National Gene Bank, ICAR-NBAGR, Karnal is dedicated to achieve Sustainable Development Goals (SDG) through conserving genetic diversity through preserving semen, somatic cell, and embryos for long term storage. Along with the conservation of animal genetic resources, assessment of genetic diversity is crucial for preserving genetic diversity and preventing the loss of undesirable alleles. This finding of this study revealed excessive heterozygosity across all the cattle populations conserved at National Gene Bank, ICAR-NBAGR. This statement can be validated by comparing the expected (0.650.01) and observed (0.720.01) heterozygosity across all the cattle population conserved.

In this study, a total of 267 alleles were identifed across all the 192 cattle bulls samples using 17 microsatellite markers (1.36 alleles/individual). However, previous studies revealed 1.2217, 1.2518, and 0.70710 alleles per individual in Indian cattle populations. The detection of a higher number of alleles per individual in conserved cattle bulls indicates that substantial amount of allelic variation is being maintained at National Gene Bank. Moreover, it is worth mentioning that smaller number of microsatellite primer pairs (17) were used for this study as compared to the previous studies, which again provides an indication towards existence of sufficient allelic variation in the conserved semen samples. Interestingly, ILSTS34 marker contributed highest number of alleles (26) in the selected individuals, which is well corroborated with the previous studies10,18.

In this study, we observed wide range of average observed number of alleles per locus, ranging from 2.2350.202 in Amritmahal to 8.6470.790 in Haryana cattle. This variation may be attributed to significant differences in the sample sizes of the conserved cattle populations at the National Gene Bank. Further, average observed number of alleles across all the populations and loci was 5.2760.145, and was lower than other research reports published elsewhere10,18,19. However, when comparing specific breeds, the allelic diversity in Sahiwal cattle (8.00.928) and Haryana cattle (8.6470.790) was found to be higher than what was previously reported in studies by Mukesh et al.17 and Sharma et al.10. At global level, less allelic diversity was observed across all the populations as compared to exotic breeds such as Burlina, Brown Swiss and Holstein Friesian cattle20. Additionally, lower value of effective number of alleles as compared to observed number of alleles across all the cattle populations suggested that there were many low frequency alleles in the populations. This reduced allelic diversity in the current scenario can be attributed to the smaller sample sizes per breed compared to previous studies. It is recommended that maximum allelic diversity be conserved in various Gene Banks established worldwide to ensure future sustainability.

The detection of a high level of observed heterozygosity (0.720.01) across all loci and populations in the conserved cattle bulls signifies a remarkable degree of genetic diversity. This can be attributed to a reduced influence of human-driven selection pressures and suggests the presence of large effective population sizes in the considered Indian cattle populations. The substantial genetic variation observed in Indian cattle breeds has likely contributed to their adaptability across diverse agroclimatic regions. This genetic diversity is likely a result of environmental pressures for adaptability and natural processes of mutation. The indigenous Indian cattle populations, managed according to local use and traditional husbandry practices, have shown no signs of inbreeding issues and have successfully maintained a higher level of genetic variability. This enhanced genetic diversity has played a crucial role in their superior adaptation to the natural environment. This genetic diversity can be well exploited for cattle genetic improvement as well as to facilitate rapid adaptation to changed breeding goals21. Genetic diversity is essential for any population to adapt and survive in their environments. It also facilitates local population or breed adaptation to dynamic environments. Further, leveraging high genetic diversity becomes crucial for expanding the genetic pool when a concerned breed or population confronts issues such as inbreeding and diminished genetic diversity, which in turn increases the risk of extinction.

The overall estimate of observed heterozygosity in the present investigation (0.720.01) was higher than previous investigations such as Tharparkar (0.643) and Rathi (0.694) cattle22, Kherigarh cattle19, and 15 other Indian cattle breeds23. Moreover, it was found higher than Indonesian cattle breeds24 Hartn del Valle, Angus, Brangus, Holstein, and Senepol cattle breeds in Colombia Montoya et al.25 and selected Ethiopian indigenous cattle26. An interesting observation was made in this study, wherein it was found that expected heterozygosity is either equal or less than observed heterozygosity in all the populations under investigation. It is worth mentioning that many studies explaining genetic diversity using microsatellite markers have found out less observed heterozygosity than expected heterozygosity10,17,20,22,27 except few28. This further confirms that a substantial level of genetic diversity is being effectively maintained in the conserved cattle bulls at the National Gene Bank, ICAR-NBAGR.

All cattle populations conserved at National Gene Bank revealed no heterozygote deficit except the Amritmahal cattle (0.058). These finding may be interpreted as cattle bulls conserved might be produced through outcrossing. Further, these results are well corroborated with the pattern expressed in estimates of heterozygosity and suggests lack of inbreeding in the conserved cattle bulls The National Gene Bank's long-term efforts in conserving cattle bulls have successfully preserved high levels of genetic diversity. In India, lack of structured breeding programme at the village level and not culling of cattle bulls may contribute to the maintenance of substantial genetic diversity within and between Indian cattle populations. In contrast, many Indian cattle populations have revealed significant homozygote excess in the previous study10,22. This heterozygote deficit might be due to collection of samples from closed herd or from sampling error.

Wrights F-statistics, and particularly FST, are valuable tools for understanding the evolutionary processes that shape the structure of genetic variation within and between populations, and they are among the most widely used descriptive statistics in population and evolutionary genetics. In population differentiation, a FST value greater than 0.15 is typically considered significant29. The highest FST value were found between Gir and Amritmahal cattle (0.185), Red Kandhari and Amritmahal (0.182), and Gangatiri and Amritmahal (0.176). This result revealed within-breed genetic variation is more than between-breed genetic variation. Further, this genetic variation could be well utilised for genetic upgradation and conservation of cattle populations in India. Further, the overall FST, F IT and FIS value across the loci and population is 0.1460.009, 0.0540.038, and 0.1050.035, respectively. These estimates obtained in the present investigation suggests lack of inbreeding in the conserved bull semen. However, these type of findings are rarely observed in natural conditions. Mostly, FIS would be positive and FIT>FST, this could be considered as evidence of inbreeding30. It is commonly hypothesized that in a population where mating occurs randomly, genes would exhibit equal levels of relatedness both within individuals and between individuals. In such conditions FIT equals FST or FIS equals zero22. Sodhi et al.22 reported F-statistics: FIS=0.1120.029, F IT=0.1690.033, F ST=0.0650.017, and interpreted departure of populations from random mating. In addition, across all the loci under investigation, FST ranged from 0.068 (ILSTS11) to 0.199 (ETH3) with an average of 0.146. This FST values revealed that the most of total allelic variation (85.4%) corresponds to differences among individuals, and only 14.5% genetic variation could be attributed to differences among breeds. Further, ETH3 (0.199), TGLA122 (0.195), MM8 (0.192), ILSTS06 (0.188), ETH10 (0.171), MM12 (0.161), BM1824 (0.156) markers might be considered as more informative to differentiate the populations under investigation. However, this statement need to be validated in large number of individuals of populations under study.

Link:
Deciphering genetic diversity in conserved cattle bulls to achieve sustainable development goals | Scientific Reports - Nature.com