Animal Genetics

Domestic dogs share a wide range of important disease conditions with humans, including cancers, diabetes and epilepsy. Many of these conditions have similar or identical underlying pathologies to their human counterparts and thus dogs represent physiologically relevant natural models of human disorders. Comparative genomic approaches whereby disease genes can be identified in dog diseases and then mapped onto the human genome are now recognized as a valid method and are increasing in popularity. The majority of dog breeds have been created over the past few hundred years and, as a consequence, the dog genome is characterized by extensive linkage disequilibrium (LD), extending usually from hundreds of kilobases to several megabases within a breed, rather than tens of kilobases observed in the human genome. Genome-wide canine SNP arrays have been developed, and increasing success of using these arrays to map disease loci in dogs is emerging. No equivalent of the human HapMap currently exists for different canine breeds, and the LD structure for such breeds is far less understood than for humans. This study is a dedicated large-scale assessment of the functionalities (LD and SNP tagging performance) of canine genome-wide SNP arrays in multiple domestic dog breeds. We have used genotype data from 18 breeds as well as wolves and coyotes genotyped by the Illumina 22K canine SNP array and Affymetrix 50K canine SNP array. As expected, high tagging performance was observed with most of the breeds using both Illumina and Affymetrix arrays when multi-marker tagging was applied. In contrast, however, large differences in population structure, LD coverage and pairwise tagging performance were found between breeds, suggesting that study designs should be carefully assessed for individual breeds before undertaking genome-wide association studies (GWAS).

Genetic studies of livestock populations focus on questions of domestication, within- and among-breed diversity, breed history and adaptive variation. In this review, we describe the use of different molecular markers and methods for data analysis used to address these questions. There is a clear trend towards the use of single nucleotide polymorphisms and whole-genome sequence information, the application of Bayesian or Approximate Bayesian analysis and the use of adaptive next to neutral diversity to support decisions on conservation.

Aim:  The  aims  are  to  study  the  genetic  diversity  and  population  structure  of  Tilapia  fish  species  in Nigeria  using  mtDNA  D-loop  region    and  time  divergence  of  these  various  groups  of  fish  to  give  a baseline  information  for  fish  management  and  conservation  programs.
Methodology:  Blood  samples  from  four  species  of  tilapia  were  collected  with  the  use  of  FTA  cards for  DNA  extraction  and  PCR  amplification.  A  941bp  long  fragment,  including  the  D-loop,  was subsequently  used  for  analysis.  Molecular  diversity  indices  and  Tajima’s  selective  test  were determined.  A  phylogenetic  tree  was  constructed  for  all  the  four  fish  species  using  UPGMA. The divergence  time  among  the  four  fish  species  using  MEGA5  software.
Place  and  Duration  of Study : The study  was  carried  out  in  the  Biotechnology  Centre,  Federal University  of  Agriculture,  Abeokuta  Nigeria  between.  Genotyping  and  Optimization  of  PCR conditions  were  carried  out  at  STAB  VIDA  Lda,  Madan  Parque,  Rua  dos  Inventores,  2825-182 Caparica  Portugal.  Total  duration  of  study  was  between  February  to  August  2015.
Results:  Sarotherodon  melanotheron  has  the  highest  nucleotide  diversity  (π),  mean  number  of pairwise  differences  and  number  of  polymorphic  site,  while  the  least  was  observed  in  Sarotherodon galiIaeus.  The  highest  number  of  monomorphic  site  and  the  highest  sequences  conservation percentage  was observed  in  Sarotherodon  galiIaeus. The  Neighbour  joining  tree  revealed  six  (6)  clusters  with  no  clear  sub-structuring  among  the sampled  fish  populations.  The  smallest  divergence  time  (about  31  mya)  was  observed  between Sarotherodon  galilaeus  and  Sarotherodon  melanotheron.  Sarotherodon  spp  diverged  from Oreochromis  niloticus  about  32.5  mya.
Conclusion:  The  present  study  revealed  that  the  sampled  Tilapia  species  from  Nigeria  represent  a single  stock.  The  existing  low  levels  of  genetic  variability  observed  here  may  compromise  the evolutionary  plasticity  of  the  Tilapia  species  population.  These  findings  indicate  an  urgent  need  for the  careful  monitoring  of  the  harvesting  of  Tilapia  species  in  Nigeria.

