climate and strategies to alleviate heat stress in livestock production.

Records on 1,180 young Angus bulls and heifers involved in performance tests were used to estimate genetic and phenotypic parameters for feed intake, feed efficiency, and other postweaning traits. The mean age was 268 d at the start of the performance test, which comprised 21-d adjustment and 70-d test periods. Traits studied included 200-d weight, 400-d weight, scrotal circumference, ultrasonic measurements of rib and rump fat depths and longissimus muscle area, ADG, metabolic weight, daily feed intake, feed conversion ratio, and residual feed intake. For all traits except the last five, additional data from the Angus Society ofAustralia pedigree and performance database were included, which increased the number of animals to 27,229. Genetic (co)variances were estimated by REML using animal models. Direct heritability estimates for 200-d weight, 400-d weight, rib fat depth, ADG, feed conversion,and residual feed intake were 0.17 +/- 0.03, 0.27 +/- 0.03, 0.35 +/- 0.04, 0.28 +/- 0.04, 0.29 +/- 0.04, and 0.39 +/- 0.03, respectively. Feed conversion ratio was genetically (r(g) = 0.66 ) and phenotypically (r(p) = 0.53) correlated with residual feed intake. Feed conversion ratio was correlated (r(g) = -0.62, r(p) = -0.74) with ADG, whereas residual feed intake was not (rg = -0.04, r(p) = -0.06). Genetically, both residual feed intake and feed conversion ratio were negatively correlated with direct effects of 200-d weight (r(g) = -0.45 and -0.21) and 400-d weight (r(g) = -0.26 and -0.09). The correlations between the remaining traits and the feed efficiency traits were near zero, except between feed intake and feed conversion ratio (r(g) = 0.31, r(p) = 0.23), feed intake and residual feed intake (r(g) = 0.69, r(p) = 0.72), and rib fat depth and residual feed intake (r(g) = 0.17, r(p) = 0.14). These results indicate that genetic improvement in feed efficiency can be achieved through selection and, in general, correlated responses in growth and the other postweaning traits will be minimal.

Genetic and phenotypic variance and covariance components for feed intake, feed efficiency, and other postweaning traits in Angus cattle

Residual feed intake (RFI) is the difference between the actual and expected feed intake of an animal based on its BW and growth rate over a specified period. The biological mechanisms underlying the variation in feed efficiency in animals with similar BW and growth rate are not well understood. This study determined the relationship of feedlot feed efficiency, performance, and feeding behavior with digestion and energy partitioning of 27 steers. The steers were selected from a total of 306 animals based on their RFI following feedlot tests at the University of Alberta Kinsella Research Station. Selected steers were ranked into high RFI (RFI >0.5 SD above the mean, n = 11), medium RFI (RFI ± 0.5 SD above and below the mean, n = 8), and low RFI (RFI 0.10). Residual feed intake was correlated with daily methane production and energy lost as methane (r = 0.44; P < 0.05). Methane production was 28 and 24% less in low-RFI animals compared with high- and medium-RFI animals, respectively. Residual feed intake tended to be associated (P < 0.10) with apparent digestibilities of DM (r = -0.33) and CP (r = -0.34). The RFI of steers was correlated with DE (r = -0.41; P < 0.05), ME (r = -0.44; P < 0.05), heat production (HP; r = 0.68; P < 0.001), and retained energy (RE; r = -0.67; P < 0.001; energy values are expressed in kcal/kg of BW). Feedlot partial efficiency of growth was correlated (P < 0.01) with methane production (r = -0.55), DE (r = 0.46), ME (r = 0.49), HP (r = -0.50), and RE (r = 0.62). With the exception of HP (r = 0.37; P < 0.05), feed conversion ratio was unrelated to the traits considered in the study. Feeding duration was correlated (P < 0.01) with apparent digestibility of DM (r = -0.55), CP (r = -0.47), methane production (r = 0.51), DE (r = -0.52), ME (r = -0.55), and RE (r = -0.60). These results have practical implications for the selection of animals that eat less at a similar BW and growth rate and for the environmental sustainability of beef production.

Relationships of feedlot feed efficiency, performance, and feeding behavior with metabolic rate, methane production, and energy partitioning in beef cattle

When a genetic marker and a quantitative trait locus (QTL) are in linkage disequilibrium (LD) in one population, they may not be in LD in another population or their LD phase may be reversed. The objectives of this study were to compare the extent of LD and the persistence of LD phase across multiple cattle populations. LD measures r and r(2) were calculated for syntenic marker pairs using genomewide single-nucleotide polymorphisms (SNP) that were genotyped in Dutch and Australian Holstein-Friesian (HF) bulls, Australian Angus cattle, and New Zealand Friesian and Jersey cows. Average r(2) was approximately 0.35, 0.25, 0.22, 0.14, and 0.06 at marker distances 10, 20, 40, 100, and 1000 kb, respectively, which indicates that genomic selection within cattle breeds with r(2) >or= 0.20 between adjacent markers would require approximately 50,000 SNPs. The correlation of r values between populations for the same marker pairs was close to 1 for pairs of very close markers (<10 kb) and decreased with increasing marker distance and the extent of divergence between the populations. To find markers that are in LD with QTL across diverged breeds, such as HF, Jersey, and Angus, would require approximately 300,000 markers.

