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Genetic diversity analysis in a set of Caricaceae accessions using resistance gene analogues

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Title Genetic diversity analysis in a set of Caricaceae accessions using resistance gene analogues
 
Creator Sengupta, Samik
Das, Basabdatta
Acharyya, Pinaki
Prasad, Manoj
Ghose, Tapas Kumar
 
Subject Carica papaya
Vasconcellea sp
DNA homologues
Rice BLB genes
 
Description Accepted date: 24 November 2014
Background: In order to assess genetic diversity of a set of 41 Caricaceae accessions, this study used 34 primer
pairs designed from the conserved domains of bacterial leaf blight resistance genes from rice, in a PCR based
approach, to identify and analyse resistance gene analogues from various accessions of Carica papaya, Vasconcellea
goudotiana, V. microcarpa, V. parviflora, V. pubescens, V. stipulata and, V. quercifolia and Jacaratia spinosa.
Results: Of the 34 primer pairs fourteen gave amplification products. A total of 115 alleles were identified from 41
accesions along with 12 rare and 11 null alleles. The number of alleles per primer pair ranged from 4 to 10 with an
average of 8.21 alleles/ primer pair. The average polymorphism information content value was 0.75/primer. The
primers for the gene Xa1 did not give any amplification product. As a group, the Indian Carica papaya accessions
produced a total of 102 alleles from 27 accessions. The similarity among the 41 accessions ranged from 1% to 53%.
The dendrogram made from Jaccard’s genetic similarity coefficient generated two major clusters showing that the
alleles of Jacaratia spinosa and Vasconcellea accessions were distinctly different from those of Carica papaya
accessions. All the alleles were sequenced and eleven of them were allotted accession numbers by NCBI. Homology
searches identified similarity to rice BLB resistance genes and pseudogenes. Conserved domain searches identified
gamma subunit of transcription initiation factor IIA (TFIIA), cytochrome P450, signaling domain of methyl-accepting
chemotaxis protein (MCP), Nickel hydrogenase and leucine rich repeats (LRR) within the sequenced RGAs.
Conclusions: The RGA profiles produced by the 14 primer pairs generated high genetic diversity. The RGA profiles
identified each of the 41 accessions clearly unequivocally. Most of the DNA sequences of the amplified RGAs from this
set of 41 accessions showed significant homology to the conserved regions of rice bacterial leaf blight resistance
genes. These information can be used in future for large scale investigation of tentative disease resistance genes of
Carica papaya and other Caricaceae genus specially Vasconcellea. Inoculation studies will be necessary to link the
identified sequences to disease resistance or susceptibility.
The authors wish to thank United States Department of Agriculture, Indian
Council of Agricultural Research, Indian Institute of Horticultural Research,
Orissa University of Agriculture and Technology and Tamil Nadu Agriculture
University for contributing the Caricaceae accessions. They also wish to
thank the Department of Science and Technology for providing the research
funding through Bose Institute and for providing the fellowship to
Basabdatta Das. Thanks are also due to the University of Calcutta for
providing fellowship to Samik Sengupta.
 
Date 2015-12-23T10:38:40Z
2015-12-23T10:38:40Z
2014
 
Type Article
 
Identifier BMC Genetics, 15: 137
1471-2156
http://172.16.0.77:8080/jspui/handle/123456789/453
http://bmcgenet.biomedcentral.com/articles/10.1186/s12863-014-0137-0
10.1186/s12863-014-0137-0
 
Language en_US
 
Publisher BioMed Central Ltd