A case study of Eucalyptus globulus fingerprinting

article

Ribeiro, M.M.A.

INRA/Springer

Ribeiro M.M.A., Sanchez L., Ribeiro C., Cunha F., Araújo J.A., Marques C.M., Borralho N.2011. A case study of Eucalyptus globulus fingerprinting for breeding. Annals of Forest Science 68 (4):701-714. DOI: 10.1007/s13595-011-0087-x

A case study of Eucalyptus globulus fingerprinting

Microsatellites
Eucalyptus globulus
Null alleles
Relatedness

2012-01-05T15:33:26Z
2012-01-05T15:33:26Z
2011

• Introduction Tree genetic improvement programs usually lack, in general, pedigree information. Since molecular markers can be used to estimate the level of genetic similarity between individuals, we genotyped a sample of a Portuguese Eucalyptus globulus breeding population—a reference population of 125 individuals—with 16 microsatellites (SSR). • Materials and methods Using genotypes from the reference population, we developed a simulation approach to recurrently generate (105 replicates) virtual offspring with different relatedness: selfed, half-sib, full-sib and unrelated individuals. Four commonly used pairwise similarity coefficients were tested on these groups of simulated offspring. Significant deficits in heterozygosity were found for some markers in the reference population, likely due to the presence of null alleles. Therefore, the impact of null alleles in the relatedness estimates was also studied. We conservatively assumed that all homozygotes in the reference population were carriers of null alleles. • Results All estimators were unbiased, but one of them was better adjusted to our data set, even when null alleles were considered. The estimator’s accuracy and precision were validated with individuals of known pedigree obtained from controlled crosses made with the same reference population’s parents. Additionally, a clustering algorithm based on the estimator of choice was constructed, in order to infer the relatedness among 24 E. globulus elite individuals. We detected four putatively related elite individuals’ pairs (six pairs considering the presence of null alleles). • Conclusions This work demonstrates that in the absence of pedigree information, our approach could be useful to identify relatives and minimize consanguinity in breeding populations.

openAccess

eng