ISSR Marker Based Population Genetic Study of<i>Melocanna baccifera</i>(Roxb.) Kurz: A Commercially Important Bamboo of Manipur, North-East India

Nilkanta, Heikrujam; Amom, Thoungamba; Tikendra, Leimapokpam; Rahaman, Hamidur; Nongdam, Potshangbam

doi:10.1155/2017/3757238

Cited by 42 publications

(37 citation statements)

References 46 publications

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“…However, we could observe that genetic variations among populations was significantly lower than that within populations indicating several subtle allelic variations among the members of each sub-populations. This was similar to previous studies for bamboo species such as Melocanna baccifera and Bashania fangiana (Dwarf bamboo) using ISSR and AFLP markers, respectively [97,98].…”

Section: Population Structure Of Asian Bamboosupporting

confidence: 91%

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Ramakrishnan

Vinod

et al. 2019

Forests

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Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. Phyllostachys genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as gag and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus Phyllostachys revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that Phyllostachys bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos.

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Section: Population Structure Of Asian Bamboosupporting

confidence: 91%

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Ramakrishnan

Vinod

et al. 2019

Forests

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“…Among molecular markers, ISSRs (Inter Simple Sequence Repeat) stand out, because they do not require prior information of the DNA sequence and present laboratory procedures with good transferability (Dias et al, 2015). ISSR are semi-arbitrarily amplified by PCR (polymerase chain reaction), using a complementary primer for a designated microsatellite (Nilkanta et al, 2017). In the Stylosanthes genus, ISSR markers have been considered more efficient than both RAPD and STR markers to detect genetic variability (Nagaich and Chandra, 2009).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity in natural populations of Stylosanthes scabra using ISSR markers

Costa¹,

Fracetto²,

Fracetto³

et al. 2018

gmr

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Genetic diversity is the basis for genetic improvement, providing genes for new cultivars. Stylosanthes scabra is a legume used in pastures, presenting economic importance in tropical and subtropical regions. Molecular markers are targeted in population studies, thus we evaluated the genetic diversity distribution of S. scabra in Brazilian semi-arid northeastern among and within populations, from molecular markers ISSR. Four natural populations of S. scabra located in the municipalities of Santa Cruz do Capibaribe, Floresta, Sertânia and Petrolina from Pernambuco state were used. We selected seven ISSR primers for amplification and analyzed 75 individuals. A total of 88 bands were amplified with a percentage of 95.27% polymorphism at the species level. AMOVA test revealed that 40.0% of the total genetic variation is within populations while 60.0% among populations. The population differentiation was 0.332 and the migrant's number per generation was 0.5. Grouping analysis confirmed a high level of differentiation among populations. The populations with the greatest variability were Santa Cruz do Capibaribe and Petrolina, and the ISSR markers were efficient for the genetic diversity quantification in S. scabra, which presented greater variability among populations than Lira Júnior MA, et al 2 Genetics and Molecular Research 17 (1): gmr16039866 within populations. In short, this variability will be very useful in future breeding programs for this species.

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“…ISSR markers are simple, randomly distributed in the genome, exhibit mostly dominant inheritance pattern and require low quantity of DNA. They are employed in species and plant varietal identification, taxonomic and genetic diversity studies, gene mapping and clonal fidelity testing of in vitro derived plants [14]. The main limitations of ISSR marker are low reproducibility and homology of co-migrating amplification products [15].…”

Section: Inter Simple Sequence Repeat (Issr)mentioning

confidence: 99%

The Use of Molecular Marker Methods in Plants: A Review

2017

IJCRR

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Different DNA markers have been utilized in the last few decades as important molecular tools in plants for genetic relation studies among individuals, hybrid and varietal identification, phylogenetic relationship among species, gene mapping and tracking quantitative trait loci. These markers can be broadly classified into hybridization and PCR based markers. Restriction fragment length polymorphism (RFLP) represents the hybridization based marker; while PCR dependent includes more reliable and advanced polymorphic markers like amplified fragment length polymorphism (AFLP), inter-simple sequence repeats (ISSR), single nucleotide polymorphism (SNP), sequence related amplified polymorphism (SRAP), start codon targeted (SCoT) and interprimer binding site (iPBS) among others. Functional markers (FMs) have also been developed from functionally characterised sequence motifs which are superior to random markers due to their complete linkage to trait locus alleles. With the advent of next generation sequencing (NGS) technology, excellent opportunities are offered for generating ample structural and functional genomic information in many important crops. The novel approach of genotyping-by-sequencing (GBS) employs NGS protocols for discovering and genotyping SNPs in many important crop genomes and populations. The present review focuses on the description of varied molecular markers, their methodologies, strengths and limitations as well as applications in plant breeding and genetic research.

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ISSR Marker Based Population Genetic Study ofMelocanna baccifera(Roxb.) Kurz: A Commercially Important Bamboo of Manipur, North-East India

Cited by 42 publications

References 46 publications

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Genetic diversity in natural populations of Stylosanthes scabra using ISSR markers

The Use of Molecular Marker Methods in Plants: A Review

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