Quantitative Trait Locus Mapping for Common Scab Resistance in a Tetraploid Potato Full-Sib Population

Pereira, Guilherme da Silva; Mollinari, Marcelo; Qu, Xinshun; Thill, Christian A.; Zeng, Zhao‐Bang; Haynes, Kathleen G.; Yencho, G. Craig

doi:10.1094/pdis-10-20-2270-re

Cited by 6 publications

(3 citation statements)

References 60 publications

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“…Common scab, caused by Streptomyces species such as Streptomyces scabies , S. acidiscabies and S. turgidiscabies (Lambert and Loria 1989 ; Miyajima et al 1998 ), is an unsightly blemish disease of potatoes occurring worldwide. Previous genetic mapping studies have identified common scab QTLs on several chromosomes viz., 1, 2, 3, 4, 6, 9, 11 and 12 (Bradshaw et al 2008 ; Braun et al 2017 ; Enciso-Rodriguez et al 2018 ; Kaiser et al 2020 ; Koizumi et al 2021 ; Pereira et al 2021a ; Yuan et al 2020 ) using diploid and tetraploid populations and deploying a range of marker types. GWAS here identified QTL-MTAs on chromosomes 1, 8, 11 and 12 (Table 5 ; Figs.…”

Section: Discussionmentioning

confidence: 99%

Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato

Sharma,

McLean,

Hedley

et al. 2024

Theor Appl Genet

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Key message De novo genotyping in potato using methylation-sensitive GBS discovers SNPs largely confined to genic or gene-associated regions and displays enhanced effectiveness in estimating LD decay rates, population structure and detecting GWAS associations over ‘fixed’ SNP genotyping platform. Study also reports the genetic architectures including robust sequence-tagged marker–trait associations for sixteen important potato traits potentially carrying higher transferability across a wider range of germplasm. Abstract This study deploys recent advancements in polyploid analytical approaches to perform complex trait analyses in cultivated tetraploid potato. The study employs a ‘fixed’ SNP Infinium array platform and a ‘flexible and open’ genome complexity reduction-based sequencing method (GBS, genotyping-by-sequencing) to perform genome-wide association studies (GWAS) for several key potato traits including the assessment of population structure and linkage disequilibrium (LD) in the studied population. GBS SNPs discovered here were largely confined (~ 90%) to genic or gene-associated regions of the genome demonstrating the utility of using a methylation-sensitive restriction enzyme (PstI) for library construction. As compared to Infinium array SNPs, GBS SNPs displayed enhanced effectiveness in estimating LD decay rates and discriminating population subgroups. GWAS using a combined set of 30,363 SNPs identified 189 unique QTL marker–trait associations (QTL-MTAs) covering all studied traits. The majority of the QTL-MTAs were from GBS SNPs potentially illustrating the effectiveness of marker-dense de novo genotyping platforms in overcoming ascertainment bias and providing a more accurate correction for different levels of relatedness in GWAS models. GWAS also detected QTL ‘hotspots’ for several traits at previously known as well as newly identified genomic locations. Due to the current study exploiting genome-wide genotyping and de novo SNP discovery simultaneously on a large tetraploid panel representing a greater diversity of the cultivated potato gene pool, the reported sequence-tagged MTAs are likely to have higher transferability across a wider range of potato germplasm and increased utility for expediting genomics-assisted breeding for the several complex traits studied.

