scholarly journals Study on Population Dynamics and Effects of Inbreeding on Performance Traits in Indian Murrah Buffalo

2021 ◽  
Author(s):  
Shabahat Mumtaz ◽  
Anupama Mukherjee ◽  
Prajwalita Pathak ◽  
Kaiser Parveen
Keyword(s):  
Genetic Diversity ◽  
Reference Population ◽  
Production Performance ◽  
Base Line ◽  
Web Based ◽  
Murrah Buffalo ◽  
Selection Strategies ◽  
Performance Traits ◽  
Genomics Tools ◽  
Productive Traits

Background: A population is continuously facing the changing environment and its directly influencing the production of animal so to adopt these changes population must be flexible and have sufficient variability to overcome the adverse affects of environment. The evaluation of animals in terms of production performance traits along with impact of inbreeding coefficient is essential to formulate breeding and selection strategies for higher genetic improvement. Methods: Genealogy data of 6429 animals maintained at ICAR-NDRI, Karnal, India was analyzed by web-based POPREP application tool (http:// poprep.tzv.fal.de) and ENDOG V5.8 used to study the population structure and genetic diversity and regression model to study the effect of inbreeding on first lactation productive traits in Murrah buffaloes. Result: The result indicated that 91.91% of the individuals had known pedigree. The maximum generation traced was 13 with mean, full and equivalent complete generation as 5.93, 1.67 and 3.25 respectively. The average generation interval was 8.28 years and longer for the sire-son pathway and 2.16% was average inbreeding in whole population. The average genetic diversity loss was 2.10% indicated that the population has been stable with sufficient diversity. The study also revealed non significant effect of inbreeding on all first lactation traits. The low inbreeding was firstly due to introduction of new genetic variant and culling of animals avoiding mating of related ones and secondly due to incompleteness of pedigree in earlier years. This can be used as a base line information of phenomic needs to be generated before applying genomics tools in particular herd to be used as reference population in future for genomic selection.

scholarly journals POLIMORPHIC CHARACTERIZATION OF ESR1 AND FOXL2 GENES AND THE ASSOCIATION OF THEIR INTERACTION WITH PRODUCTIVE TRAITS OF BROWN LOCAL IRAQI CHICKENS

2021 ◽  
Vol 52 (6) ◽  
pp. 1391-1400
Author(s):  
R. I. A. Abu-Rekaiba ◽  
E. H. AL-Anbari ◽  
W. M. Razuki
Keyword(s):  
Production Performance ◽  
Production Traits ◽  
Chi Square ◽  
Beneficial Effects ◽  
Egg Formation ◽  
Hardy Weinberg Equilibrium ◽  
Productive Traits ◽  
Chi Square Analysis ◽  
New Evidence

The estrogen receptor 1(ESR1) and fork-head box L2 (FOX L2) genes play a pivotal role in regulation of egg formation in poultry. this study aimed to investigate interaction between ESR1 and FOXL2 in the productive performance of brown local Iraqi chickens (BLIC). A total of 104 BLIC represented from the F4th generation of local chicken selected for high egg productions were used. Two novel single nucleotide polymorphism (SNPs), one of them in ESR1 (T57198C) intron 3, and another of FOX L2 (C919T) gene within encoding region were identified through PCR-DNA sequencing. Six haplotypes (H1=TTCC, H2=TTCT, H3=TCCC, H4=TCCT, H5=CCCC, H6=CCCT) were obtained due to interaction between these two SNPs. Chi-square analysis showed no significant  in genotypic and allelic frequencies for each SNP which revealed that both genes were agreement with Hardy-Weinberg equilibrium. Association analysis of haplotypes with production traits revealed that individuals have H4 genotype achieved higher body weight at sexual maturity, at 60 weeks of age and egg weight at 45 and 60 weeks of age, whereas, the higher number of eggs were exhibited in individual with H6 from onset egg till 60 weeks of age. The two haplotypes; H4(TCCT) and H6(CCCT) showed better combination than others with respect to production performance. In conclusion, our findings provided new evidence that the two genes (ESR1 and FOXLl2) with special interaction may have potential effects on productive traits of chickens and beneficial effects in laying breeding programs.

scholarly journals Production performances of cows of different origin and housing method

