Pedigree Completeness
There were total 2603 animals in the pedigree out of which 2213 had both parents known (Table 1). Pedigree completeness in a population indicates the availability of information on ancestors and enhances the depth of pedigree. Pedigree completeness declined as the maximum generation increased, explaining the fact that fewer ancestors had contributed to the lineage to each parental generation. Completeness of pedigree to the maximum known generation plays an important role for accurate inbreeding estimates. For Saanen x Beetal crossbred flock, completeness of pedigree (with both known parents) percentage was 90.58% and maximum of 18 ancestral pathways were observed. Pedigree completeness in first, second, third and fourth were 88.8%, 66.12%, 49.32% and 39.02% respectively. These findings suggested good depth in pedigree information of this breed.
Table 1
Summary of Pedigree Analysis in Saanen x Beetal goats
Items | Whole Population | Male | Female |
Total number of animals in whole population | 2603 | 1222 | 1381 |
Number of inbred animals | 1236 | 627 | 609 |
Number of non-inbred animals | 1367 | 595 | 772 |
Number of animals with both parent unknown (founder) | 193 | 88 | 105 |
Number of animals with only one parent known | 145 | 79 | 66 |
Number of animals in base population (one or more parent unknown) | 391 | 140 | 251 |
Number of animals with both known parents | 2213 | 1055 | 1158 |
Number of animals with known parents | 2358 | 1134 | 1224 |
Mean inbreeding coefficient (% F) for whole population | 4.20% | 4.49% | 3.94% |
Mean inbreeding coefficient (% F) for reference population | 10.78% | 9.8% | 11.7% |
Genetic Conservation Index (GCI) for the whole population | 4.72 | 2.30 | 2.42 |
Total number of animals in reference population (2014–2017) | 90 | 45 | 45 |
Maximum, Complete And Equivalent Number Of Generation
Analysis revealed that maximum number of generations was 18 for Saanen x Beetal goats. We observed that 193 animals were present in base population whose ancestors couldn’t be traced back further (Table 2). Maximum number of animals were present in 6th generation i.e., 250. Average relatedness showed inclination with subsequent increase in the generations. Average relatedness percentage increased from base population (0th generation) and attained its peak at 15th generation and then decreased gradually till 18th generation. Mean inbreeding coefficient increased to maximum at 17th generation and finally reached to 11.42%. Percentage of inbred animals increased till 18th generation. Maximum inbred percentage was found in 17th and 18th generation. Saanen x Beetal goats had 5 complete generations excluding founders (0th generation) (Table 3). In the pedigree, 390 animals were present in the base population. Maximum number of animals were present in second generation and it eventually decreased till last generation. Average Inbreeding, Average inbreeding for Inbred animals and Average Relatedness increased with subsequent generation.
Table 2
Estimates of population parameters for Maximum Number of Generation in Saanen x Beetal goats
Maximum Generation | Animals (N) | Average Inbreeding (F%) | % Inbred (POR%) | Average F For Inbred (FP%) | Average Relatedness (AR%) | Effective Population Size (NE) |
0 | 193 | 0.00 | | | 0.44 | |
1 | 187 | 0.00 | | | 0.98 | |
2 | 406 | 0.12 | 0.004926 | 25.00 | 1.59 | 406 |
3 | 96 | 3.13 | 0.25 | 12.50 | 7.17 | 16.6 |
4 | 105 | 8.50 | 0.619048 | 13.73 | 9.18 | 9 |
5 | 156 | 4.57 | 0.307692 | 14.87 | 9.21 | |
6 | 250 | 3.70 | 0.432 | 8.58 | 8.59 | |
7 | 175 | 2.83 | 0.56 | 5.06 | 8.17 | |
8 | 191 | 4.55 | 0.73822 | 6.16 | 8.33 | |
9 | 141 | 5.81 | 0.808511 | 7.19 | 9.90 | |
10 | 128 | 5.55 | 0.898438 | 6.17 | 9.94 | |
