Expression Quantitative Trait Loci Analysis of Carotenoid Metabolism-related Genes in Citrus

Abstract

The expression profiles of carotenoid metabolism pathway genes are one of the important factors that regulate carotenoid content and composition in the fruit of Citrus cultivars. To identify regulatory factors of gene expressions in the carotenoid pathway, expression quantitative trait loci (eQTL) analysis was applied using a hybrid population. In the analyzed population, significant eQTLs for phytoene synthase (PSY), phytoene desaturase (PDS), z-carotene desaturase (ZDS), b-ring hydroxylase (HYb), and zeaxanthin epoxidase (ZEP) were detected. Among these eQTLs, eQTLs for HYb and ZEP were located on their responsible gene loci, respectively. This result indicates that the expression level of HYb and ZEP was influenced by cis-elements in their up-stream regions. Conversely, eQTLs for PDS and ZDS were located in different loci from those of the responsible genes, indicating that the loci were trans-regulating factors. It also suggested that expression levels of PDS and ZDS were regulated by a common transcription factor because their eQTLs were co-localized. Significant eQTL of lycopene b-cyclase (LCYb) and 9-cis-epoxycarotenoid dioxygenase (NCED) were not detected in this population. The major factors to control gene expression depend on each carotenoid metabolism gene, and their combination might cause complex carotenoid metabolism and extend the variation of content and composition in citrus varieties. eQTL analysis was demonstrated as a powerful tool to identify cis-or trans-regulation for carotenoid metabolism genes, as well as in generating functionally defined markers for marker-assisted selection to increase the carotenoid content of citrus in breeding programs.

Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch]

“…Therefore, in order to determine candidate genes related to targeted traits, transcript abundances had been used as quantitative trait data in the QTL analysis (Druka et al, 2010; Galpaz et al, 2018; García-Gómez et al, 2019). Multiple authors have noted the usefulness of gene expression analysis based on qPCR for the experimental validation of QTLs in fruit crops (Huang et al, 2014; Sugiyama et al, 2014; García-Gómez et al, 2019), confirming the correlation between genotype and gene expression levels (Conesa et al, 2016).…”

QTL and eQTL mapping associated with host response to Candidatus Liberibacter asiaticus in citrandarins

“…Comparing the eQTL obtained based on the relative expression data of the target genes and the QTL of the starch quantification in the inoculated group and CLas quantification (Ct values), it was expected that some eQTL would contribute to the phenotypes. This was evidenced by the finding of overlaps between eQTL and QTL, indicating the existence of complex regulatory networks for both gene expression and phenotype (Sugiyama et al 2014;Lima et al 2018). It was observed that the positions in cM from the beginning of the overlapping eQTL/QTL were fairly close, with some exceptions showing a relatively large distance; QTL usually cover large regions of the genome (at least 20 cM) (Gion et al 2000;Brown et al 2003;Lima et al 2018).…”

“…The co-localization of eQTL and QTL represents the association between the allelic state of genomic regions with the quantification of gene transcripts within QTL involved in the variation of phenotypic characteristics (Sugiyama et al 2014;Lima et al 2018). With the exception of the T6PP and BAC2 genes, all of the genes presented eQTL co-located with QTL, independent of the map and the phenotypic characteristics (CLas or starch quantification).…”

“…Jansen and Nap (2001) proposed genomic genetics as a technique in which mapping of quantitative loci and gene expression analysis is used to identify the association between the allelic status of a genome region and the levels of gene transcripts. In citrus, a few eQTL mapping studies have been conducted, including studies of carotenoid metabolism (Sugiyama et al 2014) and resistance to Phytophthora nicotianae Breda de Haan (Phytophthora parasitica Dastur) in a population of C. sunki and P. trifoliata hybrids (Lima et al 2018).…”

Molecular Basis of Carotenoid Accumulation in Horticultural Crops

“…Various QTLs for other carotenoid components were also detected, but most of them expressed low LOD values. Sugiyama et al (2014) extended the study to compare the genetic locus and expression QTL (eQTL) of carotenoid metabolic genes using AG population. Firstly, genetic loci of the major carotenoid metabolic genes were mapped as follows: PSY on linkage group (LG)-4, PDS on LG-3, ZDS on LG-9, CHYB on LG-3, and ZEP on LG-2.…”