scholarly journals Population genomics of sorghum (Sorghum bicolor) across diverse agroclimatic zones of Niger

Genome ◽  
2018 ◽  
Vol 61 (4) ◽  
pp. 223-232 ◽  
Author(s):  
Fanna Maina ◽  
Sophie Bouchet ◽  
Sandeep R. Marla ◽  
Zhenbin Hu ◽  
Jianan Wang ◽  
...  
Keyword(s):  
Sorghum Bicolor ◽  
Local Adaptation ◽  
Population Genomics ◽  
Geographic Origin ◽  
Genome Scan ◽  
Genomic Diversity ◽  
Chromosome 9 ◽  
Local Varieties ◽  
A Genome ◽  
Agroclimatic Zones

Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed 516 Nigerien accessions for which local variety name, botanical race, and geographic origin were known. We discovered 144 299 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). We performed discriminant analysis of principal components (DAPC), which identified six genetic groups, and performed a genome scan for loci with high discriminant loadings. The highest discriminant coefficients were on chromosome 9, near the putative ortholog of maize flowering time adaptation gene Vgt1. Next, we characterized differentiation among local varieties and used a genome scan of pairwise FST values to identify SNPs associated with specific local varieties. Comparison of varieties named for light- versus dark-grain identified differentiation near Tannin1, the major gene responsible for grain tannins. These findings could facilitate genomics-assisted breeding of locally adapted and farmer-preferred sorghum varieties for Niger.

scholarly journals Correction: A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species

PLoS Genetics ◽  
2015 ◽  
Vol 11 (9) ◽  
pp. e1005488 ◽  
Author(s):  
Shosei Kubota ◽  
Takaya Iwasaki ◽  
Kousuke Hanada ◽  
Atsushi J. Nagano ◽  
Asao Fujiyama ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Genome Scan ◽  
A Genome ◽  
Arabidopsis Species

Sequence differentiation in regions identified by a genome scan for local adaptation

2008 ◽  
Vol 17 (13) ◽  
pp. 3123-3135 ◽  
Author(s):  
HENRY M. WOOD ◽  
JOHN W. GRAHAME ◽  
SEAN HUMPHRAY ◽  
JANE ROGERS ◽  
ROGER K. BUTLIN
Keyword(s):  
Local Adaptation ◽  
Genome Scan ◽  
A Genome

scholarly journals A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species

PLoS Genetics ◽  
2015 ◽  
Vol 11 (7) ◽  
pp. e1005361 ◽  
Author(s):  
Shosei Kubota ◽  
Takaya Iwasaki ◽  
Kousuke Hanada ◽  
Atsushi J. Nagano ◽  
Asao Fujiyama ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Genome Scan ◽  
A Genome ◽  
Arabidopsis Species

scholarly journals Coherence of Microcystis species revealed through population genomics

2019 ◽  
Author(s):  
Olga M. Pérez-Carrascal ◽  
Yves Terrat ◽  
Alessandra Giani ◽  
Nathalie Fortin ◽  
Charles W. Greer ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Population Genomics ◽  
Genomic Analysis ◽  
Geographic Location ◽  
Biological Species ◽  
Genomic Diversity ◽  
Cyanobacterial Blooms ◽  
Colony Morphology ◽  
Population Genomic