Aim: Native rabbits in smallholder system are considered as important genetic resources, and the present study was aimed to study the genetic and phenotypic characterization and detection of the maternal origin of the native rabbit populations located at the Middle of Egypt. Materials and Methods: A survey of native rabbit populations was conducted in three governorates (Fayum [FY], Beni Suef [BN], and El Menia [MN]). The phenotypic characterization of rabbits included the profile body of the head, ears, eyes, neck, and legs and the coat colors. The blood samples were collected for genetic characterization based on mitochondrial (cytochrome b) and the microsatellite markers. Results: The phenotypic characterization of the body parts in the three populations was almost similar. The body weight of the mature rabbits in MN government was significantly heaviest, and the measurements for the main body parts (body length, chest circumference, and abdominal girth) were the highest compared to the two populations. The results of mitochondrial (cytochrome b) analysis revealed that the rabbits from the three governments belonged to lineage A except one animal was recorded as lineage G from MN's rabbit population. The results of the microsatellite markers revealed that the genetic diversity between the three populations showed genetic interferences; however, a closer genetic relationship was observed between BN and MN than FY. The majority of the genetic diversity was the individual variability. Conclusion: The mitochondrial lineage A is the major lineage in rabbit populations in the area of the Middle Egypt understudy. The genetic populations' structure is the interferences among the three populations. A large-scale survey should be done on native rabbit populations for the sustainable management and conservation of the local breeds' genetic resources.

A total 62 milk samples from Ongole herd were collected with the objective of assessing milk compositions of Ongole cattle and to investigate the effect of parity and stage of lactation on test-day milk yield and milk constituent traits. Milk compositions were determined by Lactoscan apparatus. The test-day milk yield was 2.78 ± 0.21 kg. Overall least-squares mean for fat, SNF, protein and lactose were 3.31 ± 0.18, 9.34 ± 0.12, 3.51 ± 0.08 and 5.12 ± 0.07 respectively. The analysis revealed that the parity and stage of lactation did not influence the fat, protein, SNF and lactose content and yields.

Background and Aim: A canine multi-drug resistance 1 (MDR1) nt230(del4) is a well-known inherited disorder that primarily affects collies and various herding breeds. The most recognized clinical implication for affected dogs is associated with an increased risk of multiple drug toxicity. To date, MDR1 gene mutations have been identified globally, especially in dogs from the USA and European countries. This study aimed to investigate the prevalence of MDR1 nt230(del4) in herding dog breeds and Thai Ridgebacks in Thailand.

Materials and Methods: We clarified the prevalence of MDR1 nt230(del4) in 263 dogs of eight purebred dog breeds in Thailand using an allele-specific multiplex polymerase chain reaction method and direct DNA sequencing.

Results: Rough Collies, Australian Shepherds, Shetland Sheepdogs, and Old English Sheepdogs were affected by the mutation with mutant allelic frequencies of 57.14%, 12.82%, 11.28%, and 8.33%, respectively. Among these populations, the prevalence of the MDR1 (+/–) genotype was 57.14% (12/21) for Rough Collies, 25.64% (10/39) for Australian Shepherds, 16.13% (15/93) for Shetland Sheepdogs, and 16.67% (2/12) for Old English Sheepdogs, whereas the MDR1 (–/–) mutation was only identified in Rough Collies and Shetland Sheepdogs, with prevalences of 28.57% (6/21) and 3.22% (3/93), respectively. However, the MDR1 nt230(del4) was not identified in Border Collies, German Shepherds, White Swiss Shepherds, or Thai Ridgebacks.

