Validation of single-step genomic predictions using the linear regression method for milk yield and heat tolerance in a Thai-Holstein population

Background and Aim: Genomic selection improves accuracy and decreases the generation interval, increasing the selection response. This study was conducted to assess the benefits of using single-step genomic best linear unbiased prediction (ssGBLUP) for genomic evaluations of milk yield and heat tolerance in Thai-Holstein cows and to test the value of old phenotypic data to maintain the accuracy of predictions. Materials and Methods: The dataset included 104,150 milk yield records collected from 1999 to 2018 from 15,380 cows. The pedigree contained 33,799 animals born between 1944 and 2016, of which 882 were genotyped. Analyses were performed with and without genomic information using ssGBLUP and BLUP, respectively. Statistics for bias, dispersion, the ratio of accuracies, and the accuracy of estimated breeding values were calculated using the linear regression (LR) method. A partial dataset excluded the phenotypes of the last generation, and 66 bulls were identified as validation individuals. Results: Bias was considerable for BLUP (0.44) but negligible (–0.04) for ssGBLUP; dispersion was similar for both techniques (0.84 vs. 1.06 for BLUP and ssGBLUP, respectively). The ratio of accuracies was 0.33 for BLUP and 0.97 for ssGBLUP, indicating more stable predictions for ssGBLUP. The accuracy of predictions was 0.18 for BLUP and 0.36 for ssGBLUP. Excluding the first 10 years of phenotypic data (i.e., 1999-2008) decreased the accuracy to 0.09 for BLUP and 0.32 for ssGBLUP. Genomic information doubled the accuracy and increased the persistence of genomic estimated breeding values when old phenotypes were removed. Conclusion: The LR method is useful for estimating accuracies and bias in complex models. When the population size is small, old data are useful, and even a small amount of genomic information can substantially improve the accuracy. The effect of heat stress on first parity milk yield is small.

Performance of Kampung Super chicken and Bangkok chicken first generation (G1) until the age of 12 weeks

<p class="MDPI17abstract"><strong>Objective: </strong>The purpose of this research was to determine the performance of the first generation (G1) Kampung Super and Bangkok chicken aged 12 weeks<span lang="EN-GB">.</span></p><p class="MDPI17abstract"><strong>Methods: </strong>The research material were G1 Kampung Super and Bangkok chicken with 174 samples for each strain. This research was using the experimental method. The data collected included body weight, body weight gain, body measurements, and selected responses. The body weight, body weight gain, and body measurements data were analyzed using t-test independent, while the average value vector of body measured using <em><span>T²-Hotelling test.</span></em> Principal Component Analysis ware used to identify the characteristics of body shape and size.<strong></strong></p><p class="MDPI17abstract"><strong>Results: </strong>The results of this study showed that body weight, body weight gain of DOC-4 weeks, 4-8 weeks, 8-12 weeks, and body measurements of G1 Kampung Super chickens were real different higher (P&lt;0.05) than G1 Bangkok. The identifier of the size of the G1 Kampung Super and Bangkok chicken is the chest circumference. The characteristics of the shape G1 Kampung Super chicken is the length of the wings and the G1 Bangkok chicken is the lower body lenght. The selection response of G1 Kampung Super is higher than G1 Bangkok<span lang="EN-GB">.</span><strong></strong></p><p><strong><span>Conclusions: </span></strong>The<span> performance of G1 Kampung Super chicken was higher than G1 Bangkok chicken but the selection response value of G1 Bangkok chicken was higher than G1 Kampung Super chicken. The highest body weight gain of G1 Kampung Super and Bangkok chickens was achieved at the age of 8-12 weks</span><span lang="EN-GB">.</span></p>

Heritability of distichiasis in Havanese dogs in Norway

Background Distichiasis is a presumed inherited eyelid disease, characterized by misplaced eyelashes. The effect on eye health and animal welfare varies between individuals; most mild cases show no clinical signs, but some affected animals develop painful corneal disease. In this study, we investigated the prevalence and heritability of distichiasis in the Norwegian population of Havanese dogs. Results A total of 1156 Havanese were included in the study. Out of these, 168 were affected with distichiasis, making the prevalence in our sample 14.5% (95% CI 12.5–16.6%). There was no sex predisposition. Most affected individuals were graded “mildly affected”. The estimates generally showed high heritabilities, which varied between 0.276 (linear model) and 0.720 (Bayesian threshold model). The linear estimates, after conversion to the underlying scale (h2l = 0.664–0.674), corresponds well to the results of the Bayesian models. Conclusions The estimated heritability of distichiasis in Havanese is high and the prevalence is moderate. The high heritability indicate that a significant selection response could be obtained by simple mass selection. To secure good animal welfare, it’s important to control the number of affected individuals and especially the severely affected.

