Microevolution of longan flowering behaviors from primitive characteristic to KClO3 induction is driven by artificial selection for agricultural benefit

Abstract

Dimocarpus longan is an economically important fruit tree primarily cultivated in various Asian countries and the Indochina region encompassing Thailand, China, Vietnam, Laos and Cambodia. Here, we report an extensive dataset of 606.72 Gb of the whole-genome resequencing data obtained from 31 Dimocarpus longan and 1 Dimocarpus obtusus samples performed on Illumina HiSeq PE150, providing the coverage over 30-fold of the reference genome (averaging 15 Gb per sample) with an addition of 12 longan accessions from China. A phylogenomic tree inferred from this analyzed dataset (19,270,513 SNPs) was constructed and results indicated that there are three separate monophyletic clades of China-USA (1), Thai (2) and Vietnam longan (3). Interestingly, however, Thai and Vietnam clades appear to be closely linked in genetic relationship based on analyses of karyotype, genomic data and certain morphological characteristics. De novo transcriptome assembly further revealed variations in gene sequences, divergent gene expression and candidate genes associated with different flowering behaviors. The greatest change in differential gene expression (51.87 %) observed between natural independent and seasonal flowering implied the microevolutionary shift observed in longan is influenced by artificial selection, resulting in gradual changes in flowering behaviors from natural independent flowering to artificial flowering induction using potassium chlorate (KClO₃). In summary, the data obtained from this study serves as the essential evidence for elucidating the microevolution of longan and shedding new light on an agronomical application of artificial flowering induction via modulation of KClO₃ responsive genes in longan or other fruits in the future.