Conclusion: This study provides the current situation regarding MDR1 nt230(del4) in herding dog breeds in Thailand. In this survey, we investigated for the first time the status of MDR1 genotype in Thai Ridgebacks. These results are helpful for veterinarians managing effective therapeutic plans for commonly affected dog breeds, and these results will encourage all breeders to improve their selective breeding programs based on the MDR1 nt230(del4) status.

Aim: This study aimed to determine the genetic and non-genetic factors affecting pre-weaning body weight (BW) and morphometry in Assam Hill goat along with the genetic parameters.

Materials and Methods: The detailed information in respect of BW and body measurements of 960 animals at birth and 3 months of age belonging to three different populations of Assam Hill goat maintained at field units, namely, Batabari, Nahira, and Tetelia under "All India Coordinated Research Project on Goat Improvement" were utilized in the present study. The data were analyzed using least squares technique.

Results: The least squares means for BW, height at withers (HW), heart girth (HG), and body length (BL) were 1.166±0.008 kg, 26.198±0.070 cm, 26.695±0.096 cm, and 29.482±0.119 cm at birth and 4.590±0.083 kg, 36.850±0.105 cm, 40.741±0.115 cm, and 39.703±0.108 cm at 3 months of age, respectively. Location had a significant effect on BW, HW, and BL at both birth and 3 months and on HG at 3 months of age. Season of birth exerted significant effect only on BL at birth, whereas the significant effect of sex was observed on HG and BL at 3 months of age. The heritability estimates for BW and body measurements were moderate indicating the scope of selection. The phenotypic and genetic correlations among BWs and body measurements at birth and 3 months of age were positive in direction and high in magnitude.

Conclusion: On the basis of the present findings, it could be concluded that the weaning weight of kids can be considered for the selection of parent stock to increase productivity and eventually the economic efficiency. Further, animals with higher body measurements at initial phases of growth will perform better with respect to even BW at later stages of growth.

Keywords: Assam Hill goat, genetic parameters, morphometric traits, non-genetic factors, pre-weaning growth.

Background and Aim: Madura cattle is local cattle in Indonesia. This cattle hasphenotypic variations in growth traits. This study aimed to identify leptin (LEP) gene polymorphism exon 2 associated with body measurements in Madura cattle. Materials and Methods: We recorded body weight (BW) and body measurements of 51 Madura cattle aged 1-4 years in Waru District, Madura. The LEP gene genotyping was conducted using the polymerase chain reaction-restricted fragment length polymorphism method with AciI restriction enzyme. Results: A 267 bp DNA fragment of the LEP gene was successfully amplified using a pair of primers. This study revealed three genotypes (TT, TC, and CC) and two alleles (T and C). The frequencies of TT, TC, and CC genotypes were 0.275, 0.45, and 0.275, respectively, whereas the frequencies of T and C alleles were 0.500 and 0.500, respectively. The c.73T>C mutation was significantly associated with BW, body length (BL), and chest girth (CG) (p<0.05). Among all genotypes, the TC had the highest BW, BL, and CG. Conclusion: Conclusively, LEP gene polymorphism (c.73T>C) exon 2 was polymorphic and associated with body measurements, especially BW, BL, and CG.

The aim of this article was to present a group of genetically determined disorders in horses. Some of the genes responsible for coat color in animals, show negative pleiotropic effect at the same time. Among others, there are mutations of KIT gene (homozygous lethal white horses), PMEL17 gene (MCOA syndrome in silver horses), EDNRB gene (white foal syndrome in overo horses), TRPM1 gene (associated with congenital stationary night blindness in leopard horses) and STX17 gene (increased incidence of melanoma in grey horses). The relationship between coat color and hareditary abnormalities deserves more attention, as mating individuals of certain genotypes leads to disease risks or lethal effects for the offspring.