Comparing Tangible Symbols, Picture Exchange and a Direct Selection Response when Teaching Requesting to Two Children with Autism Spectrum Disorder

<p>Children diagnosed with Autism Spectrum Disorder (ASD) who fail to develop functional speech are candidates for augmentative and alternative communication (AAC) systems. One of the primary intentions of AAC is to provide an alternative method of communicating in the absence of speech (Mirenda, 2003). In order to select the most beneficial AAC system for a user, in regards to the ease of acquisition and successfully communicating with AAC systems, it is considered important to undertake research comparing various AAC systems and to assess users’ preferences for using one system over another. Empirical evidence from previous studies comparing AAC indicates that users often learn to use AAC systems with varying degrees of proficiency and at various acquisition rates. Additionally, assessing users’ preferences for different AAC systems has been shown to influence acquisition rates and long term maintenance of AAC systems and is suggested to be an important component when carrying out AAC intervention. In the present study a tangible symbol (TS) communication system was compared, in terms of acquisition rates and preference, with Picture Exchange (PE) and an additional direct selection (DS) method of gaining access to desired stimuli in two young boys with ASD. Two male participants diagnosed with ASD were taught via systematic instructional procedures to request/gain access to the continuation of preferred cartoon movies by using TS, PE, and DS. Additionally, preference assessments were implemented during intervention and follow-up phases to determine whether the participants showed a preference for using one of these three requesting/access methods over the other two, and whether any such preferences remained stable throughout follow-up sessions. Results indicated that both participants successfully learned to request each of the six cartoon movies using each of the three methods. Specifically, acquisition rates for TS and PE were comparable across both participants, and overall both participants preferred to request using the TS. During intervention sessions, one participant preferred to use DS, however this preference changed during follow-up where he chose to use TS more overall. These data suggest that TS is a viable AAC option for children with ASD who do not speak, and can be learned to a high proficiency after receiving systematic teaching procedures as used in the present study.</p>

Comparing Tangible Symbols, Picture Exchange and a Direct Selection Response when Teaching Requesting to Two Children with Autism Spectrum Disorder

<p>Children diagnosed with Autism Spectrum Disorder (ASD) who fail to develop functional speech are candidates for augmentative and alternative communication (AAC) systems. One of the primary intentions of AAC is to provide an alternative method of communicating in the absence of speech (Mirenda, 2003). In order to select the most beneficial AAC system for a user, in regards to the ease of acquisition and successfully communicating with AAC systems, it is considered important to undertake research comparing various AAC systems and to assess users’ preferences for using one system over another. Empirical evidence from previous studies comparing AAC indicates that users often learn to use AAC systems with varying degrees of proficiency and at various acquisition rates. Additionally, assessing users’ preferences for different AAC systems has been shown to influence acquisition rates and long term maintenance of AAC systems and is suggested to be an important component when carrying out AAC intervention. In the present study a tangible symbol (TS) communication system was compared, in terms of acquisition rates and preference, with Picture Exchange (PE) and an additional direct selection (DS) method of gaining access to desired stimuli in two young boys with ASD. Two male participants diagnosed with ASD were taught via systematic instructional procedures to request/gain access to the continuation of preferred cartoon movies by using TS, PE, and DS. Additionally, preference assessments were implemented during intervention and follow-up phases to determine whether the participants showed a preference for using one of these three requesting/access methods over the other two, and whether any such preferences remained stable throughout follow-up sessions. Results indicated that both participants successfully learned to request each of the six cartoon movies using each of the three methods. Specifically, acquisition rates for TS and PE were comparable across both participants, and overall both participants preferred to request using the TS. During intervention sessions, one participant preferred to use DS, however this preference changed during follow-up where he chose to use TS more overall. These data suggest that TS is a viable AAC option for children with ASD who do not speak, and can be learned to a high proficiency after receiving systematic teaching procedures as used in the present study.</p>

