Identification of Chilling Accumulation-Associated Genes for Litchi Flowering by Transcriptome-Based Genome-Wide Association Studies.

Litchi is an important Sapindaceae fruit tree. Flowering in litchi is triggered by low temperatures in autumn and winter. It can be divided into early-, medium-, and late-flowering phenotypes according to the time for floral induction. Early-flowering varieties need low chilling accumulation level for floral induction, whereas the late-flowering varieties require high chilling accumulation level. In the present study, RNA-Seq of 87 accessions was performed and transcriptome-based genome-wide association studies (GWAS) was used to identify candidate genes involved in chilling accumulation underlying the time for floral induction. A total of 98,155 high-quality single-nucleotide polymorphism (SNP) sites were obtained. A total of 1,411 significantly associated SNPs and 1,115 associated genes (AGs) were identified, of which 31 were flowering-related, 23 were hormone synthesis-related, and 27 were hormone signal transduction-related. Association analysis between the gene expression of the AGs and the flowering phenotypic data was carried out, and differentially expressed genes (DEGs) in a temperature-controlled experiment were obtained. As a result, 15 flowering-related candidate AGs (CAGs), 13 hormone synthesis-related CAGs, and 11 hormone signal transduction-related CAGs were further screened. The expression levels of the CAGs in the early-flowering accessions were different from those in the late-flowering ones, and also between the flowering trees and non-flowering trees. In a gradient chilling treatment, flowering rates of the trees and the CAGs expression were affected by the treatment. Our present work for the first time provided candidate genes for genetic regulation of flowering in litchi using transcriptome-based GWAS.

Identification of Genes Involved in Low Temperature-Induced Senescence of Panicle Leaf in Litchi chinensis.

Warm winters and hot springs may promote panicle leaf growing and repress floral development. To identify genes potentially involved in litchi panicle leaf senescence, eight RNA-sequencing (RNA-Seq) libraries of the senescing panicle leaves under low temperature (LT) conditions and the developing panicle leaves under high temperature (HT) conditions were constructed. For each library, 4.78⁻8.99 × 106 clean reads were generated. Digital expression of the genes was compared between the senescing and developing panicle leaves. A total of 6477 upregulated differentially expressed genes (DEGs) (from developing leaves to senescing leaves), and 6318 downregulated DEGs were identified, 158 abscisic acid (ABA)-, 68 ethylene-, 107 indole-3-acetic acid (IAA)-, 27 gibberellic acid (GA)-, 68 cytokinin (CTK)-, 37 salicylic acid (SA)-, and 23 brassinolide (BR)-related DEGs. Confirmation of the RNA-Seq data by quantitative real-time PCR (qRT-PCR) analysis suggested that expression trends of the 10 candidate genes using qRT-PCR were similar to those revealed by RNA-Seq, and a significantly positive correlation between the obtained data from qRT-PCR and RNA-Seq were found, indicating the reliability of our RNA-Seq data. The present studies provided potential genes for the future molecular breeding of new cultivars that can induce panicle leaf senescence and reduce floral abortion under warm climates.