The Experts below are selected from a list of 318 Experts worldwide ranked by ideXlab platform
Mathews M Dida - One of the best experts on this subject based on the ideXlab platform.
-
population structure and diversity in Finger Millet eleusine coracana germplasm
Tropical Plant Biology, 2008Co-Authors: Mathews M Dida, Jeffrey L Bennetzen, Nelson Wanyera, Melanie Harrison L Dunn, Katrien M DevosAbstract:A genotypic analysis of 79 Finger Millet accessions (E. coracana subsp. coracana) from 11 African and five Asian countries, plus 14 wild E. coracana subsp. africana lines collected in Uganda and Kenya was conducted with 45 SSR markers distributed across the Finger Millet genome. Phylogenetic and population structure analyses showed that the E. coracana germplasm formed three largely distinct subpopulations, representing subsp. africana, subsp. coracana originating from Africa and subsp. coracana originating from Asia. A few lines showed admixture between the African and Asian cultivated germplasm pools and were the result of either targeted or accidental intercrossing. Evidence of gene flow was also seen between the African wild and cultivated subpopulations, indicating that hybridizations among subspecies occur naturally where both species are sympatric. The genotyping, combined with phylogenetic and population structure analyses proved to be very powerful in predicting the origin of breeding materials. The genotypic study was complemented by a phenotypic evaluation. The wild and cultivated accessions differed by a range of domestication-related characters, such as tiller number, plant height, peduncle length, seed color and grain yield. Significant differences in plant architecture and yield were also identified between the Asian and African subpopulations. The observed population structure within cultivated Finger Millet is consistent with the theory that, after the introduction of Finger Millet from Africa into India via the trade routes some 3000 years ago, the two germplasm pools remained largely isolated until recent times. The significantly lower diversity present within the Asian subpopulation also suggests that it arose from a relatively small number of founder plants.
-
comparative analyses reveal high levels of conserved colinearity between the Finger Millet and rice genomes
Theoretical and Applied Genetics, 2007Co-Authors: Mathews M Dida, M D Gale, Katrien M DevosAbstract:Finger Millet is an allotetraploid (2n = 4x = 36) grass that belongs to the Chloridoideae subfamily. A comparative analysis has been carried out to determine the relationship of the Finger Millet genome with that of rice. Six of the nine Finger Millet homoeologous groups corresponded to a single rice chromosome each. Each of the remaining three Finger Millet groups were orthologous to two rice chromosomes, and in all the three cases one rice chromosome was inserted into the centromeric region of a second rice chromosome to give the Finger Millet chromosomal configuration. All observed rearrangements were, among the grasses, unique to Finger Millet and, possibly, the Chloridoideae subfamily. Gene orders between rice and Finger Millet were highly conserved, with rearrangements being limited largely to single marker transpositions and small putative inversions encompassing at most three markers. Only some 10% of markers mapped to non-syntenic positions in rice and Finger Millet and the majority of these were located in the distal 14% of chromosome arms, supporting a possible correlation between recombination and sequence evolution as has previously been observed in wheat. A comparison of the organization of Finger Millet, Panicoideae and Pooideae genomes relative to rice allowed us to infer putative ancestral chromosome configurations in the grasses.
-
the genetic map of Finger Millet eleusine coracana
Theoretical and Applied Genetics, 2006Co-Authors: Mathews M Dida, Sujatha Ramakrishnan, Jeffrey L Bennetzen, M D Gale, Katrien M DevosAbstract:Restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), expressed-sequenced tag (EST), and simple sequence repeat (SSR) markers were used to generate a genetic map of the tetraploid Finger Millet (Eleusine coracana subsp. coracana) genome (2n = 4x = 36). Because levels of variation in Finger Millet are low, the map was generated in an inter-subspecific F2 population from a cross between E. coracana subsp. coracana cv. Okhale-1 and its wild progenitor E. coracana subsp. africana acc. MD-20. Duplicated loci were used to identify homoeologous groups. Assignment of linkage groups to the A and B genome was done by comparing the hybridization patterns of probes in Okhale-1, MD-20, and Eleusine indica acc. MD-36. E. indica is the A genome donor to E. coracana. The maps span 721 cM on the A genome and 787 cM on the B genome and cover all 18 Finger Millet chromosomes, at least partially. To facilitate the use of marker-assisted selection in Finger Millet, a first set of 82 SSR markers was developed. The SSRs were identified in small-insert genomic libraries generated using methylation-sensitive restriction enzymes. Thirty-one of the SSRs were mapped. Application of the maps and markers in hybridization-based breeding programs will expedite the improvement of Finger Millet.