Laying performance of 5th generation of BLRI improved native duck

This research was aimed to improve the egg production performances and to estimate the selection response of fifth generation (G5) of deshi white (Rupali) and white breasted black (Nageswari) duck genotypes through an individual selection program. All the ducks were reared in an open sided duck house. Diet containing 17.5% CP and 2750 Kcal ME/kg and fresh water provided twice daily in the morning and evening. Individual egg production was recorded from each duck. After 40 weeks of age, female ducks were selected on the basis of selection index and selection differences, selection intensity and responses were also measured. Egg weight, egg production and feed intake were recorded and FCR, egg mass was calculated. All recorded data were analyzed by SAS and differences were determined by DMRT. The selection criteria of fifth generation (G5) of both duck genotypes were studied. As a result of selection, age at sexual maturity (day), egg weight (g) and egg production % were expected to improve by -1.63d, 0.60g, 1.01% and -0.85day, 0.39g, 0.47% for Rupali and Nageswari ducks, respectively. Egg mass was significantly (p<0.05) higher in Rupali (40.24g) than Nageswari (37.55g) duck whereas, egg weight was not significantly differ in both genotypes. Egg production in Rupali and Nageswari duck was 65.41% and 62.74%, respectively. Rupali ducks were significantly (p<0.05) consumed more feed (134.54 g) than Nagesswari ducks (126.23 g). The FCR was significantly (p<0.05) better in Rupali (3.34) than Nageswari (3.61) ducks. The egg quality results showed that egg shell thickness of Rupali duck was significantly (p<0.05) higher than Nageswari. Higher values for albumen width (p<0.05) was also found in Rupali (65.03mm) than Nageswari (59.11mm) duck egg. On the other hand shape index, albumen index, yolk index and haugh unit were not found significantly different in both genotypes but the yolk color score of Nageswari found highest score than Rupali duck egg. Proximate composition of eggs was not significantly different of both duck genotypes. Based on the results it is revealed that Rupali duck was better in terms of egg weight, egg mass and egg production, but starting lay egg is earlier in Nageswari than Rupali duck. Bang. J. Livs. Res. Vol. 27 (1&2), 2020: P. 15-23

Comprehensive functional core microbiome comparison in genetically obese and lean hosts under the same environment

Our study provides an exhaustive comparison of the microbiome core functionalities (captured by 3,936 microbial gene abundances) between hosts with divergent genotypes for intramuscular lipid deposition. After 10 generations of divergent selection for intramuscular fat in rabbits and 4.14 phenotypic standard deviations (SD) of selection response, we applied a combination of compositional and multivariate statistical techniques to identify 122 cecum microbial genes with differential abundances between the lines (ranging from −0.75 to +0.73 SD). This work elucidates that microbial biosynthesis lipopolysaccharides, peptidoglycans, lipoproteins, mucin components, and NADH reductases, amongst others, are influenced by the host genetic determination for lipid accretion in muscle. We also differentiated between host-genetically influenced microbial mechanisms regulating lipid deposition in body or intramuscular reservoirs, with only 28 out of 122 MGs commonly contributing to both. Importantly, the results of this study are of relevant interest for the efficient development of strategies fighting obesity.

Eight cycles of half-sib family recurrent selection to improve rubber yield in russian dandelion

Russian dandelion (Taraxacum kok-saghyz) produces natural rubber which can complement the world’s supply of this strategic commodity, derived mainly from the Para rubber tree (Hevea brasiliensis). Four cycles of half-sib family recurrent selection conducted previously in russian dandelion improved rubber yield nearly 50%. The objectives of this research were to continue selection for four additional cycles and evaluate progress from eight generations of breeding, and assess the potential for future gains. Rubber yield increased from 0.205 to 0.378 g/plant from Cycle 0 (C0) to C8, representing an 84% improvement, or 10% per cycle. Increases from C0 to C4 were similar to those from C4 to C8. Root dry weight did not increase from selection and improved yield only resulted from enhancing rubber percentage which changed from 4.35 to 7.62%. Selection response has not plateaued and phenotypic variation has not decreased, indicating continued gains can occur with additional breeding.

Population genetic bottleneck has only marginal effects on fitness evolution and its repeatability in dioecious C. elegans

Evolution is a key process by which populations can adapt to novel conditions, but it is not well understood how predictable this process is. Predictability is expected to depend on the ratio of deterministic and stochastic processes that contribute to evolutionary change and this ratio is modulated by the effective population size. Smaller effective populations harbor less genetic diversity and stochastic processes are generally expected to play a larger role, leading to less repeatable evolutionary trajectories. Empirical insight into the relationship between effective population size and repeatability is limited and biased towards asexual unicellular organisms. Here, we used populations of obligately outcrossing Caenorhabditis elegans to test whether fitness increase and selection response were more heterogeneous after a moderate or strong population bottleneck compared to a scenario without bottleneck. Nematodes were exposed to a novel bacterial prey and lower temperature. Population sizes after one week of growth (as a proxy of fitness) were measured before and after 15 generations of evolution. We found that replicates across all (no/moderate/strong bottleneck) treatments evolved higher fitness and no significant difference in average or maximum fitness was found among treatments. Partitioning fitness variance among effects from selection and effects from chance showed that a strong (but not a moderate) bottleneck reduced the relative contribution of selection effects to fitness variation. However, the reduced contribution from selection did not translate to a significant reduction in the repeatability of fitness evolution. Thus, although a strong bottleneck reduced the contribution of deterministic evolutionary change, we found only marginal effects on quantitative measurements of repeatability in evolution. We conclude that the extent to which evolution is predictable may not universally depend on effective population size.