Effect of insulin-like growth factor 1 gene on growth traits of Kejobong goat and its growth analysis

AIM

This study aimed to identify the effect of the insulin-like growth factor 1 (IGF1) gene on growth, to uncover the genetic marker at the IGF1 gene, and to predict growth performance by analyzing growth models of Kejobong goats based on their genotype.

MATERIALS AND METHODS

DNA and records of body weight (BW) and body measurements (BM) of Kejobong goats were collected, the IGF1 gene was amplified from the DNA template by polymerase chain reaction (PCR); the PCR products were then sequenced to determine single nucleotide polymorphisms (SNP). Linear mixed model (LMM) was used to analyze the association between SNP and growth traits. Four non-linear growth models were analyzed using non-LMM to describe the growth model and to compare the growth within genotypes.

RESULTS

An SNP at intron 4 (g5752G→C) genotyped into GG and CC was significantly associated with BW and BM. Goats of genotype GG had a significantly higher BW and BM (p<0.05) than those of genotype CC. Growth analysis showed that the von Bertalanffy model was the most fit for describing BW, the Brody model for chest width and hip height, the Gompertz and Logistic models for heart girth, and the von Bertalanffy and Gompertz models for hip width.

CONCLUSION

An SNP at intron 4 of the IGF1 gene was associated with the growth trait and was usable as a genetic marker candidate for improvement of growth traits of Kejobong goats while von Bertalanffy model provides proper and accurate estimates of parameters to describe the growth performance of Kejobong goats.

Genetics of heifer reproductive traits in Japanese Black cattle

Objective

The objective of this study was to identify environmental factors strongly associated with and to estimate genetic parameters of reproductive traits in Japanese Black heifers.

Methods

Data included reproduction records of Japanese Black heifers born between 2004 and 2014. First service non-return rate (NRR) to 56 days from first to successful insemination (FS), number of services per conception (IN), age at first calving (AFC) and gestation length were analyzed with the use of the general linear model. Genetic parameters were estimated with the use of the univariate animal model of the residual maximum likelihood.

Results

Averages of reproductive traits over eleven years were assessed, and the effects of farm, year, month, artificial insemination technician and interaction of farm×year on the traits were determined. Estimated heritability of FS was very low and that of AFC was higher than that of the other traits. A close genetic relation was observed among NRR, IN, and FS; however, their heritabilities were very low. AFC shows favorable genetic correlation with IN and FS.

Conclusion

Low heritabilities of most reproductive traits in Japanese Black heifers are strongly influenced by farm management practices, and that large residual variances make genetic evaluation difficult. Among the reproductive traits, AFC is potentially more useful for genetic improvement of heifer reproductive traits because it has high heritability and favorable genetic correlations with IN and FS.

Bayesian estimates of genetic parameters of non-return rate and success in first insemination in Japanese Black cattle

Objective

The objective of present study was to estimate heritability of non-return rate (NRR) and success of first insemination (SFI) by using the Bayesian approach with Gibbs sampling.

Methods

Heifer Traits were denoted as NRR-h and SFI-h, and cow traits as NRR-c and SFI-c. The variance covariance components were estimated using threshold model under Bayesian procedures THRGIBBS1F90.

Results

The SFI was more relevant to evaluating success of insemination because a high percentage of animals that demonstrated no return did not successfully conceive in NRR. Estimated heritability of NRR and SFI in heifers were 0.032 and 0.039 and the corresponding estimates for cows were 0.020 and 0.027. The model showed low values of Geweke (p-value ranging between 0.012 and 0.018) and a low Monte Carlo chain error, indicating that the amount of a posteriori for the heritability estimate was valid for binary traits. Genetic correlation between the same traits among heifers and cows by using the two-trait threshold model were low, 0.485 and 0.591 for NRR and SFI, respectively. High genetic correlations were observed between NRR-h and SFI-h (0.922) and between NRR-c and SFI-c (0.954).

Conclusion

SFI showed slightly higher heritability than NRR but the two traits are genetically correlated. Based on this result, both two could be used for early indicator for evaluate the capacity of cows to conceive.

Different penalty methods for assessing interval from first to successful insemination in Japanese Black heifers

Objective

The objective of this study was to determine the best approach for handling missing records of first to successful insemination (FS) in Japanese Black heifers.

