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Kalyana Babu B.,Vivekananda Parvateeya Krishi Anusanthan Sansthan VPKAS | Agrawal P.K.,Vivekananda Parvateeya Krishi Anusanthan Sansthan VPKAS | Pandey D.,University of the Humanities | Jaiswal J.P.,University of the Humanities | Kumar A.,University of the Humanities
Molecular Biology Reports | Year: 2014

Identification of alleles responsible for various agro-morphological characters is a major concern to further improve the finger millet germplasm. Forty-six genomic SSRs were used for genetic analysis and population structure analysis of a global collection of 190 finger millet genotypes and fifteen agro-morphological characters were evaluated. The overall results showed that Asian genotypes were smaller in height, smaller flag leaf length, less basal tiller number, early flowering and early maturity nature, small ear head length, and smaller in length of longest finger. The 46 SSRs yielded 90 scorable alleles and the polymorphism information content values varied from 0.292 to 0.703 at an average of 0.442. The gene diversity was in the range of 0.355 to 0.750 with an average value of 0.528. The 46 genomic SSR loci grouped the 190 finger millet genotypes into two major clusters based on their geographical origin by the both phylogenetic clustering and population structure analysis by STRUCTURE software. Association mapping of QTLs for 15 agro-morphological characters with 46 genomic SSRs resulted in identification of five markers were linked to QTLs of four traits at a significant threshold (P) level of ≤0.01 and ≤0.001. The QTL for basal tiller number was strongly associated with the locus UGEP81 at a P value of 0.001 by explaining the phenotypic variance (R 2) of 10.8 %. The QTL for days to 50 % flowering was linked by two SSR loci UGEP77 and UGEP90, explained 10 and 8.7 % of R 2 respectively at a P value of 0.01. The SSR marker, FM9 found to have strong association to two agro-morphological traits, flag leaf width (P-0.001, R 2-14.1 %) and plant height (P-0.001, R 2-11.2 %). The markers linked to the QTLs for above agro-morphological characters found in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of alleles into locally well adapted germplasm. © 2014 Springer Science+Business Media. Source


Kalyana Babu B.,University of the Humanities | Pandey D.,University of the Humanities | Agrawal P.K.,Vivekananda Parvateeya Krishi Anusanthan Sansthan VPKAS | Sood S.,Vivekananda Parvateeya Krishi Anusanthan Sansthan VPKAS | Kumar A.,University of the Humanities
Molecular Biology Reports | Year: 2014

In recent years, the increased availability of the DNA sequences has given the possibility to develop and explore the expressed sequence tags (ESTs) derived SSR markers. In the present study, a total of 1956 ESTs of finger millet were used to find the microsatellite type, distribution, frequency and developed a total of 545 primer pairs from the ESTs of finger millet. Thirty-two EST sequences had more than two microsatellites and 1357 sequences did not have any SSR repeats. The most frequent type of repeats was trimeric motif, however the second place was occupied by dimeric motif followed by tetra-, hexa- and penta repeat motifs. The most common dimer repeat motif was GA and in case of trimeric SSRs, it was CGG. The EST sequences of NBS-LRR region of finger millet and rice showed higher synteny and were found on nearly same positions on the rice chromosome map. A total of eight, out of 15 EST based SSR primers were polymorphic among the selected resistant and susceptible finger millet genotypes. The primer FMBLEST5 could able to differentiate them into resistant and susceptible genotypes. The alleles specific to the resistant and susceptible genotypes were sequenced using the ABI 3130XL genetic analyzer and found similarity to NBS-LRR regions of rice and finger millet and contained the characteristic kinase-2 and kinase 3a motifs of plant R-genes belonged to NBS-LRR region. The In-silico and comparative analysis showed that the genes responsible for blast resistance can be identified, mapped and further introgressed through molecular breeding approaches for enhancing the blast resistance in finger millet. © Springer Science+Business Media 2014. Source


Babu B.K.,University of the Humanities | Agrawal P.K.,Vivekananda Parvateeya Krishi Anusanthan Sansthan VPKAS | Pandey D.,University of the Humanities | Sood S.,Vivekananda Parvateeya Krishi Anusanthan Sansthan VPKAS | And 2 more authors.
Sabrao Journal of Breeding and Genetics | Year: 2014

The major limiting factor for production and productivity of finger millet is blast disease caused by Magnaporthe grisea. In the present study, most of the exotic genotypes showed highly resistant to moderately resistant reaction to neck blast and finger blast disease. Neck blast found to have significant and positive correlation with finger blast (0.612**), but a poor correlation was observed with leaf blast (0.08**). Fifty-eight genic SSRs were used for genetic diversity analysis of a global collection of 190 finger millet genotypes. Three SSR markers (RM23842, RM5963 and RM262) were found to be most highly polymorphic loci for differentiating the 190 global collections of finger millet genotypes. The SSR marker RM5963 containing the trimer repeat motif CAG showed highest PIC values, followed by tetra (RM23842) and di (RM262) repeat motif containing SSRs. The 58 genic SSR loci of blast disease grouped the 190 finger millet genotypes into 4 major clusters based on their blast disease response by phylogenetic clustering as revealed by Power Marker software. The average gene diversity existing among all the inbred lines was relatively high (49%), indicating existence of high levels of polymorphisms among the finger millet. Among the genotypes of NW Himalayan region of India, VHC3997 and VHC3930 found highly resistant to neck blast which can be used as donor parents for production of blast resistant finger millet varieties. © Society for the Advancement of Breeding Research in Asia and Oceania (SABRAO) 2014. Source

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