Population Structure and Genomewide Association Analysis of Resistance to Disease and Insensitivity to Ptr Toxins in Canadian Spring Wheat Using 90K SNP Array

Crop Science ◽  
2017 ◽  
Vol 57 (3) ◽  
pp. 1522-1539 ◽  
Author(s):  
Enid Perez-Lara ◽  
Kassa Semagn ◽  
Van Anh Tran ◽  
Izabela Ciechanowska ◽  
Hua Chen ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Analysis ◽  
Spring Wheat ◽  
Snp Array ◽  
Genomewide Association ◽  
90K Snp Array

scholarly journals Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kassa Semagn ◽  
Muhammad Iqbal ◽  
Nikolaos Alachiotis ◽  
Amidou N’Diaye ◽  
Curtis Pozniak ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Spring Wheat ◽  
Snp Array ◽  
Categorical Variables ◽  
Selective Sweeps ◽  
Wheat Cultivars ◽  
Breeding Programs ◽  
The Impact

AbstractPrevious molecular characterization studies conducted in Canadian wheat cultivars shed some light on the impact of plant breeding on genetic diversity, but the number of varieties and markers used was small. Here, we used 28,798 markers of the wheat 90K single nucleotide polymorphisms to (a) assess the extent of genetic diversity, relationship, population structure, and divergence among 174 historical and modern Canadian spring wheat varieties registered from 1905 to 2018 and 22 unregistered lines (hereinafter referred to as cultivars), and (b) identify genomic regions that had undergone selection. About 91% of the pairs of cultivars differed by 20–40% of the scored alleles, but only 7% of the pairs had kinship coefficients of < 0.250, suggesting the presence of a high proportion of redundancy in allelic composition. Although the 196 cultivars represented eight wheat classes, our results from phylogenetic, principal component, and the model-based population structure analyses revealed three groups, with no clear structure among most wheat classes, breeding programs, and breeding periods. FST statistics computed among different categorical variables showed little genetic differentiation (< 0.05) among breeding periods and breeding programs, but a diverse level of genetic differentiation among wheat classes and predicted groups. Diversity indices were the highest and lowest among cultivars registered from 1970 to 1980 and from 2011 to 2018, respectively. Using two outlier detection methods, we identified from 524 to 2314 SNPs and 41 selective sweeps of which some are close to genes with known phenotype, including plant height, photoperiodism, vernalization, gluten strength, and disease resistance.

scholarly journals Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios

2016 ◽  
Vol 129 (9) ◽  
pp. 1711-1724 ◽  
Author(s):  
Giorgio Tumino ◽  
Roeland E. Voorrips ◽  
Fulvia Rizza ◽  
Franz W. Badeck ◽  
Caterina Morcia ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Analysis ◽  
Signal Intensity ◽  
Snp Array ◽  
Frost Tolerance ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
Intensity Ratios

scholarly journals Genomewide Association Analysis in Diverse Inbred Mice: Power and Population Structure

Genetics ◽  
2007 ◽  
Vol 176 (1) ◽  
pp. 675-683 ◽  
Author(s):  
Phillip McClurg ◽  
Jeff Janes ◽  
Chunlei Wu ◽  
David L. Delano ◽  
John R. Walker ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Analysis ◽  
Inbred Mice ◽  
Genomewide Association

Mapping QTLs Controlling Agronomic Traits in the ‘Attila’ × ‘CDC Go’ Spring Wheat Population under Organic Management using 90K SNP Array

Crop Science ◽  
2016 ◽  
Vol 57 (1) ◽  
pp. 365-377 ◽  
Author(s):  
Jun Zou ◽  
Kassa Semagn ◽  
Muhammad Iqbal ◽  
Amidou N'Diaye ◽  
Hua Chen ◽  
...  
Keyword(s):  
Spring Wheat ◽  
Agronomic Traits ◽  
Snp Array ◽  
Organic Management ◽  
Wheat Population ◽  
90K Snp Array

A joint genomewide association analysis of pig leg weakness and its related traits in an F2 population and a Sutai population1

2013 ◽  
Vol 91 (9) ◽  
pp. 4060-4068 ◽  
Author(s):  
Y. M. Guo ◽  
X. F. Zhang ◽  
J. Ren ◽  
H. S. Ai ◽  
J. W. Ma ◽  
...  
Keyword(s):  
Association Analysis ◽  
F2 Population ◽  
Leg Weakness ◽  
Genomewide Association

scholarly journals Multiplex genomewide association analysis of breast milk fatty acid composition extends the phenotypic association and potential selection of FADS1 variants to arachidonic acid, a critical infant micronutrient