The brown planthopper (BPH) is one of the most serious insect pests of rice throughout Asia. In this study, we constructed a linkage map to determine the locus for BPH resistance gene, using an F2 population from a cross between a resistant indica cultivar, ‘Col.5 Thailand’, and a susceptible cultivar ‘02428’. Insect resistance was evaluated using 147 F3 families and the genotype of each F2 plant was inferred from the phenotype of corresponding F3 families. Two QTLs was detected on chromosome 2 (explains 29.4% phenotypic variation) and 6 (46.2% variation explained) associated with resistance to BPH in the mapping population. Comparison of the chromosomal locations and reactions to BPH biotypes indicated that the gene on chromosome 6 is different from at least 18 of the 19 previously identified BPH resistance genes. These two genes have large effects on BPH resistance and may be a useful BPH resistance resource for rice breeding programs.

Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between the individuals in a population. It is an important source of genetic variation in an individual which is now being utilized rather than single nucleotide polymorphisms (SNPs), as it covers the more genomic region. CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs). Earlier, researchers extensively utilized SNPs as the main source of genetic variation. But now, the focus is on identification of CNVs associated with complex traits. With the recent advances and reduction in the cost of sequencing, arrays are developed for genotyping which cover the maximum number of SNPs at a time that can be used for detection of CNVRs and underlying quantitative trait loci (QTL) for the complex traits to accelerate genetic improvement. CNV studies are also being carried out to understand the evolutionary mechanism in the domestication of livestock and their adaptation to the different environmental conditions. The main aim of the study is to review the available data on CNV and its role in genetic variation among the livestock.

Background and Aim: Heat shock proteins (HSPs) are a group of proteins that play a significant role in protecting cells against cellular stress. HSP70 is a conserved, sensitive, and abundant gene associated with heat stress's physiological adaptability. The objective of this study was to reveal the polymorphisms of the partial sequences of the HSP70 gene (5' untranslated region [UTR]) in seven cattle populations in Indonesia.

Materials and Methods: Polymerase chain reaction products (551 bp) of the HSP70 gene amplified from 102 animals representing seven cattle populations (Bali, Belgian Blue × Peranakan Ongole [PO] cross, Galekan, Jabres, Madura, PO, and Rambon) were sequenced by DNA sequencing method.

Results: Fourteen single-nucleotide polymorphisms (SNPs), generally found at a low frequency, were detected. Among these SNPs, only 1117G>A, 1125A>C, and 1204T>C were polymorphic in all the analyzed breeds. A Chi-square test showed that the majority of the loci were in Hardy–Weinberg equilibrium (p>0.05). Varying levels of observed (0.050-0.571) and expected heterozygosity (0.049-0.500) were noted. The polymorphism information content values (0.048-0.375) indicated that the SNPs in the HSP70 gene showed low-to-moderate polymorphism in the studied populations. Thirty-six haplotypes were defined according to the identified SNPs, of which haplotype Hap5 (CGACGAGAGTGTCC) and Hap4 (CGACGAGAGTGCCC) were generally dominant in the studied samples. The phylogenetic tree showed a close relationship between Bali and Rambon cattle and between Galekan and Jabres cattle, while the Belgian Blue × PO crossbred cattle were farther apart.

Conclusion: The polymorphisms in the 5' UTR of the HSP70 gene identified in this study should be further investigated in a larger population to unravel the association between the SNPs and thermotolerance in Indonesian local cattle populations.

Background and Aim: The genetic improvement of cattle through livestock section is based on quantitative, qualitative, and molecular characteristics. This study examined polymorphisms of the melanocortin-4 receptor (MC4R) and leptin genes as a reference for the selection of superior breeds in Madrasin cattle.

Materials and Methods: The leptin and MC4R genes of Madrasin cattle were amplified using polymerase chain reaction (PCR); then, restriction fragment length polymorphism of the leptin gene was performed using the restriction enzyme BsaA1, at site 2793 with ACGT point position.

Results: The leptin gene was divided into three bands, namely, AA with one fragment (522 bp), CG with two fragments (441 bp and 81 bp), and AG with three fragments (522 bp, 441 bp, and 81 bp). The MCR-4 gene was divided into three bands, namely, 493 bp, 318 bp, and 175 bp.

Conclusion: The MC4R and leptin genes can act as molecular markers for growth traits in Madrasin cattle and can be used to genetically optimize and improve growth. The GG allele of the MC4R gene and the AA allele of the leptin gene can be used in Madrasin cattle.