11 | 126 | 7.37 | 0.849206 | 8.68 | 10.29 | |
12 | 126 | 7.73 | 0.936508 | 8.25 | 10.62 | |
13 | 91 | 8.04 | 0.868132 | 9.26 | 10.37 | |
14 | 58 | 9.49 | 0.827586 | 11.47 | 10.39 | 46 |
15 | 45 | 11.42 | 0.955556 | 11.95 | 11.04 | 23.4 |
16 | 59 | 10.42 | 0.949153 | 10.97 | 10.74 | |
17 | 56 | 12.11 | 1 | 12.11 | 10.46 | 64.4 |
18 | 14 | 11.42 | 1 | 11.42 | 10.38 | |
Table 3
Estimates of population parameters for Complete Number of Generation for Saanen x Beetal goats
Complete Generation | Animals (N) | Average Inbreeding (F%) | % Inbred (POR%) | Average F For Inbred (FP%) | Average Relatedness (AR%) | Effective Population Size (NE) |
0 | 390 | 0.00 | | | 1.67 | |
1 | 982 | 0.40 | 0.078411 | 5.16 | 3.97 | 123.5 |
2 | 602 | 5.59 | 0.880399 | 6.35 | 9.78 | 9.6 |
3 | 370 | 10.07 | 1 | 10.07 | 11.53 | 10.5 |
4 | 206 | 12.43 | 1 | 12.43 | 12.25 | 19 |
5 | 53 | 16.57 | 1 | 16.57 | 12.32 | 10.5 |
In Saanen x Beetal goats, mean maximum generation was found to be 6.53 which means that the average number of generations separating an offspring from its furthest ancestor was 6.53. Mean complete generation was found to be 1.68 implying number of generation tracing from offspring to all known ancestors was around 2. Increasing in inbreeding by maximum, complete and equivalent generations was 0.67%, 3.68% and 3.34% respectively. Oravcova (2013) reported mean value of complete number of generations, maximum number of generations and equivalent complete generations to be 1.97, 5.62 and 3.04 respectively in White Shorthaired goats. Mandal et al. (2021) reported mean value for complete number of generations as 1.18, maximum number of generations as 4.92 and equivalent complete generations as 2.24 in Jamunapari goats. Different estimates were obtained owing to breeding practices and population size of the flock in different breeds.
Generation Interval, Inbreeding And Average Relatedness
Generation Interval for whole population and reference population were estimated from four pathways in Saanen x Beetal goats i.e., Sire-son, Sire-daughter, Dam-son and Dam-daughter as shown in Table 4. For the whole population, Mean Generation Interval was found to be 3.44 ± 0.06 years. The pathway of Dam-son was having largest GI value i.e., 4.06 ± 0.14 years whereas pathway of Dam-Daughter were having least GI value i.e., 2.97 ± 0.07 years. For reference population, Mean Generation Interval was found to be 3.10 ± 0.15 years. Sire-Daughter pathway was having the least generation interval i.e., 2.76 ± 0.38 years whereas Dam-son pathway were having highest generation interval i.e., 4.33 ± 0.81 years.
Table 4
Generation intervals (GI) in years for four pathways of Saanen x Beetal goats for whole and the reference population.
Pathway | Whole Population | Reference Population |
| No. | GI ± SE | No. | GI ± SE |
Sire-Son | 82 | 3.91 ± 0.29 | 6 | 3.42 ± 0.53 |
Sire-Daughter | 689 | 3.79 ± 0.12 | 29 | 2.76 ± 0.38 |
Dam-Son | 83 | 4.06 ± 0.14 | 7 | 4.33 ± 0.81 |
Dam-Daughter | 673 | 2.97 ± 0.07 | 30 | 3.08 ± 0.50 |
Total | 1527 | 3.44 ± 0.06 | 72 | 3.10 ± 0.15 |
(GI- Generation intervals; SE- Standard error) |
Different estimates of generation interval were obtained for Girgentana goats as 2.5 years by Portolano et al. (2004), 1.9 years in Dutch Landrace by Mucha and Windig, (2009), 5.28 years in Brazilian Marota goats (Barros et al., 2011), 2.77 years in Spanish Murciano-Granadina goats (Oliveria et al., 2016), 2.87 years in Adani goats (Banch et al., 2020) and 3.33 years in Jamunapari goats (Mandal et al., 2021). Various estimates of generation interval observed among breeds are basically due to genetic differences among breeds along with breeding policy and management decisions carried out at farm level.
