The objective of this study was to obtain (co) variance components and genetic parameter estimates for post-weaning body measurements such as body length (BL), height at withers (HW), and chest girth ...(HG) recorded at six (SBL, SHW, and SHG), nine (NBL, NHW, and NHG) and twelve (YBL, YHW, and YHG) months of age along with yearling weight (YW) in Nellore sheep maintained at livestock research station, Palamaner, Andhra Pradesh, India and also the association among body measurements with YW was studied.
Data on 2,076 Nellore sheep (descended from 75 sires and 522 dams) recorded between 2007 and 2016 (10 years) were utilized in the study. Lambing year, sex of lamb, season of lambing and parity of dam were included in the model as fixed effects and ewe weight was kept as a covariate. Analyses were conducted with six animal models with different combinations of direct and maternal genetic effects using restricted maximum likelihood procedure. Best model for each trait was determined based on Akaike's information criterion.
Moderate estimates of direct heritability were obtained for the studied traits viz., BL (0.02 to 0.24), HW (0.31 to 0.49), and CG (0.08 to 0.35) and their corresponding maternal heritability estimates were in the range of 0.00 to 0.07 (BL), 0.13 to 0.17 (HW), and 0.07 to 0.13 (CG), respectively. Positive direct genetic and phenotypic correlations among the traits and they ranged from 0.07 (YBL-YW) to 0.99 (SBL-SHG, SHG-YW, and NBL-YBL) and 0.01 (SBL-YBL) to 0.99 (NBL-NHG), respectively. Further, the genetic correlations among all the body measurements and YW were positive and ranged from 0.07 (YW and YBL) to 0.99 (YW and SHG).
There was a strong association of chest girth at six months with YW. Further, it is indicated that moderate improvement of post-weaning body measurements in Nellore sheep would be possible through selection.
Background
In the evolutionary time scale, selection shapes the genetic variation and alters the architecture of genome in the organisms. Selection leaves detectable signatures at the genomic ...coordinates that provide clues about the protein-coding regions. Sahiwal is a valuable indicine cattle adapted to tropical environments with desirable milk attributes. Insights into the genomic regions under putative selection may reveal the molecular mechanisms affecting the quantitative and other important traits. To understand this, the present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip.
Result
De-correlated composite of multiple selection signals (DCMS), which combines five different univariate statistics, was computed in the dataset to detect the signatures of selection in the Sahiwal genome. Gene annotations, Quantitative Trait Loci (QTL) enrichment, and functional analyses were carried out for the identification of significant genomic regions. A total of 117 genes were identified, which affect a number of important economic traits. The QTL enrichment analysis highlighted 14 significant False Discovery Rate (FDR)-corrected
p
-value ≤ 0.05 regions on chromosomes BTA 1, 3, 6, 11, 20, and 21. The top three enriched QTLs were found on BTA 6, 20, and 23, which are associated with exterior, health, milk production, and reproduction traits. The present study on selection signatures revealed some key genes related with coat color (
PDGFRA, KIT
, and
KDR
), facial pigmentation (
LEF
), milk fat percent (
MAP3K1, HADH, CYP2U1
, and
SGMS2
), sperm membrane integrity (
OSTC
), lactation persistency (
MRPS30, NNT, CCL28, HMGCS1, NIM1K, ZNF131
, and
CCDC152
), milk yield (
GHR
and
ZNF469
), reproduction (
NKX2-1
and
DENND1A
), and bovine tuberculosis susceptibility (
RNF144B
and
PAPSS1
). Further analysis of candidate gene prioritization identified four hub genes, viz.,
KIT, KDR, MAP3K1
, and
LEF
, which play a role in coat color, facial pigmentation, and milk fat percentage in cattle. Gene enrichment analysis revealed significant Gene ontology (GO) terms related to breed-specific coat color and milk fat percent.
Conclusion
The key candidate genes and putative genomic regions associated with economic traits were identified in Sahiwal using single nucleotide polymorphism data and the DCMS method. It revealed selection for milk production, coat color, and adaptability to tropical climate. The knowledge about signatures of selection and candidate genes affecting phenotypes have provided a background information that can be further utilized to understand the underlying mechanism involved in these traits in Sahiwal cattle.
The main objectives of the present study are to assess the genetic diversity, population structure and also to appraise the efficiency of ongoing selective breeding program in the closed nucleus herd ...of Nellore sheep through pedigree analysis.
Information utilized in the study was collected from the pedigree records of Livestock Research Station, Palamaner during the period from1989 to 2016. Genealogical parameters like generation interval, pedigree completeness, inbreeding level, average relatedness among the animals and genetic conservation index were estimated based on gene origin probabilities. Lambs born during 2012 and 2016 were considered as reference population. Two animal models either with either the use of F_i or∆F_ias linear co-variable were evaluated to know the effects of inbreeding on the growth traits of Nellore sheep.
