Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops

For populations to maintain optimal fitness, harmful mutations must be
efficiently purged from the genome. Yet, under circumstances that diminish
the effectiveness of natural selection, such as the process of plant and
animal domestication, deleterious mutations are predicted to accumulate.
Here, we compared the load of deleterious mutations in 21 accessions from
natural populations and 19 domesticated accessions of the common sunflower
using whole-transcriptome single nucleotide polymorphism data. Although we
find that genetic diversity has been greatly reduced during domestication,
the remaining mutations were disproportionally biased toward nonsynonymous
substitutions. Bioinformatically predicted deleterious mutations affecting
protein function were especially strongly over-represented. We also
identify similar patterns in two other domesticated species of the
sunflower family (globe artichoke and cardoon), indicating that this
phenomenon is not due to idiosyncrasies of sunflower domestication or the
sunflower genome. Finally, we provide unequivocal evidence that
deleterious mutations accumulate in low recombining regions of the genome,
due to the reduced efficacy of purifying selection. These results
represent a conundrum for crop improvement efforts. Although the
elimination of harmful mutations should be a long-term goal of plant and
animal breeding programs, it will be difficult to weed them out because of
limited recombination.