scholarly journals Exploring Genome-Wide Diversity in the National Peach (Prunus persica) Germplasm Collection at CITA (Zaragoza, Spain)

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 481
Author(s):  
Jorge Mas-Gómez ◽  
Celia M. Cantín ◽  
María Á. Moreno ◽  
Ángela S. Prudencio ◽  
Mar Gómez-Abajo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Prunus Persica ◽  
Association Studies ◽  
Germplasm Collection ◽  
Genome Wide Association Studies ◽  
Northern Spain ◽  
Snp Chip ◽  
Genome Wide ◽  
Northern Regions

Peach (Prunus persica (L.) Batsch) is one of the most produced and studied stone fruits. Many genetic and genomic resources are available for this species, including a high-quality genome. More recently, a new high-density Illumina peach Single Nucleotide Polymorphism (SNP) chip (9+9K) has been developed by an international consortium as an add-on to the previous 9K array. In the current study, this new array was used to study the genetic diversity and population structure of the National Peach Germplasm Collection of the Agrifood Research and Technology Centre of Aragon (CITA), located in Zaragoza (northern Spain). To accomplish this, 90 peach accessions were genotyped using the new peach SNP chip (9+9K). A total of 9796 SNPs were finally selected for genetic analyses. Through Identity-By-Descent (IBD) estimate analysis, 15 different groups with genetically identical individuals were identified. The genetic diversity and population structure elucidated a possible exchange of germplasm material among regions, mainly in the northern regions of Spain. This study will allow for more efficient management of the National Peach Germplasm Collection by classifying valuable individuals for genetic diversity preservation and will benefit forthcoming Genome-Wide Association Studies (GWAS) of commercially important fruit traits in peach.

scholarly journals Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1298
Author(s):  
Caléo Panhoca de Almeida ◽  
Jean Fausto de Carvalho Paulino ◽  
Sérgio Augusto Morais Carbonell ◽  
Alisson Fernando Chiorato ◽  
Qijian Song ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Diversity ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Association Mapping Approach

Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.

scholarly journals The USDA Barley Core Collection: Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies

PLoS ONE ◽  
2014 ◽  
Vol 9 (4) ◽  
pp. e94688 ◽  
Author(s):  
María Muñoz-Amatriaín ◽  
Alfonso Cuesta-Marcos ◽  
Jeffrey B. Endelman ◽  
Jordi Comadran ◽  
John M. Bonman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Core Collection ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

The power of genetic diversity in genome-wide association studies of lipids

Nature ◽  
2021 ◽  
Author(s):  
Sarah E. Graham ◽  
Shoa L. Clarke ◽  
Kuan-Han H. Wu ◽  
Stavroula Kanoni ◽  
Greg J. M. Zajac ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Controlling the false discovery rate in GWAS with population structure

2020 ◽  
Author(s):  
Matteo Sesia ◽  
Stephen Bates ◽  
Emmanuel Candès ◽  
Jonathan Marchini ◽  
Chiara Sabatti
Keyword(s):  
Population Structure ◽  
False Discovery Rate ◽  
Markov Models ◽  
State Of The Art ◽  
Hidden Markov ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
False Discovery ◽  
Identical By Descent ◽  
Genome Wide

AbstractThis paper proposes a novel statistical method to address population structure in genome-wide association studies while controlling the false discovery rate, which overcomes some limitations of existing approaches. Our solution accounts for linkage disequilibrium and diverse ancestries by combining conditional testing via knockoffs with hidden Markov models from state-of-the-art phasing methods. Furthermore, we account for familial relatedness by describing the joint distribution of haplotypes sharing long identical-by-descent segments with a generalized hidden Markov model. Extensive simulations affirm the validity of this method, while applications to UK Biobank phenotypes yield many more discoveries compared to BOLT-LMM, most of which are confirmed by the Japan Biobank and FinnGen data.

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