Genetic evaluation using random regression models with different covariance functions for test‐day milk yield in an admixture population of Thailand goats

The objectives of this study were to compare covariance functions (CF) and estimate the heritability of milk yield from test‐day records among exotic (Saanen, Anglo‐Nubian, Toggenburg and Alpine) and crossbred goats (Thai native and exotic breed), using a random regression model. A total of 1472 records of test‐day milk yield were used, collected from 112 does between 2003 and 2006. CF of the study were Wilmink function, second‐ and third‐order Legendre polynomials, and linear splines 4 knots located at 5, 25, 90 and 155 days in milk (SP25–90) and 5, 35, 95 and 155 of days in milk (SP35–95). Variance components were estimated by restricted maximum likelihood method (REML). Goodness of fit, Akaike information criterion (AIC), percentage of squared bias (PSB), mean square error (MSE), and empirical correlation (RHO) between the observed and predicted values were used to compare models. The results showed that CF had an impact on (co)variance estimation in random regression models (RRM). The RRM with splines 4 knots located at 5, 25, 90 and 155 of days in milk had the lowest AIC, PSB and MSE, and the highest RHO. The heritability estimated throughout lactation obtained with this model ranged from 0.13 to 0.23.     

The empirical bias of estimates by restricted maximum likelihood, Bayesian method, and method R under selection for additive, maternal, and dominance models.

Bayesian analysis via Gibbs sampling, restricted maximum likelihood (REML), and Method R were used to estimate variance components for several models of simulated data. Four simulated data sets that included direct genetic effects and different combinations of maternal, permanent environmental, and dominance effects were used. Parents were selected randomly, on phenotype across or within contemporary groups, or on BLUP of genetic value. Estimates by Bayesian analysis and REML were always empirically unbiased in large data sets. Estimates by Method R were biased only with phenotypic selection across contemporary groups; estimates of the additive variance were biased upward, and all the other estimates were biased downward. No empirical bias was observed for Method R under selection within contemporary groups or in data without contemporary group effects. The bias of Method R estimates in small data sets was evaluated using a simple direct additive model. Method R gave biased estimates in small data sets in all types of selection except BLUP. In populations where the selection is based on BLUP of genetic value or where phenotypic selection is practiced mostly within contemporary groups, estimates by Method R are likely to be unbiased. In this case, Method R is an alternative to single-trait REML and Bayesian analysis for analyses of large data sets when the other methods are too expensive to apply.     

Detection of bovine leukocyte antigen DRB3 alleles as candidate markers for clinical mastitis resistance in Holstein x Zebu

Bovine leukocyte antigen DRB3 alleles from Holstein x Zebu crossbred dairy cows (n = 409) were analyzed using the PCR-RFLP technique. Exon II of DRB3 was amplified using locus-specific primers (HLO30/HLO32), followed by digestion with 3 restriction enzymes (RsaI, BstyI, and HaeIII). Forty alleles were found with frequency ranging from 0.005 to 0.139. The most frequently detected alleles of Holstein x Zebu were DRB3*16, *51, *23, *11, *8, and *1, accounting for 61.12% of the alleles in the population. Detection of candidate alleles for clinical mastitis occurrence was performed by logistic regression. It was found that percentage of Holstein fraction in crossbred cows had a nonsignificant effect (P > 0.05). However, parity had a significant effect on mastitis occurrence. In addition, DRB3*1 and *52 were the most associated with the occurrence of clinical mastitis, whereas *15, *51, and *22 were associated with resistance in crossbred populations. This is the first report of association of DRB3*15 and *51 with mastitis resistance. The association was validated by examining the candidate alleles in another commercial population. Highly susceptible (n = 43) and resistant (n = 42) groups of Holstein x Zebu cows were investigated. The result confirmed that DRB3*1 and *52 could be considered as susceptibility alleles, whereas *15, *51, and *22 could be considered as resistant alleles in Holstein x Zebu raised under tropical conditions. In addition, allele effects on 305-d milk production were estimated by BLUP. It was shown that most alleles associated with high clinical mastitis occurrence were related to increased milk yield. This study revealed that allele DRB3*10 had the greatest effect on increasing milk yield with moderate resistance to clinical mastitis, which could be used as a potential marker for selection in dairy genetic evaluation.     