Inbreeding level shows the homozygosity of alleles in a particular population and inbreeding increases within a closed nucleus flock. In Saanen x Beetal goats, an increment in inbreeding level was observed over subsequent years due to closed nature of the flock (Fig. 1). Mean inbreeding coefficient was found to be 4.20% and 10.78% for whole and reference population respectively. These estimates were comparatively higher than the earlier mean inbreeding coefficient reported by Joezy-Shekalgorabi et al. (2017) in Adani goats as 0.24% and 0.56% whereas Mandal et al. (2021) reported average inbreeding coefficient as 0.46% and 0.77% in whole and reference population respectively. For whole population, inbred mating proportions were estimated. In Saanen x Beetal goats, 3 (0.12%) mating between full sibs, 103 (3.96%) mating between half sibs and 16 (0.61%) mating between parent-offspring was observed. Higher inbreeding level in the population also lead to higher average relatedness in the population as both measures the relatedness of an individual with other in a population. Average relatedness for the whole population and reference population were found to be 6.87% and 10.80% respectively, illustrating the fact that animals in the flock were closely related with each other as the offspring produced in this flock were used for further breeding purpose. Mandal et al. (2021) reported that average relatedness in case of Jamunapari goats was 1.06% in whole population and 3.87 in reference population. This is mainly due to the fact that the flock referred in Mandal et al. (2021) had observed several incidences of influx of Jamunapari genetics from outside the flock, however the studied flock in this report was closed throughout.
Effective Population Size
In order to deduce possible loss in genetic diversity in future, effective population size is studied. The number of animals that reproduce in an ideal population and produce the same increment in inbreeding levels in the population under study is considered the effective population size (Hill, 1979). Decline in effective population size is an indicator of loss in genetic diversity of the population. For the whole population in case of Saanen x Beetal goats, effective size obtained from regression on the birth date and effective size obtained from log regression on the birth date was 58.33 and 56.57 respectively (Table 5). According to the United Nations Food and Agriculture Organisation (FAO 1998), 50 is the figure considered as a threshold for concern. In our study, we observed that in Saanen x Beetal goats, effective population size was little over 50 nearing to the threshold level due to closed nature of the flock. These figures indicates absence of influx of outside breeding animals.
Table 5
Parameters characterizing probability of gene origin in Saanen x Beetal goats
Parameters characterizing probability of gene origin | Value |
Total number of animals | 2603 |
Whole Population |
Number of founders contributing to whole population | 390 |
Effective population size of founders | 28.00 |
Effective number of founders (fe) for whole population | 22 |
Number of ancestors contributing to whole population | 261 |
Effective number of ancestors (fa) in whole population | 20 |
Effective size obtained from regression on the birth date | 58.33 |
Effective size obtained from Log regression on the birth date | 56.57 |
fe/f for whole population | 0.79 |
Reference Population |
Number of animals in reference population | 90 |
Number of founders contributing to reference population | 62 |
Effective number of founders (fe) for reference population | 15 |
Number of ancestors contributing to reference population | 32 |
Effective number of ancestors (fa) in reference population | 7 |
Effective number of founder genome equivalent (fg) | 3.11 |
Comparision between Parameters |
fe/fa for whole population | 1.1 |
fe/fa for reference population | 2.14 |
fe/fg for reference population | 2.1 |
1/(2fa )for reference population (in %) | 7.14 |
Expected inbreeding (%) due to unequal founder contributions | 1.79%. |
Number of ancestors describing 50%, 75% and 100% of the gene pool in whole population | 8, 24, 261 |
Number of ancestors explaining 50% of the gene pool in reference population | 3 |
Mean average relatedness (% AR) for whole population | 6.87% |
Mean average relatedness (% AR) for reference population | 10.80% |
In contrast to our study, most of the review reported higher estimates for effective population size. Oravcova (2013) reported \(\stackrel{-}{{N}_{e}}\) as 182 in White Shorthaired goats. Danchin-Burge et al. (2012) reported estimates of (\(\stackrel{-}{{N}_{e}}\)) in Alpine, Saanen and Angora goats as 149,129 and 76, respectively. Similarly, estimates of \({N}_{e}\) were 84 in Markhoz goat (Rashidi et al. 2015) and 332in Raeini Cashmere goats (Mokhtari et al., 2017). Mandal et al. (2021) reported estimates of \(\stackrel{-}{{N}_{e}}\) as 210.25 in Jamunapari goats.
