Genetic diversity and classification of Nelumbo germplasm of different origins by RAPD and ISSR analysis

Zuo, Li; Liu, Xiu‐Qun; Gituru, Robert Wahiti; Juntawong, Niran; Zhou, Mingjie; Chen, Long-Qing

doi:10.1016/j.scienta.2010.05.005

Cited by 46 publications

(35 citation statements)

References 17 publications

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“…All N. nucifera accessions were divided into two sub-clusters (Clusters Ia and Ib) based on their appearance and utilization value. The same results were reported by Yang et al (2012b) and Li et al (2010). Interestingly, the genetic relationship between these lotus accessions was not based on their geographical sources, as was found in previous reports (Guo et al, 2007).…”

Section: Assessment Of Genetic Diversity Among Varieties and Wild Lotussupporting

confidence: 89%

“…Fu et al (2011) and Hu et al (2012) reported genetic variation between N. nucifera and N. lutea. Genetic diversity between China and Thailand lotus plants were evaluated using ISSR by Chen et al (2008) and Li et al (2010), which improved understanding of lotus germplasm classification. Although the development of a number of SSRs was reported by Tian et al (2008a), Kubo et al (2009), Pan et al (2010), and Xue et al (2012), few SSR markers have been exploited, particularly in Nelumbo molecular quantity genetic studies and molecular assistance breeding.…”

Section: Introductionmentioning

confidence: 99%

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Development and characterization of genic-SSR markers from different Asia lotus (Nelumbo nucifera) types by RNA-seq

et al. 2015

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ABSTRACT. Nelumbo nucifera is an important economic vegetable and traditional medicine, but available genetic resources remain limited. Next generation sequencing has proven to be a rapid and effective means of identifying genic simple sequence repeat (genic-SSR) markers. This study developed genic-SSRs for N. nucifera using Illumina sequencing technology to assess diversity across cultivated and wild lotus. A total of 105,834 uni-contigs were produced with an average read length of 722 bp. Exactly 11,178 genic-SSR loci were identified in 9523 uni-contigs. Di-nucleotide (64.5%) was the most abundant SSR, followed by trinucleotide (23%), tetra-nucleotide (8.9%), penta-nucleotide (2.5%), and hexa-nucleotide (1%) repeat types. The most common di-and tri-nucleotide repeat motifs were AG/CT (51%) and AAG/CTT (8%), respectively. Based on these SSRs sequences, 6568 primer pairs were designed, of which 72 primers were randomly selected for synthesis and validation, and 38 in-silico polymorphic primers were obtained using in-house perl scripts. A total of 110 primers were screened in the lotus samples and the results showed that 101 primers yielded amplification products, of which 80 were polymorphs. The number of alleles ranged from 2 to 17 and the PIC (polymorphism information content) ranged from 0.19 to 0.87 with a mean value of 0.55. An Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram based on Jaccard's similarity coefficients showed that the correlation between geographical source and genotype was low. This study describes the distribution of genic-SSRs in the expressed portion of the lotus genome. These genic-SSRs have an important role to play in molecular mapping, diversity analysis, and marker-assisted selection strategies in Nelumbo.

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Section: Assessment Of Genetic Diversity Among Varieties and Wild Lotussupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Development and characterization of genic-SSR markers from different Asia lotus (Nelumbo nucifera) types by RNA-seq

et al. 2015

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“…Therefore, in the present investigation, RAPD and ISSR were used as genetic markers to characterize the 16 germplasms of E. ferox. In the last three decades, both ISSR and RAPD markers have played an important role in genetic variability studies of different populations [11,12,22,23]. In the present investigation, 21 ISSR and 40 RAPD primers produced 747 polymorphic bands that clearly discriminated 16 E. ferox germplasms into three main clusters.…”

Section: Discussionmentioning

confidence: 56%

RAPD and ISSR Marker-Based Comparative Evaluation of Genetic Diversity Among Indian Germplasms of Euryale ferox: an Aquatic Food Plant

