Allelic profiles at microsatellite loci
The results obtained for number of alleles, their sizes and frequencies at egg production associated microsatellites loci has been presented in Table 2. The average number of alleles per locus was 3.7, ranging from two to seven alleles at different loci and with frequency of 0.0146 to 0.9545. The size of most frequent allele was 204 bp at locus MCW0145 and least frequent one as 173 bp at MCW0069. Two to three alleles at various polymorphic loci with an average of 2.41 alleles per locus were reported across the breeds (Deshmukh et al., 2015). The polymorphic loci having two to six alleles with an average of 3.5 alleles and two to five alleles with average of 4 alleles per locus were observed in selected strain of Rhode Island Red chicken (Rahim et al., 2017). Thus, present findings were in close agreement to the earlier findings in chicken and demonstrated their applicability.
Table 2
Number of alleles, molecular sizes and frequencies at egg production associated microsatellites loci in RIR chicken
Microsatellites | Chromosome location | No. of alleles | Allele code | Allele size (bp) | Allele frequency |
ADL0023 | 5 | 3 | A | 190 | 0.1748 |
| B | 178 | 0.3398 |
| C | 172 | 0.4854 |
ADL00158 | E29 | 4 | A | 212 | 0.0485 |
| B | 200 | 0.2524 |
| C | 194 | 0.6408 |
| D | 182 | 0.0583 |
ADL0176 | 2 | 7 | A | 220 | 0.0340 |
| B | 215 | 0.2524 |
| C | 210 | 0.0583 |
| D | 205 | 0.2621 |
| E | 200 | 0.0971 |
| F | 195 | 0.2670 |
| G | 190 | 0.0291 |
ADL0273 | Z | 3 | A | 150 | 0.0291 |
| B | 147 | 0.5243 |
| C | 144 | 0.4466 |
MCW0044 | 2 | 4 | A | 150 | 0.0388 |
| B | 147 | 0.2621 |
| C | 141 | 0.4466 |
| D | 138 | 0.2525 |
MCW0069 | 26 | 5 | A | 173 | 0.0146 |
| B | 169 | 0.1359 |
| C | 165 | 0.1893 |
| D | 161 | 0.1214 |
| E | 157 | 0.5388 |
MCW0103 | 3 | 2 | A | 300 | 0.4854 |
| B | 292 | 0.5146 |
MCW0110 | E48 | 4 | A | 116 | 0.2670 |
| B | 112 | 0.2718 |
| C | 104 | 0.2087 |
| D | 100 | 0.2525 |
MCW0145 | 1 | 2 | A | 220 | 0.0485 |
| B | 204 | 0.9515 |
MCW0258 | Z | 3 | A | 170 | 0.5340 |
| B | 158 | 0.4078 |
| C | 146 | 0.0582 |
Mean ± SE | | 3.70 ± 0.47 | | | |
Population structure
Nei’s heterozygosity of microsatellite (MS) loci was 0.55 ± 0.06 ranging from 0.09 (MCW0145) to 0.78 (ADL0176). Similar estimates for different microsatellites were reported of in various poultry breeds (Vijh and Tantia, 2004; Pandey et al., 2005). The observed and expected heterozygosity were 0.1922 ± 0.0687 and 0.5607 ± 0.06, respectively showing that the population was in Hardy-Weinberg disequilibrium. It might be due to the association of microsatellite loci with economic traits as the population was undergoing continuous selection for part-period egg production trait and was also small in size. Similar to the present findings, the observed and expected heterozygosities were reported in Ankaleshwar at ADL0023 as 0.333 and 0.804, at ADL0176 as 0.816 and 0.740 and at ADL0158 as 0.605 and 0.594, respectively (Pandey et al., 2005). There was a report of high observed and expected heterozygosities for ADL0023 (0.91 and 0.79), ADL0158 (0.92 and 0.72), ADL0176 (0.90 and 0.80), MCW0044 (0.27 and 0.49) and MCW0110 (0.73 and 0.73) loci in Kadaknath and Aseel breeds of chicken (Chatterjee et al., 2010a). Earlier reports (El-Sayed et al., 2011; Suh et al., 2014; Debnath, Kumar, Yadav, et al., 2015) also demonstrated similar estimates of observed and expected heterozygosities. The estimates were comparable to the earlier reports in RIR chicken. Five out of 10 MS loci had polymorphic information content (PIC) value more than 50%. The estimated average PIC value was 0.498 ± 0.06, which was ranging from 0.0880 (MCW0145) to 0.7489 (ADL0176), respectively and were in accordance with the earlier findings in RIR population (Vijh and Tantia, 2004; Pandey et al., 2005), although a few contrary reports are also available for the studied MS loci (Chatterjee et al., 2008a, Chatterjee et al., 2010; Deshmukh et al., 2015). The differences in PIC values may be due to the differences in genetic architecture of population analyzed or due to loss or fixation of some of the alleles during long-term selection.
