Development and crosstransferability of functionally relevant microsatellite markers in Dendrocalamus latiflorus and related bamboo species

Bhandawat, Abhishek; Sharma, Vikas; Sharma, Himanshu; Sood, Anil K.; Sharma, Ram Kumar

doi:10.1007/s12041-014-0377-9

Cited by 16 publications

(10 citation statements)

References 12 publications

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“…Moreover, India has 2nd richest bamboo bioresource after China, with ~130 species representing 18 genera (Kumar, 2004), spanning large area of temperate, subtropics and tropics. Previously, genetic marker based phylogeny clearly distinguished temperate and tropical/subtropical species (Sharma et al, 2008; Bhandawat et al, 2014, 2016; Bhandawat, 2016). Dendrocalamus hamiltonii (hexaploid; 2n = 6x = 72) is a giant, sympodial, fast growing subtropical bamboo with a life cycle of about 30 years and high commercial importance (Tewari, 1992; Bedell, 2006).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Transcriptional Profiling to Elucidate Key Candidates Involved in Bud Burst and Rattling Growth in a Subtropical Bamboo (Dendrocalamus hamiltonii)

et al. 2017

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Bamboo, one of the fastest growing plants, can be a promising model system to understand growth. The study provides an insight into the complex interplay between environmental signaling and cellular machineries governing initiation and persistence of growth in a subtropical bamboo (Dendrocalamus hamiltonii). Phenological and spatio-temporal transcriptome analysis of rhizome and shoot during the major vegetative developmental transitions of D. hamiltonii was performed to dissect factors governing growth. Our work signifies the role of environmental cues, predominantly rainfall, decreasing day length, and high humidity for activating dormant bud to produce new shoot, possibly through complex molecular interactions among phosphatidylinositol, calcium signaling pathways, phytohormones, circadian rhythm, and humidity responses. We found the coordinated regulation of auxin, cytokinin, brassinosteroid signaling and cell cycle modulators; facilitating cell proliferation, cell expansion, and cell wall biogenesis supporting persistent growth of emerging shoot. Putative master regulators among these candidates were identified using predetermined Arabidopsis thaliana protein-protein interaction network. We got clues that the growth signaling begins far back in rhizome even before it emerges out as new shoot. Putative growth candidates identified in our study can serve in devising strategies to engineer bamboos and timber trees with enhanced growth and biomass potentials.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Transcriptional Profiling to Elucidate Key Candidates Involved in Bud Burst and Rattling Growth in a Subtropical Bamboo (Dendrocalamus hamiltonii)

et al. 2017

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“…Simple sequence repeats (SSRs) are preferred tool for plant genotyping because they are abundant in genome, informative, codominant and multi-allelic genetic markers; that are also experimentally reproducible and transferable among related species (Mason 2015). In the last decade, several microsatellite markers have been identified in bamboo either by mining from the sequence information available in database ( Barkley et al 2005;Dong et al 2011;Bhandawat et al 2014) or development of novel markers using method based on microsatellite-enriched genomic library (Nayak and Rout 2005;Kaneko et al 2008;Abreu et al 2011;Ndiaye et al 2013). Availability of draft genome sequence of Phyllostachys heterocycla var.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and structure of Dendrocalamus hamiltonii natural metapopulation: a commercially important bamboo species of northeast Himalayas

et al. 2019

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Dendrocalamus hamiltonii is a commercially important bamboo species of India, experiencing population depletion due to heavy extraction from natural forests. Nuclear simple sequence repeats (nSSRs) were used to study the genetic diversity and population genetic structure of 19 natural stands of D. hamiltonii distributed across the northeast Himalayas. A total of 68 nSSR primer pairs of D. latiflorus and Bambusa arundinacea have been tested in D. hamiltonii for their transferability, out of which 17 primers showing positive and polymorphic amplification were used for genotyping. A total of 130 alleles were generated in 535 individuals of all the populations using selected primer pairs. The marker analysis indicated that D. hamiltonii populations have maintained a low level of genetic diversity (h = 0.175, I = 0.291) in northeastern region of India. Despite a large proportion of the genetic variation (83.47%) confined within the populations, a moderate level of genetic differentiation (F ST = 0.165) was observed among the populations. The clustering pattern obtained in UPGMA and STRU CTU RE analysis revealed that most of the populations were clustered in accordance with their geographical distribution. Two populations (DH03 and DH13) exhibiting significant genetic admixture were identified and recommended for in situ conservation. In addition, six highly diverse populations were also suggested for conservation in different geographical area under study. The study has revealed useful nSSR markers for D. hamiltonii, which were lacking earlier and the information generated herein is of paramount importance in devising programs for species conservation and genetic improvement.

