Identification of resistance loci against new pathotypes of Plasmodiophora brassicae in Brassica napus based on genome-wide association mapping

AbstractGenetic resistance is a successful strategy for management of clubroot (Plasmodiophora brassicae) of brassica crops, but resistance can break down quickly. Identification of novel sources of resistance is especially important when new pathotypes arise. In the current study, the reaction of 177 accessions of Brassica napus to four new, virulent pathotypes of P. brassicae was assessed. Each accession was genotyped using genotyping by sequencing to identify and map novel sources of clubroot resistance using mixed linear model (MLM) analysis. The majority of accessions were highly susceptible (70–100 DSI), but a few accessions exhibited strong resistance (0–20 DSI) to pathotypes 5X (21 accessions), 3A (8), 2B (7), and 3D (15), based on the Canadian Clubroot Differential system. In total, 301,753 SNPs were mapped to 19 chromosomes. Population structure analysis indicated that the 177 accessions belong to seven major populations. SNPs were associated with resistance to each pathotype using MLM. In total, 13 important SNP loci were identified, with 9 SNPs mapped to the A-genome and 4 to the C-genome. The SNPs were associated with resistance to pathotypes 5X (2 SNPs), 3A (4), 2B (5) and 3D (6). A Blast search of 1.6 Mb upstream and downstream from each SNP identified 13 disease-resistance genes or domains. The distance between a SNP locus and the nearest resistance gene ranged from 0.04 to 0.74 Mb. The resistant lines and SNP markers identified in this study can be used to breed for resistance to the most prevalent new pathotypes of P. brassicae in Canada.

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Identification of new QTLs for resistance to Plasmodiophora brassicae in Brassica napus using genome wide association mapping

10.21203/rs.2.14300/v1 ◽

2019 ◽

Author(s):

Abdulsalam Dakouri ◽

Mebarek Lamara ◽

Md. Masud Karim ◽

Jinghe Wang ◽

Qilin Chen ◽

...

Keyword(s):

Brassica Napus ◽

Association Mapping ◽

Resistance Genes ◽

Plasmodiophora Brassicae ◽

Snp Markers ◽

Genome Wide Association ◽

Sources Of Resistance ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome

Abstract Background Clubroot of canola ( Brassica napus ), caused by the obligate pathogen Plasmodiophora brassicae Woronin, is a major disease worldwide. Genetic resistance remains the best strategy to manage this disease. The objective of the study was to identify and map new sources of resistance to clubroot in B. napus using genome-wide association mapping. The reaction of a collection of 177 accessions to four highly virulent pathotypes of P. brassicae was assessed. These pathotypes were selected because they were most recently identified and showed different virulence patterns on the Canadian clubroot differential (CCD) lines. The collection was then genotyped using genotyping by sequencing (GBS) method. Multi-locus mixed linear model (MMLM) was used to perform the association analysis. Results The majority of accessions were highly susceptible (70 –100 DSI), while few individual accessions showed strong resistance (0–20 DSI) to 5X (2 accessions), 2B (7 accessions), 3A (8 accessions) and 3D (15 accessions). In total, 301,753 SNPs were mapped to 19 chromosomes. Population structure analysis indicated that the 177 accessions belong to two major populations. SNPs were associated with resistance to each pathotype using MLMM. In total, 23 significant SNP loci were identified, with 14 SNPs mapped to the A-genome and 9 to the C-genome. The SNPs were associated with resistance to pathotypes 5X (4 SNPs), 2B (9), 3A (5) and 3D (5). A blast search of 2 Mb upstream and downstream identified 61 disease resistance genes, of which 24 belonged to TIR-NBS-LRR proteins and 20 belonged to CC-NBS-LRR proteins. The distance between a SNP locus and the nearest resistance genes ranged from 0.11–1.66 Mb. This indicated that NBS-LRR gene family might have an important role in clubroot resistance in B. napus . Conclusion The resistant B. napus lines and the SNP markers identified in this study can be used for breeding for resistance to clubroot and contribute to understanding the genetic mechanism of resistance to clubroot.

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MULTI-TRAIT MODELS FOR GENOMIC REGIONS ASSOCIATED WITH MAL DE RÍO CUARTO AND BACTERIAL DISEASE IN MAIZE

Journal of Basic and Applied Genetics ◽

10.35407/bag.2021.32.01.03 ◽

2021 ◽

Vol 32 (Issue 1) ◽

pp. 25-33

Author(s):

M. Ruiz ◽

E.A. Rossi ◽

N.C. Bonamico ◽

M.G. Balzarini

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Mixed Linear Model ◽

Snp Markers ◽

Genome Wide Association ◽

Bacterial Disease ◽

Maize Germplasm ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

Maize (Zea Mays L.) production has been greatly benefited from the improvement of inbred lines in regard to the resistance to diseases. However, the absence of resistant genotypes to bacteriosis is remarkable. The aim of the study was to identify genomic regions for resistance to Mal de Río Cuarto (MRC) and to bacterial disease (BD) in a diverse maize germplasm evaluated in the Argentinian region where MRC virus is endemic. A maize diverse population was assessed for both diseases during the 2019-2020 crop season. Incidence and severity of MRC and BD were estimated for each line and a genome wide association study (GWAS) was conducted with 78,376 SNP markers. A multi-trait mixed linear model was used for simultaneous evaluation of resistance to MRC and BD in the scored lines. The germplasm showed high genetic variability for both MRC and BD resistance. No significant genetic correlation was observed between the response to both diseases. Promising genomic regions for resistance to MRC and BD were identified and will be confirmed in further trials. Key words: maize disease; genome wide association study; SNP; multi-trait model

