Journal
TREE GENETICS & GENOMES
Volume 10, Issue 2, Pages 241-249Publisher
SPRINGER HEIDELBERG
DOI: 10.1007/s11295-013-0673-1
Keywords
Pedigree-free model; Pedigree reconstruction; Marker-based pair-wise relationship; Genetic parameter estimates; Open-pollinated families; SSR; Larix occidentalis
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Funding
- Natural Sciences and Engineering Research Council of Canada
- Johnson's Family Forest Biotechnology Endowment
- National Agency for Agricultural Research (NAZV) [QJ1320013]
- Ministry of Education, Youth and Sports (KONTAKT II) [LH13021]
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The availability and affordability of genetic markers made it possible to estimate quantitative genetic parameters without mating designs' structured pedigree. Here, we compared 4-year height's heritability and individuals' breeding values for a western larch common-garden population of 1,418 offspring representing 15 open-pollinated families from a 41-clone seed orchard using (a) classical pedigree models such as half- and full-sib families and (b) a molecular marker-based pedigree-free model using four pair-wise relationship estimation methods using eight informative SSR markers. The results highlighted the commonly observed inflated estimates of genetic parameters often obtained from half-sib analyses, as well as demonstrating some of the full-sib analyses' caveats. The pedigree reconstruction permitted the identification of selfed individuals, thus allowing evaluating the impact of selfing on marker-based genetic parameter estimation. The results demonstrated the utility of marker-based methods as an alternative to the classical pedigree-based approaches. Unlike the pedigree-based methods, the marker-based approach allowed better partitioning the variance components as well as separating the non-additive and additive genetic variance. The theoretical underpinning of the marker-based approach was discussed.
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