Production performance
The least squares analysis of variance of body weight at 20 weeks of age (BW20) and various layer economic traits viz., age at sexual maturity (ASM), egg weight at 28 (EW28) and 40 (EW40) weeks of age and egg production up to 40 (EP40) weeks of age presented in Table 3. Sire had significant effect on layer traits EW40 and EP40. Hatch had significant effect (P ≤ 0.05) on ASM and EW28. The least squares mean for BW20 and layer economic traits viz., ASM, EW28, EW40 and EP40 have been presented in Table 4. The overall least-squares mean of ASM, EW28, EW40 and EP40 were 134.98 ± 1.30days, 42.54 ± 0.32g, 48.15 ± 0.56g and 121.47 ± 2.44eggs, respectively. Least-squares means of body weight revealed that the birds of 1st hatch showed highest BW20 (1378.27 ± 53.33g) followed by 3rd (1372.71 ± 48.13g), 4th (1347.96 ± 32.32g), 5th (1336.05 ± 35.63g) and 2nd (1280.58 ± 54.93g) hatch. Least squares mean of layer economic traits also revealed that pullets of 5th hatch showed highest EW28 (44.84 ± 0.66g), and 2nd hatch showed highest EW40 (49.96 ± 1.26g), and 1st hatch showed highest EP40 (127.92 ± 5.55). Though, same management practices followed for all the hatches, still there was significant hatch effect. It might be due to micro-environmental variability as well as quick environmental fluctuations among the hatches which were beyond the human control. Similar findings were reported for significant hatch effect on early egg weights (Smith and Bohren, 1975), on egg production (King and Henderson, 1954) and on ASM in the coloured Punjab Broiler-II (PB2) dam line (Nwagu et al., 2007; Das, 2013; Debnath, Kumar, Bhanja, et al., 2015).
Table 3
Least squares analysis of variance of layer traits in Rhode Island Red chicken
Source of variation | df | Mean sum of squares |
ASM | BW20 | EW28 | EW40 | EP40 |
Sire | 27 | 121.05 | 22286.35 | 7.13 | 19.82* | 375.81* |
Hatch | 4 | 380.73* | 11556.03 | 23.13** | 20.98 | 143.70 |
Error/ Remainder | 59 | 115.30 | 21695.30 | 6.22 (55) | 10.17 (55) | 203.91 (55) |
df = Degrees of freedom; *P < 0.05; **P < 0.01; Figures within parentheses denote degrees of freedom |
Table 4
Least squares mean ± S.E of layer traits in Rhode Island Red chicken
Factors | Least squares mean ± standard errors |
N | ASM (days) | BW20 (g) | EW28 (g) | EW40 (g) | EP40 |
Overall | 91 | 134.98 ± 1.30 | 1343.12 ± 17.65 | 42.54 ± 0.32 (87) | 48.15 ± 0.56 (87) | 121.47 ± 2.44 (87) |
Hatch | 1 | 12 | 140.75 ± 3.89a | 1378.27 ± 53.33 | 41.39 ± 0.92b | 47.56 ± 1.23 | 127.92 ± 5.55 |
2 | 9 | 132.54 ± 4.01cd | 1280.58 ± 54.93 | 42.71 ± 0.94b | 49.96 ± 1.26 | 123.16 ± 5.66 |
3 | 12 | 139.86 ± 3.51ab | 1372.71 ± 48.13 | 41.47 ± 0.82b | 47.25 ± 1.12 | 119.46 ± 5.01 |
4 | 28 | 134.77 ± 2.36bc | 1347.96 ± 32.32 | 42.29 ± 0.567b | 46.74 ± 0.81 | 119.64 ± 3.60 |
5 | 30 | 126.99 ± 2.60d | 1336.05 ± 35.63 | 44.84 ± 0.66a (26) | 49.24 ± 0.93 (26) | 117.17 ± 4.10 (26) |
N = Number of observations; Means with same superscript in a column do not differ significantly (P ≤ 0.05); Figures within parentheses denote number of observations. |
Genetic parameters of layer economic traits