Background and Aim: The production of male calf beef cattle is an agricultural innovation needed to increase the farm's productivity as a provider of meat sources. This study aimed to determine the sex ratio of the offspring of cows inseminated with Y-bearing sperm enriched by Percoll density gradient centrifugation and swim up, combined with delayed fixed-time artificial insemination (FTAI).

Materials and Methods: Ejaculates of Simmental bulls were divided into four equal portions and grouped as T0 (control, non-sexed semen), T1 and T2 were sexed semen using Percoll density gradient centrifugation three and five levels, respectively, and T3 was sexed semen using swim-up. After the sex was sorted, the semen was diluted in a tris egg yolk extender, packaged in French mini-straws containing 50 million live sperm cells, and frozen. Pre-sexed, post-sexed, and post-thawed spermatozoa were evaluated based on progressive motility, viability, intact plasma membrane, and abnormality. The post-thawed semen of T0 was artificially inseminated to recipient cows at 12 h after onset of estrus (not delayed FTAI). Meanwhile, the delayed FTAI was conducted 18 20 h after onset of estrus using the T0, the best of T1 and T2, and the T3 post-thawed semen.

Results: The Percoll density gradient centrifugation reduced motility, viability, and intact plasma membrane but increased sperm abnormalities. Meanwhile, the swim up process increased motility, viability, and intact plasma membrane of sperm cells but decreased sperm abnormalities. Post-thawed semen decreased motility, viability, and intact plasma membrane of sperm cells but increased sperm abnormalities. The sex ratio of the Simmental crossbred offspring was 96.08% and 100% in T1 and T3, respectively, compared to 48.25% and 67.39% in T0 not delayed and delayed FTAI, respectively.

Conclusion: The Percoll density gradient centrifugation and swim-up methods are prospective for obtaining male offspring.

The Korean freshwater crayfish, Cambaroides similis, has recently suffered from range reduction and habitat degradation caused by environmental changes and water pollution. For the conservation and restoration of this species, it is necessary to understand the current population structures of Korean C. similis using estimation of their genetic variation. In this study, eight microsatellite loci were developed and characterized from 49 individuals collected from four locations: one population from Mt. Bukhan (BH) and three populations from Mt. Gwanak (GA) in Seoul, Korea. As a result, the number of alleles per locus ranged from 2 to 12. The observed heterozygosities and expected heterozygosities ranged from 0.000 to 0.833 and from 0.125 to 0.943, respectively, and the former values were significantly lower than the latter ones expected under the Hardy-Weinberg equilibrium. No significant linkage disequilibrium was revealed between any of the locus pairs after Bonferroni correction. From the pairwise Fst results over all samples, higher differentiation between GA-BH population pairs (mean 0.1789) was observed than between GA population pairs (mean 0.0454). This was also supported by Mantel's test showing that the genetic distances of these crayfish populations were significantly correlated with geographic distances. This result may show the regional differentiation caused by restricted gene flow between northern (BH) and southern (GA) populations within Seoul. These microsatellite markers have the potential for use in analyses of the genetic diversity and population structure of C. similis species, with implications for its conservation and management plans.

