Genetic diversity of a nucleus flock of Malpura sheep through pedigree analyses

Demography and Genealogical Analysis of Massese Sheep, a Native Breed of Tuscany

This study investigates the genealogical and demographic trends of the Massese sheep breed in Tuscany from 2001 to 2021. The Herd Book kept by the Italian Sheep and Goat Breeders Association (Asso.Na.Pa) provided the data. The descriptive statistics were analyzed using JMP software. The pedigree parameters of a total of 311,056 animals (whole population-WP) were analyzed using CFC, ENDOG, and Pedigree viewer software. A total of 24,586 animals born in the period 2007-2021 represented the Reference Population (RP), and 18,554 animals the Base Population (BP). The demographic results showed an inconsistent trend of offspring registration. This study showed a short period of productivity for both ewes and rams, with means of 1.47 and 19.2 registered newborn ewes and rams, respectively. The genealogical analysis revealed incomplete data, highlighting inaccurate assessments of the relationships among the animals, and inbreeding with large differences among provinces. The average inbreeding coefficient in the WP was 1.16%, and it was 2.26% in the RP. The total number of inbreds was 2790 in the WP, with an average FPED of 13.56%, and 2713 in the RP, with an average FPED of 12.82%. The use of pedigree data is a key and economical approach to calculating inbreeding and relationship coefficients. It is the primary step in genetic management, playing a crucial role in the preservation of a breed. The regular updating of genealogical data is the first step to ensuring the conservation of animal genetic resources, and this study is compromised by the lack of such updates.

Explicating the genetic diversity and population structure of Saanen × Beetal goats using pedigree analysis

Pedigree analysis is required to assess the genetic diversity and population structure of a close breeding population in order to effectively manage the breeding program and keep inbreeding under acceptable limits. Saanen × Beetal is a crossbred population of goats, reared at the National Dairy Research Institute (NDRI), Karnal, for the last five decades. This germplasm has been acclimated to a tropical climate and has a higher milk potential and prolificacy. The objective of this study was to elucidate the genetic diversity, population structure, and inbreeding in the flock of the Saanen × Beetal goats. The data were collected from the Animal Genetics and Breeding Division of ICAR-NDRI, Karnal, for 2603 animals from the year 1971 to 2021. Animals born between 2014 and 2017 were considered as a reference cohort. Results revealed that the average generation interval was 3.44 years for the complete pedigree. The average inbreeding coefficient and the average relatedness were 4.20% and 6.87%, respectively, for the complete pedigree and 10.78% and 10.80% for the reference population. Higher inbreeding coefficient and average relatedness in the reference cohort demonstrated the impact of the enclosed gene pool and demands immediate intervention for managing diversity in the closed nucleus under study. Ancestors contributing 50% of the gene pool were 8 and 3 for the complete pedigree and reference cohort, respectively, which illustrates the fact that very few ancestors were responsible for genetic diversity in the flock, which results in the decline of effective population size. Effective numbers of founders (fe), ancestors (fa), and founder genome equivalents (fg) were 15, 7, and 3.11, respectively. The (fe/fa) ratio in the reference population was 2.14, indicating the occurrence of the bottleneck effect in the flock. We observed that inbreeding was non-significant for all reproductive traits except for age at first service and age at first kidding. To lessen inbreeding and augment genetic diversity in the flock, the stratified breeding plan needs to be followed, where mate selection would be based on relatedness. Furthermore, the introduction of unrelated Saanen and Beetal crosses will help alleviate the inbreeding accumulation.

Performance evaluation of Marwari lambs for growth traits and impact of inbreeding