Genetic parameters, viz., heritability, genetic and phenotypic correlations amongst body weight at 20 weeks of age (BW20) and various layer economic traits have been presented in Table 5. The heritability estimate for BW20 was 0.38 ± 0.48. Quite comparable heritability estimates with present investigation were reported by some of the researchers (Das, 2013; Qadri et al., 2013; Rahim et al., 2017). However, some authors have reported high heritability for BW20 chicken (Jilani et al., 2005), which might be due to differences in the genetic stocks evaluated. The heritability estimates were high for ASM (0.49 ± 0.48), EW40 (0.97 ± 0.50) and EP40 (0.86 ± 0.50), but low for EW28 (0.19 ± 0.46). Similar heritability for ASM has been reported by earlier researchers also (Laxmi et al., 2010; Rahim, 2015). Lower heritability estimates indicated that it was difficult to improve this trait through genetic selection. However, contrary to the present findings, some workers have reported lower heritability estimate for EW28, EW40 and EP40 (Barot et al., 2008; Anees et al., 2010; Rajkumar et al., 2011; Vasu et al., 2022). Genetic correlations (rG) of BW20 with EW28 and EW40 were positive, but negative with EP40. The rG of ASM with BW20, EW28 and EP40 were negative, but positive with EW40. The rG of EW28 was positive with EW40, but negative with EP40. The rG of EW40 was negative with EP40. The phenotypic correlations (rP) of ASM with all other traits were negative except EW28. The rP of BW20 was positive with EW28, EW40 and EP40. The rP of EW28 was positive and high with EW40, but negative with EP40. Likewise, EW40 had negative rP with EP40. Similar negative genetic correlations of ASM with layer traits have also been reported earlier (Laxmi et al., 2010; Qadri et al., 2013; Rahim, 2015). A few earlier reports demonstrated that BW20 had positive genetic correlations with EW28 and EW40 (Das et al., 2015), and negative with ASM and EP40 in selected strain of RIR chicken (Rahim, 2015).
Table 5
Heritability (at diagonal), genetic (above diagonal) and phenotypic (below diagonal) correlations amongst various layer traits
Traits | ASM | BW20 | EW28 | EW40 | EP40 |
ASM | 0.49 ± 0.48 (91) | -0.74 ± 1.18 (91) | -0.49 ± 1.27 (87) | 0.34 ± 0.59 (87) | -0.58 ± 0.77 (87) |
BW20 | -0.26 (91) | 0.38 ± 0.48 (91) | 0.59 ± 1.26 (87) | 0.12 ± 0.60 (87) | -0.06 ± 0.62 (87) |
EW28 | 0.005 (87) | 0.16 (87) | 0.19 ± 0.46 (87) | 0.20 ± 0.77 (87) | -0.32 ± 1.06 (87) |
EW40 | -0.06 (87) | 0.14 (87) | 0.46 (87) | 0.97 ± 0.50 (87) | -0.62 ± 0.47 (87) |
EP40 | -0.28 (87) | 0.07 (87) | -0.16 (87) | -0.05 (87) | 0.86 ± 0.50 (87) |
Figures within parentheses denote number of observations |
Association of microsatellite genotypes with layer economic traits
All the experimental birds were genotyped for their profiles for 10 microsatellites, all of them were found polymorphic. Least squares analysis of variance of layer economic traits to determine the effects of MS genotypes taking it as independent factor in the model and MS genotype-wise LS means of various traits are given in Table 6 and Table 7, respectively.