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MULTI-TRAIT MODELS FOR GENOMIC REGIONS ASSOCIATED WITH MAL DE RÍO CUARTO AND BACTERIAL DISEASE IN MAIZE

Journal of Basic and Applied Genetics ◽

10.35407/bag.2020.32.01.03 ◽

2021 ◽

Vol 32 (Issue 1) ◽

pp. 25-33

Author(s):

M. Ruiz ◽

E.A. Ross ◽

N.C. Bonamico ◽

M.G. Balzarini

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Mixed Linear Model ◽

Snp Markers ◽

Genome Wide Association ◽

Bacterial Disease ◽

Maize Germplasm ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

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Development of an SNP Marker Set for Marker-Assisted Backcrossing Using Genotyping-By-Sequencing in Tetraploid Perilla

10.21203/rs.3.rs-1177284/v1 ◽

2021 ◽

Author(s):

Yun-Joo Kang ◽

Bo-Mi Lee ◽

Jangmi Kim ◽

Moon Nam ◽

Myoung-Hee Lee ◽

...

Keyword(s):

Recurrent Selection ◽

Diploid Species ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Genetic Maps ◽

Linkage Maps ◽

Linkage Groups ◽

Genome Wide ◽

A Genome ◽

Marker Assisted Backcrossing

Abstract High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2,326 and 2,454 SNP markers that spanned a total genetic distance of 2,133 cM across 16 linkage groups and 2,169 cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1,123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.

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Genome-Wide Association Mapping of Resistance to Fusarium Head Blight Spread and Deoxynivalenol Accumulation in Chinese Elite Wheat Germplasm

Phytopathology ◽

10.1094/phyto-12-18-0484-r ◽

2019 ◽

Vol 109 (7) ◽

pp. 1208-1216 ◽

Cited By ~ 7

Author(s):

Lei Wu ◽

Yu Zhang ◽

Yi He ◽

Peng Jiang ◽

Xu Zhang ◽

...

Keyword(s):

Fusarium Head Blight ◽

Genome Wide Association Study ◽

Snp Array ◽

Snp Markers ◽

Genome Wide Association ◽

Head Blight ◽

Sources Of Resistance ◽

Wheat Germplasm ◽

Genome Wide ◽

A Genome

Improving resistance to Fusarium head blight (FHB) in wheat is crucial in the integrated management of the disease and prevention of deoxynivalenol (DON) contamination in grains. To identify novel sources of resistance, a genome-wide association study (GWAS) was performed using a panel of 213 accessions of elite wheat germplasm of China. The panel was evaluated for FHB severity in four environments and DON content in grains in two environments. High correlations across environments and high heritability were observed for FHB severity and DON content in grains. The panel was also genotyped with the 90K Illumina iSelect single nucleotide polymorphism (SNP) array and 11,461 SNP markers were obtained. The GWAS revealed a total of six and three loci significantly associated with resistance to fungal spread and DON accumulation in at least two environments, respectively. QFHB-2BL.1 tagged by IWB52433 and QFHB-3A tagged by IWB50548 were responsible for resistance to both fungal spread and DON accumulation. In summary, this study provided an overview of FHB resistance resources in elite Chinese wheat germplasm and identified novel resistance loci that could be used for wheat improvement.

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A Genome-Wide Genetic Diversity Scan Reveals Multiple Signatures of Selection in a European Soybean Collection Compared to Chinese Collections of Wild and Cultivated Soybean Accessions

Frontiers in Plant Science ◽

10.3389/fpls.2021.631767 ◽

2021 ◽

Vol 12 ◽

Author(s):