Kumar

Priya

Singh

et al. 2016

Appl Biochem Biotechnol

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Euryale ferox Salisbury is an important aquatic food plant cultivated largely in eastern India. E. ferox is a monotypic genus, and breeding programmes have mostly relied on the variability present in the primary gene pool. Knowledge of the genetic structure of the population is limited, and there are very few reports available on the genetic diversity of E. ferox. In this study, comprehensive research on the genetic diversity of 16 germplasms of E. ferox was carried out using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Out of 320 RAPD and 95 ISSR primers screened initially, 61 primers (40 RAPD and 21 ISSR) gave reproducible bands and were selected for further work. Amplification of the 40 RAPD primers gave 533 polymorphic bands with an average of 13.32 polymorphic bands per primer. The percentage of polymorphism ranged from 37.5 to 100, with an average of 88.3 %. The 21 ISSR primers produced 259 bands, of which 214 were polymorphic, with an average of 10.19 polymorphic bands per primer. The percentage of polymorphism using ISSR primers ranged from 50 to 100, with a mean of 82.6 %. Jaccard's coefficient ranged from 0.45 to 0.69 (RAPD), 0.50 to 0.77 (ISSR) and 0.48 to 0.71 (RAPD and ISSR). Molecular characterization of different germplasms of E. ferox not only is essential for its conservation but also can be used in further breeding programmes.

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“…These methods differ in their ease of use, cost, and reproducibility of results (Li et al, 2010). Methods previously used to study the genetic diversity in garlic can be divided into three groups, i.e., methods based on morphological markers (Pooler and Simon, 1993;Baghalian et al, 2006), those based on biochemical markers (Pooler and Simon, 1993;Lallemand et al, 1997), and those based on DNA markers (Bark and Havey, 1995;Maab and Klaas, 1995;Lampasona et al, 2003;Volk et al, 2004;Ovesná et al, 2007;Buso et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Genetic divergence among Brazilian garlic cultivars based on morphological characters and AFLP markers

Morales¹,

Resende²,

Resende³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. Outside its centers of origin, garlic propagates only asexually. Since asexual reproduction leads to the absence of meiotic recombination, the main garlic cultivars available for cultivation have arisen from the accumulation of somatic mutations in early cultivars. Thus, it is common for a single clone to have different names in different regions. This study aimed to evaluate the genetic diversity of 20 garlic cultivars by using morphological characters and amplified fragment length polymorphism (AFLP) markers to identify possible duplicate cultivars. We assessed 28 morphological characters related to the leaves, bulbs, and bulbils of the garlic plant and divided them into two categories: quantitative and qualitative (14 characters each). Genetic divergence among Brazilian garlic cultivars For molecular marker-based analysis, we used three AFLP primer combinations. Genetic divergence was calculated using the Jaccard coefficient; the cultivars were grouped using unweighted pair-group mean analysis. The average genetic divergence detected using the morphological characters was 2.30 (range, 0.45-4.70). Plant height and coat adhesion exhibited the highest divergence among the cultivars. The average genetic diversity based on AFLP data was 43% (range, 0-79%). Dendrograms derived from both techniques divided the cultivars into two groups: noble and semi-noble. Together with the divergence within groups, the correlation between morphological and molecular data suggested that the cultivars in the noble group had greater phenotypic stability than those in the semi-noble group. Analysis of Jonas and Quitéria cultivars using these two techniques revealed only slight differences, suggesting that these cultivars may be clones or have a high degree of kinship.

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Genetic diversity and classification of Nelumbo germplasm of different origins by RAPD and ISSR analysis

Cited by 46 publications

References 17 publications

Development and characterization of genic-SSR markers from different Asia lotus (Nelumbo nucifera) types by RNA-seq

Development and characterization of genic-SSR markers from different Asia lotus (Nelumbo nucifera) types by RNA-seq

RAPD and ISSR Marker-Based Comparative Evaluation of Genetic Diversity Among Indian Germplasms of Euryale ferox: an Aquatic Food Plant

Genetic divergence among Brazilian garlic cultivars based on morphological characters and AFLP markers

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