Effects of forage ensiling and ration fermentation on total mixed ration pH,ruminal fermentation and performance of growing Holstein‐Zebu cross steers

Our objective was to determine the effect of forage ensiling and ration fermentation on total mixed ration pH, ruminal fermentation and animal performance. Thirty Holstein‐Zebu cross steers were allotted to feeding treatments for 188 days in a randomized complete block design including: fresh grass‐total mixed ration (GTMR; pH 4.7), grass silage‐TMR (STMR; pH 4.0) and fermented‐TMR (FTMR; pH 3.5). Average daily gain for STMR was greatest during the first 3 months period; however, that for FTMR tended to be greater than GTMR during the second 3 months period (P < 0.10). During the second period dry matter intake for STMR was the greatest (P < 0.01), but feed conversion ratio (P < 0.01) and cost per gain (P < 0.01) were the least for FTMR. Protein digestibility tended (P < 0.10) to be greater for FTMR than STMR and fat digestibility was greater (P < 0.05) for GTMR and FTMR than STMR. FTMR had less (P < 0.01) ruminal NH₃‐N content than STMR. Total volatile fatty acids post‐feeding was greatest for GTMR (P < 0.01). Ruminal proportions of acetic and butyric acids were greater for FTMR than GTMR (P < 0.05); in contrast, propionic acid was greater for GTMR (P < 0.05). Utilizing silage or total ration fermentation did not negatively impact on ruminal pH. STMR and FTMRs can be used to maintain performance of growing crossbred Holstein steers.     

Droplet digital polymerase chain reaction assay for identifying and quantifying pork products

Halal products are growing in consumer markets worldwide, and pork meat is classified as non-halal. Manufacturers of processed foods and products must ensure that their products follow Islamic dietary law because pork is prohibited for Muslims. Droplet digital polymerase chain reaction (PCR) (ddPCR) is a novel method for identifying pig species and quantifying pork products. This experiment aimed to investigate pork species and establish the proportion of pork in meat products using the mitochondrial cytochrome b gene (CYTB). The study found that the correlation coefficient between the meat weight and DNA concentration of pork was 0.997, and the correlation coefficient between the DNA concentration and the target DNA copy number of pork was 0.998. The accuracy of the ddPCR assay was verified using a sample of a known proportion of pork, and it was revealed that this method is highly precise in quantifying pork products. Nine products contained an undeclared meat proportion (90%). The limit of detection for pork was 0.0001 ng. The analysis indicated that the ddPCR assay has high accuracy and sensitivity for quantifying pork products. Therefore, the predictive model can be used in routine laboratories for quality assurance of halal food products.     

Production of acute hepatopancreatic necrosis disease toxin is affected by addition of cell‐free supernatant prepared from AI‐2‐producing Vibrio harveyi mutant

Acute hepatopancreatic necrosis disease (AHPND) causes massive mortality in shrimp ponds within the first month poststocking. The causative agent is a specific strain of Vibrio parahaemolyticus (VP_AHPND) that has acquired the capability to produce virulent binary toxins called ToxA and ToxB. This study aims to test the effect of the addition of an autoinducer‐2‐containing cell‐free supernatant (CFS) from the mutant Vibrio harveyi (VH) on growth and toxin production of VP_AHPND. The relative AI‐2‐like activity in CFS was detected by luminescence assay. The effect of CFS (5 and 9%) on growth and toxin production of VP_AHPND was evaluated. Compared to the control culture (without CFS‐VH addition), the addition of either 5 or 9% CFS‐VH affected the growth at the initial stage of VP_AHPND. Similar growth profiles of VP_AHPND were found with the addition of CFS‐VH at both concentrations. Western blot analysis suggests that the addition of CFS‐VH affected the production of both toxins. ToxA could be detected at the early hour post‐CFS‐VH inoculation, whereas the high amount of ToxB was detected when 5% CFS‐VH was added. However, interfering with the AI‐2 function with furanone, the AI‐2 antagonist resulted in a slight delay in the production of both toxins. Results from this study will help to design a novel strategy to control AHPND in shrimp culture.     

Genetic characterization of Thai indigenous chickens compared with commercial lines

A total of 210 chicken samples, from seven strains, were genotyped using 20 microsatellite loci of which 16 are recommended by the Food and Agriculture Organization. The genetic variability and divergence of four Thai indigenous strains and three commercial lines were assessed to generate baseline information for conservation, promotion, and make sustainable utilization of indigenous chicken resources in Thailand. A total of 227 alleles were distributed ranging from six (MCW 111) to 16 (MCW 183 and LEI 166) alleles per locus. The highest (0.81) and lowest (0.77) average of expected heterozygosities were observed in indigenous chicken (Dang) and commercial layer (Isa Brown), respectively. All microsatellite loci were in the Hardy–Weinberg equilibrium, except for MCW111 and ADL372 in the Isa Brown line. The subpopulation division coefficient (F _ST ) was strong with the value of 0.183 indicating the genetic differentiation among the studied groups. Four genetic clusters were detected: the first group consisted of layers (Isa Brown and White Leghorn); the second group was broiler; the third group consisted of non-black feather indigenous chicken (Chee, Dang, and Leung Hang Khoa); and the fourth group was black feather indigenous chicken (Pradu Hang Dam). The results of this study also suggested that Pradu Hang Dam is suitable to be developed as a meat type chicken due to lower genetic distance between Pradu Hang Dam and broiler.     

