Decryption of favourable haplotypes and potential candidate genes for five fibre quality properties using a relatively novel genome-wide association study procedure in upland cotton.
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| Title: | Decryption of favourable haplotypes and potential candidate genes for five fibre quality properties using a relatively novel genome-wide association study procedure in upland cotton. |
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| Authors: | Su, Junji1 (AUTHOR) sujunjicotton@126.com, Wang, Caixiang1 (AUTHOR), Yang, Delong1 (AUTHOR) yangdl@gsau.edu.cn, Shi, Chunhui1 (AUTHOR), Zhang, Ai1 (AUTHOR), Ma, Qi2 (AUTHOR), Liu, Juanjuan1 (AUTHOR), Zhang, Xianliang3 (AUTHOR), Huang, Long4 (AUTHOR), Ma, Xiongfeng1,3,5 (AUTHOR) maxiongfeng@caas.cn |
| Source: | Industrial Crops & Products. Dec2020, Vol. 158, pN.PAG-N.PAG. 1p. |
| Subjects: | Cotton, Single nucleotide polymorphisms, Haplotypes, Fibers, Genes, Linkage disequilibrium |
| Abstract: | • A relatively novel GWAS procedure was used in upland cotton. • SNP linkage disequilibrium block-based alleles were used for whole-genome scanning. • A total of 344 QTLs were detected for five fibre quality properties. • Nine stable QTLs were identified, and their haplotype/allele effects were estimated. • 79 likely candidate genes were related to fibre quality properties. To understand the genetic basis of crop economic characteristics, identifying whole-genome quantitative trait loci (QTLs) in breeding resources via genome-wide association studies (GWASs) is important, but conventional GWAS procedures have mainly concentrated on identifying regions of major QTLs. In this study, to reveal whole-genome QTLs controlling cotton fibre quality traits, a total of 1,236,418 single-nucleotide polymorphism (SNP) markers were explored in a natural population of 315 upland cotton accessions using the specific-locus amplified fragment sequencing (SLAF-seq) method, and 13,391 high-quality SNPs were organized into 9244 SNP linkage disequilibrium blocks (SNPLDBs) to develop molecular markers with multiple haplotypes/alleles. A relatively novel procedure for restricted two-stage multi-locus multi-allele GWAS (RTM-GWAS) involving two methods was applied, including multiple environments and four single environments. In total, 75, 77, 66, 66, and 60 significant SNPLDBs associated with the upper half mean length (UHML), fibre strength (FS), fibre micronaire (FM), fibre uniformity index (FUI), and fibre elongation (FE), respectively, were identified via the multiple-environment RTM-GWAS method. Based on these results, the haplotype/allele effects of the significant SNPLDB loci were estimated, and QTL-allele matrices were established to provide the abbreviated genetic composition of the population. Most importantly, nine stable SNPLDB loci were simultaneously detected in multiple environments and two or more single test environments with large –lg(P) values and percentages of explained phenotypic variation. Furthermore, favourable haplotypes/alleles of the nine stable SNPLDB loci were identified, and 79 potential candidate genes related to UHML and FS traits were predicted from RNA-seq data. Favourable haplotypes/alleles, potential candidate genes and QTL-allele matrices can offer important insights into the genetic basis of fibre quality traits in upland cotton and may facilitate the breeding of cotton varieties with excellent fibre quality properties. [ABSTRACT FROM AUTHOR] |
| Copyright of Industrial Crops & Products is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 147181986 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Decryption of favourable haplotypes and potential candidate genes for five fibre quality properties using a relatively novel genome-wide association study procedure in upland cotton. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Su%2C+Junji%22">Su, Junji</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> sujunjicotton@126.com</i><br /><searchLink fieldCode="AR" term="%22Wang%2C+Caixiang%22">Wang, Caixiang</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Yang%2C+Delong%22">Yang, Delong</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> yangdl@gsau.edu.cn</i><br /><searchLink fieldCode="AR" term="%22Shi%2C+Chunhui%22">Shi, Chunhui</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Zhang%2C+Ai%22">Zhang, Ai</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Ma%2C+Qi%22">Ma, Qi</searchLink><relatesTo>2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Liu%2C+Juanjuan%22">Liu, Juanjuan</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Zhang%2C+Xianliang%22">Zhang, Xianliang</searchLink><relatesTo>3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Huang%2C+Long%22">Huang, Long</searchLink><relatesTo>4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Ma%2C+Xiongfeng%22">Ma, Xiongfeng</searchLink><relatesTo>1,3,5</relatesTo> (AUTHOR)<i> maxiongfeng@caas.cn</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Industrial+Crops+%26+Products%22">Industrial