Average generation interval and realized effective population size for the reference cohort were estimated as 3.38±0.10and 91.56±1.58, respectively and the average inbreeding coefficient for reference population was 3.32%. Similarly, the effective number of founders, ancestors and founder genome equivalent of the reference population were observed as 47, 37 and 22.48, respectively. Fifty per cent of the genetic variability was explained by 14 influential ancestors in the reference cohort. The ratio fe/fa obtained in the study was 1.21, which is an indicator of any bottlenecks in the population. The number of equivalent generations obtained in the study was 4.23 and this estimate suggested the fair depth of the pedigree.
Study suggested that the population had decent levels of genetic diversity and non-significant influence of inbreeding coefficient on growth traits of Nellore lambs. However, little portion of genetic diversity lost due to disproportionate contribution of founders and bottlenecks. Hence, breeding strategies which improve the genetic gain, widens the selection process and with optimum levels of inbreeding are recommended in the herd.
Runs of homozygosity (ROH) are contiguous genomic regions, homozygous across all sites which arise in an individual due to the parents transmitting identical haplotypes to their offspring. The ...genetic improvement program of Sahiwal cattle after decades of selection needs re-assessment of breeding strategy and population phenomena. Hence, the present study was carried out to optimize input parameters in PLINK for ROH estimates, to explore ROH islands and assessment of pedigree and genome-based inbreeding in Sahiwal cattle. The sliding window approach with parameters standardized to define ROH for the specific population under study was used for the identification of runs. The optimum maximum gap, density, window-snp and window-threshold were 250 Kb, 120 Kb/SNP, 10, 0.05 respectively and ROH patterns were also characterized. ROH islands were defined as the short homozygous genomic regions shared by a large proportion of individuals in a population, containing significantly higher occurrences of ROH than the population specific threshold level. These were identified using the –homozyg-group function of the PLINK v1.9 program. Our results indicated that the Islands of ROH harbor a few candidate genes, ACAD11, RFX4, BANP, UBA5 that are associated with major economic traits. The average F
PED
(Pedigree based inbreeding coefficient), F
ROH
(Genomic inbreeding coefficient), F
HOM
(Inbreeding estimated as the ratio of observed and expected homozygous genotypes), F
GRM
(Inbreeding estimated on genomic relationship method) and F
GRM0.5
(Inbreeding estimated from the diagonal of a GRM with allele frequencies near to 0.5) were 0.009, 0.091, 0.035, -0.104 and -0.009, respectively. Our study revealed the optimum parameter setting in PLINK viz. maximal gaps between two SNPs, minimal density of SNPs in a segment (in kb/SNP) and scanning window size to identify ROH segments, which will enable ROH estimation more efficient and comparable across various SNP genotyping-based studies. The result further emphasized the significant role of genomics in unraveling population diversity, selection signatures and inbreeding in the ongoing Sahiwal breed improvement programs.
Karan Fries (KF), a high-producing composite cattle was developed through crossing indicine Tharparkar cows with taurine bulls (Holstein Friesian, Brown Swiss, and Jersey), to increase the milk yield ...across India. This composite cattle population must maintain sufficient genetic diversity for long-term development and breed improvement in the coming years. The level of linkage disequilibrium (LD) measures the influence of population genetic forces on the genomic structure and provides insights into the evolutionary history of populations, while the decay of LD is important in understanding the limits of genome-wide association studies for a population. Effective population size (Ne) which is genomically based on LD accumulated over the course of previous generations, is a valuable tool for e valuation of the genetic diversity and level of inbreeding. The present study was undertaken to understand KF population dynamics through the estimation of Ne and LD for the longterm sustainability of these breeds.
The present study included 96 KF samples genotyped using Illumina HDBovine array to estimate the effective population and examine the LD pattern. The genotype data were also obtained for other crossbreds (Santa Gertrudis, Brangus, and Beefmaster) and Holstein Friesian cattle for comparison purposes.
The average LD between single nucleotide polymorphisms (SNPs) was r2 = 0.13 in the present study. LD decay (r2 = 0.2) was observed at 40 kb inter-marker distance, indicating a panel with 62,765 SNPs was sufficient for genomic breeding value estimation in KF cattle. The pedigree-based Ne of KF was determined to be 78, while the Ne estimates obtained using LD-based methods were 52 (SNeP) and 219 (genetic optimization for Ne estimation), respectively.
KF cattle have an Ne exceeding the FAO's minimum recommended level of 50, which was desirable. The study also revealed significant population dynamics of KF cattle and increased our understanding of devising suitable breeding strategies for longterm sustainable development.
