Genetic diversity of cultivated and wild Ussurian Pear (Pyrus ussuriensis Maxim.) in China evaluated with M13-tailed SSR markers

Cao, Yufen; Tian, Lili; Gao, Yuan; Liu, Fengzhi

doi:10.1007/s10722-011-9661-1

Cited by 37 publications

(22 citation statements)

References 13 publications

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“…In this study, the average value of heterozygosity and an average number of effective allele were 0.61 and 14.3 in 109 accessions by the nine SSR same as our previous study. In this study, observed heterozygosities (H o ) for individual loci with an average value of 0.61, which is comparable with a value of 0.63 (Kimura et al 2002;Bao et al 2007;Cao et al 2011a). However, this value is much higher than the values of 0.50 for 58 Iwate accessions (Katayama et al 2007), 0.48 for 114 European and Asian pears (Bassil and Postman 2010), 0.44 for 63 European pear accessions (Wünsch and Hormaza 2007).…”

Section: Discussionsupporting

confidence: 78%

Identification of Chinese white pear cultivars using SSR markers

Tian

Gao

Cao

et al. 2012

Genet Resour Crop Evol

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109 Pyrus accessions including 92 local Chinese accessions of P. bretschneideri were identified genetically using nine microsatellite loci developed from apple and pear. The nine SSR loci revealed 129 alleles in 109 pear accessions and 114 alleles in 92 Chinese white pears. Among the 92 local Chinese accessions of P. bretschneideri, 70 could be differentiated successfully except for 10 sets of synonymous or mutants. For the 92 accessions, the number of putative alleles per locus ranged from seven to 18, with an average of 12.67; the average values of observed heterozygosity and Shannon's Information index were 0.60 and 1.85, respectively. A phenogram based on the SSR (simple sequence repeat) genotypes was obtained. The 109 accessions clustered into 11 groups based on geographical origin. The European pears and the Asian pears did not form independent two groups, but three P. communis cultivars grouped together independently. The Japanese P. pyrifolia cultivars mingled together with the Chinese P. bretschneideri cultivars, but four P. ussuriensis cultivars except for one (Jianbali) grouped together independently. The results indicated that the relationship of P. bretschneideri cultivars and P. pyrifolia cultivars was much closer than others.

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Section: Discussionsupporting

confidence: 78%

Identification of Chinese white pear cultivars using SSR markers

Tian

Gao

Cao

et al. 2012

Genet Resour Crop Evol

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“…Terzopoulos and Bebeli (2008) suggested that using only morphological/agronomic traits is not adequate for the development of gene pools since either these traits are influenced by environmental factors and stage of plant development or they reveal only limited variation. The rapid development of molecular markers has provided new tools for evaluating germplasm and assessing the genetic diversity and population structure of plant species (Baranski et al 2012;Boczkowska et al 2012;Cao et al 2012;Mir et al 2012;Roy et al 2012;Sardos et al 2012;Wang and Li 2012). Different types of markers such as isozymes, random amplification of polymorphic DNAs (RAPDs), restriction fragment length polymorphisms (RFLPs), target region amplification polymorphisms (TRAPs), sequence-specific amplification polymorphisms (SSAPs), and amplified fragment length polymorphisms (AFLPs) have already been used for the assessment of genetic variability and diversity and to perform fingerprinting of Vicia species and V. faba L. accessions (Van de Ven et al 1990;Przybylska et al 1998;Gresta et al 2010;Kwon et al 2010;Liu and Hou 2010;Ouji et al 2012;Waly et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Genetic Relationship and Diversity Analysis of Faba Bean (Vicia Faba L. var. Minor) Genetic Resources Using Morphological and Microsatellite Molecular Markers

