scholarly journals Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet

Genome ◽  
2011 ◽  
Vol 54 (6) ◽  
pp. 498-506 ◽  
Author(s):  
Ryoko Hirano ◽  
Ken Naito ◽  
Kenji Fukunaga ◽  
Kazuo N. Watanabe ◽  
Ryo Ohsawa ◽  
...  
Keyword(s):  
Foxtail Millet ◽  
Crop Evolution ◽  
Setaria Italica ◽  
Entire Genome ◽  
Transposon Display ◽  
Green Foxtail ◽  
Genome Wide ◽  
History Of ◽  
Genetic Structures ◽  
The Relationship

Although the origin and domestication process of foxtail millet (Setaria italica subsp. italica (L.) P. Beauv.) has been studied by several groups, the issue is still ambiguous. It is essential to resolve this issue by studying a large number of accessions with sufficient markers covering the entire genome. Genetic structures were analyzed by transposon display (TD) using 425 accessions of foxtail millet and 12 of the wild ancestor green foxtail (Setaria italica subsp. viridis (L.) P. Beauv.). We used three recently active transposons (TSI-1, TSI-7, and TSI-10) as genome-wide markers and succeeded in demonstrating geographical structures of the foxtail millet. A neighbor-joining dendrogram based on TD grouped the foxtail millet accessions into eight major clusters, each of which consisted of accessions collected from adjacent geographical areas. Eleven out of 12 green foxtail accessions were grouped separately from the clusters of foxtail millet. These results indicated strong regional differentiations and a long history of cultivation in each region. Furthermore, we discuss the relationship between foxtail millet and green foxtail and suggest a monophyletic origin of foxtail millet domestication.

scholarly journals Current State and Perspectives in Population Genomics of the Common Bean

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 330 ◽  
Author(s):  
Gaia Cortinovis ◽  
Giulia Frascarelli ◽  
Valerio Di Vittori ◽  
Roberto Papa
Keyword(s):  
Common Bean ◽  
Population Genomics ◽  
Crop Evolution ◽  
Entire Genome ◽  
Sequencing Technologies ◽  
Specific Effects ◽  
Current State ◽  
Genome Wide ◽  
History Of ◽  
Genomic Basis

Population genomics integrates advances in sequencing technologies, bioinformatics tools, statistical methods and software into research on evolutionary and population genetics. Its application has provided novel approaches that have significantly advanced our understanding of new and long-standing questions in evolutionary processes. This has allowed the disentangling of locus-specific effects from genome-wide effects and has shed light on the genomic basis of fitness, local adaptation and phenotypes. “-Omics” tools have provided a comprehensive genome-wide view of the action of evolution. The specific features of the Phaseolus genus have made it a unique example for the study of crop evolution. The well-documented history of multiple domestications in Phaseolus vulgaris L. (common bean) and its further adaptation to different environments have provided the opportunity to investigate evolutionary issues, such as convergent evolution in the same species across different domestication events. Moreover, the availability of the P. vulgaris reference genome now allows adaptive variations to be easily mapped across the entire genome. Here, we provide an overview of the most significant outcomes obtained in common bean through the use of different computational tools for analysis of population genomics data.

scholarly journals Variation in VKORC1 Is Associated with Vascular Dementia

2021 ◽  
Vol 80 (3) ◽  
pp. 1329-1337
Author(s):  
Jure Mur ◽  
Daniel L. McCartney ◽  
Daniel I. Chasman ◽  
Peter M. Visscher ◽  
Graciela Muniz-Terrera ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Vascular Dementia ◽  
Genetic Variant ◽  
Warfarin Dose ◽  
Uk Biobank ◽  
Parental History ◽  
Genome Wide ◽  
History Of ◽  
First Time ◽  
The Relationship