Crops & Products</searchLink>. Dec2020, Vol. 158, pN.PAG-N.PAG. 1p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Cotton%22">Cotton</searchLink><br /><searchLink fieldCode="DE" term="%22Single+nucleotide+polymorphisms%22">Single nucleotide polymorphisms</searchLink><br /><searchLink fieldCode="DE" term="%22Haplotypes%22">Haplotypes</searchLink><br /><searchLink fieldCode="DE" term="%22Fibers%22">Fibers</searchLink><br /><searchLink fieldCode="DE" term="%22Genes%22">Genes</searchLink><br /><searchLink fieldCode="DE" term="%22Linkage+disequilibrium%22">Linkage disequilibrium</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: • A relatively novel GWAS procedure was used in upland cotton. • SNP linkage disequilibrium block-based alleles were used for whole-genome scanning. • A total of 344 QTLs were detected for five fibre quality properties. • Nine stable QTLs were identified, and their haplotype/allele effects were estimated. • 79 likely candidate genes were related to fibre quality properties. To understand the genetic basis of crop economic characteristics, identifying whole-genome quantitative trait loci (QTLs) in breeding resources via genome-wide association studies (GWASs) is important, but conventional GWAS procedures have mainly concentrated on identifying regions of major QTLs. In this study, to reveal whole-genome QTLs controlling cotton fibre quality traits, a total of 1,236,418 single-nucleotide polymorphism (SNP) markers were explored in a natural population of 315 upland cotton accessions using the specific-locus amplified fragment sequencing (SLAF-seq) method, and 13,391 high-quality SNPs were organized into 9244 SNP linkage disequilibrium blocks (SNPLDBs) to develop molecular markers with multiple haplotypes/alleles. A relatively novel procedure for restricted two-stage multi-locus multi-allele GWAS (RTM-GWAS) involving two methods was applied, including multiple environments and four single environments. In total, 75, 77, 66, 66, and 60 significant SNPLDBs associated with the upper half mean length (UHML), fibre strength (FS), fibre micronaire (FM), fibre uniformity index (FUI), and fibre elongation (FE), respectively, were identified via the multiple-environment RTM-GWAS method. Based on these results, the haplotype/allele effects of the significant SNPLDB loci were estimated, and QTL-allele matrices were established to provide the abbreviated genetic composition of the population. Most importantly, nine stable SNPLDB loci were simultaneously detected in multiple environments and two or more single test environments with large –lg(P) values and percentages of explained phenotypic variation. Furthermore, favourable haplotypes/alleles of the nine stable SNPLDB loci were identified, and 79 potential candidate genes related to UHML and FS traits were predicted from RNA-seq data. Favourable haplotypes/alleles, potential candidate genes and QTL-allele matrices can offer important insights into the genetic basis of fibre quality traits in upland cotton and may facilitate the breeding of cotton varieties with excellent fibre quality properties. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Industrial Crops & Products is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1016/j.indcrop.2020.113004 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 1 StartPage: N.PAG Subjects: – SubjectFull: Cotton Type: general – SubjectFull: Single nucleotide polymorphisms Type: general – SubjectFull: Haplotypes Type: general – SubjectFull: Fibers Type: general – SubjectFull: Genes Type: general – SubjectFull: Linkage disequilibrium Type: general Titles: – TitleFull: Decryption of favourable haplotypes and potential candidate genes for five fibre quality properties using a relatively novel genome-wide association study procedure in upland cotton. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Su, Junji – PersonEntity: Name: NameFull: Wang, Caixiang – PersonEntity: Name: NameFull: Yang, Delong – PersonEntity: Name: NameFull: Shi, Chunhui – PersonEntity: Name: NameFull: Zhang, Ai – PersonEntity: Name: NameFull: Ma, Qi – PersonEntity: Name: NameFull: Liu, Juanjuan – PersonEntity: Name: NameFull: Zhang, Xianliang – PersonEntity: Name: NameFull: Huang, Long – PersonEntity: Name: NameFull: Ma, Xiongfeng IsPartOfRelationships: – BibEntity: Dates: – D: 15 M: 12 Text: Dec2020 Type: published Y: 2020 Identifiers: – Type: issn-print Value: 09266690 Numbering: – Type: volume Value: 158 Titles: – TitleFull: Industrial Crops & Products Type: main |
| ResultId | 1 |
