scholarly journals Molecular Evidence for Two Domestication Events in the Pea Crop

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 535 ◽  
Author(s):  
Oldřich Trněný ◽  
Jan Brus ◽  
Iveta Hradilová ◽  
Abhishek Rathore ◽  
Roma Das ◽  
...  
Keyword(s):  
Gene Flow ◽  
Natural Variation ◽  
Wide Distribution ◽  
Hybrid Origin ◽  
Molecular Evidence ◽  
Wild Relative ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide Analysis ◽  
Genome Wide

Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide analysis of 11,343 polymorphic single nucleotide polymorphisms (SNPs) on a set of wild P. elatius (134) and P. fulvum (20) and 74 domesticated accessions (64 P. sativum landraces and 10 P. abyssinicum), we demonstrated that domesticated P. sativum and the Ethiopian pea (P. abyssinicum) were derived from different P. elatius genepools. Therefore, pea has at least two domestication events. The analysis does not support a hybrid origin of P. abyssinicum, which was likely introduced into Ethiopia and Yemen followed by eco-geographic adaptation. Both P. sativum and P. abyssinicum share traits that are typical of domestication, such as non-dormant seeds. Non-dormant seeds were also found in several wild P. elatius accessions which could be the result of crop to wild introgression or natural variation that may have been present during pea domestication. A sub-group of P. elatius overlaps with P. sativum landraces. This may be a consequence of bidirectional gene-flow or may suggest that this group of P. elatius is the closest extant wild relative of P. sativum.

Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences

10.1038/79981 ◽  
2000 ◽  
Vol 26 (2) ◽  
pp. 233-236 ◽  
Author(s):  
Kris Irizarry ◽  
Vlad Kustanovich ◽  
Cheng Li ◽  
Nik Brown ◽  
Stanley Nelson ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Increased individual homozygosity is correlated with low fitness in a fragmented lizard population

2019 ◽  
Vol 128 (4) ◽  
pp. 952-962 ◽  
Author(s):  
Javier Pérez-Tris ◽  
Alejandro Llanos-Garrido ◽  
Paul Bloor ◽  
Roberto Carbonell ◽  
José Luis Tellería ◽  
...  
Keyword(s):  
Gene Flow ◽  
Restricted Gene Flow ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Anthropogenic Habitat ◽  
Geographical Scale ◽  
Psammodromus Algirus ◽  
Fragmented Population ◽  
The Impact

Abstract Isolation owing to anthropogenic habitat fragmentation is expected to increase the homozygosity of individuals, which might reduce their fitness as a result of inbreeding depression. Using samples from a fragmented population of the lizard Psammodromus algirus, for which we had data about two correlates of fitness, we genotyped individuals for six microsatellite loci that correctly capture genome-wide individual homozygosity of these lizards (as validated with an independent sample of lizards genotyped for both these microsatellites and > 70 000 single nucleotide polymorphisms). Our data revealed genetic structure at a very small geographical scale, which was compatible with restricted gene flow among populations disconnected in a matrix of inhospitable habitat. Lizards from the same fragment were genetically more related to one another than expected by chance, and individual homozygosity was greater in small than in large fragments. Within fragments, individual homozygosity was negatively associated with adult body size and clutch mass, revealing a link among reduced gene flow, increased homozygosity and lowered fitness that might reduce population viability deterministically. Our results contribute to mounting evidence of the impact of the loss of genetic diversity on fragmented wild populations.

Genome-wide analysis of single nucleotide polymorphisms in Bordetella pertussis using comparative genomic sequencing

2008 ◽  
Vol 159 (9-10) ◽  
pp. 602-608 ◽  
Author(s):  
Ram P. Maharjan ◽  
Chong Gu ◽  
Peter R. Reeves ◽  
Vitali Sintchenko ◽  
Gwendolyn L. Gilbert ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Bordetella Pertussis ◽  
Comparative Genomic ◽  
Genomic Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome-wide analysis of thyroid function in Australian adolescents highlights SERPINA7 and NCOA3

2021 ◽  
Author(s):  
James Nolan ◽  
Purdey J Campbell ◽  
Suzanne J Brown ◽  
Gu Zhu ◽  
Scott Gordon ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Thyroid Function ◽  
Association Analysis ◽  
Genetic Factors ◽  
Meta Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Objective Genetic factors underpin the narrow intraindividual variability of thyroid function, although precise contributions of environmental versus genetic factors remain uncertain. We sought to clarify the heritability of thyroid function traits and thyroid peroxidase antibody (TPOAb) positivity and identify single nucleotide polymorphisms (SNPs) contributing to the trait variance. Methods Heritability of thyroid stimulating hormone (TSH), free T4 (fT4), free T3 (fT3) and TPOAb in a cohort of 2854 euthyroid, dizygous and monozygous twins (age range 11.9-16.9 years) from the Brisbane Longitudinal Twin Study (BLTS) was assessed using structural equation modelling. A genome-wide analysis was conducted on 2832 of these individuals across 7,522,526 single nucleotide polymorphisms as well as gene-based association analyses. Replication analysis of the association results was performed in the Raine Study (n= 1115) followed by meta-analysis to maximise power for discovery. Results Heritability of thyroid function parameters in the BLTS was 70.8% (95% CI: 66.7-74.9%) for TSH, 67.5% (59.8-75.3%) for fT4, 59.7% (54.4-65.0%) for fT3 and 48.8% (40.6-56.9%) for TPOAb. The genome-wide association study (GWAS) in the discovery cohort identified a novel association between rs2026401 upstream of NCOA3 and TPOAb. GWAS meta-analysis found associations between TPOAb and rs445219, also near NCOA3, and fT3 and rs12687280 near SERPINA7. Gene-based association analysis highlighted SERPINA7 for fT3 and NPAS3 for fT4. Conclusion Our findings resolve former contention regarding heritability estimates of thyroid function traits and TPOAb positivity. GWAS and gene-based association analysis identified variants accounting for a component of this heritability.

scholarly journals Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 784 ◽  
Author(s):  
Katie E Fowler ◽  
Ricardo Pong-Wong ◽  
Julien Bauer ◽  
Emily J Clemente ◽  
Christopher P Reitter ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Copy Number ◽  
Copy Number Variants ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide Analysis ◽  
Pig Breeds ◽  
Genome Wide

scholarly journals Genome-Wide Analysis of MicroRNA-related Single Nucleotide Polymorphisms (SNPs) in Mouse Genome

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Gideon Omariba ◽  
Fuyi Xu ◽  
Maochun Wang ◽  
Kai Li ◽  
Yuxun Zhou ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Mouse Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome-Wide Analysis of Single Nucleotide Polymorphisms Uncovers Population Structure in Northern Europe

PLoS ONE ◽  
2008 ◽  
Vol 3 (10) ◽  
pp. e3519 ◽  
Author(s):  
Elina Salmela ◽  
Tuuli Lappalainen ◽  
Ingegerd Fransson ◽  
Peter M. Andersen ◽  
Karin Dahlman-Wright ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Northern Europe ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide Analysis ◽  
Genome Wide
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