Microsatellite markers of genetic diversity and population structure of <i>Carica papaya</i>

Matos, Edneide Luciana Santiago; Oliveira, E. J. de; Jesus, O. N. de; Dantas, J. L. L.

doi:10.1111/aab.12053

Cited by 19 publications

(19 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, this is also probable due to the gene flow via seeds movement among farmers of different geographic origins and to the self-incompatibility allogamy of this species, resulting in an increase in allele distribution among different accessions. This is consistent with the results found by various authors in other fruit trees as Carica papaya L. (Ocampo et al, 2007;Matos et al, 2013), P. ligularis (Bernal et al, 2014) and Physalis peruviana L. (Chacón et al, 2016) who argued that genetic polymorphism can be associated with the allogamous nature of the species and the exchange of seeds between producers, which tends to favor the conservation of a high percentage of heterozygote genotypes.…”

Section: Genetic Diversity and Structuresupporting

confidence: 92%

“…The set of results of cluster and structure analyses show that the accessions analyzed are genetically heterogeneous and indicate that there is low correspondence with geographic distribution of accessions, and this is similar to other studies reported for cultivated accessions of P. ligularis (Bernal et al, 2014) and Carica papaya (Matos et al, 2013). In contrast, Ortiz et al (2012) reported a high genetic homogeneity in cultivated material of P. edulis f. edulis (purple passion fruit) in Colombia with microsatellite markers and AFLP, and without a consistency with the origin of the samples analyzed by department or location.…”

Section: Genetic Diversity and Structuresupporting

confidence: 86%

See 1 more Smart Citation

Variability and genetic structure of yellow passion fruit (Passiflora edulis f. flavicarpa Degener) in Colombia using microsatellite DNA markers

Ocampo¹,

Acosta-Barón²,

Fernández³

2017

Agron. colomb.

View full text Add to dashboard Cite

Colombia is one of the leading producers of yellow passion fruit but the genetic studies based on molecular markers from commercial plantations have not been considered to select interesting market material. The goal of this study was to assess the genetic variability and the population structure of 51 Colombian commercial yellow passion fruit accessions (102 individuals), and to provide the necessary information for prospective selection and breeding programs. Thus, a total of six microsatellites were amplified with 58 alleles identified and an average of 9.66 alleles per locus, including nine private and 31 rare. Diversity indexes showed polymorphic information content values of 0.74 (PIC), an observed (Ho) and expected (He) heterozygosity average of 0.52 and 0.78, respectively. Spatial distribution showed the greatest allelic richness (11 to 14) in most of the Valle del Cauca accessions. The average genetic distance among accessions was 0.68, and the cluster analysis showed three main groups poorly supported (bootstrap <50%), with slight geographical structure and high differentiation between individuals of the same accession. Structure analysis indicated K=4 as the genetic structure's uppermost hierarchical level, while Bayesian clustering showed a division of individuals into four genetically distinct groups. The low geographic structure and high variability of the accessions could be explained by allogamy and seed exchange frequency among farmers. Results issued suggest a complementary agro-morphological assessment to establish total genetic variability and implement a breeding program through assisted selection of superior genotypes in search of more productive and resistant cultivars to phytosanitary problems.

show abstract

Section: Genetic Diversity and Structuresupporting

confidence: 92%

Section: Genetic Diversity and Structuresupporting

confidence: 86%

Variability and genetic structure of yellow passion fruit (Passiflora edulis f. flavicarpa Degener) in Colombia using microsatellite DNA markers

Ocampo¹,

Acosta-Barón²,

Fernández³

2017

Agron. colomb.

View full text Add to dashboard Cite

show abstract

“…The highest allelic diversity was observed for in CP16 (eight alleles) and lowest for 23 loci (CP code: 06,09,11,20,22,23,24,27,28,29,33,36,38, CPM2288CC, P3K2351CC, P3K3143C0, P3K3187CC, P3K3579CC, P3K5504A5, P3K5988CC, P6K883CC, P8K277CC and P8K594A5) exhibiting only two alleles (Table 6). This average number of alleles was consistent with previous observations made by other authors, who reported averages of 4.02 (Oliveira et al 2010b) and 4.53 alleles per locus (Matos et al 2013) in the analysis of Brazilian papaya genotypes. In contrast, a higher average number of alleles per locus (6.60) was found by Ocampo Pérez et al (2007), who analyzed 72 papaya genotypes with 15 microsatellite markers, and by Asudi et al (2013), who analyzed 42 papaya genotypes from six regions in Kenya, in which 11.93 alleles per locus were observed.…”

