Genome-Wide Association Study of Resistance to Potato Common Scab

Yuan, Jiazheng; Bizimungu, Benoît; Koeyer, David De; Rosyara, Umesh R.; Zhang, Wen; Lagüe, M.

doi:10.1007/s11540-019-09437-w

Cited by 35 publications

(28 citation statements)

References 44 publications

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“…in present) estimated in diploid populations of S. stenotomum and S. phureja ( H 2 = 0.59) by using the diameter of the rotten area as a measure of the degree of resistance (Wolters and Collins 1991). The broad-sense heritability of DS was also similar or lower than the heritability for resistance to common scab, other bacterial disease caused by Streptomyces scabies , evaluated in field trials in a diploid population of S. tuberosum and S. chacoense ( H 2 in range from 0.48 to 0.72) (Braun et al 2017), and lower than that estimated for common scab resistance in potato clones and breeding lines ( H 2 = 0.81) (Yuan et al 2020). The broad-sense heritability of DI in our study was low ( H 2 = 0.24).…”

Section: Discussionmentioning

confidence: 80%

“…Resistance QTLs for other bacterial diseases of potato, such as common scab, have recently been mapped in a genome–wide association study in 143 Canadian potato cultivars and advanced breeding clones (Yuan et al 2020). Three QTLs for potato tuber resistance to this pathogen, explaining 21%, 8%, and 12% of phenotypic variance, were identified on potato chromosomes II, IV and XII, respectively.…”

Section: Discussionmentioning

confidence: 99%

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QTLs for potato tuber resistance toDickeya solaniare located on chromosomes II and IV

Lebecka

Śliwka

Grupa-Urbańska

et al. 2021

Preprint

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Soft rot is a bacterial disease that causes heavy losses in potato production worldwide. The goal of this study was to identify quantitative trait loci (QTLs) for potato tuber resistance to bacterium Dickeya solani and for tuber starch content to study the relationship between these traits. A highly resistant diploid hybrid of potato was crossed with a susceptible hybrid to generate the F1 mapping population. Tubers that were wound-inoculated with bacteria were evaluated for disease severity expressed as the mean weight of rotted tubers, and disease incidence measured as the proportion of rotten tubers. Diversity array technology (DArTseq) was used for genetic map construction and QTLs analysis. The most prominent QTLs for disease severity and incidence were identified in overlapping regions on potato chromosome IV and explained 22.4% and 22.9% of the phenotypic variance, respectively. The second QTL for disease severity was mapped to chromosome II and explained 16.5% of the variance. QTLs for starch content were detected on chromosomes III, V, VI, VII, VIII, IX, XI, and XII in regions different than the QTLs for soft rot resistance. Two strong and reproducible QTLs for resistance to Dickeya solani on potato chromosomes IV and II might be useful for further study of candidate genes and marker development in potato breeding programs. The relationship between tuber resistance to bacteria and the starch content in potato tubers was not confirmed by QTL mapping, which makes the selection of genotypes highly resistant to soft rot with a desirable starch content feasible.

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Section: Discussionmentioning

confidence: 80%

Section: Discussionmentioning

confidence: 99%

QTLs for potato tuber resistance toDickeya solaniare located on chromosomes II and IV

Lebecka

Śliwka

Grupa-Urbańska

et al. 2021

Preprint

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“…GWASpoly ( [Rosyara et al, 2016]) is an R package designed for GWAS in polyploid species used in several studies in plants ([Berdugo-Cely et al, 2017, Ferrão et al, 2018, Sharma et al, 2018, Yuan et al, 2019). GWASpoly uses a Q+K linear mixed model with biallelic SNPs that account for population structure and relatedness.…”

Section: Gwaspolymentioning

confidence: 99%

MultiGWAS: An integrative tool for Genome Wide Association Studies (GWAS) in tetraploid organisms

