scholarly journals Morpho-agronomic Classification of Some Native and Exotic Finger Millet (Eleusine coracana L.) Germplasm Accessions in Ethiopia

2011 ◽  
Vol 4 (1) ◽  
Author(s):  
D Chemeda ◽  
K Gemechu
Keyword(s):  
Finger Millet ◽  
Eleusine Coracana ◽  
Germplasm Accessions

scholarly journals Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

2020 ◽  
Author(s):  
Nathan Daniel Hall ◽  
Jinesh D Patel ◽  
Joseph Scott McElroy ◽  
Leslie Richard Goertzen
Keyword(s):  
Finger Millet ◽  
Draft Genome ◽  
Synonymous Substitution ◽  
Eleusine Coracana ◽  
Eastern Africa ◽  
Syntenic Block ◽  
Individual Gene ◽  
A Genome ◽  
Synonymous Substitution Rates

Abstract Background: Finger millet (Eleusine coracana 2n=4x=36 ) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs. Results: We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A , 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes. Examination of expression within the circadian rhythm pathway suggests A subgenomic preference. Conclusion: The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.

scholarly journals Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Nathan D. Hall ◽  
Jinesh D. Patel ◽  
J. Scott McElroy ◽  
Leslie R. Goertzen
Keyword(s):  
Finger Millet ◽  
Draft Genome ◽  
Synonymous Substitution ◽  
Eleusine Coracana ◽  
Eastern Africa ◽  
Syntenic Block ◽  
Individual Gene ◽  
A Genome ◽  
Synonymous Substitution Rates

AbstractBackgroundFinger millet (Eleusine coracana2n = 4x = 36) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome forE. indicaexisted. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs.ResultsWe produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within theEleusinegenus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A, 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes.ConclusionThe evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.

scholarly journals Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

2021 ◽  
Author(s):  
Nathan Daniel Hall ◽  
Jinesh D Patel ◽  
Joseph Scott McElroy ◽  
Leslie Richard Goertzen
Keyword(s):  
Finger Millet ◽  
Draft Genome ◽  
Synonymous Substitution ◽  
Eleusine Coracana ◽  
Eastern Africa ◽  
Syntenic Block ◽  
Individual Gene ◽  
A Genome ◽  
Synonymous Substitution Rates

Abstract Background: Finger millet (Eleusine coracana 2n=4x=36 ) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs. Results: We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A , 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes. Examination of transcript counts within the Circadian Rhythm Pathway suggests a possible A subgenomic preference. Conclusion: The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.

scholarly journals Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

2020 ◽  
Author(s):  
Nathan Daniel Hall ◽  
Jinesh D Patel ◽  
Joseph Scott McElroy ◽  
Leslie Richard Goertzen
Keyword(s):  
Finger Millet ◽  
Draft Genome ◽  
Synonymous Substitution ◽  
Eleusine Coracana ◽  
Eastern Africa ◽  
Syntenic Block ◽  
Individual Gene ◽  
A Genome ◽  
Synonymous Substitution Rates

Abstract Background: Finger millet (Eleusine coracana 2n=4x=36 ) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs.Results: We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes supports A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A , 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes. Examination of expression within the ciradian rhythm pathway suggests A subgenomic preference.Conclusion: The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.

scholarly journals Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

2021 ◽  
Author(s):  
Nathan Daniel Hall ◽  
Jinesh D Patel ◽  
Joseph Scott McElroy ◽  
Leslie Richard Goertzen
Keyword(s):  
Finger Millet ◽  
Draft Genome ◽  
Synonymous Substitution ◽  
Eleusine Coracana ◽  
Eastern Africa ◽  
Syntenic Block ◽  
Individual Gene ◽  
A Genome ◽  
Synonymous Substitution Rates

Abstract Background: Finger millet (Eleusine coracana 2n=4x=36 ) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs. Results: We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A , 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes.Conclusion: The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.

scholarly journals Adaptability and genotype-environment interaction of finger millet (Eleusine coracana (L.) Gaertn) varieties in North Eastern Ethiopia

2018 ◽  
Vol 13 (26) ◽  
pp. 1331-1337
Author(s):  
Mamo Mulugeta ◽  
Worede Fisseha ◽  
Bezie Yemata ◽  
Assefa Solomon ◽  
Gebremariam Tsegaye
Keyword(s):  
Finger Millet ◽  
Eleusine Coracana ◽  
Environment Interaction ◽  
Eastern Ethiopia ◽  
Genotype Environment Interaction ◽  
North Eastern
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