Transcriptome Analysis of Domesticated Breadfruit and Its Wild Relatives

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Underutilized crops have the potential to economically benefit developing countries and to improve global food security. Breadfruit (Artocarpus altilis, Moraceae) is one such crop that can provide essential nutrients and requires relatively low-energy input to maintain compared to major crops. Humans have selected for many cultivars of breadfruit since its domestication began approximately 3,500 years ago. They selected for different traits and dispersed the new cultivars throughout the islands of Oceania as they migrated in an eastward direction from Melanesia to Polynesia and north into Micronesia. The goal of this research was to provide a better understanding of the genomic effects of the domestication process and, ultimately, to develop genomic resources that may facilitate the development of improved breadfruit cultivars in the future. In this study, a reference transcriptome of breadfruit was de novo assembled and characterized, and 24 transcriptomes of breadfruit and its wild relatives were analyzed to reveal genetic patterns correlated with the domestication gradient. This analysis suggested that signals of positive selection did not increase along a domestication gradient, but the presence of positive selection in certain genes varied according to ploidy level and taxon. In addition, over 1,000 genes were indicated as being driven by positive selection, many of which localized to plastids. Nucleotide sites and individuals under positive selection were also discovered in MADS-box genes and carotenoid biosynthesis genes. Overall, this research revealed several effects of the domestication process, provided candidate genes for further study, and produced new genomic resources for breadfruit.

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  • 12/01/2017
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