Identification of a Simple Sequence Repeat molecular-marker set for large-scale analyses of pear germplasm

Dequigiovanni, Gabriel; Rech, Fernanda; Gomes, Felippe George Gatti; Cerotti, Ivan Somensi; Faoro, Ivan Dagoberto; Oliveira, P. R. D. de; Quecini, Vera; Ritschel, P. S.

doi:10.1590/s1984-70332012000200004

Cited by 6 publications

(5 citation statements)

References 22 publications

(24 reference statements)

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“…Bartlett is a mutant that probably originated from seeds derived from 'Bon Chrétien Williams' circa 1880; Packham's Triumph was selected around 1886-1887 from a cross conducted in Australia between 'Uvedale St. Germain' and 'Williams Bon Chrétien'. Our results differ from those obtained by Dequigiovanni et al (2012) as the Williams cultivar was distant from the cultivars Red Bartlett and Packham's Triumph, although the latter two grouped close together.…”

Section: Resultscontrasting

confidence: 99%

“…Although all of these cultivars were clustered within the group of European pears in the present study, the Williams and Abatel Fetel pears grouped very close together, but distant from the Packham's Triumph cultivar. Dequigiovanni et al (2012) evaluated pear cultivars using SRR markers and reported that the cultivars Williams, Red Bartlett, and Packham's Triumph corresponded to the European pear variety Bon Chrétien Williams. Bartlett is a mutant that probably originated from seeds derived from 'Bon Chrétien Williams' circa 1880; Packham's Triumph was selected around 1886-1887 from a cross conducted in Australia between 'Uvedale St. Germain' and 'Williams Bon Chrétien'.…”

Section: Resultsmentioning

confidence: 99%

“…The results for the number of alleles per locus were within the ranges reported for other studies of Pyrus sp. cultivars (Kimura et al, 2002;Fernández-Fernández et al, 2006;Miranda et al, 2010;Dequigiovanni et al, 2012). Heterozygosity summarizes the fundamental variations of genetic diversity in a population (Berg and Harmik, 1997), and is therefore commonly employed in studies of diversity.…”

Section: Resultsmentioning

confidence: 99%

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Simple sequence repeat (SSR) markers are effective for identifying pear cultivars and selections

Stracieri¹,

Magalhães²,

Resende³

et al. 2015

Afr. J. Biotechnol.

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Section: Resultscontrasting

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Simple sequence repeat (SSR) markers are effective for identifying pear cultivars and selections

Stracieri¹,

Magalhães²,

Resende³

et al. 2015

Afr. J. Biotechnol.

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“…Wolko et al [ 42 ] found PIC values were in the range of 0.42 to 0.89 with an average of 0.65 for the 19 high polymorphic SSR markers selected from 40 tested SSR markers. Dequigiovanni et al [ 43 ] reported PIC values for 62 SSR loci among 42 pear accessions ranged from 0.48 to 0.87, with an average of 0.67. Yue et al [ 17 ] reported an average PIC value of 0.58 for 28 SSRs in 28 Pyrus accessions (0.26 to 0.91).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide characterization of simple sequence repeats in Pyrus bretschneideri and their application in an analysis of genetic diversity in pear

et al. 2018

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BackgroundPear (Pyrus spp.) is an economically important temperate fruit tree worldwide. In the past decade, significant progress has been made in pear molecular genetics based on DNA research, but the number of molecular markers is still quite limited, which hardly satisfies the increasing needs of geneticists and breeders.ResultsIn this study, a total of 156,396 simple sequence repeat (SSR) loci were identified from a genome sequence of Pyrus bretschneideri ‘Dangshansuli’. A total of 101,694 pairs of SSR primers were designed from the SSR loci, and 80,415 of the SSR loci were successfully located on 17 linkage groups (LGs). A total of 534 primer pairs were synthesized and preliminarily screened in four pear cultivars, and of these, 332 primer pairs were selected as clear, stable, and polymorphic SSR markers. Eighteen polymorphic SSR markers were randomly selected from the 332 polymorphic SSR markers in order to perform a further analysis of the genetic diversity among 44 pear cultivars. The 14 European pears and their hybrid materials were clustered into one group (European pear group); 29 Asian pear cultivars were clustered into one group (Asian pear group); and the Zangli pear cultivar ‘Deqinli’ from Yunnan Province, China, was grouped in an independent group, which suggested that the cultivar ‘Deqinli’ is a distinct and valuable germplasm resource. The population structure analysis partitioned the 44 cultivars into two populations, Pop 1 and Pop 2. Pop 2 was further divided into two subpopulations. Results from the population structure analysis were generally consistent with the results from the UPGMA cluster analysis.ConclusionsThe results of the present study showed that the use of next-generating sequencing to develop SSR markers is fast and effective, and the developed SSR markers can be utilized by researchers and breeders for future pear improvement.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4822-7) contains supplementary material, which is available to authorized users.

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“…However, in other fruit species such as pear, Dequigiovanni et al (2012) differentiated 42 individuals using 11 microsatellite markers, whose combined PI was 2.47 9 10 -16 . Likewise, Cardoso et al (2014) differentiated 50 common bean cultivars based on 24 microsatellite markers, with combined PI of 7.05 9 10 -17 and a PEC [99.99 %.…”

Section: Markers With Discriminatory Powermentioning

confidence: 99%

Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya

2015

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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.

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Identification of a Simple Sequence Repeat molecular-marker set for large-scale analyses of pear germplasm

Abstract: -

Cited by 6 publications

References 22 publications

Simple sequence repeat (SSR) markers are effective for identifying pear cultivars and selections

Simple sequence repeat (SSR) markers are effective for identifying pear cultivars and selections

Genome-wide characterization of simple sequence repeats in Pyrus bretschneideri and their application in an analysis of genetic diversity in pear

Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya

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