Identification of potential gene‐associated major traits using <scp>GBS</scp>‐<scp>GWAS</scp> for Korean apple germplasm collections

Lee, So Jin; Ban, Seung Hyun; Kim, Gi Hoon; Kwon, Sanghoon; Kim, Jeong Hee; Choi, Cheol

doi:10.1111/pbr.12544

Cited by 18 publications

(8 citation statements)

References 31 publications

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“…In the GWAS approach, the collections of unrelated genotypes exhibit much more limited linkage disequilibrium (LD) between pairs of neighboring markers, and therefore a large number of markers are needed to cover the genome (Sonah, O'Donoughue, Cober, Rajcan, & Belzile, 2015). Genotyping-by-sequencing (GBS), a complexity reduction approach based on restriction-enzyme digestion, can efficiently generate a large number of The Plant Genome single nucleotide polymorphisms (SNPs) distributed throughout the genome for conducting an effective GWAS (He et al, 2014;Lee et al, 2017). GWAS based on GBS-derived markers has been used to study population structure and genetic relationships, and identify novel genes influencing crucial traits in rice (Begum et al, 2015), wheat (Juliana et al, 2013), maize (Wallace et al, 2014), sorghum (Morris et al, 2013), and soybean (Sonah et al, 2015).…”

Section: Core Ideasmentioning

confidence: 99%

“…This is because of breeding difficulties that occur as a result of the long juvenile stage, the large physical stature of the plants, and the large genome. A recent study detected SNPs significantly associated with skin chroma and acidity on chromosomes 3 and 9 of Korean apple germplasm collections by GBS‐GWAS (Lee et al., 2017). In recent years, whole‐genome assemblies of Chinese jujube cultivars ‘Dongzao’ and ‘Junzao’ were released (Huang et al., 2016; Liu et al., 2014), which enables researchers to identify candidate genes if the trait mapped intervals can be sufficiently resolved.…”

Section: Introductionmentioning

confidence: 99%

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Genome‐wide association studies of fruit quality traits in jujube germplasm collections using genotyping‐by‐sequencing

Hou

Zhang

et al. 2020

The Plant Genome

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Chinese jujube (Ziziphus jujuba Mill.) is an important fruit crop and harbors many highly diverse traits of potential economic importance. Fruit size, stone size, and fruit cracking have an important influence on the commercial value of jujube. This study is the first to conduct a genome-wide association study (GWAS) on 180 accessions of jujube and focuses on locating single-nucleotide polymorphisms (SNPs) associated with nine important fruit quality traits. Genotyping was performed using genotyping-by-sequencing and 4651 high-quality SNPs were identified. A genetic diversity analysis revealed the presence of three distinct groups, and rapid linkage disequilibrium decay was observed in this jujube population. Using a mixed linear model, a total of 45 significant SNPtrait associations were detected, among which 33 SNPs had associations with fruit size-related traits, nine were associated with stone size-related traits, and three with fruit cracking-related traits. In total, 21 candidate genes involved in cell expansion, abiotic stress responses, hormone signaling, and growth development were identified from the genome sequences of jujube. These results are useful as basic data for GWAS of other jujube traits, and these significant SNP loci and candidate genes should aid marker-assisted breeding and genomic selection of improved jujube cultivars.

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Section: Core Ideasmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome‐wide association studies of fruit quality traits in jujube germplasm collections using genotyping‐by‐sequencing

Hou

Zhang

et al. 2020

The Plant Genome

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“…With the development of next-generation sequencing (NGS) technology, genotyping-by-sequencing (GBS) has been used widely as a high-throughput and low-cost genotyping platform for discovering genome-wide single-nucleotide polymorphisms (SNPs) in many crops, including tobacco ( Elshire et al, 2011 ; Lee et al, 2017 ; Sakiroglu and Brummer, 2017 ). 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 ).…”

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.

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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.

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“…GWAS have been conducted for various traits and have identified a series of genes and molecular mechanisms underlying phenotypic variation. Advanced GWAS has been conducted in mainly model plants and major crops; however, GWAS has also been reported in other plants with considerably less dense SNPs and population, such as apple (Amyotte et al, 2017;Farneti et al, 2017;Lee et al, 2017), beans (Sallam et al, 2016;Zuiderveen et al, 2016), and other vegetables (Nimmakayala et al, 2016;Han et al, 2018;Okada et al, 2019). Such kinds of studies in various plants will be conducted to promote NGS platform and resource collection.…”

Section: Conclusion and Perspectivementioning

confidence: 99%

Genome-wide Association Studies of Agronomic Traits Consisting of Field- and Molecular-based Phenotypes

Nakano

Kobayashi

2020

RAS

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Genome-wide association study (GWAS) is a powerful approach to identify the genetic factors underlying the intraspecific phenotypic variations. Recent advances in DNA sequencing technology, including next generation sequencing has enabled us to easily genotype high density genome-wide SNPs. In addition, many accessions of various plant species have been widely collected in recent years. These genetic resources have made GWAS a markedly more popular approach for investigation of natural variations occurring in various traits using large populations. In addition to genotyping technology, advances in high-throughput phenotyping technologies have enabled us to acquire variation data on a large number of accessions characterized for various traits, including not only the field traits (e.g., yield and disease resistance) but also molecular traits (e.g., gene expression level and metabolite content). Thus, it is possible to expand the range of application of GWAS and enhance the detection power of genomic association. In this review, we summarize recent GWAS of various agronomic traits at field and molecular scale, following which we highlight the integration approach involving GWAS and high-throughput phenotyping technologies including transcriptome, ionome and metabolome.

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Identification of potential gene‐associated major traits using GBS‐GWAS for Korean apple germplasm collections

Cited by 18 publications

References 31 publications

Genome‐wide association studies of fruit quality traits in jujube germplasm collections using genotyping‐by‐sequencing

Genome‐wide association studies of fruit quality traits in jujube germplasm collections using genotyping‐by‐sequencing

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

Genome-wide Association Studies of Agronomic Traits Consisting of Field- and Molecular-based Phenotypes

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