Molecular characterization of tall fescue germplasm using SNP markers: population structure, linkage disequilibrium, and association mapping of yield-related traits.
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| Title: | Molecular characterization of tall fescue germplasm using SNP markers: population structure, linkage disequilibrium, and association mapping of yield-related traits. |
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| Authors: | Shahabzadeh, Zeynab1 (AUTHOR), Darvishzadeh, Reza1 (AUTHOR) r.darvishzadeh@urmia.ac.ir, Mohammadi, Reza2 (AUTHOR), Jafari, Morad1 (AUTHOR), Alipour, Hadi1 (AUTHOR) ha.alipour@urmia.ac.ir |
| Source: | Plant Biotechnology Reports. Apr2023, Vol. 17 Issue 2, p171-190. 20p. |
| Subjects: | Linkage disequilibrium, Tall fescue, Single nucleotide polymorphisms, Forage plants, Germplasm, Chromosomes |
| Abstract: | Tall fescue (Festuca arundinacea) from Poaceae family is an allohexaploid (2n=6x=42) and cross pollinated plant that is used throughout the world as a forage plant. This research was conducted to identify the genomic regions associated with 10 agro-morphological traits using 15,881 SNP markers in a diverse tall fescue germplasm. UPGMA, Structure, and PCA analyses illustrated high genetic differentiation between forage, turf, and hybrid tall fescue samples. Correcting r2 for population structure and kinship effects revealed the fact that the r2v (corrected for kinship) is much smaller than r2 (uncorrected) illustrating the necessity of removing the effect of coancestry to reduce the inflation of r2 estimates. Analysis of linkage disequilibrium revealed that the amount of SNP pairs in LD differs between sub-genomes and chromosomes and any increase in the distance among SNPs reduces the amount of SNP pairs in LD. A total of 111 and 17 marker-trait associations were identified via GLM and MLM methods for the investigated traits, respectively. Most of the significant MTAs belonged to plant height and days to anthesis. Gene ontology results revealed that 34% of MTAs were located in protein-coding regions. Most of the MTAs were located on chromosomes 1B and 1D. The MTAs for plant height and days to anthesis located within the coding regions can be utilized in genome-based breeding in tall fescue breeding programs. [ABSTRACT FROM AUTHOR] |
| Copyright of Plant Biotechnology Reports is the property of Springer Nature 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 |
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| Header | DbId: egs DbLabel: Engineering Source An: 163387475 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Molecular characterization of tall fescue germplasm using SNP markers: population structure, linkage disequilibrium, and association mapping of yield-related traits. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Shahabzadeh%2C+Zeynab%22">Shahabzadeh, Zeynab</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Darvishzadeh%2C+Reza%22">Darvishzadeh, Reza</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> r.darvishzadeh@urmia.ac.ir</i><br /><searchLink fieldCode="AR" term="%22Mohammadi%2C+Reza%22">Mohammadi, Reza</searchLink><relatesTo>2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Jafari%2C+Morad%22">Jafari, Morad</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Alipour%2C+Hadi%22">Alipour, Hadi</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> ha.alipour@urmia.ac.ir</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Plant+Biotechnology+Reports%22">Plant Biotechnology Reports</searchLink>. Apr2023, Vol. 17 Issue 2, p171-190. 20p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Linkage+disequilibrium%22">Linkage disequilibrium</searchLink><br /><searchLink fieldCode="DE" term="%22Tall+fescue%22">Tall fescue</searchLink><br /><searchLink fieldCode="DE" term="%22Single+nucleotide+polymorphisms%22">Single nucleotide polymorphisms</searchLink><br /><searchLink fieldCode="DE" term="%22Forage+plants%22">Forage plants</searchLink><br /><searchLink fieldCode="DE" term="%22Germplasm%22">Germplasm</searchLink><br /><searchLink fieldCode="DE" term="%22Chromosomes%22">Chromosomes</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Tall fescue (Festuca arundinacea) from Poaceae family is an allohexaploid (2n=6x=42) and cross pollinated plant that is used throughout the world as a forage plant. This research was conducted to identify the genomic regions associated with 10 agro-morphological traits using 15,881 SNP markers in a diverse tall fescue germplasm. UPGMA, Structure, and PCA analyses illustrated high genetic differentiation between forage, turf, and hybrid tall fescue samples. Correcting r2 for population structure and kinship effects revealed the fact that the r2v (corrected for kinship) is much smaller than r2 (uncorrected) illustrating the necessity of removing the effect of coancestry to reduce the inflation of r2 estimates. Analysis of linkage disequilibrium revealed that the amount of SNP pairs in LD differs between sub-genomes and chromosomes and any increase in the distance among SNPs reduces the amount of SNP pairs in LD. A total of 111 and 17 marker-trait associations were identified via GLM and MLM methods for the investigated traits, respectively. Most of the significant MTAs belonged to plant height and days to anthesis. Gene ontology results revealed that 34% of MTAs were located in protein-coding regions. Most of the MTAs were located on chromosomes 1B and 1D. The MTAs for plant height and days to anthesis located within the coding regions can be utilized in genome-based breeding in tall fescue breeding programs. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Plant Biotechnology Reports is the property of Springer Nature 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: 10.1007/s11816-022-00769-7 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 20 StartPage: 171 Subjects: – SubjectFull: Linkage disequilibrium Type: general – SubjectFull: Tall fescue Type: general – SubjectFull: Single nucleotide polymorphisms Type: general – SubjectFull: Forage plants Type: general – SubjectFull: Germplasm Type: general – SubjectFull: Chromosomes Type: general Titles: – TitleFull: Molecular characterization of tall fescue germplasm using SNP markers: population structure, linkage disequilibrium, and association mapping of yield-related traits. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Shahabzadeh, Zeynab – PersonEntity: Name: NameFull: Darvishzadeh, Reza – PersonEntity: Name: NameFull: Mohammadi, Reza – PersonEntity: Name: NameFull: Jafari, Morad – PersonEntity: Name: NameFull: Alipour, Hadi IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 04 Text: Apr2023 Type: published Y: 2023 Identifiers: – Type: issn-print Value: 18635466 Numbering: – Type: volume Value: 17 – Type: issue Value: 2 Titles: – TitleFull: Plant Biotechnology Reports Type: main |
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