Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes

Rauscher, Gilda; Šimko, Ivan

doi:10.1186/1471-2229-13-11

Cited by 41 publications

(43 citation statements)

References 35 publications

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“…Interestingly, our data are consistent with previous studies in faba bean which revealed a larger genetic variation and differentiation within than between population (Terzopoulos and Bebeli 2008; Ouji et al 2011;Oliveira et al 2016). Moreover, this was consistent with the findings from other species such as grapevine (De Andrés et al 2012), olive (Belaj et al 2007), apple ) and lettuce (Rauscher and Simko 2013).…”

Section: Discussionsupporting

confidence: 91%

Genetic variability in Tunisian populations of faba bean (Vicia faba L. var. major) assessed by morphological and SSR markers

Rebaa¹,

Abid²,

Aouida³

et al. 2017

Physiol Mol Biol Plants

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The genetic diversity of 21 faba bean populations was examined using morphological and molecular markers. DNA was extracted from 189 individuals and 8 microsatellite markers were genotyped individually in these 21 populations. A total of 53 alleles were obtained in all populations, with an average of 6.62 alleles per locus. The expected and observed heterozygosity was 0.38 and 0.62 respectively. The average polymorphism index content of SSR markers was 0.61, ranging from 0.31 to 0.81. The unweighted pair group method with arithmetic mean dendrogram clustered all the populations into two groups, each for them subdivided into 3 sub-groups according to geographical origin. Morphological variation showed that the populations were not grouped according to their geographical origin. Therefore, patterns of differentiation of morphological traits did not coincide with molecular differentiation, indicating that morphological variation does not reflect genetic subdivision in studied faba bean populations. Analysis of molecular variance revealed high levels of genetic variation (83%) within population and provides a good base for designing genetic improvement programs. The result of Principal Component Analysis (PCA) revealed that three dimensional principal components (PC1, PC2 and PC3) contributed 40.56% of the total variability and accounted with values of 20.64, 11.22 and 8.70%, respectively. Cluster analysis based on PCA indicated three separate groups of populations. The genetic relationships found between the 21 populations samples were the same in both the PCA and STRUCTURE analysis which support the results observed. These data may serve as a foundation for the development of faba bean breeding programs.

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Section: Discussionsupporting

confidence: 91%

Genetic variability in Tunisian populations of faba bean (Vicia faba L. var. major) assessed by morphological and SSR markers

Rebaa¹,

Abid²,

Aouida³

et al. 2017

Physiol Mol Biol Plants

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“…In our study, the mean value of PIC (0.63) was less than that (0.67) previously reported for genomic-SSRs (Jiao et al, 2012), but significantly higher than the figure (0.44) for EST-SSRs (Zhang et al, 2012). Our results are in agreement with that reported in lettuce (Rauscher and Simko, 2013). Compared with ESTSSRs, genomic-SSRs have relatively high polymorphism and good genome coverage, so they can be used in constructing a linkage map.…”

Section: Ssr Polymorphismsupporting

confidence: 87%

Development of 107 SSR markers from whole genome shotgun sequences of Chinese bayberry (Myrica rubra) and their application in seedling identification

Jia

Shen

Jiao

et al. 2014

J. Zhejiang Univ. Sci. B

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Chinese bayberry (Myrica rubra Sieb. et Zucc.) is one of the important subtropical fruit crops native to the South of China and Asian countries. In this study, 107 novel simple sequence repeat (SSR) molecular markers, a powerful tool for genetic diversity studies, cultivar identification, and linkage map construction, were developed and characterized from whole genome shotgun sequences. M13 tailing for forward primers was applied as a simple method in different situations. In total, 828 alleles across 45 accessions were detected, with an average of 8 alleles per locus. The number of effective alleles ranged from 1.22 to 10.41 with an average of 4.08. The polymorphic information content (PIC) varied from 0.13 to 0.89, with an average of 0.63. Moreover, these markers could also be amplified in their related species Myrica cerifera (syn. Morella cerifera) and Myrica adenophora. Seventy-eight SSR markers can be used to produce a genetic map of a cross between 'Biqi' and 'Dongkui'. A neighbor-joining (NJ) tree was constructed to assess the genetic relationships among accessions, and the elite accessions 'Y2010-70', 'Y2012-140', and 'Y2012-145', were characterized as potential new genotypes for cultivation.

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“…This result was higher than 0.32 reported by [10] but lower than 0.55 of [19] and 0.56 of [20]. This may be mainly due to genetic background of tested cultivars and chromosome loci linked to SSR marker.…”

Section: Est-ssr Polymorphisms In Lettucecontrasting

confidence: 67%

Construction of EST-SSR Databases for Effective Cultivar Identification and Their Applicability to Complement for Lettuce (Lactuca sativa L.) Distinctness Test

Hong¹,

Kwon²,

Mishra³

et al. 2015

AJPS

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The objectives of this study were to construct a database of expressed sequence tag (EST)-simple sequence repeat (SSR) markers to identify lettuce cultivars. A set of 370 EST-SSR primer pairs were applied for fingerprinting the lettuce cultivars. Fifty-eight EST-SSR markers showed hyper-variability and were able to differentiate 92 cultivars. A total of 176 polymorphic amplified fragments were obtained by the 58 markers, and two to eight SSR alleles were detected for each l˚Cus with an average of three alleles per locus. Average polymorphism information content (PIC) was 0.425, ranging from 0.022 to 0.743. Cluster analysis was based on Jaccard's distance coefficients using the method of unweighted pair group. In this method we used arithmetical averages (UPGMA) algorithm categorized 4 major groups, which were in accordance to morphological traits. The eight cultivars of three groups with 100% genetic similarity through SSR analysis were investigated by phenotypic traits. These cultivars including these pairs are very similar in 27 morphological characteristics. Therefore, these EST-SSR markers could be used to select similar cultivars through management of reference collection to complement distinctiveness test of lettuce cultivars.

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Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes

Cited by 41 publications

References 35 publications

Genetic variability in Tunisian populations of faba bean (Vicia faba L. var. major) assessed by morphological and SSR markers

Genetic variability in Tunisian populations of faba bean (Vicia faba L. var. major) assessed by morphological and SSR markers

Development of 107 SSR markers from whole genome shotgun sequences of Chinese bayberry (Myrica rubra) and their application in seedling identification

Construction of EST-SSR Databases for Effective Cultivar Identification and Their Applicability to Complement for Lettuce (Lactuca sativa L.) Distinctness Test

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