Genome‐wide association mapping identifies novel loci underlying fire blight resistance in apple

Thapa, Ranjita; Singh, Jugpreet; Gutierrez, Benjamin; Arro, Jie; Khan, Awais

doi:10.1002/tpg2.20087

Cited by 14 publications

(8 citation statements)

References 81 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genome-wide association studies (GWAS) can use these millions of SNPs as molecular markers to screen many accessions simultaneously without needing to construct segregating populations in advance ( Buckler and Thornsberry, 2002 ; Flint-Garcia et al, 2003 ; Yu et al, 2006 ; Wang et al, 2016 ; Zhang et al, 2019 ). For instance, Thapa et al (2021) identified 23 and 38 QTNs associated with shoot and blossom blight resistance, respectively, using GBS markers in 273 apple accessions, while Jing et al (2021) identified 18 QTNs related to Sclerotinia stem rot resistance in soybean. Thus, GWAS is an efficient tool for QTN identification in natural populations with high-quality SNPs to overcome the shortcomings of bi-parental QTL mapping ( Zhang et al, 2019 ) and has great potential for discovering interrelationships among complex traits conditioned by multiple genes/alleles ( Buckler and Thornsberry, 2002 ; Yu et al, 2006 ; Hyun et al, 2021 ; Thapa et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…For instance, Thapa et al (2021) identified 23 and 38 QTNs associated with shoot and blossom blight resistance, respectively, using GBS markers in 273 apple accessions, while Jing et al (2021) identified 18 QTNs related to Sclerotinia stem rot resistance in soybean. Thus, GWAS is an efficient tool for QTN identification in natural populations with high-quality SNPs to overcome the shortcomings of bi-parental QTL mapping ( Zhang et al, 2019 ) and has great potential for discovering interrelationships among complex traits conditioned by multiple genes/alleles ( Buckler and Thornsberry, 2002 ; Yu et al, 2006 ; Hyun et al, 2021 ; Thapa et al, 2021 ). However, no GWAS studies have been undertaken to detect QTNs associated with TBW resistance in tobacco.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco (Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies

Lai

Ikram

et al. 2021

Front. Plant Sci.

View full text Add to dashboard Cite

Tobacco bacterial wilt (TBW) is a devastating soil-borne disease threatening the yield and quality of tobacco. However, its genetic foundations are not fully understood. In this study, we identified 126,602 high-quality single-nucleotide polymorphisms (SNPs) in 94 tobacco accessions using genotyping-by-sequencing (GBS) and a 94.56 KB linkage disequilibrium (LD) decay rate for candidate gene selection. The population structure analysis revealed two subpopulations with 37 and 57 tobacco accessions. Four multi-locus genome-wide association study (ML-GWAS) approaches identified 142 quantitative trait nucleotides (QTNs) in E1–E4 and the best linear unbiased prediction (BLUP), explaining 0.49–22.52% phenotypic variance. Of these, 38 novel stable QTNs were identified across at least two environments/methods, and their alleles showed significant TBW-DI differences. The number of superior alleles associated with TBW resistance for each accession ranged from 4 to 24; eight accessions had more than 18 superior alleles. Based on TBW-resistant alleles, the five best cross combinations were predicted, including MC133 × Ruyuan No. 1 and CO258 × ROX28. We identified 52 candidate genes around 38 QTNs related to TBW resistance based on homologous functional annotation and KEGG enrichment analysis, e.g., CYCD3;2, BSK1, Nitab4.5_0000641g0050, Nitab4.5_0000929g0030. To the best of our knowledge, this is the first comprehensive study to identify QTNs, superior alleles, and their candidate genes for breeding TBW-resistant tobacco varieties. The results provide further insight into the genetic architecture, marker-assisted selection, and functional genomics of TBW resistance, improving future breeding efforts to increase crop productivity.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco (Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies

Lai

Ikram

et al. 2021

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…In this approach, mostly a collection of diverse individual genotypes or diverse populations that are unrelated and can capture all possible recombination events are used. Such a population structure results in increased mapping resolution, improved transferability from one family to another, and increased discovery of SNPs across the whole genome ( Kumar et al., 2012a ; Peace et al., 2019 ; Thapa et al., 2021 ).…”

Section: Fruit Growthmentioning

confidence: 99%

“…Finally, markers controlling harvest date were co-localized with the coding region of a NAC transcription factor that regulates fruit ripening and maturity in apple ( Larsen et al., 2019 ). Recently, a genome-wide methods was applied to study other physiological traits such as fruit texture ( Di Guardo et al., 2017 ), fire blight resistance loci ( Thapa et al., 2021 ), scab resistance ( McClure et al., 2018 ), and flesh browning ( Kunihisa et al., 2021 ). Findings of these studies indicate that genome-wide techniques can facilitate increased mapping resolution, increased detection of multiple alleles at the same locus, and a high number of SNPs that adequately cover the whole genome.…”

Section: Fruit Growthmentioning

confidence: 99%

Fruit growth and development in apple: a molecular, genomics and epigenetics perspective

Jahed

Hirst

2023

Front. Plant Sci.

View full text Add to dashboard Cite

Fruit growth and development are physiological processes controlled by several internal and external factors. This complex regulatory mechanism comprises a series of events occurring in a chronological order over a growing season. Understanding the underlying mechanism of fruit development events, however, requires consideration of the events occurring prior to fruit development such as flowering, pollination, fertilization, and fruit set. Such events are interrelated and occur in a sequential order. Recent advances in high-throughput sequencing technology in conjunction with improved statistical and computational methods have empowered science to identify some of the major molecular components and mechanisms involved in the regulation of fruit growth and have supplied encouraging successes in associating genotypic differentiation with phenotypic observations. As a result, multiple approaches have been developed to dissect such complex regulatory machinery and understand the genetic basis controlling these processes. These methods include transcriptomic analysis, quantitative trait loci (QTLs) mapping, whole-genome approach, and epigenetics analyses. This review offers a comprehensive overview of the molecular, genomic and epigenetics perspective of apple fruit growth and development that defines the final fruit size and provides a detailed analysis of the mechanisms by which fruit growth and development are controlled. Though the main emphasis of this article is on the molecular, genomic and epigenetics aspects of fruit growth and development, we will also deliver a brief overview on events occurring prior to fruit growth.

show abstract

“…Diverse set of 566 apple accessions identified significant marker trait associations for fire blight of apple caused by Erwinia amylovora . A total of 23 and 38 MTAs significantly (p<.001) associated with shoot and blossom blight resistance, respectively ( Thapa et al., 2021 ). GWAS based on 195 accessions and 145,456 genome-wide SNPs identified five SNPs and six candidate genes significantly associated with gummosis disease resistance in peach ( Li et al., 2021b ).…”

Section: Other Key Cropsmentioning

confidence: 99%

Two decades of association mapping: Insights on disease resistance in major crops

et al. 2022

View full text Add to dashboard Cite

Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.

show abstract

Genome‐wide association mapping identifies novel loci underlying fire blight resistance in apple

Cited by 14 publications

References 81 publications

Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco (Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies

Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco (Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies

Fruit growth and development in apple: a molecular, genomics and epigenetics perspective

Two decades of association mapping: Insights on disease resistance in major crops

Contact Info

Product

Resources

About