Aamir Saleem ◽

Hilde Muylle ◽

Jonas Aper ◽

Tom Ruttink ◽

Jiao Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Oil Content ◽

Selective Sweep ◽

Germplasm Collection ◽

Snp Markers ◽

Selective Sweeps ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome ◽

Signatures Of Selection

Targeted and untargeted selections including domestication and breeding efforts can reduce genetic diversity in breeding germplasm and create selective sweeps in crop genomes. The genomic regions at which selective sweeps are detected can reveal important information about signatures of selection. We have analyzed the genetic diversity within a soybean germplasm collection relevant for breeding in Europe (the EUCLEG collection), and have identified selective sweeps through a genome-wide scan comparing that collection to Chinese soybean collections. This work involved genotyping of 480 EUCLEG soybean accessions, including 210 improved varieties, 216 breeding lines and 54 landraces using the 355K SoySNP microarray. SNP calling of 477 EUCLEG accessions together with 328 Chinese soybean accessions identified 224,993 high-quality SNP markers. Population structure analysis revealed a clear differentiation between the EUCLEG collection and the Chinese materials. Further, the EUCLEG collection was sub-structured into five subgroups that were differentiated by geographical origin. No clear association between subgroups and maturity group was detected. The genetic diversity was lower in the EUCLEG collection compared to the Chinese collections. Selective sweep analysis revealed 23 selective sweep regions distributed over 12 chromosomes. Co-localization of these selective sweep regions with previously reported QTLs and genes revealed that various signatures of selection in the EUCLEG collection may be related to domestication and improvement traits including seed protein and oil content, phenology, nitrogen fixation, yield components, diseases resistance and quality. No signatures of selection related to stem determinacy were detected. In addition, absence of signatures of selection for a substantial number of QTLs related to yield, protein content, oil content and phenological traits suggests the presence of substantial genetic diversity in the EUCLEG collection. Taken together, the results obtained demonstrate that the available genetic diversity in the EUCLEG collection can be further exploited for research and breeding purposes. However, incorporation of exotic material can be considered to broaden its genetic base.

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Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

Frontiers in Plant Science ◽

10.3389/fpls.2017.00648 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 24

Author(s):

Qinghong Zhou ◽

Can Zhou ◽

Wei Zheng ◽

Annaliese S. Mason ◽

Shuying Fan ◽

...

Keyword(s):

Brassica Napus ◽

Snp Markers ◽

Brassica Napus L ◽

Genome Wide

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Genome-wide association for heifer reproduction and calf performance traits in beef cattle

Genome ◽

10.1139/gen-2015-0031 ◽

2015 ◽

Vol 58 (12) ◽

pp. 549-557 ◽

Cited By ~ 5

Author(s):

Everestus C. Akanno ◽

Graham Plastow ◽

Carolyn Fitzsimmons ◽

Stephen P. Miller ◽

Vern Baron ◽

...

Keyword(s):

Beef Cattle ◽

Genome Wide Association Study ◽

Average Daily Gain ◽

Snp Markers ◽

Genome Wide Association ◽

Research Centre ◽

Genome Wide ◽

A Genome ◽

Starting Point ◽

And Performance

The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5–7, 9, 13–16, 19–21, 24, 25, and 27–29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.

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SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis 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 ◽

10.1139/g10-079 ◽

2010 ◽

Vol 53 (11) ◽

pp. 948-956 ◽

Cited By ~ 35

Author(s):

G. Durstewitz ◽

A. Polley ◽

J. Plieske ◽

H. Luerssen ◽

E. M. Graner ◽

...

Keyword(s):

Genetic Analysis ◽

Oilseed Rape ◽

Expressed Sequence Tag ◽

Diploid Species ◽

Amplicon Sequencing ◽

Snp Markers ◽

Snp Analysis ◽

Genome Wide ◽

A Genome ◽

Illumina Goldengate

Oilseed rape ( Brassica napus ) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

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Genome-wide association analysis of resistance to Pseudoperonospora cubensis in citron watermelon

Plant Disease ◽

10.1094/pdis-08-21-1611-re ◽

2021 ◽

Author(s):

Dennis Katuuramu ◽

Sandra Branham ◽

Amnon Levi ◽

Patrick Wechter

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Citrullus Lanatus ◽

Phenotypic Variability ◽

Germplasm Collection ◽

Snp Markers ◽

Genome Wide Association ◽

Pseudoperonospora Cubensis ◽

Genome Wide ◽

A Genome

Cultivated sweet watermelon (Citrullus lanatus) is an important vegetable crop for millions of people around the world. There are limited sources of resistance to economically important diseases within C. lanatus, whereas Citrullus amarus has a reservoir of traits that can be exploited to improve C. lanatus for resistance to biotic and abiotic stresses. Cucurbit downy mildew (CDM), caused by Pseudoperonospora cubensis, is an emerging threat to watermelon production. We screened 122 C. amarus accessions for resistance to CDM over two tests (environments). The accessions were genotyped by whole-genome resequencing to generate 2,126,759 single nucleotide polymorphic (SNP) markers. A genome-wide association study was deployed to uncover marker-trait associations and identify candidate genes underlying resistance to CDM. Our results indicate the presence of wide phenotypic variability (1.1 - 57.8%) for leaf area infection, representing a 50.7-fold variation for CDM resistance across the C. amarus germplasm collection. Broad-sense heritability estimate was 0.55, implying the presence of moderate genetic effects for resistance to CDM. The peak SNP markers associated with resistance to P. cubensis were located on chromosomes Ca03, Ca05, Ca07, and Ca11. The significant SNP markers accounted for up to 30% of the phenotypic variation and were associated with promising candidate genes encoding disease resistance proteins, leucine-rich repeat receptor-like protein kinase, and WRKY transcription factor. This information will be useful in understanding the genetic architecture of the P. cubensis-Citrullus spp. patho-system as well as development of resources for genomics-assisted breeding for resistance to CDM in watermelon.

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