Assessment of genetic diversity and conservation priority of Omani local chickens using microsatellite markers

Abstract

Designing strategies for conservation and improvement livestock should be based on assessment of genetic characteristics of populations under consideration. In Oman, conservation programs for local livestock breeds have been started. The current study assessed the genetic diversity and conservation potential of local chickens from Oman. Twenty-nine microsatellite markers were analyzed in 158 birds from six agroecological zones: Batinah, Dhofar, North Hajar, East Hajar, Musandam, and East Coast. Overall, a total of 217 alleles were observed. Across populations, the average number of alleles per locus was 7.48 and ranged from 2 (MCW98 and MCW103) to 20 (LEI094). The mean expected heterozygosity (H _E) was 0.62. Average fixation index among populations (F _ST) was 0.034, indicating low population differentiation, while the mean global deficit of heterozygotes across populations (F _IT) was 0.159. Based on Nei’s genetic distance, a neighbor-joining tree was constructed for the populations, which clearly identified the Dhofar population as the most distant one of the Omani chicken populations. The analysis of conservation priorities identified Dhofar and Musandam populations as the ones that largely contribute to the maximal genetic diversity of the Omani chicken gene pool.

Appendix 1: parameters and formulas used for conservation analyses

To assess conservation priorities, two methods were used as described by Caballero and Toro (2002). For the first method, for each population i, the global genetic diversity GD_tli is calculated excluding this population, then the loss of genetic diversity (L _GD ) is calculated as follows:

$$ {L}_{\mathrm{GD}}=\left(\left({\mathrm{GD}}_{\mathrm{t}}-{\mathrm{GD}}_{\mathrm{t}\mathrm{l}i}\right)/{\mathrm{GD}}_{\mathrm{t}}\right)\times 100 $$

(1)

where GD_t is the total genetic diversity, GD_tli the global genetic diversity after removing population i, and L _GD the loss of genetic diversity.

Therefore, the higher the contribution of a population to the global genetic diversity is, the higher will be the decrease of genetic diversity when that population is excluded from the analysis. Negative values indicate that global genetic diversity is increased when that population is excluded.

For the second method, the contribution that a population i will add to a pool with maximum genetic diversity (GD_pool) could be achieved by obtaining the values of c _i that maximize GD_pool as follows:

$$ \mathrm{GDpool}=1-{{\displaystyle \sum}}_{i=1}^n{c}_i\left\lfloor {f}_{ii}-{{\displaystyle \sum}}_{j=1}^n{D}_{ij}{c}_j\right\rfloor $$

(2)

where c _i is restricted to c ≥ 0 and ∑  ⁿ _i = 1 c _i  = 1 with n being the number of populations, f _ii the coancestry coefficient within population i, and D _ij Nei’s minimum distance between population i and j (Caballero and Toro 2002).