Section: Characterization Of Minisatellite and Microsatellite Locisupporting

confidence: 93%

“…According to Matos et al (2013), an analysis of the population structure of 96 Brazilian papaya accessions based on 15 microsatellite loci indicated a higher DK value for six groups. However, even identifying a high degree of ancestry between different groups, revealing the presence of mixture in these populations, these authors did not establish a minimum assignment probability to form different groups.…”

Section: Analysis Of Population Structurementioning

confidence: 99%

Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya

2015

View full text Add to dashboard Cite

The objective of this study was to evaluate information on minisatellite and microsatellite markers in papaya (Carica papaya L.). Forty minisatellites and 91 microsatellites were used for genotyping 24 papaya accessions. Estimates of genetic diversity, genetic linkage and analyses of population structure were compared. A lower average number of alleles per locus was observed in minisatellites (3.10) compared with microsatellites (3.57), although the minisatellites showed rarer alleles (18.54 %) compared with microsatellite (13.85 %). Greater expected (He = 0.52) and observed (Ho = 0.16) heterozygosity was observed in the microsatellites compared with minisatellites (He = 0.42 and Ho = 0.11), possibly due to the high number of hermaphroditic accessions, resulting in high rates of self-fertilization. The polymorphic information content and Shannon-Wiener diversity were also higher for microsatellites (from 0.47 to 1.10, respectively) compared with minisatellite (0.38 and 0.85, respectively). The probability of paternity exclusion was high for both markers (>0.999), and the combined probability of identity was from 1.65(-13) to 4.33(-38) for mini- and micro-satellites, respectively, which indicates that both types of markers are ideal for genetic analysis. The Bayesian analysis indicated the formation of two groups (K = 2) for both markers, although the minisatellites indicated a substructure (K = 4). A greater number of accessions with a low probability of assignment to specific groups were observed for microsatellites. Collectively, the results indicated higher informativeness of microsatellites. However, the lower informative power of minisatellites may be offset by the use of larger number of loci. Furthermore, minisatellites are subject to less error in genotyping because there is greater power to detect genotyping systems when larger motifs are used.

show abstract

“…The DAPC has been used for large data volumes, particularly generated by SNP markers. Recently, the DAPC was used to structure the germplasm of Carica papaya L. with microsatellite markers (Matos et al, 2013) and cassava with SNPs markers (Oliveira et al, 2014).…”

Section: Analysis Of Parental Diversity Available For Breedingmentioning

confidence: 99%

Molecular-assisted selection for resistance to cassava mosaic disease in Manihot esculenta Crantz

Carmo

Silva

Oliveira

et al. 2015

Sci. agric. (Piracicaba, Braz.)

View full text Add to dashboard Cite

The geminivirus complex known as cassava mosaic disease (CMD) is one of the most devastating viruses for cassava (Manihot esculenta Crantz). The aim of this study was to use molecular-assisted selection (MAS) to identify CMD-resistant accessions and ascertain promising crosses with elite Brazilian varieties. One thousand two hundred twenty-four accessions were genotyped using five molecular markers (NS169, NS158, SSRY028, SSRY040 and RME1) that were associated with resistance to CMD, along with 402 SNPs (single-nucleotide polymorphism). The promising crosses were identified using a discriminant analysis of main component (DAPC), and the matrix of genomic relationship was estimated with SNP markers. The CMD1 gene, previously described in M. glaziovii, was not found in M. esculenta. In contrast, the CMD2 gene was found in 5, 4 and 5 % of cassava accessions, with flanking markers NS169+RME1, NS158+RME1 and SSRY28+RME1, respectively. Only seven accessions presented all markers linked to the CMD resistance. The DAPC of the seven accessions along with 17 elite cassava varieties led to the formation of three divergent clusters. Potential sources of resistance to CMD were divided into two groups, while the elite varieties were distributed into three groups. The low estimates of the genomic relationship (ranging from -0.167 to 0.681 with an average of 0.076) contributed to the success in identifying contrasting genotypes. The use of MAS in countries where CMD is a quarantine disease constitutes a successful strategy not only for identifying the resistant accessions but also for determining the promising crosses.

show abstract

Microsatellite markers of genetic diversity and population structure of Carica papaya

Cited by 19 publications

References 43 publications

Variability and genetic structure of yellow passion fruit (Passiflora edulis f. flavicarpa Degener) in Colombia using microsatellite DNA markers

Variability and genetic structure of yellow passion fruit (Passiflora edulis f. flavicarpa Degener) in Colombia using microsatellite DNA markers

Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya

Molecular-assisted selection for resistance to cassava mosaic disease in Manihot esculenta Crantz

Contact Info

Product

Resources

About