QTLs and eQTLs mapping related to citrandarins’ resistance to citrus gummosis disease

Abstract

BackgroundPhytophthora nicotianae Breda de Haan (Phytophthora parasitica Dastur) causes severe damage to citrus crops worldwide. A population of citrandarins was created from the cross between the susceptible parent Citrus sunki Hort. Ex Tan. and the resistant parent Poncirus trifoliata (L.) Raf. cv. Rubidoux, both parents and two reference rootstocks (Rangpur lime and Swingle citrumelo) were grafted in a greenhouse on Rangpur lime. Inoculations were performed at 10 cm and 15 cm above the grafting region and the resulting lesions were evaluated by measuring the lesion length 60 days after inoculation. As control, non-inoculated plants of each genotype were used. In addition, we evaluated the expression of 19 candidate genes involved in citrus defense response 48 h after pathogen infection by quantitative Real-Time PCR (qPCR). We mapped genomic regions of Quantitative Trait Loci (QTLs) and Expression Quantitative Trait Loci (eQTLs) associated with resistance to P. parasitica in the linkage groups (LGs) of the previously constructed maps of C. sunki and P. trifoliata.ResultsWe found disease severity differences among the generated hybrids, with lesion lengths varying from 1.15 to 11.13 mm. The heritability of the character was 65%. These results indicate that there is a great possibility of success in the selection of resistant hybrids within this experiment. The analysis of gene expression profile demonstrated a great variation of responses regarding the activation of plant defense pathways, indicating that citrandarins have several defense strategies to control oomycete infection. The information of the phenotypic and gene expression data made possible to detect genomic regions associated with resistance. Three QTLs and 84 eQTLs were detected in the linkage map of P. trifoliata, while one QTL and 110 eQTLs were detected in C. sunki.ConclusionsThis is the first study to use eQTLs mapping in the Phytophthora-citrus interaction. Our results from the QTLs and eQTLs mapping allow us to conclude that the resistance of some citrandarins to the infection by P. parasitica is due to a favorable combination of QTLs and eQTLs transmitted by both parents.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4888-2) contains supplementary material, which is available to authorized users.

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

“…It was expected that a large number of eQTL would be found in the gene expression profiles for each candidate gene because we observed high heritability of the phenotypic characteristics and high saturation of the maps for each parent according to Curtolo et al (2018); in addition, the population of hybrids selected for eQTL mapping consisted of 72 individuals. We found In parentheses is the position from the beginning in cM CARBOX and MEX1 NAC2 and PP2B10 10 CARBOX, GLUC, GALAC, BAM3 and PP2B10 -a higher number of eQTL per gene for C. sunki (six) than for P. trifoliata (four), consistent with the results of Lima et al (2018). The UDP gene presented the highest number of eQTL (six) on the map of the P. trifoliata genitor, while in the C. sunki map, a greater number, seven eQTL, were found for the CARBOX gene.…”

“…The second one was the logistic regression for categorical traits which was slight superior than regression interval mapping but this difference reduces as the sample size increases and the distribution is symmetric. The sample size used in this work is consistent with the literature (Lima et al 2018), especially dealing with a perennial crop. Considering the aspects present by Rebaï (1997) and Li et al (2006), we chose to assume normality as a starting point for revealing information about related traits to HBL disease, once results are not frequent in literature.…”

“…According to Anderson et al (2007), many QTL mapping studies detect few loci with moderate R 2 values, while several other loci with small effects are found, similar to the findings of the present study. Lima et al (2018) mapped QTL associated with resistance to P. parasitica, the causative agent of citrus gummosis, in the same population of citrandarins and also found few loci with moderate R 2 values and many with small effects.…”

“…Two treatments were considered in the study: plants inoculated with CLas (infected group) and mock-inoculated (control group). Relative amounts, expression levels, fold change values and the stability of expression of endogenous genes were determined according to Lima et al (2018). The amplification efficiency and Ct data were calculated for each qPCR reaction using Real-time PCR Miner software (Zhao and Fernald 2005).…”

“…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).…”