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Article|15 Nov 2017|OPEN
Genome resequencing and transcriptome profiling reveal structural diversity and expression patterns of constitutive disease resistance genes in Huanglongbing-tolerant Poncirus trifoliata and its hybrids
Nidhi Rawat1 , Brajendra Kumar2 , Ute Albrecht3 , Dongliang Du4 , Ming Huang4 , Qibin Yu4 , Yi Zhang4 , Yong-Ping Duan5 , Kim D Bowman5 , Fred G Gmitter Jr4 and Zhanao Deng,1 ,
1University of Florida, IFAS, Gulf Coast Research and Education Center, Wimauma, FL, USA
2Ocimum BioSolutions Ltd., Royal Demeure, Plot no. 12/2, Sector- 1, HUDA Techno Enclave, Madhapur, Hyderabad, India
3University of Florida, IFAS, Southwest Florida Research and Education Center, Immokalee, FL, USA
4University of Florida, IFAS, Citrus Research and Education Center, Lake Alfred, FL, USA
5U.S. Horticultural Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Fort Pierce, FL, USA
*Corresponding author. E-mail: zdeng@ufl.edu

Horticulture Research 4,
Article number: 64 (2017)
doi: https://doi.org/10.1038/hortres.2017.64
Views: 755

Received: 26 Jul 2017
Revised: 06 Oct 2017
Accepted: 10 Oct 2017
Published online: 15 Nov 2017

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 P. 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 genomes, 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 upregulated in HLB-tolerant, Poncirus hybrids as revealed by real-time PCR analysis. These two CDR genes seem to be good candidate genes for future studies of their role in citrus-CLas interactions.