This study aimed at the performance evaluation of a closed flock of Marwari sheep and also to study the effect of accumulated inbreeding on the growth traits using a linear mixed model methodology. The data generated for 39 years (1981 to 2020) on Marwari sheep maintained at ICAR-Central Sheep & Wool Research Institute, Arid Region Campus (CSWRI, ARC), Bikaner, Rajasthan, India were used for analysis on growth traits. The overall least-squares means (LSM) of live weights at birth (BWT), weaning (3MWT), 6 months (6MWT), 9 months (9MWT) and 12 months (12MWT) were observed to be 3.02 ± 0.01, 14.30 ± 0.04, 20.12 ± 0.05, 23.68 ± 0.06 and 26.39 ± 0.07 kg, respectively. Overall LSM for average daily gain from birth to 3 months (ADG1), 3 to 6 months (ADG2) and 6 to 12 months (ADG3) were 125.44 ± 0.40, 67.37 ± 0.40 and 35.83 ± 0.29 g/day, respectively. Kleiber ratio (KR) from birth to 3 months (KR1), 3 to 6 months (KR2), and 6 to 12 months (KR3) were 16.78 ± 0.02, 6.58 ± 0.04 and 3.05 ± 0.02, respectively. Results revealed a 4.36, 25.83, 36.33, 31.50 and 28.99% improvement in the live weights since the inception of the improvement programme. This is also reflected by a significant effect of sire on all the growth traits. The estimate of inbreeding in the flock was 1.55%. Highly inbred animals were 5.13% (>5% Fi). The study revealed the non-significant effect of inbreeding level on all growth traits except for BWT and KR3. For BWT, inbreeding classes had variation; however, a negative effect was not seen. The inbreeding class (>5% Fi) was reduced by 0.05 units for KR3 as against its preceding class. Dam's age at lambing and weight influenced the birth weight and subsequent weights. The study concluded that the selection programme of Marwari sheep is in the right direction; however, regular monitoring of inbreeding is necessary and factors affecting growth must be monitored to attain better growth rates in the nucleus.

Effects of inbreeding on performance traits in Karan Fries crossbred cattle

Present study includes the effect of inbreeding on expected genetic gain and estimation of regression with respect to first lactation production, reproduction and lifetime traits in Karan Fries crossbred cattle maintained at ICAR-NDRI, Karnal. Out of total, only 36.97% were found to be inbred with an average inbreeding coefficient 3.68%. Overall least squares mean for reproduction traits (days) AFC, SP, DP and CI were 1020.41 ± 5.49, 141.42± 3.86, 74.54 ± 2.04 and 421.20 ± 3.81 respectively. For production traits (kg) were 305MY, LL, LTMY, FY and SNFY were 3169.15 ± 37.87, 353.25 ± 4.18, 3686.10 ± 55.10, 266.19 ± 4.66 and 127.81 ± 2.26 respectively and lifetime traits like LTMY and stayability were 14588.47 ± 486.09 (kg) and 2444.69 ± 41.26 (days) respectively. Among reproduction traits (days), AFC increased by +3.70, DP +3.66 and CI +68.44 however SP decreased by -0.85 d and production traits (kg), 305MY decreased by -10.2 TMY -16.09, LL -1.23 d, 305FY -1.75, 305SNFY - 0.26, LTMY 202.02 and stayability -17.37 days per unit increase in the inbreeding coefficient. Although there was no inbreeding depression in any of the traits except AFC. The expected genetic gain of AFC increased two folds in IBL2 (Fx >5%) as compared to IBL1 (Fx<5) group that is not desirable, so in future, to maintain the optimum genetic gain we should keep inbreeding at optimum level and so more precise pedigree recording and planned mating strategies should be adopted to avoid inbreeding depression in next generation.

Selecting sheep for Haemonchus contortus resistance and susceptibility: Flock dynamics and genetic architecture

The study was carried out in the selected strains of Malpura and Avikalin sheep for nematode resistance versus susceptibility (Malpura resistant: MR, Malpura susceptible: MS, Avikalin resistant: AR and Avikalin susceptible: AS). Strains were selected since 2004 and inter-se breeding followed since year 2007. The objective was to decipher the genetic structure of strains and to estimate genetic parameters for fecal egg count (FEC). The population size was small (107-279); however, all the four flocks had sizable effective population size (f_e) for founders. The ratio for f_e to effective number of ancestors (f_a) was nearly 1 indicating genetic stability. Inbreeding was under control. The log transformed FEC (LFEC) was significantly (P < .05) affected by sex, year and month of recording for all 4 strains. Generation had desired genetic trend. There was low heritability for LFEC in MR(0.02), MS(0.06), AR(0.07) and AS(0.02). The estimate of the permanent environment effect (c²) was low. Repeatability (ρ) for LFEC were 0.05, 0.11, 0.07 and 0.06 for MR, MS, AR and AS, respectively. Pruning the data for repeated records in peak infection period (1: "Aug-Sep" and 2: only "Sep") resulted in considerable increase in ρ for MR (Aug-Sep: 0.07 ± 0.03 and Sep: 0.12 ± 0.07) and AR (Aug-Sep: 0.05 ± 0.04 and Sep: 0.09 ± 0.10). Results revealed genotype x environment interaction for repeated measures across months. Low flock size and low genetic variability are hurdles for improvement in R strains. It is recommended to incorporate new candidates post selection from the other breeding flocks and admit them in the R strains for selective breeding.

