Genome resequencing and transcriptome profiling reveal structural diversity and expression patterns of constitutive disease resistance genes in Huanglongbing-tolerant Poncirus trifoliata and its hybrids

Authors: DENG, Z. - Gulf Coast Research Laboratory; RAWAT, N. - Gulf Coast Research Laboratory; KUMAR, B. - Osmania University; ALBRECHT, UTE - Southwest Florida Research And Education Center; DU, D. - University Of Florida; HUANG, M. - University Of Florida; YU, Q. - University Of Florida; ZHANG, Y. - University Of Florida; Duan, Ping; Bowman, Kim; GMITTER, F. - University Of Florida

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/10/2017
Publication Date: 11/15/2017
Citation: Deng, Z., Rawat, N., Kumar, B., Albrecht, U., Du, D., Huang, M., Yu, Q., Zhang, Y., Duan, Y., Bowman, K.D., Gmitter, F. 2017. Genome resequencing and transcriptome profiling reveal structural diversity and expression patterns of constitutive disease resistance genes in Huanglongbing-tolerant Poncirus trifoliata and its hybrids. Horticulture Research. 4:17064. https://doi.org/10.1038/hortes.2017.64.
DOI: https://doi.org/10.1038/hortes.2017.64

Interpretive Summary: Huanglongbing (HLB) is the most destructive disease of citrus worldwide, and threatens all United States citrus production areas. Most citrus is severely damaged by HLB, but the trifoliate orange and some of its hybrids with citrus are tolerant to the disease. A class of disease resistance genes, designated as constitutive disease resistance (CDR) genes, were identified as being expressed in HLB-tolerant hybrids and are examined in more detail in this study. Eight individual CDR genes were identified in the trifoliate orange, and two of these genes, PtCDR2 and PtCDR8, were revealed to become especially active in the HLB-tolerant hybrids following inoculation with HLB. The findings on these two CDR genes warrant further studies on their roles in HLB disease development.

Technical Abstract: Huanglongbing (HLB) is the most destructive bacterial disease of citrus worldwide. While most citrus varieties are susceptible to HLB, Poncirus trifoliata, a close relative of Citrus, and some of its hybrids with Citrus are tolerant to HLB. No specific HLB tolerance genes have been identified in Poncirus trifoliata but recent studies have shown that constitutive disease resistance (CDR) genes were expressed at much higher levels in HLB-tolerant Poncirus hybrids and the expression of CDR genes was modulated by Candidatus Liberibacter asiaticus (CLas), the pathogen of HLB. The current study was undertaken to mine and characterize the CDR gene family in Citrus and Poncirus and to understand its association with HLB tolerance in Poncirus. We identified 17 CDR genes in two citrus genome databases, deduced their structures, and investigated their phylogenetic relationships. We revealed that the expansion of the CDR family in Citrus seems to be due to segmental and tandem duplication events. Through genome resequencing and transcriptome sequencing, we identified eight CDR genes in the Poncirus genome (PtCDR1-PtCDR8). The number of SNPs was the highest in PtCDR2 and the lowest in PtCDR7. Most of the deletion and insertion events were observed in the UTR regions of Citrus and Poncirus CDR genes. PtCDR2 and PtCDR8 were in abundance in the leaf transcriptomes of two HLB-tolerant Poncirus genotypes and were also up-regulated in HLB-tolerant Poncirus hybrids as revealed by real-time PCR analysis. The findings on these two CDR genes warrant further studies on their roles in citrus-CLas interactions.