Table 6
Estimated mean sum of squares of layer economic traits under different microsatellite loci in Rhode Island Red chicken
Source of variation | Mean sum of squares |
df | ASM | BW20 | EW28 | EW40 | EP40 |
ADL0023 | 3 | 58.47 | 80830.27** | 5.72 | 4.90 | 188.24 |
ADL0158 | 3 | 239.98 | 5697.87 | 5.20 | 10.57 | 144.30 |
ADL0176 | 8 | 117.34 | 20385.26 | 8.21 | 5.44 | 77.99 |
ADL0273 | 2 | 67.69 | 58488.71$ | 25.18* | 14.31 | 2.36 |
MCW0044 | 3 | 133.52 | 17993.42 | 3.03 | 1.93 | 23.12 |
MCW0069 | 6 | 48.24 | 6015.21 | 6.03 | 13.92 | 286.92 |
MCW0103 | 1 | 34.45 | 20299.47 | 4.19 | 0.15 | 9407.69 |
MCW0110 | 8 | 96.61 | 24455.32 | 8.941 | 10.07 | 72.59 |
MCW0145 | 1 | 3.28 | 52603.44 | 0.06 | 13.69 | 11.20 |
MCW0258 | 4 | 37.68 | 20809.26 | 11.17 | 11.53 | 41.17 |
df = Degrees of freedom; $P ≤ 0.07; *P ≤ 0.05; **P ≤ 0.01 |
Table 7
Least squares mean ± S.E of layer traits for different genotypes at microsatellite loci in Rhode Island Red chicken
Microsatellite | Genotype | Least squares mean ± standard error |
ASM (days) (n = 110) | BW20 (g) (n = 110) | EW28(g) (n = 108) | EW40(g) (n = 103) | EP40 (n = 110) |
ADL0023 | AA | 132.832 ± 3.63 | 1496.34a ± 45.52 | 42.18 ± 0.89 | 48.08 ± 1.20 | 118.07 ± 5.42 |
BB | 136.63 ± 2.88 | 1295.52b ± 36.01 | 42.54 ± 0.68 | 47.39 ± 0.94 | 124.39 ± 4.27 |
CC | 134.62 ± 2.63 | 1325.76 b ± 32.89 | 42.77 ± 0.63 | 48.74 ± 0.93 | 126.14 ± 4.23 |
AB | 141.50 ± 6.25 | 1334.04b ± 78.34 | 40.04 ± 1.47 | 48.81 ± 2.11 | 134.72 ± 9.45 |
ADL0158 | BB | 139.76 ± 3.97 | 1313.12 ± 55.98 | 42.09 ± .95 | 47.85 ± 1.25 | 121.65 ± 5.71 |
CC | 135.66 ± 2.30 | 1351.37 ± 30.93 | 42.56 ± .52 | 47.90 ± .81 | 124.06 ± 3.69 |
DD | 134.36 ± 4.99 | 1398.58 ± 70.83 | 44.16 ± 1.21 | 48.89 ± 1.64 | 124.51 ± 7.51 |
AB | 125.74 ± 4.69 | 1326.84 ± 66.44 | 41.27 ± 1.13 | 50.37 ± 1.46 | 132.48 ± 6.68 |
ADL0176 | BB | 137.20 ± 3.23 | 1276.81 ± 44.50 | 43.26 ± 0.76 | 47.63 ± 1.04 | 120.52 ± 4.86 |
DD | 135.47 ± 3.69 | 1435.39 ± 50.86 | 44.01 ± 0.87 | 48.86 ± 1.19 | 127.38 ± 5.54 |
FF | 132.79 ± 5.22 | 1285.72 ± 71.94 | 40.17 ± 1.21 | 47.38 ± 1.64 | 123.65 ± 7.549 |
AB | 120.25 ± 9.27 | 1396.75 ± 127.90 | 40.67 ± 2.16 | 52.57 ± 2.85 | 112.61 ± 13.06 |
AD | 136.68 ± 8.68 | 1490.25 ± 119.72 | 43.67 ± 2.02 | 48.50 ± 2.73 | 126.17 ± 12.53 |
CD | 134.81 ± 7.30 | 1363.10 ± 100.67 | 43.75 ± 1.70 | 49.81 ± 2.26 | 127.69 ± 10.39 |
CE | 138.76 ± 5.95 | 1375.91 ± 82.01 | 41.79 ± 1.39 | 47.37 ± 1.85 | 133.77 ± 8.52 |