Effect of environmental factors on estrus synchronization and artificial insemination success in farmers flock in sheep under semi-arid tropical region

Environmental cues in the different seasons might influence the estrus and lambing percentages. The present study was conducted to assess the effect of environmental factors on estrus synchronization (ES) and artificial insemination success in sheep. During the period from 2012 to 2017, a total of 1,197 ewes of Kheri and Malpura breeds of 34 farms originating from 10 villages were synchronized for estrus and then fixed-time artificial insemination (FTAI) was done. Oestrous synchronization was done by intravaginal progesterone sponges and eCG protocol. Fixed-time cervical insemination was performed 48 and 56 hr after sponge removal in ewes exhibiting estrus, using liquid chilled semen containing 100 million sperm per dose of Patanwadi/Malpura rams. Mean sunshine hours, maximum and minimum ambient temperatures, temperature amplitude, mean relative humidity (RH), temperature-humidity index (THI), mean temperature during sponge-in to sponge-out-12-day period, sponge-out and next day, AI day and AI to next 15 days have been calculated. The estrus response and lambing percentage were higher (p < .05) when ES and FTAI were done during hot-humid with rainfall season. Successful (p < .05) ES occur when the minimum temperature was higher in cold-humid season, and the sunshine hour was higher in hot-humid with scanty rainfall season during sponge-in to sponge-out period. The success of the lambing percentage was higher (p < .05) when maximum temperature, minimum temperature, mean temperature and THI was higher on the day of AI and the next 15-day period, irrespective of the season. The success of FTAI indicates the adaptability of the local breed to tolerate the harsh climate of the hot semi-arid region without much hindrance in lambing percentages.

The breeding structure for the small ruminant resources in India

Intense selection for a few desired traits has resulted in reduction of the effective population size (Ne) in most of the plant and livestock populations across the world. The objective of the research was to assess the impact of Ne on the genetic architecture of the population in a simulated data with variable Ne for general population under selection. Along with this, the estimate of Ne and its ratio to adult breeding population (N_B) in the census data of small ruminants of India were also investigated. Results indicated that the average inbreeding ([Formula: see text]) decreases with increase in Ne; similarly, increase in [Formula: see text] per generation was highest in population with lowest Ne. Correlation of estimated breeding value (EBV) with true breeding value (TBV) was not much affected with effective population size. An effective number of chromosome segments (Me) in the populations under selection were significantly affected by magnitude of Ne, with linear positive relation between Ne and Me. Results on livestock census data revealed that all the sheep and goat breeds have sufficiently large Ne based on derived and actual census data. The median for ratio of effective population size to adult census size in sheep breeds was 0.120 and for goat breeds was 0.131. Karnah and Poonchi sheep shares the status of endangered breeds due to a smaller number of breeding female population and hence need attention for conservation. The Ne was large in sheep and goat due to less selection pressure as a result of low coverage of breed improvement programs, availability of large number of breeding males, and absence of artificial insemination (AI) in the field flocks. The estimates of Ne and its ratio to the adult census size (N_B) excluded several factors such as fluctuating population size and overlapping generations. Study revealed introspection from most of the industrial breeding programs on the issue of Ne for populations under selection. Similarly, in small ruminants, large Ne indicates huge genetic diversity and scope of improvement in the productivity in near future.

Evaluation of selection program by assessing the genetic diversity and inbreeding effects on Nellore sheep growth through pedigree analysis

Objective

The main objectives of the present study were to assess the genetic diversity, population structure and to appraise the efficiency of ongoing selective breeding program in the closed nucleus herd of Nellore sheep through pedigree analysis.

Methods

Information utilized in the study was collected from the pedigree records of Livestock Research Station, Palamaner during the period from 1989 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 the use of F_i or ΔF_i as linear co-variables were evaluated to know the effects of inbreeding on the growth traits of Nellore sheep.