Methods

Of a total of 2,367 records of heifers born between 2003 and 2015 used, 206 (8.7%) of open heifers were missing. Four penalty methods based on the number of inseminations were set as follows: C1, FS average according to the number of inseminations; C2, constant number of days, 359; C3, maximum number of FS days to each insemination; and C4, average of FS at the last insemination and FS of C2. C5 was generated by adding a constant number (21 d) to the highest number of FS days in each contemporary group. The bootstrap method was used to compare among the 5 methods in terms of bias, mean squared error (MSE) and coefficient of correlation between estimated breeding value (EBV) of non-censored data and censored data. Three percentages (5%, 10%, and 15%) were investigated using the random censoring scheme. The univariate animal model was used to conduct genetic analysis.

Results

Heritability of FS in non-censored data was 0.012±0.016, slightly lower than the average estimate from the five penalty methods. C1, C2, and C3 showed lower standard errors of estimated heritability but demonstrated inconsistent results for different percentages of missing records. C4 showed moderate standard errors but more stable ones for all percentages of the missing records, whereas C5 showed the highest standard errors compared with non-censored data. The MSE in C4 heritability was 0.633×10⁻⁴, 0.879×10⁻⁴, 0.876×10⁻⁴ and 0.866 ×10⁻⁴ for 5%, 8.7%, 10%, and 15%, respectively, of the missing records. Thus, C4 showed the lowest and the most stable MSE of heritability; the coefficient of correlation for EBV was 0.88; 0.93 and 0.90 for heifer, sire and dam, respectively.

Conclusion

C4 demonstrated the highest positive correlation with the non-censored data set and was consistent within different percentages of the missing records. We concluded that C4 was the best penalty method for missing records due to the stable value of estimated parameters and the highest coefficient of correlation.

Partial diallel cross for assessing genetic merit of local rabbit breed

This study was carried out to estimate general combining ability (GCA) and specific combining ability (SCA) of pre-and post-weaning traits from a partial diallel cross in three rabbit breeds: Local rabbit (L), Flemish Giant (F), and Rex (R). Body weight at 0 (BW0), 30 (BW30), 42 (BW42), and 63 (BW63) days of age, average daily gains from 0 to 30 d of age (ADG0-30), from 30 to 42 d of age (ADG30-42), from 42 to 63 d of age (ADG42-63), and from 30 to 63 d of age (ADG30-63), litter size at birth (LS0) and at weaning (LS42), and mortality at weaning (MR42) were studied in crossing LL, FF, RR, LF, LR, and FR. Local breed had the highest GCA for BW0, BW30, BW42, and average daily gain before weaning (ADG0-30, and ADG30-42) compared to Flemish Giant and Rex, while GCA of Local breed for average daily gain after weaning (ADG42-63), litter size (LS0, and LS42), and mortality (MR42) was higher than for Rex and similar to that of Flemish Giant. Crossing LF and LR showed higher SCA for BW30, BW42, BW63, ADG0-30, ADG42-63 and ADG30-63 than FR. In conclusion, based on GCA and SCA, the Indonesian Local breed has a high genetic potential in the crossing with Flemish Giant and Rex breeds.

Relation between body condition score and conception rate of Japanese Black cows

Objective

This study analyzes interactions of body condition score (BCS) with other factors and the effect of BCS on estimates of genetic paremeters of conception rate (CR) in Japanese Black cows.

Methods

Factors affecting CR were analyzed through the linear mixed model, and genetic parameters of CR were estimated through the threshold animal model.

Result

The interactions between BCS and each season and the number of artificial inseminations (AI) was significant (p<0.05), but that between BCS and parity showed no significance for CR. High CR was observed with BCS 3 in autumn (0.56 ± 0.01) and BCS 4 in summer (0.56 ± 0.02). The highest CR with BCS 3 (0.56 ± 0.02) and BCS 4 (0.55 ± 0.01) was observed at first AI. With BCS 5, however, the highest CR (0.55 ± 0.08) was observed at second AI.

Conclusion

The model with BCS was notably conducive to the estimation of genetic parameters because of a low deviance information criterion (DIC) of heritability that, nevertheless, was slightly lower than the model without BCS.

Revealing the complete mtDNA genome sequence of Cemani chicken (Gallus gallus) by using Nanopore sequencing analysis

OBJECTIVE

This study aimed to identify, discover and explore the characteristics of the mtDNA genomes of Cemani chicken (Gallus gallus).

METHODS

This study used gDNA of Cemani chicken isolated from liver tissue. mtDNA sequencing was performed using WGS mtDNA analysis with nanopore technology by Oxford Nanopore Technologies GridION. Bioinformatics and data analysis were then performed.

