scholarly journals Multi-Parental Populations Suitable for Identifying Sources of Resistance to Powdery Mildew in Winter Wheat

2021 ◽  
Vol 11 ◽  
Author(s):  
Nana Vagndorf Nordestgaard ◽  
Tine Thach ◽  
Pernille Sarup ◽  
Julian Rodriguez-Algaba ◽  
Jeppe Reitan Andersen ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Association Studies ◽  
Genetic Difference ◽  
Synthetic Hexaploid Wheat ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Sources Of Resistance ◽  
Genome Association ◽  
Whole Genome Association ◽  
Disease Pressure

Wheat (Triticum aestivum L.) is one of the world’s staple food crops and one of the most devastating foliar diseases attacking wheat is powdery mildew (PM). In Denmark only a few specific fungicides are available for controlling PM and the use of resistant cultivars is often recommended. In this study, two Chinese wheat landraces and two synthetic hexaploid wheat lines were used as donors for creating four multi-parental populations with a total of 717 individual lines to identify new PM resistance genetic variants. These lines and the nine parental lines (including the elite cultivars used to create the populations) were genotyped using a 20 K Illumina SNP chip, which resulted in 8,902 segregating single nucleotide polymorphisms for assessment of the population structure and whole genome association study. The largest genetic difference among the lines was between the donors and the elite cultivars, the second largest genetic difference was between the different donors; a difference that was also reflected in differences between the four multi-parental populations. The 726 lines were phenotyped for PM resistance in 2017 and 2018. A high PM disease pressure was observed in both seasons, with severities ranging from 0 to >50%. Whole genome association studies for genetic variation in PM resistance in the populations revealed significant markers mapped to either chromosome 2A, B, or D in each of the four populations. However, linkage disequilibrium between these putative quantitative trait loci (QTL) were all above 0.80, probably representing a single QTL. A combined analysis of all the populations confirmed this result and the most associated marker explained 42% of the variation in PM resistance. This study gives both knowledge about the resistance as well as molecular tools and plant material that can be utilised in marker-assisted selection. Additionally, the four populations produced in this study are highly suitable for association studies of other traits than PM resistance.

scholarly journals Sampling strategies for whole genome association studies in aquaculture and outcrossing plant species

2009 ◽  
Vol 91 (6) ◽  
pp. 367-371 ◽  
Author(s):  
B. J. HAYES ◽  
I. M. MACLEOD ◽  
M. BARANSKI
Keyword(s):  
Plant Species ◽  
Association Studies ◽  
Whole Genome ◽  
Minimal Effect ◽  
Sampling Strategies ◽  
False Discovery ◽  
Breeding Populations ◽  
Genome Association ◽  
Whole Genome Association ◽  
Sib Families

SummaryA number of farmed species are characterized by breeding populations of large full-sib families, including aquaculture species and outcrossing plant species. Whole genome association studies in such species must account for stratification arising from the full-sib family structure to avoid high rates of false discovery. Here, we demonstrate the value of selective genotyping strategies which balance the contribution of families across high and low phenotypes to greatly reduce rates of false discovery with a minimal effect on power.

scholarly journals Calibrating the Performance of SNP Arrays for Whole-Genome Association Studies

PLoS Genetics ◽  
2008 ◽  
Vol 4 (6) ◽  
pp. e1000109 ◽  
Author(s):  
Ke Hao ◽  
Eric E. Schadt ◽  
John D. Storey
Keyword(s):  
Association Studies ◽  
Whole Genome ◽  
Snp Arrays ◽  
Genome Association ◽  
Whole Genome Association

Exploring Genetic Basis of GVHD by Whole-Genome Association Studies in a Large Series from the Japan Marrow Donation Program (JMDP).

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3232-3232
Author(s):  
Yasuhito Nannya ◽  
Makoto Onizuka ◽  
Koichi Kashiwase ◽  
Masashi Sanada ◽  
Yoshiki Akatsuka ◽  
...  
Keyword(s):  
Large Scale ◽  
Genetic Basis ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Whole Genome ◽  
Minor Histocompatibility Antigens ◽  
Therapeutic Benefits ◽  
Gvhd Prophylaxis ◽  
Genome Association ◽  
Whole Genome Association

Abstract Allogeneic stem cell transplantation (allo-HSCT) has been established as one of the most effective therapeutic options for hematopoietic malignancies. Its major therapeutic benefits are obtained from allo-immunity directed against patients’ tumor cells (graft-versus-tumor effects, GVT). However, the same kind of allo-immune reactions can also be directed to normal host tissues resulting in graft-versus-host disease (GVHD) and subsequently offset the potential benefit from GVT. Because both reactions are initiated by donor T-cells that recognize minor histocompatibility antigens (mHA) that are incompatible between donor and recipient, the knowledge of these mHA is of particular importance to develop a new measure to prevent GVHD while harnessing the antitumor potential of allo-HSCT. On the other hand, the incompatibility of mHAs, as well as other predispositions to development of GVHD, is basically determined genetically, and thus, are plausible targets of genetic association studies, which have recently been enabled with the advent of large-scale genotyping technology. In the current study, we explored genetic basis of GVHD by whole genome association studies, in which relevant SNPs to GVHD development were explored by genotyping a large cohort of GVHD-positive and negative transplantations performed through the Japan Marrow Donor Program (JMDP). Among 7,800 transplants genotyped for HLA types, we selected 1856 transplants (3712 donors/recipients) for large scale genotyping of more than 500,000 SNPs using Affymetrix® GeneChip® 500K arrays, according to the following criteria: HLA A, B, C, DR, DQ loci were completely matched at the DNA level Short term MTX (stMTX) + CyA or stMTX + FK506 was employed as GVHD prophylaxis, and Genome DNA from both donor and recipient and record of clinical course was available. Based on the genotyping data, possible association was tested for each SNP in donors and recipients with regard to the development of GVHD. Association of genotype incompatibilities was also investigated for major HLA subtypes to identify the mHA loci that are relevant to GVHD pathogenesis. In the intermediate analysis, a number of candidate polymorphisms in donors and recipients have been identified together with possible mHA loci.

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 A Randomization Test for Controlling Population Stratification in Whole-Genome Association Studies

2007 ◽  
Vol 81 (5) ◽  
pp. 895-905 ◽  
Author(s):  
Gad Kimmel ◽  
Michael I. Jordan ◽  
Eran Halperin ◽  
Ron Shamir ◽  
Richard M. Karp
Keyword(s):  
Population Stratification ◽  
Association Studies ◽  
Randomization Test ◽  
Whole Genome ◽  
Genome Association ◽  
Whole Genome Association
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