Application of random amplified polymorphic DNA to study genetic diversity in Paspalum scrobiculatum L. (Kodo millet, Poaceae)

M'Ribu, H. Kaburu; Hilu, Khidir W.

doi:10.1007/bf00123272

Cited by 28 publications

(16 citation statements)

References 16 publications

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“…Genomic DNA was isolated following Doyle and Doyle [56] procedure as modified in M'ribu and Hilu [57]. The matK gene was amplified as described in Crawley and Hilu [8].…”

Section: Methodsmentioning

confidence: 99%

Impact of Gene Molecular Evolution on Phylogenetic Reconstruction: A Case Study in the Rosids (Superorder Rosanae, Angiosperms)

Hilu¹,

Black²,

Oza³

2014

PLoS ONE

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Rate of substitution of genomic regions is among the most debated intrinsic features that impact phylogenetic informativeness. However, this variable is also coupled with rates of nonsynonymous substitutions that underscore the nature and degree of selection on the selected genes. To empirically address these variables, we constructed four completely overlapping data sets of plastid matK, atpB, rbcL, and mitochondrial matR genes and used the rosid lineage (angiosperms) as a working platform. The genes differ in combinations of overall rates of nucleotide and amino acid substitutions. Tree robustness, homoplasy, accuracy in contrast to a reference tree, and phylogenetic informativeness are evaluated. The rapidly evolving/unconstrained matK faired best, whereas remaining genes varied in degrees of contribution to rosid phylogenetics across the lineage's 108 million years evolutionary history. Phylogenetic accuracy was low with the slowly evolving/unconstrained matR despite least amount of homoplasy. Third codon positions contributed the highest amount of parsimony informative sites, resolution and informativeness, but magnitude varied with gene mode of evolution. These findings are in clear contrast with the views that rapidly evolving regions and the 3rd codon position have inevitable negative impact on phylogenetic reconstruction at deep historic level due to accumulation of multiple hits and subsequent elevation in homoplasy and saturation. Relaxed evolutionary constraint in rapidly evolving genes distributes substitutions across codon positions, an evolutionary mode expected to reduce the frequency of multiple hits. These findings should be tested at deeper evolutionary histories.

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“…Genomic DNA was isolated following Doyle and Doyle [56] procedure as modified in M'ribu and Hilu [57]. The matK gene was amplified as described in Crawley and Hilu [8].…”

Section: Methodsmentioning

confidence: 99%

Impact of Gene Molecular Evolution on Phylogenetic Reconstruction: A Case Study in the Rosids (Superorder Rosanae, Angiosperms)

Hilu¹,

Black²,

Oza³

2014

PLoS ONE

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“…Molecular techniques like restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNA (RAPDs) have been used in the genus Paspalum to study, for instance, genetic diversity (Liu et al 1994;M'Ribu and Hilu 1996;Jarret et al 1998;Pereira et al 2000), the phylogenetic relationship among closely related species of this genus (Pereira et al 1999;Casa 1995) and to analyze the mode of reproduction (Ortiz et al 1997) In the studied area, the populations of this species show a predominance of apomictic biotypes. Therefore, these populations, like populations of the autogamous biotypes, might show reduced variability within population and wide diversity among populations.…”

Section: Introductionmentioning

confidence: 99%

Genetic variability in natural populations of Paspalum dilatatum Poir. analyzed by means of morphological traits and molecular markers

