Genome-wide SNP analysis reveals an increase in adaptive genetic
variation through selective breeding of coral
Abstract
Summer heat waves are the principal global driver of mortality in
reef-building corals. Resilience-based genetic management may increase
coral heat tolerance, but it is unclear how temperature responses are
regulated at a genomic level and thus how corals may adapt to warming
naturally or through selective breeding. Here we combine phenotypic,
pedigree, and genomic marker data from colonies sourced from a warm reef
on the Great Barrier Reef reproductively crossed with conspecific
colonies from a cooler reef to produce combinations of warm and cool
purebred and hybrid larvae and juveniles. Intra-population breeding
created significantly greater genetic diversity across the coral genome
and maintained diversity in key regions associated with heat tolerance
and fitness. High-density genome-wide scans of single nucleotide
polymorphisms (SNPs) identified alleles significantly associated with
offspring reared at 27.5°C (87 – 2,224 loci), including loci putatively
associated with proteins involved in responses to heat stress (cell
membrane formation, metabolism, and immune responses). Underlying
genetics explained 43% of PCoA variation in juvenile survival, growth,
and bleaching responses at 27.5°C and 31°C between the multilocus
genotypes. Genetic marker contribution to total variation in fitness
traits (narrow-sense heritability) were high for survival but not for
growth and bleaching in juveniles, with heritability of these traits
influenced more at 31°C relative to 27.5°C. Using only a limited number
of crosses, the mechanistic understanding presented here demonstrates
that allele frequencies are affected by one generation of selective
breeding, key information for the assessments of genetic intervention
feasibility and modelling of reef futures.