https://www.genetics.org/content/genetics/179/3/1503.full.pdf

Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle

Evidence for genetic variation in feed efficiency of beef cattle is reviewed in this paper, and ways in which this variation might be used in selection programs to improve beef cattle in Australia are discussed. Efficiency of beef production systems is determined by feed and other inputs of all classes of animals in the production system as well as outputs in terms of slaughter progeny and cull cows. Different indices have been used to express aspects of efficiency on cattle over certain periods of the production cycle. Use of these indices is discussed, and then evidence for genetic variation in both growing animals and mature animals is reviewed. Genetic variation in feed efficiency exists in both growing and mature cattle, although information is lacking to determine whether variation in total production system efficiency exists. The physiological basis for observed variation in feed efficiency is discussed, with differences in requirements for maintenance, body composition, proportions of visceral organs, level of physical activity, and digestion efficiency identified as possible sources of variation. Selection to improve efficiency might be achieved by measuring feed intake of growing animals and utilising genetic correlations that are likely to exist between efficiency of growing animals and mature animals. Measurement of feed intake might occur in central test stations, or methods may be developed to measure feed intake on-farm. Ways of utilising information generated in genetic evaluations are discussed, and it is concluded that estimated breeding values for feed intake after a phenotypic adjustment for growth performance would be most practical, although not theoretically optimal. Such estimated breeding values would best be used in an economic selection index to account for genetic correlations with other traits, including feed intake of the breeding herd, and the economic value of feed in relation to other traits. Future research should be directed towards understanding the genetic relationships between feed intake and other traits in the breeding objective, and to find ways to reduce the cost of measurement of feed intake, including a search for genetic markers.

Potential for selection to improve efficiency of feed use in beef cattle: a review

The optimum duration of test for measurement of growth rate, feed intake, feed conver- sion, and residual feed intake was examined using postweaning feed intake and weight data from 760 Angus, Hereford, Polled Hereford, and Shorthorn heifer and Angus bull progeny from 78 sires. Variance components, heritability, phenotypic and genetic correlations, and the efficiency of selection using shortened tests compared with a 119-d test were used as criteria to assess the optimum test length. The results indicated that a 35-d test was sufficient for measurement of feed intake, whereas a 70-d test was required to measure growth rate, feed conversion, and residual feed intake without compromising the ac- curacy of measurement. When a 70-d test is used to measure growth rate, feed conversion, and residual feed intake there is minimal loss in accuracy when weights are collected every 2 wk instead of weekly, but a further increase in the interval between weights to 5 wk caused a decline in the accuracy of the test. Therefore a 70-d test with cattle weighed every 2 wk seems to be optimal for measuring these traits in British breed cattle.

Optimum postweaning test for measurement of growth rate, feed intake, and feed efficiency in British breed cattle

There is considerable individual animal variation in feed intake above and below that expected or predicted on the basis of size and growth rate. This difference in intake is calculated as residual (or net) feed intake (RFI). Genetic variation in RFI of beef cattle exists both during growth (slaughter generation and replacement females; heritability estimates since 1996 range from 0.16 to 0.43) and in adult cattle (the breeding herd; the one published heritability estimate is 0.23). Evidence shows that selection for lower RFI measured postweaning will lead to a decrease in feed intake by young cattle and by cows, with no compromise in growth performance or increase in cow size. Results from a single generation of divergent selection on postweaning RFI between 8 to 12 mo of age demonstrated favorable correlated changes in average daily feed intake (9.2 ± 0.2 vs. 9.8 ± 0.2 kg/d), RFI (−0.20 ± 0.11 vs. 0.17 ± 0.10 kg/d), and feed:gain ratio (F:G; 7.0 ± 0.2 vs. 7.6 ± 0.2 kg/kg) in Angus feedlot steers. In Angus cattle, the genetic correlation between postweaning RFI with av- erage daily feed intake by the cow is high (0.64), and

Reducing the cost of beef production through genetic improvement in residual feed intake: Opportunity and challenges to application 1

Residual feed intake measures variation in feed intake independent of liveweight and liveweight gain First generation steer progeny (n = 33) of parents previously selected for low or high post-weaning residual feed intake were examined to determine metabolic processes contributing to variation in residual feed intake Blood samples were taken from the steers from weaning through to slaughter These samples were analysed for key metabolites and hormones Total urine and total faecal collections were taken from the steers in an animal-house experiment to estimate dry matter digestibility, microbial protein production and protein turnover At weaning, there were phenotypic correlations between concentrations in plasma of β-hydroxy butyrate (r = 055, P 005) Neither the ratio of 3-methyl histidine : creatinine in urine, as a measure of rate of muscle breakdown, nor the dry matter digestibility measured in the animal house were correlated with residual feed intake in the animal house (r = 004, P>005), or residual feed intake over the whole experiment (r = –022, P>005), and neither were associated with genetic variation in residual feed intake It is hypothesised that high-RFI (low-efficiency) steers have higher tissue energy requirements, are more susceptible to stress and utilise different tissue substrates (partly as a consequence of differences in body composition) to generate energy required in response to exposure to a stressful stimulus

J. A. Archer

Papers

Genetic and phenotypic variance and covariance components for feed intake, feed efficiency, and other postweaning traits in Angus cattle

Potential for selection to improve efficiency of feed use in beef cattle: a review

Optimum postweaning test for measurement of growth rate, feed intake, and feed efficiency in British breed cattle

Reducing the cost of beef production through genetic improvement in residual feed intake: Opportunity and challenges to application 1

Metabolic differences in Angus steers divergently selected for residual feed intake