EF | 125.40 ± 8.30 | 1154.59 ± 114.42 | 41.31 ± 1.94 | 46.83 ± 2.58 | 122.25 ± 11.84 |
EG | 142.39 ± 6.23 | 1302.03 ± 85.90 | 40.65 ± 1.45 | 48.25 ± 1.92 | 122.92 ± 8.85 |
ADL0273 | AA | 137.60 ± 5.85 | 1530.30a ± 77.34 | 45.01a ± 1.50 | 52.41 ± 2.31 | 124.32 ± 10.63 |
BB | 136.59 ± 2.17 | 1365.01b ± 28.79 | 43.26a ± 0.58 | 48.33 ± 0.97 | 124.26 ± 4.36 |
CC | 132.87 ± 2.79 | 1305.50c ± 36.95 | 41.16b ± 0.69 | 47.76 ± 1.08 | 125.01 ± 4.88 |
MCW0044 | AA | 139.43 ± 7.51 | 1373.84 ± 103.81 | 43.78 ± 1.81 | 47.28 ± 2.29 | 119.00 ± 10.42 |
BB | 136.93 ± 3.27 | 1293.06 ± 44.97 | 41.91 ± 0.79 | 47.99 ± 1.06 | 124.58 ± 4.85 |
CC | 132.84 ± 2.63 | 1371.75 ± 36.10 | 42.58 ± 0.63 | 48.48 ± 0.87 | 125.23 ± 4.012 |
DD | 139.11 ± 3.76 | 1364.84 ± 51.83 | 43.03 ± 0.90 | 47.78 ± 1.18 | 123.58 ± 5.41 |
MCW0069 | CC | 134.37 ± 5.17 | 1285.23 ± 71.38 | 43.81 ± 1.19 | 48.28 ± 1.57 | 134.50 ± 7.08 |
DD | 133.63 ± 4.96 | 1332.67 ± 68.52 | 41.85 ± 1.16 | 50.83 ± 1.60 | 127.40 ± 7.23 |
EE | 134.90 ± 2.79 | 1366.64 ± 38.53 | 42.80 ± 0.66 | 48.42 ± 0.90 | 118.57 ± 4.06 |
AE | 142.48 ± 7.04 | 1414.44 ± 97.26 | 39.40 ± 1.92 | 42.22 ± 2.36 | 133.09 ± 10.65 |
BD | 134.30 ± 5.50 | 1359.18 ± 76.06 | 42.12 ± 1.28 | 48.88 ± 1.62 | 135.38 ± 7.29 |
BE | 132.58 ± 3.19 | 1347.84 ± 44.17 | 41.90 ± 0.74 | 47.54 ± 1.02 | 121.75 ± 4.59 |
CE | 137.83 ± 3.53 | 1325.33 ± 48.84 | 42.87 ± 0.81 | 48.28 ± 1.06 | 126.98 ± 4.77 |
MCW0103 | AA | 134.39 ± 1.84 | 1366.63 ± 24.88 | 42.20 ± 0.43 | 48.18 ± 0.61 | 125.99 ± 2.78 |
BB | 135.91 ± 1.78 | 1329.67 ± 24.06 | 42.73 ± 0.41 | 48.18 ± 0.58 | 123.32 ± 2.69 |
MCW0110 | AA | 136.66 ± 3.66 | 1301.64 ± 48.78 | 42.89 ± 0.84 | 48.74 ± 1.14 | 123.16 ± 5.41 |
BB | 136.65 ± 3.75 | 1265.68 ± 50.04 | 41.37 ± 0.89 | 46.89 ± 1.23 | 125.93 ± 5.83 |
CC | 136.93 ± 6.88 | 1336.34 ± 92.10 | 42.01 ± 1.57 | 46.61 ± 2.02 | 120.81 ± 9.62 |
DD | 139.42 ± 4.90 | 1409.39 ± 65.53 | 44.05 ± 1.13 | 50.80 ± 1.47 | 122.14 ± 6.97 |
AC | 135.38 ± 3.21 | 1382.04 ± 42.71 | 41.95 ± 0.78 | 48.57 ± 1.05 | 124.46 ± 4.99 |
AD | 134.43 ± 5.89 | 1402.08 ± 78.85 | 40.80 ± 1.34 | 50.72 ± 1.74 | 134.03 ± 8.28 |
BC | 121.14 ± 7.32 | 1532.04 ± 98.12 | 45.80 ± 2.07 | 49.18 ± 2.67 | 127.92 ± 12.69 |
BD | 131.87 ± 3.23 | 1362.80 ± 43.04 | 43.68 ± 0.76 | 47.47 ± 1.026 | 122.01 ± 4.84 |
CD | 135.61 ± 6.41 | 1407.59 ± 85.91 | 43.51 ± 1.46 | 48.85 ± 1.89 | 131.12 ± 8.97 |
MCW0145 | BB | 135.12 ± 1.83 | 1356.02 ± 24.24 | 42.49 ± 0.42 | 48.03 ± 0.72 | 124.69 ± 3.28 |