Katrien M Devos - One of the best experts on this subject based on the ideXlab platform.
-
population structure and diversity in Finger Millet eleusine coracana germplasm
Tropical Plant Biology, 2008Co-Authors: Mathews M Dida, Jeffrey L Bennetzen, Nelson Wanyera, Melanie Harrison L Dunn, Katrien M DevosAbstract:A genotypic analysis of 79 Finger Millet accessions (E. coracana subsp. coracana) from 11 African and five Asian countries, plus 14 wild E. coracana subsp. africana lines collected in Uganda and Kenya was conducted with 45 SSR markers distributed across the Finger Millet genome. Phylogenetic and population structure analyses showed that the E. coracana germplasm formed three largely distinct subpopulations, representing subsp. africana, subsp. coracana originating from Africa and subsp. coracana originating from Asia. A few lines showed admixture between the African and Asian cultivated germplasm pools and were the result of either targeted or accidental intercrossing. Evidence of gene flow was also seen between the African wild and cultivated subpopulations, indicating that hybridizations among subspecies occur naturally where both species are sympatric. The genotyping, combined with phylogenetic and population structure analyses proved to be very powerful in predicting the origin of breeding materials. The genotypic study was complemented by a phenotypic evaluation. The wild and cultivated accessions differed by a range of domestication-related characters, such as tiller number, plant height, peduncle length, seed color and grain yield. Significant differences in plant architecture and yield were also identified between the Asian and African subpopulations. The observed population structure within cultivated Finger Millet is consistent with the theory that, after the introduction of Finger Millet from Africa into India via the trade routes some 3000 years ago, the two germplasm pools remained largely isolated until recent times. The significantly lower diversity present within the Asian subpopulation also suggests that it arose from a relatively small number of founder plants.
-
comparative analyses reveal high levels of conserved colinearity between the Finger Millet and rice genomes
Theoretical and Applied Genetics, 2007Co-Authors: Mathews M Dida, M D Gale, Katrien M DevosAbstract:Finger Millet is an allotetraploid (2n = 4x = 36) grass that belongs to the Chloridoideae subfamily. A comparative analysis has been carried out to determine the relationship of the Finger Millet genome with that of rice. Six of the nine Finger Millet homoeologous groups corresponded to a single rice chromosome each. Each of the remaining three Finger Millet groups were orthologous to two rice chromosomes, and in all the three cases one rice chromosome was inserted into the centromeric region of a second rice chromosome to give the Finger Millet chromosomal configuration. All observed rearrangements were, among the grasses, unique to Finger Millet and, possibly, the Chloridoideae subfamily. Gene orders between rice and Finger Millet were highly conserved, with rearrangements being limited largely to single marker transpositions and small putative inversions encompassing at most three markers. Only some 10% of markers mapped to non-syntenic positions in rice and Finger Millet and the majority of these were located in the distal 14% of chromosome arms, supporting a possible correlation between recombination and sequence evolution as has previously been observed in wheat. A comparison of the organization of Finger Millet, Panicoideae and Pooideae genomes relative to rice allowed us to infer putative ancestral chromosome configurations in the grasses.
