Computational protocol: Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers

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Protocol publication

[…] Estimates of within-breed genetic diversity were obtained with GENETIX 4.05.2 software [], namely observed (Ho) and unbiased expected (He) heterozygosities, mean number of alleles (MNA) per breed and geographical breed group. This software was also used to estimate F statistics according to Weir and Cockerham []. Allelic richness (Rt) over all loci per breed was calculated with FSTAT v. 2.9.3 software [].Analysis of conservation priorities depends on how the metapopulation is defined to investigate partial contributions to global genetic diversity. Also, breed prioritization will vary considerably according to the relative importance of the within- and between-breed components of genetic diversity in each breed and to the genetic relationships among breeds. Given the extensive collection of cattle specimens available for this study and for the sake of simplicity, we took into consideration two dimensions that were analyzed separately i.e., (1) the 27 Creole cattle populations and (2) the 13 major geographical breed groups defined above. From the perspective of practical applications, we chose to consider geographical breed groups with their specificities, rather than the complete worldwide distribution of cattle included in a single metapopulation.For the conservation analyses, we followed the methods described by Cañon et al. [] and outlined below. For a better understanding of the statistical procedures involved, we categorized the different approaches as follows: methods that aim at minimizing the overall kinship coefficient of the metapopulation (kinship-based methods), a method that reflects only the between-breed diversity component (Weitzman approach) and combined approaches that take into consideration both the within- and between-breed components of global genetic diversity. [...] We applied the Core Set methods of Eding et al. [] to investigate the population contributions to global diversity that account for within- and between-breed kinship coefficients by minimizing the overall kinship coefficient of the metapopulation considered and eliminating the genetic overlap between breeds in the core set []. Estimation of possible negative contributions by a given population is avoided through an iterative process that gives the lowest value a zero and recalculates the contributions after removal of the population.In the absence of genealogical data, kinships were estimated from molecular data with different methods: (1) marker-estimated kinships (MEK) obtained from individual genotypes, as described by Eding and Meuwissen []; (2) a variation of the MEK method based on log-linear regressions [] obtained with the weighted log-linear model (WLM); (3) same as (2) but the log-linear regressions were obtained with the mixed model (WLMM); and (4) average molecular coancestries (fm) based on allele frequencies []. MEK were estimated with a macro function in Excel [], whereas the solutions for WLM and WLMM were obtained with matrices built with the MATLAB® software (The MathWorks, Inc., USA). Average coancestry coefficients within (fii) and between (fij) each Creole breed and geographical breed group were calculated with the MOLKIN3 software []. Analyses of conservation priorities based on these similarity matrices (MEK, WLM, WLMM and fm) were carried-out with a FORTRAN program developed and kindly shared by Eding and Meuwissen.We derived pairwise kinship distances from the MEK coefficients following Eding et al. [] as: d(i, j) = fii + fjj - 2fij. Kinship genetic distances were used to construct the neighbor-net phylogenies of the Creole breeds and geographical breed groups with the SPLITS TREE4 4.12.6 software []. Genetic relationships were used to classify the Creole breeds and groups of breeds- and then to build contour plots of kinship coefficients (MEK and fm) with the MATLAB® software (The MathWorks, Inc., USA).In order to assess within-breed genetic diversity directly, the partial contributions of each Creole breed and each geographical breed group were also calculated as the proportional variation in expected heterozygosity of the metapopulation after removal of each breed or breed group (PCHe). […]

Pipeline specifications

Software tools GENETIX, Molkin
Applications Phylogenetics, Population genetic analysis
Organisms Bos taurus, Bos indicus
Diseases Genetic Diseases, Inborn