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A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives ( Artocarpus spp.)
Author(s) -
Laricchia Kristen M.,
Johnson Matthew G.,
Ragone Diane,
Williams Evelyn W.,
Zerega Nyree J. C.,
Wickett Norman J.
Publication year - 2018
Publication title -
american journal of botany
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.218
H-Index - 151
eISSN - 1537-2197
pISSN - 0002-9122
DOI - 10.1002/ajb2.1095
Subject(s) - biology , moraceae , domestication , transcriptome , artocarpus , gene , germplasm , selection (genetic algorithm) , botany , genetics , gene expression , artificial intelligence , computer science
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 3500 years ago. The goal of this research was 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 on carotenoid biosynthesis genes, which can impact the nutritional quality of the fruit. Key Results Over 1000 genes showed signals of positive selection, and these genes were enriched for localization to plastids. Nucleotide sites and individuals under positive selection were discovered in MADS ‐box genes and carotenoid biosynthesis genes, with several sites located in cofactor or DNA ‐binding domains. A McDonald–Kreitman test comparing wild to cultivated samples revealed selection in one of the carotenoid biosynthesis genes, abscisic acid 8′‐hydroxylase 3. Conclusions This research highlights some of the many genes that may have been intentionally or unintentionally selected for during the human‐mediated dispersal of breadfruit and stresses the importance of conserving a varied germplasm collection. It has revealed candidate genes for further study and produced new genomic resources for breadfruit.