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“…1 or 2 alleles per individual ( Figure 1a) but rest 7 exhibited more than 2 bands in single individual when the PCR products resolved in high resolution agarose gel (Figure 1b), this may be attributed to the polyploid nature of the species. The multiple alleles generated with these primer sets were also reported in the parent literature where the primers were developed for D. latiflorus and tested their cross transferability in 36 other bamboo species of various ploidy level (Bhandawat et al, 2014). The problem remained persistent with the different set of SSR primers developed in bamboos (Bhandawat et al, 2015;Bhandawat et al, 2019) as well as other polyploid plant species viz.…”

Section: Research Notementioning

confidence: 98%

“…The detailed geographic information of sampling location is given in supplementary table 1. The SSR primers used in the current study were validated through cross-transferability; a total of 62 primer pairs of D. latiflorus (Bhandawat et al, 2014) were screened in D. hamiltonii, and 17 of these demonstrated polymorphic banding pattern (supplementary table 2). Among these, 10 primers gave typical banding pattern of microsatellite markers i.e.…”

Section: Research Notementioning

confidence: 99%

“…will be lost but the results generated here will be more reliable than the dominant markers. Therefore, in majority of studies data generated with SSR markers were analyzed by transforming allelic data into binary matrix (Teixeira et al, 2014;Bhandawat et al, 2014Bhandawat et al, , 2015Bhandawat et al, and 2019. Also, the quantitative as well as non-quantitative measure calculated with non-allelic data set could be used to characterize and describe the populations.…”

Section: Research Notementioning

confidence: 99%

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Usage of microsatellite markers for characterization of polyploids: a case study in reference to hexaploid bamboo species

2020

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Microsatellite markers are most valuable tools for characterization of plant genetic resources or population genetic analysis. Since they are codominant and allelic markers, utilizing them in polyploid species remained doubtful. In such cases, microsatellite markers are usually analyzed by treating them as dominant marker. In the current study, it has been showed that despite of losing the advantage of co-dominance, microsatellite markers are still powerful tool for genotyping of polyploid species because of availability of large number of reproducible alleles per locus. It has been studied by genotyping of nineteen sub populations of Dendrocalamus hamiltonii (hexaploid bamboo species) with seventeen polymorphic SSR primer pairs. Among these, ten primers gave typical banding pattern of microsatellite marker as expected in diploid species but rest seven gave unusual pattern i.e. more than two bands per locus per genotype. In such case genotyping data are generally analyzed by considering as dominant markers. Given these facts, data were analyzed in both ways as dominant and codominant. All the seventeen primer were first scored as non-allelic data and analyzed; later ten primer pairs giving standard banding pattern were analyzed as allelic data and the results were compared. The UPGMA clustering and genetic structure showed that results obtained with both the data sets were very similar, and therefore the SSR marker could be utilized to characterize polyploid species by considering them as dominant marker. The study is highly useful to widen the scope of SSR markers applications and beneficial to the researchers dealing with polyploid species.

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Development and crosstransferability of functionally relevant microsatellite markers in Dendrocalamus latiflorus and related bamboo species

Cited by 16 publications

References 12 publications

Genome-Wide Transcriptional Profiling to Elucidate Key Candidates Involved in Bud Burst and Rattling Growth in a Subtropical Bamboo (Dendrocalamus hamiltonii)

Genome-Wide Transcriptional Profiling to Elucidate Key Candidates Involved in Bud Burst and Rattling Growth in a Subtropical Bamboo (Dendrocalamus hamiltonii)

Genetic diversity and structure of Dendrocalamus hamiltonii natural metapopulation: a commercially important bamboo species of northeast Himalayas

Usage of microsatellite markers for characterization of polyploids: a case study in reference to hexaploid bamboo species

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