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Section: Discussionmentioning

confidence: 99%

Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato

Sharma,

McLean,

Hedley

et al. 2024

Theor Appl Genet

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“…The software described in this study and used in this analysis has been previously used to create linkage maps and map QTL for various traits in other polyploid crops. The MAPpoly and QTLpoly software have been successfully used to map common scab resistance in autotetraploid potatoes ( da Silva Pereira et al, 2021 ) and fruit firmness in autotetraploid blueberry ( Cappai et al, 2020 ). This software has been used extensively to study autohexaploid sweet potatoes for root-knot nematode resistance ( Oloka et al, 2021 ), carotenoid, and starch biosynthesis ( Gemenet et al, 2020 ) and yield component traits ( da Silva Pereira et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations

et al. 2022

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Rose rosette disease (RRD), caused by the Rose rosette emaravirus (RRV), is a major threat to the garden rose industry in the United States. There has been limited work on the genetics of host plant resistance to RRV. Two interconnected tetraploid garden rose F1 biparental mapping populations were created to develop high-quality tetraploid rose linkage maps that allowed the discovery of RRD resistance quantitative trait loci (QTLs) on linkage groups (LGs) 5, 6, and 7. These QTLs individually accounted for around 18–40% of the phenotypic variance. The locus with the greatest effect on partial resistance was found in LG 5. Most individuals with the LG 5 QTL were in the simplex configuration; however, two individuals were duplex (likely due to double reduction). Identification of resistant individuals and regions of interest can help the development of diagnostic markers for marker-assisted selection in a breeding program.

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“…Genetic interactions regulate PVY resistance and have an impact on tuber quality and quantity [6]. Furthermore, potato surveys benefit from the availability of the potato genome and sequencing progress with increasing precision genomic information, pan-genomics [7,8], advanced segregant populations [9,10], and genome editing techniques [11,12]. Tilling, ecotilling, and virus-induced gene silencing techniques have been used to link traits to genetic variants in potato [13].…”

Section: Introductionmentioning

confidence: 99%

Genotyping-by-sequencing and weighted gene co-expression network analysis of genes responsive against Potato virus Y in commercial potato cultivars

Hajibarat,

Saidi,

Zeinalabedini

et al. 2024

PLoS ONE

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Potato is considered a key component of the global food system and plays a vital role in strengthening world food security. A major constraint to potato production worldwide is the Potato Virus Y (PVY), belonging to the genus Potyvirus in the family of Potyviridae. Selective breeding of potato with resistance to PVY pathogens remains the best method to limit the impact of viral infections. Understanding the genetic diversity and population structure of potato germplasm is important for breeders to improve new cultivars for the sustainable use of genetic materials in potato breeding to PVY pathogens. While, genetic diversity improvement in modern potato breeding is facing increasingly narrow genetic basis and the decline of the genetic diversity. In this research, we performed genotyping-by-sequencing (GBS)-based diversity analysis on 10 commercial potato cultivars and weighted gene co-expression network analysis (WGCNA) to identify candidate genes related to PVY-resistance. WGCNA is a system biology technique that uses the WGCNA R software package to describe the correlation patterns between genes in multiple samples. In terms of consumption, these cultivars are a high rate among Iranian people. Using population structure analysis, the 10 cultivars were clustered into three groups based on the 118343 single nucleotide polymorphisms (SNPs) generated by GBS. Read depth ranged between 5 and 18. The average data size and Q30 of the reads were 145.98 Mb and 93.63%, respectively. Based on the WGCNA and gene expression analysis, the StDUF538, StGTF3C5, and StTMEM161A genes were associated with PVY resistance in the potato genome. Further, these three hub genes were significantly involved in defense mechanism where the StTMEM161A was involved in the regulation of alkalization apoplast, the StDUF538 was activated in the chloroplast degradation program, and the StGTF3C5 regulated the proteins increase related to defense in the PVY infected cells. In addition, in the genetic improvement programs, these hub genes can be used as genetic markers for screening commercial cultivars for PVY resistance. Our survey demonstrated that the combination of GBS-based genetic diversity germplasm analysis and WGCNA can assist breeders to select cultivars resistant to PVY as well as help design proper crossing schemes in potato breeding.

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Quantitative Trait Locus Mapping for Common Scab Resistance in a Tetraploid Potato Full-Sib Population

Cited by 6 publications

References 60 publications

Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato

Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato

Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations

Genotyping-by-sequencing and weighted gene co-expression network analysis of genes responsive against Potato virus Y in commercial potato cultivars

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