Abstract
Complete pedigree information is a prerequisite for modern breeding and the ranking of parents and offspring for selection and deployment decisions. DNA fingerprinting and pedigree reconstruction can substitute for artificial matings, by allowing parentage delineation of naturally produced offspring. Here, we report on the efficacy of a breeding concept called “Breeding without Breeding” (BwB) that circumvents artificial matings, focusing instead on a subset of randomly sampled, maternally known but paternally unknown offspring to delineate their paternal parentage. We then generate the information needed to rank those offspring and their paternal parents, using a combination of complete (full-sib: FS) and incomplete (half-sib: HS) analyses of the constructed pedigrees. Using a random sample of wind-pollinated offspring from 15 females (seed donors), growing in a 41-parent western larch population, BwB is evaluated and compared to two commonly used testing methods that rely on either incomplete (maternal half-sib, open-pollinated: OP) or complete (FS) pedigree designs. BwB produced results superior to those from the incomplete design and virtually identical to those from the complete pedigree methods. The combined use of complete and incomplete pedigree information permitted evaluating all parents, both maternal and paternal, as well as all offspring, a result that could not have been accomplished with either the OP or FS methods alone. We also discuss the optimum experimental setting, in terms of the proportion of fingerprinted offspring, the size of the assembled maternal and paternal half-sib families, the role of external gene flow, and selfing, as well as the number of parents that could be realistically tested with BwB.
Highlights
Plant breeding, including tree improvement, typically follows the classical recurrent selection scheme, which is characterized by systematic and repetitive cycles of breeding, testing, and selection [1], [2]
To alleviate the efforts associated with generating offspring with complete pedigree information, for early generation testing, forest geneticists have adopted simplified protocols, ranging from those not requiring a pedigree
The concept of marker-assisted estimation of quantitative genetic parameters was introduced by Ritland [20], whereby traits’ heritabilities and the magnitude and direction of their genetic correlations are derived from regressing pair-wise phenotypic similarity on their corresponding pair-wise genetic relatedness
Summary
Plant breeding, including tree improvement, typically follows the classical recurrent selection scheme, which is characterized by systematic and repetitive cycles of breeding, testing, and selection [1], [2] These programs deal with multiple populations (e.g., base, breeding, and deployment) and large numbers of parents and offspring, planted over multiple sites and years, and requiring extensive monitoring and maintenance. Data analyses with incomplete pedigrees often require invoking and/or accepting untestable assumptions related to the genetic constitution of the tested families and the numbers of male parents involved in their formation, as well as their proportionate contributions Since these assumptions are not inordinately realistic in practice, the resulting genetic parameters and their associated inferences are often biased, leading to various degrees of inaccuracy and inefficiency [8]–[10]
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