Increasing Breeding without Breeding (BwB) Efficiency: Full- vs. Partial-Pedigree Reconstruction in Lodgepole Pine

Abstract

The advantage of paternity assignment in assembling structured pedigree for breeding is investigated using two sampling methods; namely, family array (known maternal parent) and random offspring (unknown maternal and paternal parents) collected from an open- pollinated lodgepole pine experimental population with known parents (N = 74) using nuclear and chloroplast microsatellite markers. Offspring of equivalent sample sizes representing the family array (n = 619) and random offspring (n = 635) were genotyped and subjected to partial and full pedigree reconstruction, respectively. The full pedigree reconstruction assembled substantially larger number of full-sib families than the partial (446 vs. 268) and interestingly the two methods detected equivalent amount of external gene flow to the experimental population. The superiority of the random offspring over the family array sampling in producing more full-sib families was attributed to its better representation of the parental population, as random sampling included offspring from most parents as compared to the parent-limited family array. Owing to the observed advantages, the full pedigree reconstruction could be employed as an alternative to the breeding phase commonly required in conventional breeding programs for the development of structured pedigree needed for genetic parameters estimation.