Genetic relationships of fertility traits with test‐day milk yield and fat‐to‐protein ratio in tropical smallholder dairy farms

The test‐day milk fat‐to‐protein ratio (TD‐FPR) could serve as a measure of energy balance status and might be used as a criterion to improve metabolic stability and fertility through genetic selection. Therefore, genetic parameters for fertility traits, test‐day milk yield (TD‐MY) and TD‐FPR, as well as, their relationships during different stages of lactation, were estimated on data collected from 25 968 primiparous Thai dairy crossbred cows. Gibbs sampling algorithms were implemented to obtain (co)variance components using both univariate linear and threshold animal models and bivariate linear‐linear and linear‐threshold animal models with random regression. Average TD‐MY and TD‐FPR were 12.60 and 1.15. Heritability estimates for TD‐MY, TD‐FPR and selected fertility traits ranged from 0.31 to 0.58, 0.17 to 0.19 and 0.02 to 0.05, respectively. Genetic correlations among TD‐FPR and TD‐MY, TD‐FPR and fertility traits, and TD‐MY and fertility traits ranged from 0.05 to ‐0.44, from ‐0.98 to 0.98 and ‐0.22 to 0.79, respectively. Selection for lower TD‐FPR would decrease numbers of inseminations per conception and increase conception at first service and pregnancy within 90 days. In addition, cow selection based only on high milk production has strong effects to prolong days to first service, days open and calving interval.     

An identification in fish of the genus Puntius Hamilton 1822 (Cypriniformes: Cyprinidae) of some wetlands in northeast Thailand with the use of random amplified polymorphic DNA technique

The experiment was carried out during the 2003 to 2006 at the Department of Fisheries, Khon Kaen University, Khon Kaen, Thailand in collaboration with the Department of Biosciences, the University of Hertfordshire, College Land, Hatfield, Herts, UK. Molecular RAPD technique was used for the determinations of DNA patterns of the fish genus Puntius Hamilton 1822. The fish samples of 1,500 individual fish were collected from fifteen wetlands in Northeast Thailand and they were used for DNA extraction. Before the experiment was carried out the fish samples were morphologically identified and it was found that the collected fish consisted of 9 species i.e., Puntius altus, P. aurotaeniatus, P. binotatus, P. gonionotus, (e) P. leiacanthus, P. orphoides, P. partipentazona, P. schwanenfeldi and P. wetmorei. Genomic DNAs were extracted from 5 mg of muscle tissues (skeleton muscles) with the use of PUREGENE DNA Isolation Kit for Laboratory Use, Gentra Systems, USA. Eighty decamer primers from four kits were subjected to a preliminary test. It was found that only 10 decamer primers were most suited for this PCR amplification. The results showed that genetic distant values being established among and between pairs of the fishes of the 9 fish species ranged from 0.191 to 0.456 for a pair between Puntius gonionotus and Puntius altus and a pair between Puntius schwanenfeldi and Puntius leiacanthus, respectively. Similarity coefficient values within the 9 fish species ranged from 0.109 to 0.231. The results on a Dendrogram of clusters showed that there were 5 minor groups of the 9 fish species but the 9 species could not be split or shifted into other genera of the fish due to small differences found within the values of similarity coefficients.     

Genetic associations between milk fat‐to‐protein ratio,milk production and fertility in the first two lactations of Thai Holsteins dairy cattle

The aims of this study were to estimate, simultaneously, the genetic parameters of test‐day milk fat‐to‐protein ratio (FPR), test‐day milk yield (MY), and days‐open (DO) in the first two lactations of Thai Holsteins. A total of 76 194 test‐day production records collected from 8874 cows with 8674 DO records between 2001 and 2011 from different lactations were treated as separated traits. The estimates of heritability for test‐day FPR in the first lactation showed an increasing trend, whereas the estimates in the second lactation showed a U‐shape trend. Genetic correlations for FPR‐DO and MY‐DO showed a decreasing trend along days in milk (DIM) in both lactations, whereas genetic correlations for FPR‐MY increased along DIM in the first lactation but decreased in the second lactation. Genetic correlations of FPR between consecutive DIM were moderate to high, which showed the effectiveness of simultaneous analyses. Selection of FPR in the early stage has no adverse effect on MY and DO for the first lactation but has a negative effect on MY and positive effect on DO for the second lactation. This study showed that genetic improvement of the energy balance using FPR, MY and DO with multi‐trait test day model could be applied in a Thailand dairy cattle breeding program.