MIM: an indirect method to assess inbreeding and coancestry in large incomplete pedigrees of selected dairy cattle

In real data, inbreeding is usually underestimated because of missing pedigree information. A method adapted to the dairy cattle situation is presented to approximate inbreeding when the stored population pedigree is incomplete. Missing parents in incomplete pedigrees were given a dummy identification and assigned to groups (up to nine for a given birth date of progeny). These groups were linked to contemporary reference groups with known parents. An explicit model considered that polygenic breeding values in a censored group were centred on a function of the average breeding value in the corresponding reference group and deviated independently. Inbreeding coefficients were obtained progressively over birth dates starting from founders. For each date considered, the parameters pertaining to its groups were computed using the parameters already obtained from groups belonging to the previous dates. The updating algorithms were given in detail. An indirect method was implemented to expedite mass computations of the relationship coefficients involved (MIM). MIM was compared to Van Raden's (VR) method using simulated populations with 20 overlapping generations and different rates of missing sires and dams. In the situation of random matings, the average inbreeding coefficients by date obtained by MIM were close to true values, whereas they were strongly underestimated by VR. In the situation of assortative matings, MIM gave average inbreeding coefficients moderately underestimated, whereas those of VR's method were still strongly underestimated. The main conclusion of this study adapted to the situation of dairy cattle with incomplete pedigrees was that corrections for inbreeding and coancestry coefficients are more efficient with an explicit appropriate genetic model than without.     

Impact of Fertility Variation on Gene Diversity and Drift in two Clonal Seed Orchards of Teak (Tectona grandis Linn. f.)

Two 25 year old teak clonal seed orchards comprising 15 (CSO-I) and 20 clones (CSO-II), respectively, selected mostly from moist forests of Western Ghats (latitude 10° N) in southern India, were evaluated for fertility, offspring diversity, and genetic drift. The orchards differed in fertility of clones as well as flower and fruit production per ramet. Fertility was highly skewed in CSO-II, where one clone (originating from higher latitude −17° N, in Eastern Ghats of peninsular India) produced 55% of the fruits and 68% of the flowers in the orchard, in contrast to a similar contribution from four most fertile clones in CSO-I. Fertility variation, measured as `sibling coefficient' (1.7 in CSO-I and 8.3 in CSO-II), was high in CSO-II resulting in high coancestry and low effective population size (3 times lower than CSO-I) in the seed crop. In CSO-I, 58% of the clones contributed effectively to seed production compared to only 12% effective contribution resulting in eight times higher genetic drift in CSO-II. Placing limits on how much seed can be collected per clone might be useful in restricting over representation of highly reproductive clones thereby increasing genetic diversity in the seed crop.     

Genetic variability in the endangered Asturcón pony assessed using genealogical and molecular information

The aim of this analysis is to assess the genetic diversity in the black-coated Asturcón pony population using genealogical and molecular methods in order to ascertain the possible impact of the inclusion of the bay Asturcón individuals on the breed's recovery programme. Pedigree information registered in the studbook of the black-coated Asturcón (including a total of 1080 individuals) was analysed. Additionally, 261 blood samples from the black-coated Asturcón individuals were obtained and genotyped for 15 microsatellites. Furthermore, 58 blood samples were obtained and genotyped from bay Asturcón individuals in order to place the results within the context of an unselected population with no known genealogies. The results indicated high losses of genetic representation of founders in the present population of black-coated Asturcón ponies. Roughly 60% and 30% of the founder stallion and dam lines, respectively, are lost in the present population. Average inbreeding was 4.7%. The equivalent number of founders and equivalent number of ancestors were 18.1 and 13. The most relevant founders and ancestors identified belonged to the three major studs involved in the recovery of the breed. However, the results highlight the dependence of the breed on the management of the government-run Cayón stud, which has increased its genetic contribution to the breed over time from 35.6% to 50.1%. At a molecular level, genetic variability assessed in the black-coated Asturcón was lower than that observed in the bay Asturcón. Expected heterozygosity, F_IS(m) and rarefacted average number of alleles per locus were 0.755 and 0.828, 4.1% and 1.3%, and 9.5 and 9.2, respectively, for the black-coated and bay Asturcón. The expected molecular coancestry in the black-coated Asturcón base population (Ef₀) took a value of 0.229, which was near to the molecular coancestry computed in the bay Asturcón (0.231). Implications of the reported results in the recovery programme of the Asturcón pony breed are discussed.     

Optimized management of genetic variability in selected pig populations

Controlling the increase of coancestry and inbreeding coefficients in selected populations is made possible through calculation of the optimal contributions allowed to breeding animals, given the current situation with regard to genetic diversity, and further, through optimal design of matings. The potential of such an approach for pig breeding was tested by retrospective optimization on the French Landrace population in reference to the matings actually carried out during a 21-week test period. The major constraint was that the average overall estimated breeding value (EBV) should be the same as the observed one, for not decreasing short-term genetic gain. Optimizing breeding allocations to boars would have led one to decrease coancestry and inbreeding coefficients by approximately 20%. This decrease would have even increased to approximately 30%, would have replacements and disposals been optimized after accounting for genetic variability, keeping the same constraint of genetic level identical to the observed one. These results showed the potential value, in the future, of completing each periodical calculation of EBVs by optimizations considering genetic variability and of releasing corresponding information to breeders, in order to enhance maintenance of genetic variability.