-
the genetic map of Finger Millet eleusine coracana
Theoretical and Applied Genetics, 2006Co-Authors: Mathews M Dida, Sujatha Ramakrishnan, Jeffrey L Bennetzen, M D Gale, Katrien M DevosAbstract:Restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), expressed-sequenced tag (EST), and simple sequence repeat (SSR) markers were used to generate a genetic map of the tetraploid Finger Millet (Eleusine coracana subsp. coracana) genome (2n = 4x = 36). Because levels of variation in Finger Millet are low, the map was generated in an inter-subspecific F2 population from a cross between E. coracana subsp. coracana cv. Okhale-1 and its wild progenitor E. coracana subsp. africana acc. MD-20. Duplicated loci were used to identify homoeologous groups. Assignment of linkage groups to the A and B genome was done by comparing the hybridization patterns of probes in Okhale-1, MD-20, and Eleusine indica acc. MD-36. E. indica is the A genome donor to E. coracana. The maps span 721 cM on the A genome and 787 cM on the B genome and cover all 18 Finger Millet chromosomes, at least partially. To facilitate the use of marker-assisted selection in Finger Millet, a first set of 82 SSR markers was developed. The SSRs were identified in small-insert genomic libraries generated using methylation-sensitive restriction enzymes. Thirty-one of the SSRs were mapped. Application of the maps and markers in hybridization-based breeding programs will expedite the improvement of Finger Millet.
Salej Sood - One of the best experts on this subject based on the ideXlab platform.
-
Phenomics and genomics of Finger Millet: current status and future prospects
Planta, 2019Co-Authors: Salej Sood, Dinesh C. Joshi, Ajay Kumar Chandra, Anil KumarAbstract:Main conclusion Diverse gene pool, advanced plant phenomics and genomics methods enhanced genetic gain and understanding of important agronomic, adaptation and nutritional traits in Finger Millet. Finger Millet ( Eleusine coracana L. Gaertn) is an important minor Millet for food and nutritional security in semi-arid regions of the world. The crop has wide adaptability and can be grown right from high hills in Himalayan region to coastal plains. It provides food grain as well as palatable straw for cattle, and is fairly climate resilient. The crop has large gene pool with distinct features of both Indian and African germplasm types. Interspecific hybridization between Indian and African germplasm has resulted in greater yield enhancement and disease resistance. The crop has shown numerous advantages over major cereals in terms of stress adaptation, nutritional quality and health benefits. It has indispensable repository of novel genes for the benefits of mankind. Although rapid strides have been made in allele mining in model crops and major cereals, the progress in Finger Millet genomics is lacking. Comparative genomics have paved the way for the marker-assisted selection, where resistance gene homologues of rice for blast and sequence variants for nutritional traits from other cereals have been invariably used. Transcriptomics studies have provided preliminary understanding of the nutritional variation, drought and salinity tolerance. However, the genetics of many important traits in Finger Millet is poorly understood and need systematic efforts from biologists across disciplines. Recently, deciphered Finger Millet genome will enable identification of candidate genes for agronomically and nutritionally important traits. Further, improvement in genome assembly and application of genomic selection as well as genome editing in near future will provide plethora of information and opportunity to understand the genetics of complex traits.
-
cross genera transferability of rice and Finger Millet genomic ssrs to barnyard Millet echinochloa spp
3 Biotech, 2018Co-Authors: Kalyana B Babu, Salej Sood, Dinesh Kumar, Anjeli Joshi, A Pattanayak, Lakshmi Kant, H D UpadhyayaAbstract:Barnyard Millet (Echinochloa spp.) is an important crop from nutritional point of view, nevertheless, the genetic information is very scarce. In the present investigation, rice and Finger Millet genomic SSRs were used for assessing cross transferability, identification of polymorphic markers, syntenic regions, genetic diversity and population structure analysis of barnyard Millet genotypes. We observed 100% cross transferability for Finger Millet SSRs, of which 91% were polymorphic, while 71% of rice markers were cross transferable with 48% polymorphic out of them. Twenty-nine and sixteen highly polymorphic Finger Millet and rice SSRs yielded a mean of 4.3 and 3.38 alleles per locus in barnyard Millet genotypes, respectively. The PIC values varied from 0.27 to 0.73 at an average of 0.54 for Finger Millet SSRs, whereas it was from 0.15 to 0.67 at an average of 0.44 for rice SSRs. High synteny was observed for markers related to panicle length, yield-related traits, spikelet fertility, plant height, root traits, leaf senescence, blast and brown plant hopper resistance. Although the rice SSRs located on chromosome 10 followed by chromosome 6 and 11 were found to be more transferable to barnyard Millet, the Finger Millet SSRs were more polymorphic and transferable to barnyard Millet genotypes. These SSR data of Finger Millet and rice individually as well as combined together grouped the 11 barnyard Millet genotypes into 2 major clusters. The results of population structure analysis were similar to cluster analysis.