Objective: The objective of this study was to obtain (co) variance components and genetic parameter estimates for post-weaning body measurements such as body length (BL), height at withers (HW), and ...chest girth (HG) recorded at six (SBL, SHW, and SHG), nine (NBL, NHW, and NHG) and twelve (YBL, YHW, and YHG) months of age along with yearling weight (YW) in Nellore sheep maintained at livestock research station, Palamaner, Andhra Pradesh, India and also the association among body measurements with YW was studied. Methods: Data on 2,076 Nellore sheep (descended from 75 sires and 522 dams) recorded between 2007 and 2016 (10 years) were utilized in the study. Lambing year, sex of lamb, season of lambing and parity of dam were included in the model as fixed effects and ewe weight was kept as a covariate. Analyses were conducted with six animal models with different combinations of direct and maternal genetic effects using restricted maximum likelihood procedure. Best model for each trait was determined based on Akaike's information criterion. Results: Moderate estimates of direct heritability were obtained for the studied traits viz., BL (0.02 to 0.24), HW (0.31 to 0.49), and CG (0.08 to 0.35) and their corresponding maternal heritability estimates were in the range of 0.00 to 0.07 (BL), 0.13 to 0.17 (HW), and 0.07 to 0.13 (CG), respectively. Positive direct genetic and phenotypic correlations among the traits and they ranged from 0.07 (YBL-YW) to 0.99 (SBL-SHG, SHG-YW, and NBL-YBL) and 0.01 (SBL-YBL) to 0.99 (NBL-NHG), respectively. Further, the genetic correlations among all the body measurements and YW were positive and ranged from 0.07 (YW and YBL) to 0.99 (YW and SHG). Conclusion: There was a strong association of chest girth at six months with YW. Further, it is indicated that moderate improvement of post-weaning body measurements in Nellore sheep would be possible through selection.
The objective of the present study was to estimate variance components and genetic parameters for average daily gain from birth to weaning (ADGa), birth to 6 months (ADGb) and 3 to 6 months (ADGc) ...and corresponding Kleiber ratios (Ka, Kb, and Kc) in Nellore sheep. Data were collected from the records maintained at Livestock Research Station, Palamaner, for analysis and the data spread from 1993 to 2016 (23 years). Lambing year, sex of lamb, season of lambing, and parity of dam were included in the model as fixed effects, and ewe weight was kept as a covariate. Six animal models were fitted with various combinations of direct and maternal genetic effects using restricted maximum likelihood procedure. The Akaike’s information criterion was employed to determine the best model for each trait. Direct heritability estimates obtained in the study for ADGa, ADGb, ADGc, Ka, Kb, and Kc were 0.37, 0.41, 0.34, 0.48, 0.46, and 0.37, respectively, and their corresponding maternal heritabilities ranged from 0.11, 0.21, 0.11, 0.24, 0.22, and 0.11, respectively. (Co)variance among the direct and maternal effects were found to be negative in all the traits. Direct genetic correlations among the studied traits were positive with few exceptions, and they ranged from − 0.03 (Ka-Kc) to 0.99 (ADGa-Ka); similarly, the phenotypic correlations ranged from low to high − 0.18 (ADGa-Kc and Ka-Kc) to 0.95 (ADGa-Ka). These results indicated the importance of maternal effects in affecting the growth rate and efficiency of feed utilization traits and also suggested the possibility of moderate genetic progress for these traits through selection.
Analyses were carried out for the estimation of (co)variance components and genetic parameters for birth weight (BWT), 6-month weight (6WT), 12-month weight (12WT), 18-month weight (18WT), 24-month ...weight (24WT), 30-month weight (30WT), 36-month weight (36WT), weight at first service (WFS), and weight at first calving(WFC) in Sahiwal cattle. Data for 802 lifetime records (raw data) were collected over a period of 30 years (1990–2019) for various growth traits in the herd for Sahiwal cows maintained at the livestock farm unit of ICAR-NDRI Karnal, Haryana, India. Bayesian estimates using the multi-trait Gibbs sampling animal model approach were calculated in the present study. Total heritability for BWT, 6WT, 12WT, 18WT, 24WT, 30WT, 36WT, WFS, and WFC by Bayesian modeling was estimated as 0.22 ± 0.0052, 0.47 ± 0.0037, 0.30 ± 0.0025, 0.65 ± 0.0021, 0.32 ± 0.0039, 0.33 ± 0.0027, 0.39 ± 0.0031, 0.49 ± 0.0020, and 0.57 ± 0.0023, respectively, along with its Monte Carlo error in Sahiwal cattle. Direct genetic covariances between body weight traits were ranging from − 2762.5 for 18WT and WFC to 4739.6 between WFS and WFC. Environmental covariances were ranging from − 169.98 for 30WT and 36WT to 4539.4 between WFS and WFC. Family relationships as well as the existing interaction effects between two or more traits in opposite direction effect lead to negative estimates for genetic covariances between some of the combinations with various growth traits. Although most of the estimates for posteriori were somewhat skewed, the marginalization effect enabled them to fit into the Gaussian distribution, by comparing the mean, mode, and median with each other. Results suggest that genetic progress through growth traits can be achieved if the selection is carried out for highly heritable 18-month weight as well as for the selection of pubertal and fertility traits, viz., 24WT, 30WT, 36WT, WFS, and WFC with a balanced feeding and optimum management.
