Abstract
Accurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains. We used SNP genotyping to characterize founder trees, five bulk seed orchard seedlots, and trees from progeny trials to assess pollen contamination and the impact of severe roguing on genetic diversity and parental contributions in a first-generation open-pollinated white spruce clonal seed orchard. After severe roguing (eliminating 65% of the seed orchard trees), we found a slight reduction in the Shannon Index and a slightly negative inbreeding coefficient, but a sharp decrease in effective population size (eightfold) concomitant with sharp increase in coancestry (eightfold). Pedigree reconstruction showed unequal parental contributions across years with pollen contamination levels between 12 and 51% (average 27%) among seedlots, and 7–68% (average 30%) among individual genotypes within a seedlot. These contamination levels were not correlated with estimates obtained using pollen flight traps. Levels of pollen contamination also showed a Pearson’s correlation of 0.92 with wind direction, likely from a pollen source 1 km away from the orchard under study. The achievement of 5% genetic gain in height at rotation through eliminating two-thirds of the orchard thus generated a loss in genetic diversity as determined by the reduction in effective population size. The use of genomic profiles revealed the considerable impact of roguing on genetic diversity, and pedigree reconstruction of full-sib families showed the unanticipated impact of pollen contamination from a previously unconsidered source.
Highlights
Accurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains
As typically observed in many tree improvement programs, orchard managers use the number of cones, seeds and pollen produced in orchards to estimate diversity parameters, parental contributions and pollen contamination to obtain government approvals for the genetic gain and genetic diversity of reforestation s tock[7,8]
The specific goals of the project were to: (1) evaluate the impact of a severe roguing on the effective population size and other diversity parameters of orchard seedlots produced in different years; (2) assess the imbalance of contributions among parents before and after severe roguing; (3) through pedigree reconstruction, obtain precise estimates of pollen contamination levels of seed orchard seedlots and families from a progeny trial associated with the breeding program; and (4) compare the methods used to estimate the effective population size and levels of pollen contamination
Summary
Accurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains. As typically observed in many tree improvement programs, orchard managers use the number of cones, seeds and pollen produced in orchards to estimate diversity parameters, parental contributions and pollen contamination to obtain government approvals for the genetic gain and genetic diversity of reforestation s tock[7,8]. Tree improvement programs often have little to no strategy for pollen management using silvicultural practices, since local orchard pollen production is believed to be sufficient to both swamp pollen from external sources and account for the high seed yields found during mast years in white spruce[15] These assumptions appear to be underestimating the impact of contamination on the genetic worth of the production seedlots we studied. In white spruce, such genotyping approaches have enhanced the evaluation of allelic diversity in selected seedlots from seed orchards compared to natural populations[24] and allowed for pedigree reconstruction[25], genomic selection[17,26], and traceability in breeding and propagation operations[27]
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