-
Comparative genetic analysis of wild Finger Millet accessions using Finger Millet and maize microsatellite markers
Applied Biological Research, 2017Co-Authors: C. Rashmi, B. Kalyana Babu, Salej SoodAbstract:The genomic information available for Finger Millet is very scarce though the plant is a rich source of highly digestible proteins and dietary fibre with good amounts of soluble and insoluble fractions. In present study, 64 maize and Finger Millet genomic SSRs were used for cross transferability, identification of polymorphic markers and genetic diversity of Finger Millet, both cultivated and wild species. Out of 64 SSRs, only 43 (67%) were amplified across the Finger Millet genotypes. The PIC values of all the polymorphic loci across the 23 Finger Millet genotypes varied from 0.04 to 0.47 (average value 0.17). Based on the parameters of PIC values ≥ 0.26, gene diversity ≥0.43, inbreeding coefficient ≥ 0.60, the SSR loci UGEP33, UMC1858, UMC1805, and UMC2163 were found highly polymorphic. Comparison of SSR polymorphism in Finger Millet genotypes revealed that microsatellites of maize were more polymorphic and were able to identify more diversity in Finger Millet genotypes than the Finger Millet SSRs. Good correlations were found between genetic diversity analysis in differentiation of Finger Millet genotypes using Finger Millet and maize microsatellite markers. Dendrogram generated through UPGMA analysis grouped all the 23 genotypes clustered them into two major groups A and B with maximum similarity found between genotype pairs T552, T622 and T507, T74. The genotype pairs T671 and T760; T187 and T 631, T824 showed lowest similarity in Finger Millet which could be selected for hybrid plant production. The present study enriched the Finger Millet genomics by identifying suitable polymorphic markers of maize and Finger Millet, which can be used for diversity analysis, cultivar identification and QTL mapping studies.
-
Genotyping-by-Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins
The Plant Genome, 2016Co-Authors: Anil Kumar, Apoorv Tiwari, J.p. Jaiswal, Divya Sharma, N. K. Singh, Salej SoodAbstract:Finger Millet [Eleusine coracana (L.) Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of Finger Millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the pres- ent investigation, attempts have been made to characterize the genetically diverse collection of 113 Finger Millet accessions through whole-genome genotyping-by-sequencing (GBS), which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the pres- ence of three subpopulations among the Finger Millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that Finger Millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO) terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput ge- notyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of Finger Millet.
-
Stability of Finger Millet genotypes under diverse environments
Indian Journal of Genetics and Plant Breeding, 2016Co-Authors: Salej Sood, Tssk Patro, Sunil KaradAbstract:The present study aimed at deciphering the stability and patterns of genotype × environment interaction (GEI) in Finger Millet genotypes tested in All India Coordinated Trials using GGE biplot technique. The combined ANOVA for grain yield of five Finger Millet cultivars at four environments showed that environments (E), genotypes (G) and GEI were highly significant (P
Anil Kumar - One of the best experts on this subject based on the ideXlab platform.