2018 ◽  
Vol 55 (7) ◽  
pp. 459-468 ◽  
Author(s):  
Josyf C Mychaleckyj ◽  
Uma Nayak ◽  
E Ross Colgate ◽  
Dadong Zhang ◽  
Tommy Carstensen ◽  
...  
Keyword(s):  
Arachidonic Acid ◽  
Fatty Acid ◽  
Breast Milk ◽  
Genetic Association ◽  
Snp Array ◽  
Genetic Selection ◽  
Milk Composition ◽  
Significance Threshold ◽  
Fa Composition ◽  
Genomewide Association

BackgroundBreast milk is the sole nutrition source during exclusive breastfeeding, and polyunsaturated fatty acids (FAs) are critical micronutrients in infant physical and cognitive development. There has been no prior genomewide association study of breast milk, hence our objective was to test for genetic association with breast milk FA composition.MethodsWe measured the fractional composition of 26 individual FAs in breast milk samples from three cohorts totalling 1142 Bangladeshi mothers whose infants were genotyped on the Illumina MEGA chip and replicated on a custom Affymetrix 30K SNP array (n=616). Maternal genotypes were imputed using IMPUTE.ResultsAfter running 33 separate FA fraction phenotypes, we found that SNPs known to be associated with serum FAs in the FADS1/2/3 region were also associated with breast milk FA composition (experiment-wise significance threshold 4.2×10−9). Hypothesis-neutral comparison of the 33 fractions showed that the most significant genetic association at the FADS1/2/3 locus was with fraction of arachidonic acid (AA) at SNP rs174556, with a very large per major allele effect size of 17% higher breast milk AA level. There was no evidence of independent association at FADS1/2/3 with any other FA or SNP after conditioning on AA and rs174556. We also found novel significant experiment-wise SNP associations with: polyunsaturated fatty acid (PUFA) 6/PUFA3 ratio (sorting nexin 29), eicosenoic (intergenic) and capric (component of oligomeric Golgi complex 3) acids; and six additional loci at genomewide significance (<5×10−8).ConclusionsAA is the primary FA in breast milk influenced by genetic variation at the FADS1/2/3 locus, extending the potential phenotypes under genetic selection to include breast milk composition, thereby possibly affecting infant growth or cognition. Breast milk FA composition is influenced by maternal genetics in addition to diet and body composition.

scholarly journals Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1441
Author(s):  
Filippo Cendron ◽  
Francesco Perini ◽  
Salvatore Mastrangelo ◽  
Marco Tolone ◽  
Andrea Criscione ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Conservation Status ◽  
Geographical Area ◽  
Snp Array ◽  
Local Economy ◽  
Conservation Strategies ◽  
Snp Analysis ◽  
Runs Of Homozygosity ◽  
Chicken Breeds

The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.

scholarly journals Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Christina Marie Rochus ◽  
Elisabeth Jonas ◽  
Anna M. Johansson
Keyword(s):  
Population Structure ◽  
Snp Array ◽  
Principal Component ◽  
Northern Sweden ◽  
The Baltic Sea ◽  
Sheep Breeds ◽  
The North ◽  
South West ◽  
Branch Lengths ◽  
The Baltic

Abstract Background Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish sheep. Five breeds were genotyped using the 600 K SNP array. Dalapäls and Klövsjö sheep are from the middle of Sweden; Gotland and Gute sheep from Gotland, an island in the Baltic Sea; and Fjällnäs sheep from northern Sweden. We studied population structure by: principal component analysis (PCA), cluster-based analysis of admixture, and an estimated population tree. Results The analyses of the five Swedish breeds revealed that these breeds are five distinct breeds, while Gute and Gotland are more closely related to each other as seen in all analyses. All breeds had long branch lengths in the population tree indicating they’ve been subjected to drift. We repeated our analyses using 39 K SNP and including 50 K SNP genotypes from other European and southwestern Asian breeds from the Sheep HapMap project and 600 K SNP genotypes from a dataset of French sheep. Results arranged breeds into five groups: south-west Asia, south-west Europe, central Europe, north Europe and north European short-tailed sheep. Within this last group, Norwegian and Icelandic breeds, Finn and Romanov sheep, Scottish breeds, and Gute and Gotland sheep were more closely related while the remaining Swedish breeds and Ouessant sheep were distinct from all breeds and had longer branches in the population tree. Conclusions We showed population structure of five Swedish breeds and their structure within European and southwestern Asian breeds. Swedish breeds are unique, distinct breeds that have been subjected to drift but group with other north European short-tailed sheep.

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