AbstractMicrocystis is a genus of freshwater cyanobacteria which causes harmful blooms in ecosystems worldwide. Some Microcystis strains produce harmful toxins such as microcystin, impacting drinking water quality. Microcystis colony morphology, rather than genetic similarity, is often used to classify Microcystis into morphospecies. However, colony morphology is a plastic trait which can change depending on environmental and laboratory culture conditions, and is thus an inadequate criterion for species delineation. Furthermore, Microcystis populations are thought to disperse globally and constitute a homogeneous gene pool. However, this assertion is based on relatively incomplete characterization of Microcystis genomic diversity. To better understand these issues, we performed a population genomic analysis of 33 newly sequenced genomes (of which 19 were resequenced to check for mutation in culture) mainly from Canada and Brazil. We identified eight Microcystis clusters of genomic similarity, only four of which correspond to named morphospecies and monophyletic groups. Notably, M. aeruginosa is paraphyletic, distributed across four genomic clusters, suggesting it is not a coherent species. Most monophyletic groups are specific to a unique geographic location, suggesting biogeographic structure over relatively short evolutionary time scales. Higher homologous recombination rates within than between clusters further suggest that monophyletic groups might adhere to a Biological Species-like concept, in which barriers to gene flow maintain species distinctness. However, certain genes – including some involved in microcystin and micropeptin biosynthesis – are recombined between monophyletic groups in the same geographic location, suggesting local adaptation. Together, our results show the importance of using genomic criteria for Microcystis species delimitation and suggest the existence of locally adapted lineages and genes.ImportanceThe genus Microcystis is responsible for harmful and often toxic cyanobacterial blooms across the world, yet it is unclear how and if the genus should be divided into ecologically and genomically distinct species. To resolve the controversy and uncertainty surrounding Microcystis species, we performed a population genomic analysis of Microcystis genome from public databases, along with new isolates from Canada and Brazil. We inferred that significant genetic substructure exists within Microcystis, with several species being maintained by barriers to gene flow. Thus, Microcystis appears to be among a growing number of bacteria that adhere to a Biological Species-like Concept (BSC). Barriers to gene flow are permeable, however, and we find evidence for relatively frequent cross-species horizontal gene transfer (HGT) of genes that may be involved in local adaptation. Distinct clades of Microcystis (putative species) tend to have distinct profiles of toxin biosynthesis genes, and yet toxin genes are also subject to cross-species HGT and local adaptation. Our results thus pave the way for more informed classification, monitoring and understanding of harmful Microcystis blooms.

scholarly journals Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jose F. Delgado-Blas ◽  
Cristina M. Ovejero ◽  
Sophia David ◽  
Natalia Montero ◽  
William Calero-Caceres ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Population Genomics ◽  
Population Diversity ◽  
Genomic Diversity ◽  
Resistant Bacteria ◽  
Aquatic Environments ◽  
E Coli ◽  
Water Ecosystems ◽  
Sequence Types

AbstractAquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant bacteria in different aquatic environments are still largely unknown. The aim of this study was to understand the population genomics and evolutionary events of Escherichia coli resistant to clinically important antibiotics including aminoglycosides, in anthropogenic and natural water ecosystems. Here we show that less different E. coli sequence types (STs) are identified in wastewater than in rivers, albeit more resistant to antibiotics, and with significantly more plasmids/cell (6.36 vs 3.72). However, the genomic diversity within E. coli STs in both aquatic environments is similar. Wastewater environments favor the selection of conserved chromosomal structures associated with diverse flexible plasmids, unraveling promiscuous interplasmidic resistance genes flux. On the contrary, the key driver for river E. coli adaptation is a mutable chromosome along with few plasmid types shared between diverse STs harboring a limited resistance gene content.

scholarly journals A genome scan for selection signatures in Taihu pig breeds using next-generation sequencing

animal ◽  
2019 ◽  
Vol 13 (4) ◽  
pp. 683-693 ◽  
Author(s):  
Z. Wang ◽  
H. Sun ◽  
Q. Chen ◽  
X. Zhang ◽  
Q. Wang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Scan ◽  
Next Generation ◽  
Selection Signatures ◽  
Pig Breeds ◽  
A Genome ◽  
Generation Sequencing

A genome scan for candidate genes involved in the adaptation of turbot (Scophthalmus maximus)

2015 ◽  
Vol 23 ◽  
pp. 77-86 ◽  
Author(s):  
Román Vilas ◽  
Sara G. Vandamme ◽  
Manuel Vera ◽  
Carmen Bouza ◽  
Gregory E. Maes ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Scan ◽  
Scophthalmus Maximus ◽  
A Genome ◽  
Turbot Scophthalmus Maximus
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