Rapid identification of red-flesh loquat cultivars using EST-SSR markers based on manual cultivar identification diagram strategy

Li, X.Y.; Xu, Hongxia; Chen, J.W.

doi:10.4238/2014.april.29.17

Cited by 8 publications

(8 citation statements)

References 34 publications

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“…Furthermore, owing to additional criteria used for selection, the new set of 6 core SSR markers were all provided with enough discriminant power, and were highly polymorphic, easily manageable, which helped in improving the identification efficiency. The capillary electrophoresis conducted in ABI 3730 sequencer was capable of providing high detection sensitivity of amplified DNA fragments, which has been proved to be a powerful and efficient technique for automated and accurate estimation of allele sizes (Brunings et al 2010 ; Li et al 2014 ). There were no differences between the two independent replicates, which both detected by the capillary electrophoresis technology, showed the detection results held stability and reproducibility.…”

Section: Discussionmentioning

confidence: 99%

An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers

et al. 2016

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Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait ‘cultivar processing-property’. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10−5, which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.

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Section: Discussionmentioning

confidence: 99%

An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers

et al. 2016

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“…Malus transitoria (Batalin) C. K. Schneider, native to China, is an important Shrubs or small trees species in the crabapple genus Malus of the family Rosaceae. It is mainly distributed in higher altitude areas such as Shaanxi, Sichuan, Gansu, Nei Mongo, and Qinghai-Tibetan (Li et al 2014;Garden 2009).…”

Section: Introductionmentioning

confidence: 99%

“…To date, some polymorphic SSR markers have been developed in the Malus Ha et al 2021;Coart et al 2003), Based on these developed SSR markers, the Genetic diversity and population structure analysis (Urrestarazu et al 2016), Germplasm identification (Li et al 2014;Liu et al 2014), fruit quality improvement, fingerprint construction and Gene mapping (Erdin et al 2006) have been investigated in several Malus species. However, the study of molecular markers and population evolution of M. transitoria has no published.…”

Section: Introductionmentioning

confidence: 99%

Development of EST-SSR markers and population genetic structure and genetic diversity of the Malus transitoria (Batalin) C. K. Schneider in Qinghai-Tibetan Plateau

Guo

Zhang

Bai

2022

Genet Resour Crop Evol

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Malus transitoria (Batalin) C. K. Schneider is a shrub or small trees species native to in and around the Qinghai Tibet Plateau (QTP). We analyzed 142 samples from 8 natural populations of M. transitoria collected from the QTP using 18 pairs of EST-SSR markers. Genetic diversity was high at the species level showed the mean expected heterozygosity (HE) and Shannon's information index (I) per population were 0.573 and 0.921, and the genetic diversity of the WD population (HE=0.595, I=0.974) was the highest, whereas that of the BS population (HE=0.541, I=0.870) was the lowest. The mean Gene Flow (Nm) was 6.076, and the genetic diversity of the MKH population (Nm = 5.034) was the lowest. Molecular variance analysis (AMOVA) showed moderate genetic differentiation among populations, that Within Populations variation (95%) was significantly higher than Among Populations variation (5%), which was consistent with the genetic differentiation coefficient (Fst = 0.057). STRUCTURE analysis showed 2 clusters grouped similar to the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA). We speculate that due to long-term orogeny, gene exchange between populations is blocked, resulting in small gene flow and loss of genetic resources. This research investigated the genetic diversity and structure of natural populations of M. transitoria to provide a scientific basis for the conservation, breeding, and rational utilization of this tree species germplasm resources in QTP.

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“…Through RAPD markers, efficient identification was performed for tomato, peach and Ribes cultivars [ 3 – 5 ]. By using EST-SSR markers, red-flesh loquat cultivars were rapidly identified [ 6 ]. SNP markers were used to genotype 260 accessions of Pummelo [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

A cost-effective barcode system for maize genetic discrimination based on bi-allelic InDel markers

et al. 2020

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Background: Maize is one of the most important cereal crop all over the world with a complex genome of about 2.3 gigabase, and exhibits tremendous phenotypic and molecular diversity among different germplasms. Along with the phenotype identification, molecular markers have been accepted extensively as an alternative tool to discriminate different genotypes. Results: By using previous re-sequencing data of 205 lines, bi-allelic insertions and deletions (InDels) all over maize genome were screened, and a barcode system was constructed consisting of 37 bi-allelic insertion-deletion markers with high polymorphism information content (PIC) values, large discriminative size among varieties. The barcode system was measured and determined, different maize hybrids and inbreds were clearly discriminated efficiently with these markers, and hybrids responding parents were accurately determined. Compared with microarray data of more than 200 maize lines, the barcode system can discriminate maize varieties with 1.57% of different loci as a threshold. The barcode system can be used in standardized easy and quick operation with very low cost and minimum equipment requirements. Conclusion: A barcode system was constructed for genetic discrimination of maize lines, including 37 InDel markers with high PIC values and user-friendly. The barcode system was measured and determined for efficient identification of maize lines.

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Rapid identification of red-flesh loquat cultivars using EST-SSR markers based on manual cultivar identification diagram strategy

Cited by 8 publications

References 34 publications

An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers

An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers

Development of EST-SSR markers and population genetic structure and genetic diversity of the Malus transitoria (Batalin) C. K. Schneider in Qinghai-Tibetan Plateau

A cost-effective barcode system for maize genetic discrimination based on bi-allelic InDel markers

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