IDENTIFICATION OF CANDIDATE RESISTANCE GENES IN POMEGRANATE (Punica granatum L.) AGAINST BACTERIAL BLIGHT CAUSED BY Xanthomonas axonopodis pv. punicae
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Date
2018-08
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University of Horticultural Sciences, Bagalkot (COLLEGE OF HORTICULTURE, BAGALKOT)
Abstract
Pomegranate (Punica granatum L.) has gained worldwide popularity because
of its highly nutritive and medicinal values. Bacterial blight caused by Xanthomonas
axonopodis pv. punicae (Xap) is impeding production of pomegranate with estimated
losses up to 80%. Breeding for bacterial blight resistant pomegranate varieties is
economically viable and sustainable approach for management of bacterial blight.
However, no genetic resistance sources are yet available and tolerant wild collections
(Nana and Daru) are burdened with undesirable agronomic traits like small fruit size,
high acidity and hard seed. For efficient utilization of wild accessions in breeding,
identification of candidate genes for bacterial blight resistance and the corresponding
bacterial effectors is crucial. The present study envisages screening of wild accessions
of pomegranate for bacterial blight resistance, identification of bacterial effectors in
Xap genomes and corresponding resistance gene analogues (RGAs) in pomegranate.
Bacterial type III effectors were predicted using pEffect and TAL effectors were
predicted using AnnoTALE suit. A total of 28 type III effectors and two TAL
effectors were identified in Xap genome and were validated. Pomegranate RGAs were
identified using RGAugury pipeline based on prediction of conserved motifs and
domains, using pomegranate genome sequence, 958 host R genes were identified
belonging to 277 nucleotide binding site (NBS) family proteins, 495 receptor-like
kinases (RLK) and 81 receptor-like protein (RLP) families. Digital differential
expression analysis of 958 RGAs using RNAseq data of bacterial blight tolerant
pomegranate accession (IC-524027) and susceptible ‘Bhagwa’ revealed differential
expression of 385 RGAs. Ten differentially expressed RGAs (fold change >5.0, 5
each of up-regulated and down regulated in tolerant) were further validated by semiquantitative
PCR reverse transcription (RT-PCR). However, no significant difference
in expression of RGAs was observed in RT-PCR between bacterial blight tolerant
(UHSP-1) and susceptible Bhagwa varieties of pomegranate. Further, these RGAs
have to be validated using more accurate quantitatjive real time PCR (qPCR). After
validation, potential R genes could be used in breeding for bacterial blight resistance
by marker assisted breeding, genetic engineering or genome editing.