A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.)

PREMISE OF THE STUDY: Underutilized crops, such as breadfruit (Artocarpus altilis, Moraceae) have the potential to improve global food security. Humans have artificially selected many cultivars of breadfruit since its domestication began approximately 3,500 years ago. The goal of this research is to identify transcriptomic signals of positive selection and to develop genomic resources that may facilitate the development of improved breadfruit cultivars in the future.
METHODS: A reference transcriptome of breadfruit was assembled de novo and annotated. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that may have resulted from local adaptation or natural selection. Emphasis was placed on MADS-box genes, which are important because they often regulate fruiting timing and structures, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.
KEY RESULTS: Over 1,000 genes sh...