-
Phenomics and genomics of Finger Millet: current status and future prospects
Planta, 2019Co-Authors: Salej Sood, Dinesh C. Joshi, Ajay Kumar Chandra, Anil KumarAbstract:Main conclusion Diverse gene pool, advanced plant phenomics and genomics methods enhanced genetic gain and understanding of important agronomic, adaptation and nutritional traits in Finger Millet. Finger Millet ( Eleusine coracana L. Gaertn) is an important minor Millet for food and nutritional security in semi-arid regions of the world. The crop has wide adaptability and can be grown right from high hills in Himalayan region to coastal plains. It provides food grain as well as palatable straw for cattle, and is fairly climate resilient. The crop has large gene pool with distinct features of both Indian and African germplasm types. Interspecific hybridization between Indian and African germplasm has resulted in greater yield enhancement and disease resistance. The crop has shown numerous advantages over major cereals in terms of stress adaptation, nutritional quality and health benefits. It has indispensable repository of novel genes for the benefits of mankind. Although rapid strides have been made in allele mining in model crops and major cereals, the progress in Finger Millet genomics is lacking. Comparative genomics have paved the way for the marker-assisted selection, where resistance gene homologues of rice for blast and sequence variants for nutritional traits from other cereals have been invariably used. Transcriptomics studies have provided preliminary understanding of the nutritional variation, drought and salinity tolerance. However, the genetics of many important traits in Finger Millet is poorly understood and need systematic efforts from biologists across disciplines. Recently, deciphered Finger Millet genome will enable identification of candidate genes for agronomically and nutritionally important traits. Further, improvement in genome assembly and application of genomic selection as well as genome editing in near future will provide plethora of information and opportunity to understand the genetics of complex traits.
-
Genotyping-by-Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins
The Plant Genome, 2016Co-Authors: Anil Kumar, Apoorv Tiwari, J.p. Jaiswal, Divya Sharma, N. K. Singh, Salej SoodAbstract:Finger Millet [Eleusine coracana (L.) Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of Finger Millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the pres- ent investigation, attempts have been made to characterize the genetically diverse collection of 113 Finger Millet accessions through whole-genome genotyping-by-sequencing (GBS), which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the pres- ence of three subpopulations among the Finger Millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that Finger Millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO) terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput ge- notyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of Finger Millet.
-
In-silico mining, type and frequency analysis of genic microsatellites of Finger Millet (Eleusine coracana (L.) Gaertn.): a comparative genomic analysis of NBS-LRR regions of Finger Millet with rice.
Molecular Biology Reports, 2014Co-Authors: B. Kalyana Babu, Salej Sood, Dinesh Pandey, P. K. Agrawal, Anil KumarAbstract: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.
Ceasar S Antony - One of the best experts on this subject based on the ideXlab platform.
-
Finger Millet eleusine coracana l gaertn improvement current status and future interventions of whole genome sequence
Frontiers in Plant Science, 2018Co-Authors: Ceasar S Antony, Theivanayagam Maharajan, T Krishna P Ajeesh, M Ramakrishnan, Roch G Victor, L Satish, S IgnacimuthuAbstract:The whole genome sequence (WGS) of the much awaited, nutrient rich and climate resilient crop, Finger Millet (Eleusine coracana (L.) Gaertn.) has been released recently. While possessing superior mineral nutrients and excellent shelf life as compared to other major cereals, multiploidy nature of the genome and relatively small plantation acreage in less developed countries hampered the genome sequencing of Finger Millet, disposing it as one of the lastly sequenced genomes in cereals. The genomic information available for this crop is very little when compared to other major cereals like rice, maize and barley. As a result, only a limited number of genetic and genomic studies has been undertaken for the improvement of this crop. Finger Millet is known especially for its superior calcium content, but the high-throughput studies are yet to be performed to understand the mechanisms behind calcium transport and grain filling. The WGS of Finger Millet is expected to help to understand this and other important molecular mechanisms in Finger Millet, which may be harnessed for the nutrient fortification of other cereals. In this review, we discuss various efforts made so far on the improvement of Finger Millet including genetic improvement, transcriptome analysis, mapping of quantitative trait loci (QTLs) for traits, etc. We also discuss the pitfalls of modern genetic studies and provide insights for accelerating the Finger Millet improvement with the interventions of WGS in near future. Advanced genetic and genomic studies aided by WGS may help to improve the Finger Millet, which will be helpful to strengthen the nutritional security in addition to food security in the developing countries of Asia and Africa.