Cross-species microsatellite amplification in Vasconcellea and related genera and their use in germplasm classification

Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea chilensis) Using GBS Tools

A genotyping by sequencing (GBS) approach was used to analyze the organization of genetic diversity in V. pubescens and V. chilensis. GBS identified 4675 and 4451 SNPs/INDELs in two papaya species. The cultivated orchards of V. pubescens exhibited scarce genetic diversity and low but significant genetic differentiation. The neutrality test yielded a negative and significant result, suggesting that V. pubescens suffered a selective sweep or a rapid expansion after a bottleneck during domestication. In contrast, V. chilensis exhibited a high level of genetic diversity. The genetic differentiation among the populations was slight, but it was possible to distinguish the two genetic groups. The neutrality test indicated no evidence that natural selection and genetic drift affect the natural population of V. chilensis. Using the Carica papaya genome as a reference, we identified critical SNPs/INDELs associated with putative genes. Most of the identified genes are related to stress responses (salt and nematode) and vegetative and reproductive development. These results will be helpful for future breeding and conservation programs of the Caricaceae family.

An integrative approach reveals five new species of highland papayas (Caricaceae, Vasconcellea) from northern Peru

The assignment of accurate species names is crucial, especially for those with confirmed agronomic potential such as highland papayas. The use of additional methodologies and data sets is recommended to establish well-supported boundaries among species of Vasconcellea. Accordingly, six chloroplast (trnL-trnF, rpl20-rps12, psbA-trnH intergenic spacers, matK and rbcL genes) and nuclear (ITS) markers were used to delimit species in the genus Vasconcellea using phylogeny and four DNA-based methods. Our results demonstrated congruence among different methodologies applied in this integrative study (i.e., morphology, multilocus phylogeny, genetic distance, coalescence methods). Genetic distance (ABGD, SPN), a coalescence method (BPP), and the multilocus phylogeny supported 22–25 different species of Vasconcellea, including the following five new species from northern Peru: V. badilloi sp. nov., V. carvalhoae sp. nov., V. chachapoyensis sp. nov., V. pentalobis sp. nov., and V. peruviensis sp. nov. Genetic markers that gave better resolution for distinguishing species were ITS and trnL-trnF. Phylogenetic diversity and DNA-species delimitation methods could be used to discover taxa within traditionally defined species.

Southern Species From the Biodiversity Hotspot of Central Chile: A Source of Color, Aroma, and Metabolites for Global Agriculture and Food Industry in a Scenario of Climate Change

Two interesting plants within the Chilean flora (wild and crop species) can be found with a history related to modern fruticulture: Fragaria chiloensis subsp. chiloensis (Rosaceae) and Vasconcellea pubescens (Caricaceae). Both species have a wide natural distribution, which goes from the Andes mountains to the sea (East-West), and from the Atacama desert to the South of Chile (North-South). The growing locations are included within the Chilean Winter Rainfall-Valdivian Forest hotspot. Global warming is of great concern as it increases the risk of losing wild plant species, but at the same time, gives a chance for usually longer term genetic improvement using naturally adapted material and the source for generating healthy foods. Modern agriculture intensifies the attractiveness of native undomesticated species as a way to provide compounds like antioxidants or tolerant plants for climate change scenario. F. chiloensis subsp. chiloensis as the mother of commercial strawberry (Fragaria × ananassa) is an interesting genetic source for the improvement of fruit flavor and stress tolerance. On the other hand, V. pubescens produces fruit with high level of antioxidants and proteolytic enzymes of interest to the food industry. The current review compiles the botanical, physiological and phytochemical description of F. chiloensis subsp. chiloensis and V. pubescens, highlighting their potential as functional foods and as source of compounds with several applications in the pharmaceutical, biotechnological, and food science. The impact of global warming scenario on the distribution of the species is also discussed.

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

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.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-014-0137-0) contains supplementary material, which is available to authorized users.

A comparative survey of genetic diversity among a set of Caricaceae accessions using microsatellite markers

A preliminary survey of genetic diversity among 34 commercially popular Carica papaya cultivars from India and abroad, 6 accessions of Vasconcellea species and 1 accession of Jacaratia spinosa, was done using 20 simple sequence repeat (SSR) markers. The SSR profiles were used to find out total number of alleles, null and rare alleles, Polymorphism Information Content (PIC) values and to calculate similarity matrix using Jaccard’s coefficient. The subsequent dendrogram was made by unweighted pair-group method of arithmetic average (UPGMA) and neighbor-joining method. Based on these parameters a comparison was made between the Indian papaya cultivars and the rest of the accessions. All the markers showed polymorphism and a total of 140 alleles were identified. The average number of alleles was 7 alleles/locus. Categorically the Vasconcellea and Jacaratia species had 54 alleles, the 7 non-Indian Carica papaya accessions had 70 and the 27 Indian accessions had 102 alleles. The average PIC value was 0.735 per marker. A total of 37 rare alleles were identified. Jacaratia spinosa had 17 rare alleles. Nineteen null alleles were detected among the Carica papaya accessions. A Carica papaya accession from South Africa, Hortus Gold had 5 null alleles. The genetic similarity among the accessions ranged from 7% to 67%. In the dendrogram, the Vasconcellea and Jacaratia spinosa accessions separated as a distinct cluster from the rest of the Carica papaya accessions. The study indicated that the accessions of Indian Carica papaya cultivars included in this survey are genetically more diverse than the non-Indian Carica papaya cultivars.