Results

Average generation interval and realized effective population size for the reference cohort were estimated as 3.38±0.10 and 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 f_e/f_a obtained in the study was 1.21, which is an indicator of 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.

Conclusion

Study suggested that the population had decent levels of genetic diversity and a non-significant influence of inbreeding coefficient on growth traits of Nellore lambs. However, small portion of genetic diversity was lost due to a 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 for the herd.

Combined effect of heat and nutritional stress on superovulation of Malpura ewes in a semi-arid region

Sheep reared in hot semi-arid environments are generally exposed to heat and nutritional stress in some seasons of the year, which affects both production and reproduction. To assess the effect of high ambient temperature and feed scarcity on superovulation, 16 adult Malpura ewes were randomly divided into two groups of 8 animals each. G1 (control) was kept under a shed and offered a maintenance diet, and G2 (combined stress) was subjected to both nutritional (30% less of maintenance diet) and heat (38-44 °C for 6 h/day) stress. Ewes were superovulated without estrus synchronization by a combination of single injection of 200 IU eCG and 8 injections of FSH (Folltropin-V) at 12-h intervals in tapering doses of 5 mg/kg body weight, starting from the day 7 of natural estrus. eCG was given with the first injection and PGF2α (10 mg) was given with the second last FSH injection. G2 increased respiration rate and rectal temperature (P < 0.01), and blood urea level (P < 0.05), whereas it decreased average daily gain, plasma T4 concentration (P < 0.01) and body weight (P < 0.05). Plasma estradiol level was lower (P < 0.05) in G2 ewes as compared to control (G1) ewes. However, the number of ewes showed a superovulatory response (88 vs 66% ewes ≥ 3 corpus luteum), ovulation rate (8.75 vs 5.88) and embryo production (5.5 vs 3.9) decreased, and the number of large follicles (anovulation) increased (1.0 vs 2.14) in G2 ewes. G2 had a comparable effect on the superovulatory response compared to control ewes although physiological changes occurred as an adaptive mechanism to stress. Therefore, the well-adapted cyclic sheep of the semi-arid region may be used for superovulation despite the stressful condition of heat exposure and nutritional insufficiency.

Genetic structure of a small closed population of the New Zealand white rabbit through pedigree analyses

The genetic structure of a small population of New Zealand White rabbits maintained at the Sheep Breeding and Research Station, Sandynallah, The Nilgiris, India, was evaluated through pedigree analyses. Data on pedigree information (n=2503) for 18 yr (1995-2012) were used for the study. Pedigree analysis and the estimates of population genetic parameters based on the gene origin probabilities were performed. The analysis revealed that the mean values of generation interval, coefficients of inbreeding and equivalent inbreeding were 1.49 yr, 13.23 and 17.59%, respectively. The proportion of population inbred was 100%. The estimated mean values of average relatedness and individual increase in inbreeding were 22.73 and 3.00%, respectively. The percentage increase in inbreeding over generations was 1.94, 3.06 and 3.98 estimated through maximum generations, equivalent generations and complete generations, respectively. The number of ancestors contributing the majority of 50% genes (f_a50) to the gene pool of reference population was only 4, which might have led to reduction in genetic variability and increased the amount of inbreeding. The extent of genetic bottleneck assessed by calculating the effective number of founders (f_e) and the effective number of ancestors (f_a), as expressed by the f_e/f_a ratio was 1.1, which is indicative of the absence of stringent bottlenecks. Up to 5th generation, 71.29% pedigree was complete, reflecting the well maintained pedigree records. The maximum known generations were 15, with an average of 7.9, and the average equivalent generations traced were 5.6, indicating a fairly good depth in pedigree. The realized effective population size was 14.93, which is very critical, and with the increasing trend of inbreeding the situation has been assessed as likely to become worse in future. The proportion of animals with the genetic conservation index (GCI) greater than 9 was 39.10%, which can be used as a scale to use such animals with higher GCI to maintain balanced contribution from the founders. From the study, it was evident that the herd was completely inbred, with a very high inbreeding coefficient, and the effective population size was critical. Recommendations were made to reduce the probability of deleterious effects of inbreeding and to improve genetic variability in the herd. The present study can help in carrying out similar studies to meet the demand for animal protein in developing countries.