RESULTS

This study showed that the length of the mtDNA genome is 16,789 bp, consisting of two ribosomal RNA (12S rRNA, 16S rRNA), 22 transfer RNA genes (trnR, trnG, trnK, trnD, trnS, trnY, trnC, trnN, trnA, trnW, trnM, trnQ, trnl, trnL, trnV, trnF, trnP, trnT, trnE, trnL, trnS, trnH), 13 protein-coding genes (PCGs) (ND4l, ND3, COX3, ATP6, ATP8, COX2, COX1, ND2, ND1, CYTB, ND6, ND5, ND4), and a noncoding control region (Dloop). Furthermore, analysis showed there were polymorphic sites and amino acid alterations when mtDNA Cemani chicken was aligned with references from GenBank.

CONCLUSION

Site (988T>*) in Dloop genes and (328A>G) in ND3 genes which alter glycine to stop codon, were specific markers found only in Cemani chicken.

Genetic diversity and phylogenetic study of Ongole Grade cattle population in Central Java based on blood protein polymorphism

Abstract. Lestari DA, Sutopo, Setiaji A, Kurnianto E. 2023. Genetic diversity and phylogenetic study of Ongole Grade cattle population in Central Java based on blood protein polymorphism. Biodiversitas 24: 617-624. This research provides useful information to reflect the genetic structure and to determine appropriate breeding strategies for the Ongole Grade cattle population in Central Java. The objectives of this research were to investigate the genetic diversity and phylogenetic relationship of the Ongole Grade cattle (Bos indicus) population in Central Java based on blood protein polymorphism. A total of 208 blood samples were collected, which belonged to 6 populations of Ongole Grade cattle in Central Java, namely Rembang, Blora, Kebumen, Semarang, Magelang, and Kudus regency. Blood protein analysis was conducted by Sodium Dodecyl Sulfate-Polyacrilamide Gel Electrophoresis (SDS-PAGE) methods to separate blood protein based on molecule weight. Results showed 4 blood protein locus were clearly identified, namely Albumin (Alb), Post Albumin (Pa), Ceruloplasmin (Cp), and Amylase-I (Amy-I), which formed 9 identified alleles and 15 genotypes. All populations had different allele and gene frequency distribution for each locus, which dominated by allele AlbB (0.525), PaB (0.556), CpF (0.608), and Amy-IB (0.639) and by genotype BB (0.312) for Alb loci, BB (0.429) for Pa loci, FS (0.423) for Cp loci and BB (0.472) for Amy-I. Ongole Grade cattle population in this study showed deviation in Hardy-Weinberg Equilibrium (HWE) (P<0.05) for Blora, Kebumen, Semarang, and Kudus, while the rest populations showed in HWE condition. Average heterozygosity and genetic distance of the Ongole Grade cattle population in the recent study were range 0.328-0.529 (for Magelang and Kebumen populations, respectively) and 0.0057-0.0955 (for the Rembang-Kebumen population and Magelang-Kebumen population), respectively. In conclusion, Ongole Grade cattle population in Central Java had high genetic diversity and was divided into two major clusters.

Genetic characteristics of complete mtDNA genome sequence of Indonesian local rabbit (Oryctolagus cuniculus)

BACKGROUND

Indonesian local rabbit (Oryctolagus cuniculus) is a local breed in Indonesia. We reveal the mitochondrial genome sequence of the Indonesian local Rabbit for the first time. A better understanding of the mechanisms underlying these beneficial aspects of local breeds over imported ones requires detailed genetic investigations, of which mtDNA genome sequencing is of particular importance. Such an investigation will solve the major issues of misidentification with Javanese hares (Lepus nigricollis) and maternal lineage. In addition, this information will guide better statistics on the Indonesian local rabbit breed population and strategies for its conservation and breeding plans. This study aimed to identify and explore the characteristics of the mtDNA genomes of Indonesian local rabbits.

RESULT

This study observed that the length of the mtDNA genome is 17,469 bp, consisting of two ribosomal RNA (12S rRNA, 16S rRNA), 22 transfer RNA genes (trnR, trnG, trnK, trnD, trnS, trnY, trnC, trnN, trnA, trnW, trnM, trnQ, trnl, trnL, trnV, trnF, trnP, trnT, trnE, trnL, trnS, trnH), 13 protein-coding genes (PCGs) (ND4l, ND3, COX3, ATP6, ATP8, COX2, COX1, ND2, ND1, CYTB, ND6, ND5, ND4), a replication origin, and a noncoding control region (D-loop).

CONCLUSIONS

mtDNA genome of Indonesian local rabbit was the longest and had the most extended D-loop sequence among the other references of Oryctolagus cuniculus. Other specific differences were also found in the percentage of nucleotides and variation in most of the PCGs when they were aligned with Oryctolagus cuniculus references from GenBank. Indonesian local Rabbits strongly suspected brought from Europe during the colonial period in Indonesia.