2020 ◽  
Vol 36 (4) ◽  
pp. 417-426
Author(s):  
Dragan Niksic ◽  
Vlada Pantelic ◽  
Dusica Ostojic-Andric ◽  
Predrag Perisic ◽  
Ljiljana Samolovac ◽  
...  
Keyword(s):  
Protein Content ◽  
Milk Yield ◽  
Milk Fat ◽  
Domestic Animals ◽  
Fat Content ◽  
Production Performance ◽  
Agricultural Producers ◽  
Rearing Method ◽  
Performance Traits ◽  
Farming Households

In order to examine the variability of production performance traits (lactation duration, milk yield for the whole lactation, milk yield in standard lactation, milk fat content, milk fat yield in standard lactation, protein content and yield in standard lactation), 954 cows, domestic and imported Simmental populations, were included in the study, with a total of 3641 completed lactations. Cows were located in the area of Toplica district, reared on individual farming households (tied system) and on the farm with intensive farming (free system). Based on the rearing method and origin, animals were divided into four groups: Group 1 (domestic animals reared by individual agricultural producers on individual farming households); Group 2 (imported animals reared by individual agricultural producers on individual farming households); Group 3 (domestic animals reared on the farm) and Group 4 (imported animals reared on the farm). The fourth group of studied cows showed the highest yield and protein content, while the cows of the third group had the longest lactation and the highest milk fat content. All production performance traits varied highly significantly (p?0.001) under the influence of the combined factor of housing/rearing method and origin.

scholarly journals Using pedigree information to study genetic diversity and re-evaluating a selection program in an experimental flock of Afshari sheep

2012 ◽  
Vol 55 (4) ◽  
pp. 375-384 ◽  
Author(s):  
F. Ghafouri-Kesbi
Keyword(s):  
Genetic Diversity ◽  
Phenotypic Selection ◽  
Reference Population ◽  
Pedigree Information ◽  
Selection Experiment ◽  
Founder Population ◽  
Effective Number ◽  
Effective Population ◽  
Breeding Values ◽  
Closed Population

Abstract. The purpose of this paper was to evaluate the inbreeding consequences of a short-term selection experiment which was initiated in 1998 in an Afshari sheep flock. Moreover, the conducted selection experiment was re-evaluated through assessing change in ranking of the first 10 influential ancestors when their genetic contributions were replaced with their breeding values. A total of 1714 animals were registered in the herdbook with a founder population comprised of 243 animals. The average coancestry (f) and inbreeding (F) in the reference population were 2.1% and 1.2%, respectively. Estimated value of the effective population size (Ne) was 50. The effective number of founders (fe) was estimated to be 40 and the effective number of ancestors (fa) was 34. Estimates of breeding values revealed that owing to phenotypic selection some ancestors with lower breeding values had greater contribution to the reference genome than those with greater breeding values and, for this reason, the population has been deprived from the maximum genetic improvement that could be achieved if selection was based on breeding values. The effective number of founder genomes (fg) was computed to be 23 and the effective number of non-founder genomes (fne) was 55. The index of genetic diversity decreased by almost 2.2% over the period studied. In general, decrease in genetic variability was low and Ne was not very low for a small-closed population under selection, indicating even in populations which undergo selection, besides achieving genetic gain, the rate of inbreeding is controllable if matings carefully planned.

scholarly journals Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

2019 ◽  
Vol 67 (6) ◽  
pp. 1457-1463 ◽  
Author(s):  
Radovan Kasarda ◽  
Nina Moravčíková ◽  
Ondrej Kadlečík ◽  
Anna Trakovická ◽  
Marko Halo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quality Control ◽  
Genomic Analysis ◽  
Genomic Data ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Snp Markers ◽  
Runs Of Homozygosity ◽  
Current Generation ◽  
Genomic Inbreeding

The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

scholarly journals Genetic Characterization of Plasmodium vivax Isolates from Pakistan Using Circumsporozoite Protein (PvCSP) and Merozoite Surface Protein-1 (PvMSP-1) genes as genetic markers 

2021 ◽  
Author(s):  
Zainab Bibi ◽  
Anam Fatima ◽  
Rehana Rani ◽  
Ayesha Maqbool ◽  
Samea Khan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Vivax ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Circumsporozoite Protein ◽  
Effective Vaccine ◽  
Population Divergence ◽  
Large Sample Size ◽  
Base Line ◽  
Merozoite Surface Protein 1

