AUTHOR=Lu Xingyu , Lü Peitao , Liu Hao , Chen Houbin , Pan Xifen , Liu Pengxu , Feng Lei , Zhong Silin , Zhou Biyan 

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

JOURNAL=Frontiers in Plant Science

VOLUME=Volume 13 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.819188

DOI=10.3389/fpls.2022.819188

ISSN=1664-462X

ABSTRACT=Litchi is an important Sapindaceae fruit tree. Flowering in litchi is triggered by low 
19 temperatures in autumn and winter. It can be divided into early-, medium-, and late-flowering 
20 phenotypes according to the time for floral induction. Early-flowering varieties need low 
21 chilling accumulation level for floral induction, while the late-flowering varieties require high 
22 chilling accumulation level. In the present study, RNA-Seq of the 87 accessions was 
23 performed and transcriptome-based genome-wide association studies (GWAS) was used to 
24 identify candidate genes involved in chilling accumulation underlying the time for floral 
25 induction. 98155 high-quality single-nucleotide polymorphism (SNP) sites were obtained.
26 1411 significantly associated SNPs and 1115 associated genes (AGs) were identified, of 
27 which 31 were flowering-related, 23 were hormone synthesis-related, and 27 were hormone 
28 signal transduction-related. Association analysis between gene expression of the AGs and the 
29 flowering phenotypic data was carried out, and differentially expressed genes (DEGs) in a
30 temperature-controlled experiment were obtained. As a result, 15 flowering-related candidate 
31 associated genes (CAGs), 13 hormone synthesis-related CAGs, and 11 hormone signal 
32 transduction-related CAGs were further screened. The expression levels of the CAGs in the 
33 early-flowering accessions were different from those in the late-flowering ones, and also 
34 between the flowering trees and non-flowering trees. In a gradient chilling treatment,
35 flowering rates of the trees and the CAGs expression were affected by the treatment. Our 
36 present work for the first time provided candidate genes for genetic regulation of flowering in 
37 litchi using transcriptome-based GWAS.