Ancestral Flock Diversity Analysis
Diversity analysis of ancestors gives a deep insight in to the diversification of the population. It was observed that the effective number of founders were less as compared with total number of founders illustrating the fact that only few individuals were used for subsequent breeding (Goyache et al., 2003). Effective number of founders and ancestors were found to be 22 and 20, respectively. These findings further explain the fact that although the main objective was to select superior germplasm for breeding purpose, it ultimately led to limiting the genetic diversity of the population. Due to the use of lesser number of individuals for subsequent breeding, the genetic diversity in the population is chiefly contributed by these individuals. These findings also explain about increase in inbreeding coefficient and average relatedness in the population along with decline in genetic diversity and allelic loss due to genetic drift. Hence, this population parameter provides useful information in formulating strategies to keep inbreeding under acceptable limits. Ratio of \({f}_{e}/ f\) gives a clear idea about the disequilibrium observed in founders contribution to the population. Estimates of \({f}_{e}/ f\) was found to be 0.79 in Saanen x Beetal goats. Other estimates of \({f}_{e}/ f\) reported were 0.25 in Girgentana goats (Portolano et al., 2004), 0.26 in White Shorthaired goats by Oravcova (2013), 0.46 in Markhoz goat (Rashidi et al., 2015), 0.23 in Cashmere goats (Joezy-Shekalgorabi et al., 2016), 0.14 in Adani goats (Baneh et al., 2020) and 0.14 in Jamunapari goats (Mandal et al., 2021).
Boichard et al. (1997) explained that ratio of \({f}_{e}/{f}_{a}\) describes loss of genetic diversity that occurred in the population due to existence of bottleneck effect. If the ratio of \({f}_{e}/{f}_{a}\) exceeds 1, it indicates the occurrence of bottleneck effect in the population resulting in reduction of diversification across the population. For the whole population and the reference population of Saanen x Beetal goats, the ratio of \({f}_{e}/{f}_{a}\) was 1.1 and 2.14, respectively. Effective number of ancestors includes both founders and non-founders; if effective number of ancestors is smaller than effective number of founders, genetic diversification is constrained due to the use of a small number of individuals, causing a bottleneck effect in the population. Similar estimates of \({f}_{e}/{f}_{a}\) such as 1.6 was observed in White Shorthaired goats by Oravcova (2013), 2.38 in Boer goats (Menezes et al., 2015), 1.32 in Markhoz goat (Rashidi et al., 2015), 1.76 in Raeini Cashmere goats (Mokhtari et al., 2017) and 1.31 in Jamunapari goats (Mandal et al., 2021).
Effective number of founder genomes, or founder genome equivalent, describes the genetic diversity that has been lost during genetic drift in a small population size even after equal contributions from founders and ancestors in a population. The estimate for fg in reference population was 3.11 in Saanen x Beetal goats. Higher estimates for effective number of founder genome ( \({\text{f}}_{\text{g}}\)) was found to be 32 in White Shorthaired goats as reported by Oravcova (2013). Moreover, \({\text{f}}_{\text{g}}\) value reported were 26 in Markhoz goat (Rashidi et al., 2015), 42.7 in Cashmere goat (Joezy-Shekalgorabi et al., 2016), 32.01 in Adani goat (Joezy-Shekalgorabi et al., 2017) and 25.8 in Jamunapari goat (Mandal et al., 2021). Estimates of fe/fg was found to be 2.1 that explained the genetic drift occurred in the population. The estimate for fg/fa in reference population was 0.44, which indicates that 44 % o the original ancestral genetic diversity is present in the reference population. This estimate was low when compared with other report in Jamunapari goat by Mandal et al. (2021), where fg/fa was 0.66.
