Determination of paternal and maternal parentage in lodgepole pine seed: full versus partial pedigree reconstruction

Estimating seed orchards' maternal and paternal gametic contributions is of importance in assessing the genetic quality of seed crops. The advantage of full over partial pedigree reconstruction in investigating the mating dynamics in a lodgepole pine (Pinus contorta Dougl. ex. Loud. ssp. latifolia Engelm.) seed orchard population (N = 74) was demonstrated using nuclear and chloroplast microsatellite markers. We analyzed offspring of equivalent sample sizes representing full (bulk seed with unknown maternal and paternal parentage (n = 635)) and partial (11 maternal family arrays (n = 619)) pedigree reconstruction methods. Small differences in selfing rate, gene flow, and male reproductive success were observed between the two methods; however, the full pedigree reconstruction enabled simultaneous estimation of female-related fertility parameters (female reproductive success and effective number of maternal parents) that partial pedigree reconstruction could not provide. The use of bulk random sample of seed from orchards' crops is recommended when male and female fertility parameters, as well as selfing and contamination rates, are needed for seed orchards' seed crops genetic rating.