Association mapping for phenological, morphological, and quality traits in canola quality winter rapeseed (Brassica napus L.)This article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 899-907 ◽  
Author(s):  
Nora Honsdorf ◽  
Heiko C. Becker ◽  
Wolfgang Ecke
Keyword(s):  
Qtl Mapping ◽  
Association Analysis ◽  
Phenotypic Variance ◽  
Brassica Napus L ◽  
Genome Wide ◽  
Breeding Research ◽  
Genome Association ◽  
Whole Genome Association ◽  
Winter Rapeseed ◽  
Canola Quality

QTL mapping by association analysis has recently gained interest in plant breeding research as an alternative to QTL mapping in segregating populations from biparental crosses. In a first experiment on whole-genome association analysis in rapeseed, 684 mapped AFLP markers were tested for association with 14 traits in a set of 84 canola quality winter rapeseed cultivars. For association analysis a general linear model was used. By testing significance of marker–trait associations against a false discovery rate of 0.2, between 1 and 34 associated markers were found for 10 of the 14 traits. Taking into account linkage disequilibrium between the significant markers, these markers represent between 1 and 22 putative QTL for the respective traits. The minimum phenotypic variance explained by the QTL for the different traits ranged from 15% to 53%. A subset of 27 markers were significantly associated with two or more traits. These markers were predominantly shared between traits that were significantly correlated at the phenotypic level. The results show clearly that in rapeseed, QTL mapping by association analysis is a viable alternative to QTL mapping in segregating populations.

Rapid variance components–based method for whole-genome association analysis

2012 ◽  
Vol 44 (10) ◽  
pp. 1166-1170 ◽  
Author(s):  
Gulnara R Svishcheva ◽  
Tatiana I Axenovich ◽  
Nadezhda M Belonogova ◽  
Cornelia M van Duijn ◽  
Yurii S Aulchenko
Keyword(s):  
Association Analysis ◽  
Variance Components ◽  
Whole Genome ◽  
Genome Association ◽  
Whole Genome Association

scholarly journals Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs

BMC Genetics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Lucas L. Verardo ◽  
Marja-Liisa Sevón-Aimonen ◽  
Timo Serenius ◽  
Ville Hietakangas ◽  
Pekka Uimari
Keyword(s):  
Association Analysis ◽  
Whole Genome ◽  
Pork Meat ◽  
Genome Association ◽  
Yorkshire Pigs ◽  
Whole Genome Association ◽  
Meat Ph

scholarly journals Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.)

2009 ◽  
Vol 120 (5) ◽  
pp. 921-931 ◽  
Author(s):  
Wolfgang Ecke ◽  
Rosemarie Clemens ◽  
Nora Honsdorf ◽  
Heiko C. Becker
Keyword(s):  
Linkage Disequilibrium ◽  
Brassica Napus ◽  
Brassica Napus L ◽  
Winter Rapeseed ◽  
Canola Quality

Whole-genome association mapping in elite inbred crop varietiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 967-972 ◽  
Author(s):  
Robbie Waugh ◽  
David Marshall ◽  
Bill Thomas ◽  
Jordi Comadran ◽  
Joanne Russell ◽  
...  
Keyword(s):  
Gene Pool ◽  
Physical Map ◽  
Association Studies ◽  
Population Substructure ◽  
Whole Genome ◽  
Data Set ◽  
Genome Wide ◽  
Marker Loci ◽  
Genome Association ◽  
Whole Genome Association

We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley ( Hordeum vulgare ) gene pool extends, on average, for <1–5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.

scholarly journals Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 30 ◽  
Author(s):  
Gwen Iris Descalsota-Empleo ◽  
Abd Aziz Shamsudin Noraziyah ◽  
Ian Paul Navea ◽  
Chongtae Chung ◽  
Maria Stefanie Dwiyanti ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Analysis ◽  
Leaf Blight ◽  
Genome Wide Association ◽  
Anthocyanin Content ◽  
Phenotypic Variance ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
Colored Rice ◽  
Resistance Traits

Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.

scholarly journals QTL mapping and genome-wide prediction of heat tolerance in multiple connected populations of temperate maize

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Delphine Van Inghelandt ◽  
Felix P. Frey ◽  
David Ries ◽  
Benjamin Stich
Keyword(s):  
Qtl Mapping ◽  
Heat Tolerance ◽  
Prediction Models ◽  
Genotypic Diversity ◽  
Phenotypic Variance ◽  
Nucleotide Polymorphisms ◽  
Prediction Ability ◽  
Specific Pcr ◽  
Genome Wide ◽  
Trait Locus

Abstract Climate change will lead to increasing heat stress in the temperate regions of the world. The objectives of this study were the following: (I) to assess the phenotypic and genotypic diversity of traits related to heat tolerance of maize seedlings and dissect their genetic architecture by quantitative trait locus (QTL) mapping, (II) to compare the prediction ability of genome-wide prediction models using various numbers of KASP (Kompetitive Allele Specific PCR genotyping) single nucleotide polymorphisms (SNPs) and RAD (restriction site-associated DNA sequencing) SNPs, and (III) to examine the prediction ability of intra-, inter-, and mixed-pool calibrations. For the heat susceptibility index of five of the nine studied traits, we identified a total of six QTL, each explaining individually between 7 and 9% of the phenotypic variance. The prediction abilities observed for the genome-wide prediction models were high, especially for the within-population calibrations, and thus, the use of such approaches to select for heat tolerance at seedling stage is recommended. Furthermore, we have shown that for the traits examined in our study, populations created from inter-pool crosses are suitable training sets to predict populations derived from intra-pool crosses.

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