Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact.
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| Title: | Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. |
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| Authors: | Zhang, Xiao1,2,3 (AUTHOR) hunterzap@163.com, Zhu, Yonghui4 (AUTHOR), Kremling, Karl A. G.3 (AUTHOR), Romay, M. Cinta3 (AUTHOR), Bukowski, Robert5 (AUTHOR), Sun, Qi5 (AUTHOR), Gao, Shibin1,2 (AUTHOR), Buckler, Edward S.3,6 (AUTHOR), Lu, Fei3,7,8,9 (AUTHOR) flu@genetics.ac.cn |
| Source: | Theoretical & Applied Genetics. Jan2022, Vol. 135 Issue 1, p273-290. 18p. |
| Subjects: | Genetic variation, Locus (Genetics), Flowering time, Gene expression, Genome-wide association studies, Corn, Nucleotide sequencing |
| Abstract: | Key message: Two read depth methods were jointly used in next-generation sequencing data to identify deletions in maize population. GWAS by deletions were analyzed for gene expression pattern and classical traits, respectively. Many studies have confirmed that structural variation (SV) is pervasive throughout the maize genome. Deletion is one type of SV that may impact gene expression and cause phenotypic changes in quantitative traits. In this study, two read count approaches were used to analyze the deletions in the whole-genome sequencing data of 270 maize inbred lines. A total of 19,754 deletion windows overlapped 12,751 genes, which were unevenly distributed across the genome. The deletions explained population structure well and correlated with genomic features. The deletion proportion of genes was determined to be negatively correlated with its expression. The detection of gene expression quantitative trait loci (eQTL) indicated that local eQTL were fewer but had larger effects than distant ones. The common associated genes were related to basic metabolic processes, whereas unique associated genes with eQTL played a role in the stress or stimulus responses in multiple tissues. Compared with the eQTL detected by SNPs derived from the same sequencing data, 89.4% of the associated genes could be detected by both markers. The effect of top eQTL detected by SNPs was usually larger than that detected by deletions for the same gene. A genome-wide association study (GWAS) on flowering time and plant height illustrated that only a few loci could be consistently captured by SNPs, suggesting that combining deletion and SNP for GWAS was an excellent strategy to dissect trait architecture. Our findings will provide insights into characteristic and biological function of genome-wide deletions in maize. [ABSTRACT FROM AUTHOR] |
| Copyright of Theoretical & Applied Genetics 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.) | |
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| Header | DbId: egs DbLabel: Engineering Source An: 154581850 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Zhang%2C+Xiao%22">Zhang, Xiao</searchLink><relatesTo>1,2,3</relatesTo> (AUTHOR)<i> hunterzap@163.com</i><br /><searchLink fieldCode="AR" term="%22Zhu%2C+Yonghui%22">Zhu, Yonghui</searchLink><relatesTo>4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Kremling%2C+Karl+A%2E+G%2E%22">Kremling, Karl A. G.</searchLink><relatesTo>3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Romay%2C+M%2E+Cinta%22">Romay, M. Cinta</searchLink><relatesTo>3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Bukowski%2C+Robert%22">Bukowski, Robert</searchLink><relatesTo>5</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Sun%2C+Qi%22">Sun, Qi</searchLink><relatesTo>5</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Gao%2C+Shibin%22">Gao, Shibin</searchLink><relatesTo>1,2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Buckler%2C+Edward+S%2E%22">Buckler, Edward S.</searchLink><relatesTo>3,6</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Lu%2C+Fei%22">Lu, Fei</searchLink><relatesTo>3,7,8,9</relatesTo> (AUTHOR)<i> flu@genetics.ac.cn</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Theoretical+%26+Applied+Genetics%22">Theoretical & Applied Genetics</searchLink>. Jan2022, Vol. 135 Issue 1, p273-290. 18p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Genetic+variation%22">Genetic variation</searchLink><br /><searchLink fieldCode="DE" term="%22Locus+%28Genetics%29%22">Locus (Genetics)</searchLink><br /><searchLink fieldCode="DE" term="%22Flowering+time%22">Flowering time</searchLink><br /><searchLink fieldCode="DE" term="%22Gene+expression%22">Gene expression</searchLink><br /><searchLink fieldCode="DE" term="%22Genome-wide+association+studies%22">Genome-wide association studies</searchLink><br /><searchLink fieldCode="DE" term="%22Corn%22">Corn</searchLink><br /><searchLink fieldCode="DE" term="%22Nucleotide+sequencing%22">Nucleotide sequencing</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Key message: Two read depth methods were jointly used in next-generation sequencing data to identify deletions in maize population. GWAS by deletions were analyzed for gene expression pattern and classical traits, respectively. Many studies have confirmed that structural variation (SV) is pervasive throughout the maize genome. Deletion is one type of SV that may impact gene expression and cause phenotypic changes in quantitative traits. In this study, two read count approaches were used to analyze the deletions in the whole-genome sequencing data of 270 maize inbred lines. A total of 19,754 deletion windows overlapped 12,751 genes, which were unevenly distributed across the genome. The deletions explained population structure well and correlated with genomic features. The deletion proportion of genes was determined to be negatively correlated with its expression. The detection of gene expression quantitative trait loci (eQTL) indicated that local eQTL were fewer but had larger effects than distant ones. The common associated genes were related to basic metabolic processes, whereas unique associated genes with eQTL played a role in the stress or stimulus responses in multiple tissues. Compared with the eQTL detected by SNPs derived from the same sequencing data, 89.4% of the associated genes could be detected by both markers. The effect of top eQTL detected by SNPs was usually larger than that detected by deletions for the same gene. A genome-wide association study (GWAS) on flowering time and plant height illustrated that only a few loci could be consistently captured by SNPs, suggesting that combining deletion and SNP for GWAS was an excellent strategy to dissect trait architecture. Our findings will provide insights into characteristic and biological function of genome-wide deletions in maize. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Theoretical & Applied Genetics 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/s00122-021-03965-1 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 18 StartPage: 273 Subjects: – SubjectFull: Genetic variation Type: general – SubjectFull: Locus (Genetics) Type: general – SubjectFull: Flowering time Type: general – SubjectFull: Gene expression Type: general – SubjectFull: Genome-wide association studies Type: general – SubjectFull: Corn Type: general – SubjectFull: Nucleotide sequencing Type: general Titles: – TitleFull: Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Zhang, Xiao – PersonEntity: Name: NameFull: Zhu, Yonghui – PersonEntity: Name: NameFull: Kremling, Karl A. G. – PersonEntity: Name: NameFull: Romay, M. Cinta – PersonEntity: Name: NameFull: Bukowski, Robert – PersonEntity: Name: NameFull: Sun, Qi – PersonEntity: Name: NameFull: Gao, Shibin – PersonEntity: Name: NameFull: Buckler, Edward S. – PersonEntity: Name: NameFull: Lu, Fei IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Text: Jan2022 Type: published Y: 2022 Identifiers: – Type: issn-print Value: 00405752 Numbering: – Type: volume Value: 135 – Type: issue Value: 1 Titles: – TitleFull: Theoretical & Applied Genetics Type: main |
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