ORAL PRESENTATION: Selective breeding produces multi-locus responses in adaptive genomic variation of lodgepole pine

Submitted by : Fady Bruno
Abstract type : Oral presentation
Session type : Conference session 3: CONSERVING and USING GENETIC DIVERSITY
Author Speaker : Ian MacLachlan

Information about other authors :

1 Department of Forest and Conservation Sciences, University of British Columbia, Canada, V6T 1Z4

2 Department of Biological Sciences, University of Calgary, 507 Campus Drive N.W., Calgary, Alberta, Canada, T2N 1N4

3 Department of Botany, University of British Columbia, Vancouver, Canada, V6T 1Z4.

4 Department of Ecosystem Science and Management, Texas A & M University, 2138 TAMU, College Station, TX 77843-2138, USA

*Corresponding Author: ian.maclachlan@alumni.ubc.ca

Abstract :

Climatic adaptation of temperate and boreal trees involves trade-offs between growth, phenology and tolerance to cold. Negative trade-offs among these traits have evolved in natural populations and can be exacerbated by selective breeding programs. Understanding the genomic basis of climatically adaptive traits and their trade-offs may allow efficient and precise adaptive genetic management strategies in response to shifting climates, and provide insights into the genomic architecture of adaptive traits.

               Our study combined seedling phenotypes (n = 2176)  for height growth, phenology and cold injury traits, genotype data for 18,600 SNPs from previous exome captures, and climatic data for 20 selectively bred and 105 wild-stand lodgepole pine seedlots sampled from across Alberta and British Columbia, Canada. GWAS was used to identify phenotype-associated SNPs of interest. We then quantified multi-locus effects of selective breeding at individual seedling and population levels by studying frequency changes in alleles associated with the greater trait value for each phenotype-associated SNP, which we termed ‘positive effect alleles’ (PEAs).

               There was substantial overlap among all traits in SNPs that had the strongest phenotypic associations, suggesting widespread pleiotropy is important to climatically adaptive trade-offs among traits despite their strongly contrasting genomic architectures. Selective breeding for increased height growth caused systematic PEA frequency increases within seedlings for SNPs associated with height, phenology and cold injury. Genomic responses to selective breeding varied substantially among regions of our sampled range and appear linked to differences in genomic architectures among traits. Modest amounts of multi-locus variation in breeding zone PEA frequencies was associated with strong phenotypic differences and climatic gradients for both natural and selectively bred seedlings, reinforcing the need for assisted gene flow to mitigate climatic maladaptation. Selectively bred seedlings had stronger phenotype-genotype relationships than natural seedlings among breeding zones for three of four traits, and for all the climate-genotype relationships, even though these differences were not statistically significant.

               Relationships among genotypes, phenotypes and climate were maintained or strengthened among the selective breeding programs we sampled, suggesting that among breeding zones the same assisted gene flow prescriptions are valid for both natural and selectively bred seedlings. Even so, the potential for trade-offs among traits due to substantial antagonistic pleiotropy was evident and should be carefully monitored as a potential source of climatic maladaptation in selectively bred seedlings. Our use of PEA frequencies demonstrated a simple, sensitive and effective method of summarizing genomic data for polygenic traits and detecting the effects of selective breeding on climatically adaptive genotypes that are relevant to breeding strategies and assisted gene flow policies.

Bibliografic references :

Keywords : Climatic adaptation, selective breeding, lodgepole pine, positive effect alleles, polygenic traits
: Pine_PEAShift_Histograms_BC-SouthvBC-Central_Nov11th2019.jpg 1.96 MB