AB | 135.88 ± 3.69 | 1260.51 ± 49.40 | 42.39 ± 0.87 | 49.70 ± 1.22 | 123.18 ± 5.60 |
MCW0258 | AA | 136.50 ± 3.46 | 1303.88 ± 46.46 | 41.70 ± 0.79 | 47.55 ± 1.07 | 124.37 ± 4.88 |
BB | 132.67 ± 3.64 | 1358.95 ± 48.84 | 42.37 ± 0.84 | 48.29 ± 1.13 | 125.58 ± 5.18 |
CC | 130.58 ± 11.37 | 1596.32 ± 152.53 | 48.87 ± 2.57 | 53.71 ± 3.35 | 118.54 ± 15.62 |
AB | 136.53 ± 4.27 | 1361.60 ± 57.31 | 43.15 ± 0.97 | 49.06 ± 1.35 | 125.94 ± 6.22 |
BC | 135.61 ± 7.01 | 1358.21 ± 94.03 | 41.76 ± 1.59 | 46.04 ± 2.06 | 118.57 ± 9.61 |
N = Number of observations; Means with same superscript in a column do not differ significantly (P < 0.05 and P < 0.07); Figures within parentheses denote number of observations. |
Genotypes at two MS loci (ADL0023 and ADL0273) were revealed significant (P ≤ 0.01) effects on layer economic traits. AA genotype at ADL0023 had revealed highest body weight (1496.34 ± 45.52 g) at BW20 which was statistically higher than those pullets having genotypes BB (1295.52 ± 36.01g), CC (1325.76 ± 32.89g) or AB (1334.04 ± 78.34g). Significant effect of genotypes at ADL0023 on BW20 had been reported by earlier researchers also (Chatterjee et al., 2008b; Das et al., 2015; Debnath et al., 2019; Rahim et al., 2017; Wardȩcka et al., 2002). ADL0273 genotypes had significant effect on BW20 (P ≤ 0.07) and EW28 (P ≤ 0.05). The pullets with AA genotype at this locus showed highest BW20 as 1530.30 ± 77.34g which was statistically higher than those pullets having BB (1365.01 ± 28.79g) and CC (1305.50 ± 36.95g). AA genotyped pullets revealed highest EW28 (45.01 ± 1.50g) which was statistically different than CC (41.16 ± 0.69g) genotyped birds, but did not differ from BB (43.26 ± 0.58g) genotyped birds. Similar to the present findings, earlier researchers had reported significant effect ADL0273 genotypes on ASM, BW20 and EW28 (Chatterjee et al., 2010b; Das et al., 2015; Debnath et al., 2015b; Radwan et al., 2014; Rahim, 2015). The rest of the MS-genotypes at other loci did not differ significantly for any of the layer economic traits. The non-significant effect of MS-genotypes at these loci was supported by previous reports (Chatterjee et al., 2008a; Das et al., 2015). Contrary to the present findings some of the reports suggested significant effect of genotypes at ADL0158, ADL0176, MCW0069, MCW0103, MCW0110, MCW0145 and MCW0258 on egg production and egg weight (Roushdy et al., 2008; Rahim et al., 2017).