Background: The genetic variant rs9923231 (VKORC1) is associated with differences in the coagulation of blood and consequentially with sensitivity to the drug warfarin. Variation in VKORC1 has been linked in a gene-based test to dementia/Alzheimer’s disease in the parents of participants, with suggestive evidence for an association for rs9923231 (p = 1.8×10–7), which was included in the genome-wide significant KAT8 locus. Objective: Our study aimed to investigate whether the relationship between rs9923231 and dementia persists only for certain dementia sub-types, and if those taking warfarin are at greater risk. Methods: We used logistic regression and data from 238,195 participants from UK Biobank to examine the relationship between VKORC1, risk of dementia, and the interplay with warfarin use. Results: Parental history of dementia, APOE variant, atrial fibrillation, diabetes, hypertension, and hypercholesterolemia all had strong associations with vascular dementia (p < 4.6×10–6). The T-allele in rs9923231 was linked to a lower warfarin dose (βperT - allele = –0.29, p < 2×10–16) and risk of vascular dementia (OR = 1.17, p = 0.010), but not other dementia sub-types. However, the risk of vascular dementia was not affected by warfarin use in carriers of the T-allele. Conclusion: Our study reports for the first time an association between rs9923231 and vascular dementia, but further research is warranted to explore potential mechanisms and specify the relationship between rs9923231 and features of vascular dementia.

scholarly journals Identification of blast-resistance loci through genome-wide association analysis in foxtail millet (Setaria italica (L.) Beauv.)

2021 ◽  
Vol 20 (8) ◽  
pp. 2056-2064
Author(s):  
Zhi-jiang LI ◽  
Guan-qing JIA ◽  
Xiang-yu LI ◽  
Yi-chu LI ◽  
Hui ZHI ◽  
...  
Keyword(s):  
Association Analysis ◽  
Blast Resistance ◽  
Foxtail Millet ◽  
Genome Wide Association ◽  
Setaria Italica ◽  
Genome Wide Association Analysis ◽  
Genome Wide

scholarly journals Phytolith Analysis for Differentiating between Foxtail Millet (Setaria italica) and Green Foxtail (Setaria viridis)

PLoS ONE ◽  
2011 ◽  
Vol 6 (5) ◽  
pp. e19726 ◽  
Author(s):  
Jianping Zhang ◽  
Houyuan Lu ◽  
Naiqin Wu ◽  
Xiaoyan Yang ◽  
Xianmin Diao
Keyword(s):  
Foxtail Millet ◽  
Setaria Italica ◽  
Setaria Viridis ◽  
Phytolith Analysis ◽  
Green Foxtail

scholarly journals Genome-wide identification and in silico characterization of chitinase gene family in Foxtail millet (Setaria italica)

2020 ◽  
Author(s):  
Motukuri S. R. Krishna ◽  
Nerella Dheeraj ◽  
Bathuru Jayasree ◽  
Chodisetty Bhavya ◽  
Nallamothu Jaswanthi
Keyword(s):  
Gene Family ◽  
In Silico ◽  
Foxtail Millet ◽  
Chitinase Gene ◽  
Setaria Italica ◽  
Genome Wide ◽  
In Silico Characterization

New evidence on the relationship between Microsporidia and Fungi: a genome-wide analysis by DarkHorse software

2014 ◽  
Vol 60 (9) ◽  
pp. 557-568 ◽  
Author(s):  
Heng Xiang ◽  
Ruizhi Zhang ◽  
David De Koeyer ◽  
Guoqing Pan ◽  
Tian Li ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Enterocytozoon Bieneusi ◽  
Entire Genome ◽  
Encephalitozoon Intestinalis ◽  
Genome Wide ◽  
A Genome ◽  
Fungal Genes ◽  
Eukaryotic Organisms ◽  
New Evidence ◽  
The Relationship