Typical features, breeding objectives and morphological as well as biometrical characters of Begait sheep breed were studied in two districts (Setit Humera and Kafta Humera) of Ethiopia. Semi-structured questionnaires, recording body weight, linear body measurements and field observations were employed. Begait sheep breed is described as long and thin tailed (up to 50-cm long), with muscular body, short and smooth hair and polled for both male and female sexes. As reported by the respondents' growth rate (0.21), tail length (0.20), appearance/conformation (0.19) and coat colour (0.18) were the most important traits in selecting breeding rams. For breeding ewes' body size (0.27), age at first service (0.15), growth rate (0.14) and coat colour and tail (0.13) were their first, second, third and fourth traits, respectively. Sites and age had significant (P < 0.01) effect on body weight and most linear body measurements. Relatively, Kafta Humera had lower values in body weight and most of the linear body measurements than Setit Humera. The overall mean body weight and body length of female Begait sheep were 31.4 ± 0.4 kg and 62.5 ± 0.5 cm, respectively. The corresponding values for male Begait sheep were 34.5 ± 0.5 kg and 66.1 ± 0.5 cm, respectively. The existing traditional herding, breeding practices and trait preferences are the key breeding components that need improvement at smallholder farmers' in Ethiopia. Résumé Les caractéristiques, les objectifs de sélection et les caractères morphologiques et biométriques des moutons Begayit ont été étudiés dans deux districts (Setit Humera et Kafta Humera) de l'Éthiopie en utilisant des questionnaires semi-structurés, l'enregistrement du poids corporel et des mensurations du corps et des observations sur le terrain. Les moutons Begayit possèdent une queue longue et mince (jusqu'à 50 cm de longueur), un corps musclé, des poils courts et lisses et, les mâles autant que les femelles, n'ont pas de cornes. Les interviewés ont signalé que le taux de croissance (0.21), la longueur de la queue (0.20), l'aspect/conformation (0.19) et la couleur de la robe (0.18) représentaient les caractères les plus importants dans la sélection des béliers reproducteurs. Pour ce qui concerne les brebis reproductrices, la taille du corps (0.27), l'âge à la première mise bas (0.15), le taux de croissance (0.14) et la robe et la queue (0.13) étaient respectivement le premier, le deuxième, le troisième et le quatrième caractère d'importance. L'emplacement et l'âge influencent (P < 0.01) le poids et la plupart des mensurations du corps. Les moutons du district Kafta Humera présentaient des valeurs concernant le poids et les mensurations du corps relativement plus faibles que les moutons du district de Setit Humera. Les moyennes générales du poids et de la longueur du corps des femelles Begayit étaient respectivement de 31.4 ± 0.4 kg et de 62.5 ± 0.5 cm. Les valeurs correspondantes pour les mâles des moutons Begayit étaient respectivement de 34.5 ± 0.5 kg et de 66.1 ± 0.5 cm. Les pratiques traditionnelles existantes d'élevage et de sélection et les préférences de caractères sont les composantes principales de sélection qu'il faut améliorer chez les petits exploitants de l'Éthiopie. Mots-clés: moutons Begayit, pratiques de sélection, préférences de caractères, caractéristiques Resumen Se estudiaron las características típicas, los objetivos de cría y los caracteres tanto morfológicos como biométricos de la raza ovina Begait en dos distritos de Etiopía (Setit Humera y Kafta Humera). Se utilizaron cuestionarios semi-estructurados con registro del peso y medidas lineales del cuerpo y de observaciones de campo. La descripción de la raza Begait es: cola larga y delgada (hasta 50 cm de largo), cuerpo musculoso, pelo corto y liso, y desprovistos de cuernos en ambos sexos masculino y femenino. Según las respuestas de los encuestados, la tasa de crecimiento (0.21), la longitud de la cola (0.20), la apariencia/conformación (0.19) y el color del pelaje (0.18) fueron las características más importantes en la selección de los carneros de reproducción. Para la cría de hem-bras el tamaño corporal (0.27), la edad de la primera cubrición (0.15), la tasa de crecimiento (0.14) y el color del pelaje y de la cola (0.13) fueron las primeras cuatro características, en ese orden. El emplazamiento y la edad tuvieron un efecto significativo (P < 0.01) en el peso corporal y en la mayoría de las medidas corporales lineales. Los ejemplares de Kafta Humera mostraron en términos relativos valores más bajos de peso corporal y de la mayoría de las medidas corporales lineales que los de Setit Humera. En conjunto, el peso corporal medio y la longitud corporal media de las hembras Begait fueron respectivamente 31.4 ± 0.4 kg y 62.5 ± 0.5 cm. Los valores correspondientes para los machos Begait fueron 34.5 ± 0.5 kg y 66.1 ± 0.5 cm, respectivamente. Las prácticas tradicionales existentes