•Moderate estimates of heritability were observed for the growth traits of Nellore sheep which was unexpected.•The estimate of heritability implies a better expected response to selection in the ...flock.•Maternal effects were found to be high at all the stages of lamb growth, surprisingly even at yearling age.•Moderate estimates of correlation were observed for the consecutively recorded traits.•This study reveals the decisive information which is necessary for implementation of optimum breeding and management strategies for growth traits in this sheep.
The main aim of this study is to estimate genetic parameters and (co) variance components for body weights at various ages in Nellore sheep born during the period from 1993 to 2016 (23 years). A total of 4822 lambs with pedigree descended from 144 sires and 1299 dams were included in this study. Bayesian analysis using Gibbs sampler multi trait animal model with and without maternal effects was studied. Traits included in this study were birth weight (BW), weaning weight (WW), six months body weight (6MW), nine months body weight (9 MW), Yearling weight (YW). Year-season of birth and sex of lamb (contemporary groups) were considered as fixed effects with ewe weight at lambing as a covariate. Estimates of direct heritability estimates for birth weight, WW, 6MW, 9MW and YW based on best model were 0.17, 0.28, 0.27, 26 and 0.23, respectively and the corresponding maternal heritability estimates were 0.12, 0.14, 0.14, 0.12 and 0.13, respectively. The direct-maternal genetic covariance was negative for all the studied traits. Strong and positive estimates of direct additive genetic correlations were observed in growth traits and they ranged from 0.16 to 0.83, whereas the direct-maternal genetic correlations were negative for all the traits and these estimates ranged from ˗0.89 to ˗0.08. Moderate estimates of heritability for the growth traits obtained in this study suggested the presence of better genetic variability and the possibility for genetic improvement of Nellore sheep through selection. Maternal genetic effects were significant in all the traits. Hence, it is recommended to incorporate these effects in the genetic analysis by including it as a genetic or environmental effect or both. The environmental variance obtained in the study suggested that the growth performance of Nellore sheep may be enhanced by improving the feeding and management aspects. Correlations among traits and effects should be considered while implementing breed improvement program.
The present study was carried out to estimate the genetic parameters for direct and maternal influences on Mecheri sheep (
Ovis aries
) growth traits using Bayesian multi-trait animal model. The ...genetic parameters were calculated using data from 2825 Mecheri lambs born between 2010 and 2020 that were kept in semi-arid tropical climate. Mecheri sheep body weight (mean ± SE) at various stages, viz. BW, WW, and BW12, were 2.6 ± 0.01, 11.1 ± 0.05, and 20.7 ± 0.13 kg, respectively. The Mecheri sheep gained 71.5 percent of their body weight at the age of 6 months. With the exception of birth weight, the weights of the animals varied considerably (
P
< 0.01) by the year of birth. The fixed effect of sex significantly (
P
< 0.01) influenced all the growth traits examined. The direct estimates of heritability (± SD) for BW, WW, BW6, and BW12 was 0.21 ± 0.041, 0.21 ± 0.041, 0.12 ± 0.052, and 0.13 ± 0.053, respectively, and the maternal heritability for BW, WW, BW6, and BW12 was 0.18 ± 0.021, 0.08 ± 0.023, 0.11 ± 0.022, and 0.13 ± 0.033, respectively. Significant variance was indicated by moderately larger direct heritability estimates for BWT and WWT, indicating that there will be more opportunities for selection response during the genetic improvement programme. For the majority of the variables examined, direct heritability values were higher than maternal heritability values. The additive genetic correlation between WW and BW6, BW9, and BW12 was 0.70 ± 0.145, 0.57 ± 0.171, and 0.50 ± 0.194, respectively. The maternal genetic correlations ranged from 0.06 ± 0.152 (BW–BW12) to 0.86 ± 0.046 (BW6–BW9), and the residual correlation varied from 0.18 ± 0.034 (BW–WW) to 0.85 ± 0.013 (BW9–BW12). The BW had a stronger genetic relationship with WW and a weaker relationship with other growth traits. The WW and BW6 showed a favourable genetic relationship, even if the tendency was decreasing in the latter stages of maturation. The BW6 and BW9 demonstrated the strongest positive genetic relationship (0.90 ± 0.052) of all the variables analysed. After examining the heritabilities and genetic correlation between WW and BW6, it was established that selection based on at WW was beneficial, since it manifests early in life and would result in moderate genetic progress through selection.
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