Microsporidia are a group of obligate intracellular eukaryotic parasites that infect a wide variety of species, including humans. Phylogenetic analysis indicates a relationship between the Microsporidia and the Fungi. However, most results are based on the analysis of relatively few genes. DarkHorse analysis involves the transformation of BLAST results into a lineage probability index (LPI) value and allows for the comparison of genes for an entire genome with those of other genomes. Thus, we can see which genes from the microsporidia score most closely based on the LPI with other eukaryotic organisms. In this analysis, we calculated the LPI for each gene from the genomes of 7 Microsporidia, Antonospora locustae, Enterocytozoon bieneusi, Encephalitozoon cuniculi, Encephalitozoon intestinalis, Nosema bombycis, Nosema ceranae, and Nematocida parisii, to analyze the genetic relationships between Microsporidia and other species. It was found that many (91%) genes were most closely correlated with genes from other microsporidial genomes and had the highest mean LPI (0.985), indicating a monophyletic origin of the Microsporidia. In a subsequent analysis, we excluded the other Microsporidia from the analysis to look for relationships before the divergence of Microsporidia, and found that 43% of the microsporidial genes scored highest with fungal genes, and a higher mean LPI was found with Fungi than with other kingdoms, suggesting that Microsporidia is closely related to Fungi at the genomic level. Microsporidial genes were functionally clustered based on the KOG (Eukaryotic COG) database, and the possible lineages for each gene family were discussed in concert with the DarkHorse results.

Genome-wide identification and expression analysis of the SNARE genes in Foxtail millet (Setaria italica) reveals its roles in drought stress

2021 ◽  
Author(s):  
Hui Wang ◽  
Dongdong Hao ◽  
Xiaoxia Wang ◽  
Haiying Zhang ◽  
Pu Yang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Expression Analysis ◽  
Foxtail Millet ◽  
Setaria Italica ◽  
Genome Wide

Breeding foxtail millet (Setaria italica) for quantitative traits after interspecific hybridization and polyploidization

Genome ◽  
1987 ◽  
Vol 29 (3) ◽  
pp. 453-456 ◽  
Author(s):  
H. Darmency ◽  
C. Ouin ◽  
J. Pernes
Keyword(s):  
Interspecific Hybridization ◽  
Seed Weight ◽  
Interspecific Cross ◽  
Foxtail Millet ◽  
Setaria Italica ◽  
Crop Species ◽  
Quantitative Characters ◽  
Green Foxtail ◽  
Developmental Traits ◽  
Nonadditive Effects

An interspecific cross was carried out between the cultivated foxtail millet, Setaria italica, and its wild relative the green foxtail, S. viridis. Quantitative characters (19 descriptors of morphology and reproduction) were studied using the F1 F2, and F3 generations. Moreover, this F2 was compared with the tetraploid F2 obtained from a colchicine-induced F1. The multivariate analysis of the diploid F2 showed two complex associations of characters: one concerning developmental traits (organs dimensions and flowering) and the other dealing with taxonomical characteristics (tillering, seed shedding, and seed weight). The tetraploidization resulted in a shift in characteristics towards the crop species, especially a twofold increase in seed weight. Nonadditive effects were found for most characters, except for the seed shedding, which was found to be encoded by at least four loci. However, cultivated type plants were easily recovered in both the diploid and the tetraploid F2. This demonstrates the potential of interspecific hybridization and polyploidization to improve the crop properties of the foxtail millet. Key words: foxtail millet, polyploid, quantitative inheritance, hybridization (interspecific).

scholarly journals Genome-Wide Investigation and Expression Analyses of WD40 Protein Family in the Model Plant Foxtail Millet (Setaria italica L.)

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e86852 ◽  
Author(s):  
Awdhesh Kumar Mishra ◽  
Mehanathan Muthamilarasan ◽  
Yusuf Khan ◽  
Swarup Kumar Parida ◽  
Manoj Prasad
Keyword(s):  
Foxtail Millet ◽  
Protein Family ◽  
Setaria Italica ◽  
Model Plant ◽  
Genome Wide
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