Originally published as Genetics Published Articles Ahead of Print on May 6, 2005.

Genetics, Vol. 170, 1313-1321, July 2005, Copyright © 2005
doi:10.1534/genetics.104.037325

Efficiency of the Use of Pedigree and Molecular Marker Information in Conservation Programs

Jesús Fernández^*,1, Beatriz Villanueva, Ricardo Pong-Wong and Miguel Ángel Toro^*

^* Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28040 Madrid, Spain
Sustainable Livestock Systems Group, Scottish Agricultural College, Edinburgh, EH9 3JG, United Kingdom
Genetics and Genomics, Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, United Kingdom

¹ Corresponding author: Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. A Coruña Km. 7,5, 28040 Madrid, Spain.
E-mail: jmj{at}inia.es

The value of molecular markers and pedigree records, separately or in combination, to assist in the management of conserved populations has been tested. The general strategy for managing the population was to optimize contributions of parents to the next generation for minimizing the global weighted coancestry. Strategies differed in the type of information used to compute global coancestries, the number and type of evaluated individuals, and the system of mating. Genealogical information proved to be very useful (at least for 10 generations of management) to arrange individuals' contributions via the minimization of global coancestry. In fact, the level of expected heterozygosity after 10 generations yielded by this strategy was 88–100% of the maximum possible improvement obtained if the genotype for all loci was known. Marker information was of very limited value if used alone. The amount and degree of polymorphism of markers to be used to compute molecular coancestry had to be high to mimic the performance of the strategy relying on pedigree, especially in the short term (for example, >10 markers per chromosome with 10 alleles each were needed if only the parents' genotype was available). When both sources of information are combined to calculate the coancestry conditional on markers, clear increases in effective population size (N_e) were found, but observed diversity levels (either gene or allelic diversity) in the early generations were quite similar to the ones obtained with pedigree alone. The advantage of including molecular information is greater when information is available on a greater number of individuals (offspring and parents vs. parents only). However, for realistic situations (i.e., large genomes) the benefits of using information on offspring are small. The same conclusions were reached when comparing the use of the different types of information (genealogical or/and molecular) to perform minimum coancestry matings.

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