Abstract Background: Plasmodium vivax contributes to over 70% malaria burden in Pakistan, but limited data exists on various aspects including genetic diversity of the parasite as compared to other parts of the world. Since the information about the genetic diversity of P. vivax assists to understand the population dynamics of the parasite, the current study was designed to understand population divergence of Plasmodium vivax in Pakistan using circumsporozoite protein (PvCSP) and merozoite surface protein-1 (PvMSP-1) genes as molecular markers. Methods: PvCSP and PvMSP-1 specific PCR and DNA sequencing were carried out for 150 blood samples collected from Islamabad and Rawalpindi, Pakistan. Genetic diversity and polymorphism was analyzed using ChromasPro, ClustalW, MEGA7, DnaSP v.5 and WebLogo programs. Results: The PCR for PvCSP and PvMSP-1 genes was carried out for 150 P. vivax isolates and resulting the PCR products ranging from 900 to 1100 bp for PvCSP and ~400bp for PvMSP-1 genes respectively. Majority (93%; 141/150) of the P. vivax isolates were of VK210 variant and only 9 isolates were found to be of VK247 variant based on PvCSP gene. Out of the numerous peptide repeat motifs (PRMs) detected, GDRADGQPA (PRM1) and GDRAAGQPA (PRM2) were more extensively dispersed among the P. vivax isolates. Partial sequences (~400bp) at the N-terminal of PvMSP-1 gene depicted high level of diversity.Conclusion: High levels of genetic diversity based on PvCSP and PvMSP-1 genes was observed in the isolated samples from the study area. Parasite typing is essential in predicting pattern of antigenic variations and drug resistance and for effective vaccine designing and development which can further assist in evaluating measures for malaria control at individual and community level. The base-line data presented here warrants future studies to investigate more into the genetic diversity of P. vivax with large sample size from across the country for better understanding of the transmission patterns of vivax malaria.

scholarly journals Polimorphic Explore of Esr1, Esr2 and Foxl2 Genes and Interaction Effect of Esri and Foxl2 with Productive Traits of Brown Local Iraqi Chickens

2021 ◽  
Vol 910 (1) ◽  
pp. 012004
Author(s):  
Raed Ibraheem A. Abu-Rekaiba ◽  
W. M. Razuki ◽  
E. H. Al-Anbari
Keyword(s):  
Estrogen Receptor ◽  
Production Performance ◽  
Production Traits ◽  
Chi Square ◽  
Beneficial Effects ◽  
Egg Formation ◽  
Hardy Weinberg Equilibrium ◽  
Productive Traits ◽  
Chi Square Analysis ◽  
And Function

Abstract The estrogen receptor 1(ESR1) and estrogen receptor 2 (ESR2) plays a crucial role in the growth and development of follicles and ovulation in chickens. Fork-head box L2 (FOX L2) gene and its protein is active in several tissues, such as the ovaries, it has a pivotal role in ovarian development and function, like regulation of egg formation in poultry. This study aimed to detect the polymorphism of ESR1, ESR2 and, FOXL2 genes and investigate interaction between ESR1 and FOXL2 in the productive performance of brown local Iraqi chickens (BLIC). A total of 104 BLIC, at 17 weeks of age. Four novel single nucleotide polymorphism (SNPs). Every polymorphism a number had been given according to its location within gene, one of them in ESR1 (T57198C) intron 3 with three genotypes: Wild(TT), Heterozygous(TC),and Homozygous(CC), and two SNPs within ESR2 were assessed, one of the identified SNPsT39565C transition located within intron 7 with two alleles(T and C)and three genotypes were found: Wild(TT), Heterozygous(TC),and Homozygous(CC), another SNPG40100A transition within (3 prime UTR), with two alleles (G and A)and three genotypes were found: Wild(GG), Heterozygous(GA)and Homozygous(AA) and the SNP in FOXL2 (C919T) gene with two genotypes: Wild(CC) and Heterozygous(CT) within encoding region were identified through PCR-DNA sequencing. An interaction between the ESR1 and FOXL2 genes has been proposed, and six haplotypes (H1=TTCC, H2=TTCT, H3=TCCC, H4=TCCT, H5=CCCC, H6=CCCT) were obtained due to interaction between these two SNPs. Chi-square analysis showed no significant in genotypic and allelic frequencies for each SNP which revealed those genes were agreement with Hardy-Weinberg equilibrium. Association analysis of haplotypes with production traits revealed that individuals have H4 genotype achieved higher body weight at sexual maturity, at 60 weeks of age and egg weight at 45 and 60 weeks of age, whereas, the higher number of eggs were exhibited to individual with H6 from onset egg till 60 weeks of age. The two genotypes; TCCT and CCCT showed better combination than others with respect to production performance. In conclusion, our findings provided new evidence that the two SNPs (ESR1 and FOXLl2) with special interaction may have potential effects on productive traits of chickens and beneficial effects in laying breeding programs.

