Abstract
BackgroundIn 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.ResultsOf 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0137-0) contains supplementary material, which is available to authorized users.
Highlights
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
Resistances to several other diseases which affect Carica papaya have been identified in the Vasconcellea genepool, including: resistance to black spot, (V. cundinamarcensis) [7]; die back, (V. parviflora) [7]; and root rot, (V. goudotiana) [7]
The other objectives of this study were, to obtain the genetic relationship amongst the 41 Caricaceae accessions using the polymorphism of the amplified DNA bands using statistical methods, and to analyze the sequences of the obtained DNA bands for the presence of homology and conserved domains
Summary
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. Other leading producers are Brazil, Mexico, Nigeria, Indonesia, China, Peru, Thailand and Philippines. Papaya is eaten both fresh and cooked, and is processed into pickles, jams, candies, fruit drinks and juices. Resistances to several other diseases which affect Carica papaya have been identified in the Vasconcellea genepool, including: resistance to black spot, (V. cundinamarcensis) [7]; die back, (V. parviflora) [7]; and root rot, (V. goudotiana) [7]. Hybridization between Carica papaya and Vasconcellea have been largely limited by post-zygotic instabilities, including embryo abortion and infertility of the hybrids [7,8]; presenting a significant barrier for the successful introgression of desirable disease resistance traits into C. papaya
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