Abid¹,

Mingeot

Udupa³

et al. 2015

Plant Mol Biol Rep

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Assessment of genetic diversity is an essential component in germplasm characterization and utilization. Molecular markers serve as a valuable tool to assess the genetic variation and germplasm identification, which play a key role for faba (Vicia faba L.) bean breeding. In this study, we analyzed the genetic diversity of faba bean accessions based on simple sequence repeats (SSRs) and morphological traits. Forty-six faba bean accessions, originating from different countries and from the ICARDA breeding program, were evaluated by using 15 morphological and agronomic traits and 17 simple sequence repeat (SSR) loci. Significant differences among accessions for the 15 morphological descriptors were observed. Analysis by SSR markers showed a high genetic diversity among the accessions: All SSRs showed polymorphism, and 101 alleles were revealed for all accessions. The number of alleles at each locus ranged from 2 to 10, with an average of 5.94 alleles per marker, and the polymorphic information content (PIC) values ranged from 0.38 to 0.84 with a mean of 0.69. Expected heterozygosity (He), observed heterozygosity (Ho), unbiased expected heterozygosity (UHe), and Shannon's information index (I) showed existence of high genetic variation between accessions from different pedigree. Analyses of genetic distance of the accessions separated the accessions into two groups and seven and five subgroups according to morphological and SSR analysis, respectively. Principal component analysis (PCA) of the SSR markers showed that the first two principal components (PCs) explained a total of 43.90 % of the genetic variation and allowed to distinguish three groups of accessions. Regardless of the method of analysis, Tunisian cultivars are grouped together. For the rest of the accessions, the geographical origin did not seem to be the main factor for structuring the variability of the studied accessions. Elite accessions from the ICARDA faba bean program differed from others and clustered together. The results obtained suggested that the faba bean microsatellite markers can be used to efficiently distinguish faba bean genotypes and to estimate their genetic diversity.

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“…By virtue of their reproducibility, multi-allelic nature, co-dominant inheritance, relative abundance, and good genome coverage (Powell et al, 1996), SSR markers have been largely applied to genetic diversity studies (Gupta and Varshney, 2000;Chen et al, 2011;Zhang et al, 2013) and used in a variety of applications related to pears, demonstrating their adaptability for Pyrus (Yamamoto et al, 2002;Bao et al, 2007;Katayama et al, 2007;Yao et al, 2010;Cao et al, 2012). SSR loci consist of randomly repeated DNA regions with motif lengths of one to six base pairs (bp) and are spread throughout the genome (Tóth et al, 2000).…”

Section: Introductionmentioning

confidence: 99%

Development of genic SSR markers from transcriptome sequencing of pear buds

Yue

Liu

Zong

et al. 2014

J. Zhejiang Univ. Sci. B

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A total of 8375 genic simple sequence repeat (SSR) loci were discovered from a unigene set assembled from 116 282 transcriptomic unigenes in this study. Dinucleotide repeat motifs were the most common with a frequency of 65.11%, followed by trinucleotide (32.81%). A total of 4100 primer pairs were designed from the SSR loci. Of these, 343 primer pairs (repeat length ≥15 bp) were synthesized with an M13 tail and tested for stable amplification and polymorphism in four Pyrus accessions. After the preliminary test, 104 polymorphic genic SSR markers were developed; dinucleotide and trinucleotide repeats represented 97.11% (101) of these. Twenty-eight polymorphic genic SSR markers were selected randomly to further validate genetic diversity among 28 Pyrus accessions. These markers displayed a high level of polymorphism. The number of alleles at these SSR loci ranged from 2 to 17, with a mean of 9.43 alleles per locus, and the polymorphism information content (PIC) values ranged from 0.26 to 0.91. The UPGMA (unweighted pair-group method with arithmetic average) cluster analysis grouped the 28 Pyrus accessions into two groups: Oriental pears and Occidental pears, which are congruent to the traditional taxonomy, demonstrating their effectiveness in analyzing Pyrus phylogenetic relationships, enriching rare Pyrus EST-SSR resources, and confirming the potential value of a pear transcriptome database for the development of new SSR markers.

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Genetic diversity of cultivated and wild Ussurian Pear (Pyrus ussuriensis Maxim.) in China evaluated with M13-tailed SSR markers

Cited by 37 publications

References 13 publications

Identification of Chinese white pear cultivars using SSR markers

Identification of Chinese white pear cultivars using SSR markers

Genetic Relationship and Diversity Analysis of Faba Bean (Vicia Faba L. var. Minor) Genetic Resources Using Morphological and Microsatellite Molecular Markers

Development of genic SSR markers from transcriptome sequencing of pear buds

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