García

Balatti

Arturi

2007

Genet Resour Crop Evol

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Native species show adaptive traits that are difficult to find in introduced species. The Pampas region in Argentina is a valuable nature reserve of grasses and Paspalum dilatatum Poir. is one of the most important grasses found there. Based on ploidy level and on morphological traits, five biotypes of P. dilatatum have been described. Two of them were included in this study: a tetraploid biotype with sexual reproduction and a pentaploid biotype with apomictic reproduction. We analyzed the genetic diversity in eight native populations from the Salado basin, Argentina, using both quantitative traits and molecular data (RAPD) with these aims: to obtain information of the degree of phenotypic variation in that area, to know which the pattern of distribution of this variation is and to look for association between molecular markers with populational or biotypic differentiation. Cluster analysis based on morphological data grouped the individuals of the different populations by ploidy level. Molecular markers showed the inverse situation because individuals were grouped by geographic origin as opposed to biotype. Moreover, since RAPD did not discriminate between biotypes with sexual or apomictic reproduction, they are probably not associated with mating system. The results let us conclude that polygenic traits such as LP, LBSR, NRT and NSP can discriminate between biotypes and molecular markers such as bands 12, 40, 19 and 46 can be used to discriminate among populations, probably because they detect neutral variation.

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“…The only genetic study available in P. scrobiculatum was based on RAPD (Random amplified polymorphic DNA) markers (M'Ribu and Hilu 1996), wherein nine Indian and seven African P. scrobiculatum accessions along with accessions from other two species were analyzed and high level of polymorphism was observed, Table 1 comparable to our studies. And genotypes were grouped in quite distinct Indian vs. African clusters.…”

Section: Genetic Diversity Based On Functional Markers (Scot and Srap)mentioning

confidence: 84%

“…These genomic resources can serve as potential sources of novel alleles for introgression into other cereals for improving nutritional properties and producing climate resilient crops (Kole et al 2015). Compared to foxtail millet, very few genomic resources and molecular characterization reports are available in kodo millet (M'Ribu and Hilu 1996;Kushwaha et al 2015 were employed to characterize kodo millet germplasm collected from 12 diverse regions of India with the objective to evaluate the level of available genetic diversity and structure among 96 accessions of kodo millet. The ISSR, SRAP and SCoT markers were used for the present study due to their universal nature, high polymorphism rates and in the absence of kodo millet specific genomic resources.…”

Section: Introductionmentioning

confidence: 99%

Neutral and functional marker based genetic diversity in kodo millet (Paspalum scrobiculatum L.)

et al. 2016

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Kodo millet (Paspalum scrobiculatum L.) is known for its high nutritive value, dietary fiber, antioxidant activity, as well as for drought tolerance. It is primarily grown as a grain in India and in Africa it is either cultivated or harvested in wild. Neutral-ISSR (inter simple sequence repeat) as well as functional-SCoT (start codon targeted) and SRAP (sequence-related amplified polymorphism) markers were employed for genetic diversity studies in 96 accessions of kodo millet collected from diverse regions of India. The genetic diversity parameters like average bands per primer, Polymorphic information content, Nei's gene diversity and Shannon's information index of 11.22, 9.69; 0.12, 0.11; 0.15 ± 0.14, 0.13 ± 0.13 and 0.26 ± 0.21, 0.22 ± 0.19 was observed with neutral and functional markers respectively. Neutral markers were showing higher values as compared to functional markers for the genetic diversity parameters as discussed. Structure based analysis placed all the accessions into four sub-groups not strictly according to their geographical locations. The accessions from Bihar followed by Karnataka were showing high diversity based on both the marker systems useful for designing exploration, conservation and germplasm enrichment strategies. Further, the set of diverse accessions selected based on these markers would serve as potential sources of unique alleles and may be exploited in future for enhancement and utilization of kodo millet germplasm. Usage of African gene pool and wild species for broadening the genetic base of Indian kodo millet was also suggested based on the present studies.

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Application of random amplified polymorphic DNA to study genetic diversity in Paspalum scrobiculatum L. (Kodo millet, Poaceae)

Cited by 28 publications

References 16 publications

Impact of Gene Molecular Evolution on Phylogenetic Reconstruction: A Case Study in the Rosids (Superorder Rosanae, Angiosperms)

Impact of Gene Molecular Evolution on Phylogenetic Reconstruction: A Case Study in the Rosids (Superorder Rosanae, Angiosperms)

Genetic variability in natural populations of Paspalum dilatatum Poir. analyzed by means of morphological traits and molecular markers

Neutral and functional marker based genetic diversity in kodo millet (Paspalum scrobiculatum L.)

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