Population parameters explaining genetic diversity in the reference population are presented in Table 5. A total of 62 founder animals were identified which contributed to reference population, but the effective number of founders (fe) was only 15. The effective number of ancestors (fa) was 7 in reference population. Number of ancestors contributing variability up to 50%, 75% and 100% of the gene pool in whole population were 8, 24, and 261, respectively. Thus, only 8 ancestors were responsible for the 50% variability of the population (Fig. 2). Genetic Conservation Index (GCI) is a population parameter helps in quantifying founders diversity. It also helps in maintaining allelic richness in a population. Higher GCI value implies that the animal is important for conservation purpose. In Saanen x Beetal goats, mean GCI for all animals, males and female in whole population were 4.72, 2.30 and 2.42 respectively (Fig. 3). In contrast to our study, higher estimate was observed for average GCI as 7.35 in Boer goat (Menezes et al., 2015), but lower estimates were also reported such as 1.64 in Murciano-Granadina goats (Oliveria et al., 2016), 2.57 in Adani goat (Baneh et al., 2020) and 3.99 in Jamunapari goats (Mandal et al., 2021).
Estimates of GD and GD* were 0.84 and 0.96, respectively. Estimate of GD*-GD revealed 12% loss in genetic diversity in this population. It actually estimated proportion of retained genetic diversity (i.e., heterozygosity) in the reference population (GD) and the proportion of retained diversity associated only with the sampling of founders (GD*). The difference (GD* − GD) estimates which was 12% in heterozygosity can be associated with genetic drift and bottleneck effect in Saanen x Beetal goats.
Impact Of Inbreeding On Reproductive Traits In Saanen X Beetal Goats
While selecting superior germplasm, animals having better genetic merit are selected for further breeding which leads to selection of specific alleles responsible for the genetic makeup of the animal. Selecting those alleles change genetic composition of whole population and hence alleles are fixed with subsequent selection for a particular trait of interest which leads to accumulation of inbreeding in the population. Hence, inbreeding up to certain extent is desirable until it negatively affects the performance status of the animal. Since this goat flock has been maintained for over 50 years, we tried to study the impact of inbreeding on reproductive traits in Saanen x Beetal goats. We observed non-significant effect of inbreeding on all reproductive traits except age at first service (AFS) and age at first kidding (AFK), where Fi influenced AFS and AFK significantly (P < 0.01) in unfavourable direction. Similar reports are available in literature where significant change in the trait phenotype in small ruminants were observed (Prince et al., 2008; Barczak et al., 2009; Pedrosa et al., 2010; Gowane et al. 2010; Gowane et al. 2013; Gowane et al. 2014). Least squares analysis revealed that for AFS and AFK, the period and season of birth were also significant sources of variation in addition to inbreeding with the R2 estimate of 16.6% and 13.1%, respectively (Table 6).
Table 6
Effect of inbreeding on reproductive traits in Saanen x Beetal goats
Particulars | AFS | AFK | SP | DP | GL | KI | LW | NKB | NFKB |
µ ± SE | 526.99 ± 4.86 | 662.96 ± 5.03 | 219.11 ± 6.25 | 109.38 ± 6.00 | 150.48 ± 0.27 | 356.63 ± 4.80 | 3.87 ± 0.05 | 1.27 ± 0.02 | 0.67 ± 0.03 |
Period of Birth | ** | ** | NS | - | NS | NS | - | - | - |
Season of Birth | ** | ** | NS | - | NS | NS | - | - | - |
Inbreeding | ** | ** | NS | NS | NS | NS | NS | NS | NS |
Period of Kidding | - | - | - | ** | - | - | ** | ** | NS |
Season of Kidding | - | - | - | NS | - | - | NS | * | NS |
Adjusted R2 | 16.6% | 13.1% | 1.6% | 3% | 0.8% | 1.6% | 6.3% | 11.3% | 0.4% |
NS- Non-Significant |
* Significant at 5% level of significance. |
** Significant at 1% level of significance. |