scholarly journals Genetic Characterization of Plasmodium vivax Isolates from Pakistan Using Circumsporozoite Protein (PvCSP) and Merozoite Surface Protein-1 (PvMSP-1) Genes as Genetic Markers

2020 ◽  
Author(s):  
Zainab Bibi ◽  
Anam Fatima ◽  
Rehana Rani ◽  
Ayesha Maqbool ◽  
Samea Khan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Vivax ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Circumsporozoite Protein ◽  
Population Divergence ◽  
Large Sample Size ◽  
Base Line ◽  
Variant Type ◽  
High Level

Abstract Background Plasmodium vivax contribute over 70% malaria burden in Pakistan. Limited data exist on various aspects including genetic diversity of the parasite as compared to other parts of the world. The information about extent of genetic diversity assists to understand the transmission patterns of the parasite in human host. The current study was designed to understand population divergence of Plasmodium vivax in Pakistan using circumsporozoite protein and merozoite surface protein-I genes as molecular markers.Methods PvCSP and PvMSP-1 specific PCR and DNA sequencing were carried out for 150 blood samples collected from Islamabad and Rawalpindi, Pakistan. Genetic diversity was analysed using ChromasPro, ClustalW, MEGA7 and DnaSP v.5 programs.Results The PCR for PvCSP and PvMSP-1 genes was carried out for 150 P. vivax isolates resulting the PCR products ranging from 900 to 1100 bp for PvCSP gene and ~ 400 bp for PvMSP-1 gene. Majority (93%; 121/150) of the P. vivax isolates were of VK210 variant type and only 9 isolates were found of VK247 variant type based on PvCSP gene. Out of the numerous peptide repeat motifs (PRMs) detected, GDRADGQPA (PRM1) and GDRAAGQPA (PRM2) were more extensively dispersed among the P. vivax isolates. Partial sequences (~ 400 bp) at the N-terminal of PvMSP-1 gene depicted high level of diversity.Conclusion High-level genetic diversity based on PvCSP and PvMSP-1 genes was observed in clinical isolated in the study area. Parasite typing is essential in predicting pattern of antigenic variations, drug resistance and for effective drug and vaccine designing and development which can further evaluate for malaria control and eradication at individual and community level. The base-line data presented here warrant future studies to investigate more into the genetic diversity of P. vivax with large sample size from across the country for better understanding of the vivax malaria transmission patterns.

scholarly journals Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear

Heredity ◽  
2012 ◽  
Vol 109 (5) ◽  
pp. 299-305 ◽  
Author(s):  
T Skrbinšek ◽  
M Jelenčič ◽  
L P Waits ◽  
H Potočnik ◽  
I Kos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Brown Bear ◽  
Reference Population

scholarly journals Genetic divergence among Brachiara humidicola (Rendle) Schweick hybrids evaluated in the Western Brazilian Amazon

2014 ◽  
Vol 14 (4) ◽  
pp. 224-231 ◽  
Author(s):  
Giselle Mariano Lessa de Assis ◽  
Cléia Florentino dos Santos ◽  
Patrícia Silva Flores ◽  
Cacilda Borges do Valle
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Nutritive Value ◽  
Recurrent Selection ◽  
Block Design ◽  
Morphological Characteristics ◽  
Plant Performance ◽  
Clustering Techniques ◽  
Selection Strategies ◽  
Randomized Block Design

The objectives of this study were to detect genetic variability among genotypes of Brachiara humidicola, study the genetic diversity and identify redundant variables in the discrimination of hybrids. Fifteen genotypes were evaluated for morphological, agronomic and nutritive characteristics in a randomized block design with six replications, in Rio Branco, Acre. Analysis of variance was performed, followed by the Scott-Knott test. Different techniques of multivariate analysis were used to study genetic diversity. Significant differences in plant performance were observed for agronomic and morphological characteristics, but not for nutritive value. There was consistency between the different clustering techniques. Four redundant characteristics were identified that can be discarded. The existence of divergent and superior hybrids that can be used in recurrent selection (sexual) programs or can be released as new (apomictic) cultivars after testing for animal response was confirmed. The lack of genetic variability in bromatological traits indicates the need for differentiated selection strategies.

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