Garreta

Cerón‐Souza

Palacio

et al. 2020

Preprint

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The Genome-Wide Association Studies (GWAS) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of model and non-model organisms. For this research question, current practice is the replication of the GWAS testing different parameters and models to validate the reproducibility of results. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software, two for polyploid data (GWASpoly and SHEsis) and two for diploids data (PLINK and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in an interface. It manages different genotype formats, including VCF. It executes both the full and naive models using several quality filters. Besides, it calculates a score to choose the best gene action model across GWASPoly and TASSEL. Finally, it generates several reports that facilitate the identification of false associations from both the significant and the best-ranked association SNP among the four software. We tested MultiGWAS with tetraploid potato data. The execution demonstrated that the Venn diagram and the other companion reports (i.e., Manhattan and QQ plots, heatmaps for associated SNP profiles, and chord diagrams to trace associated SNP by chromosomes) were useful to identify associated SNP shared among different models and parameters. Therefore, we confirmed that MultiGWAS is a suitable wrapping tool that successfully handles GWAS replication in both diploid and tetraploid organisms.

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“…For potato, strategies based on genotyping-by-sequencing (Uitdewilligen et al, 2013; Sverrisdóttir et al, 2017) or chip arrays (Felcher et al, 2012; Vos et al, 2015) can now provide allele intensity information of thousands of single nucleotide polymorphisms (SNPs). After dosage calling is carried out (Schmitz Carley et al, 2017; Zych et al, 2019), these variants can be ultimately utilized in several applications such as linkage and quantitative trait locus (QTL) analyses (Hackett et al, 2014; Chen et al, 2018; Pereira et al, 2020b), genome-wide association studies (GWAS; Rosyara et al, 2016; Yuan et al, 2019), or genomic-assisted prediction (Sverrisdóttir et al, 2017; Enciso-Rodriguez et al, 2018). In the case of QTL identification of resistance to common scab in potato, only two studies have been carried out, one in a tetraploid population (227 F 1 clones; Bradshaw et al, 2008), and another in a diploid population (49~91 F 2 clones; Braun et al, 2017a).…”

Section: Introductionmentioning

confidence: 99%

“…In the case of QTL identification of resistance to common scab in potato, only two studies have been carried out, one in a tetraploid population (227 F 1 clones; Bradshaw et al, 2008), and another in a diploid population (49~91 F 2 clones; Braun et al, 2017a). In addition, GWAS was performed in a tetraploid diversity panel (143 clones; Yuan et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Quantitative trait locus mapping for common scab resistance in a tetraploid potato full-sib population

Pereira¹,

Mollinari

et al. 2020

Preprint

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Despite the negative impact of common scab (Streptomyces spp.) to the potato industry, little is known about the genetic architecture of resistance to this bacterial disease in the crop. We evaluated a mapping population (~150 full-sibs) derived from a cross between two tetraploid potatoes ('Atlantic' × B1829-5) in three environments (MN11, PA11, ME12) under natural common scab pressure. Three measures to common scab reaction were assessed, namely percentage of scabby tubers, and disease area and lesion indices, which were highly correlated (>0.76). Due to large environmental effect, heritability values were zero for all three traits in MN11, but moderate to high in PA11 and ME12 (0.44~0.79). We identified a single quantitative trait locus (QTL) for lesion index in PA11, ME12 and joint analyses on linkage group 3, explaining 22~30% of the total variation. The identification of QTL haplotypes and candidate genes contributing to disease resistance can support genomics-assisted breeding approaches.

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Genome-Wide Association Study of Resistance to Potato Common Scab

Cited by 35 publications

References 44 publications

QTLs for potato tuber resistance toDickeya solaniare located on chromosomes II and IV

QTLs for potato tuber resistance toDickeya solaniare located on chromosomes II and IV

MultiGWAS: An integrative tool for Genome Wide Association Studies (GWAS) in tetraploid organisms

Quantitative trait locus mapping for common scab resistance in a tetraploid potato full-sib population

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