Integrating RTM-GWAS and meta‑QTL data revealed genomic regions and candidate genes associated with the first fruit branch node and its height in upland cotton.
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| Title: | Integrating RTM-GWAS and meta‑QTL data revealed genomic regions and candidate genes associated with the first fruit branch node and its height in upland cotton. |
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| Authors: | Su, Junji1,2 (AUTHOR) sujj@gsau.edu.cn, Li, Dandan1 (AUTHOR), Yuan, Wenmin1 (AUTHOR), Li, Ying2 (AUTHOR), Ju, Jisheng1 (AUTHOR), Wang, Ning3 (AUTHOR), Ling, Pingjie1 (AUTHOR), Feng, Keyun3 (AUTHOR), Wang, Caixiang1 (AUTHOR) wangcaix@gsau.edu.cn |
| Source: | Theoretical & Applied Genetics. Sep2024, Vol. 137 Issue 9, p1-18. 18p. |
| Abstract: | Key message: Two genomic regions associated with FFBN and HFFBN and a potential regulatory gene (GhE6) of HFFBN were identified through the integration of RTM-GWAS and meta‑QTL analyses. Abstract The first fruit branch node (FFBN) and the height of the first fruit branch node (HFFBN) are two important traits that are related to plant architecture and early maturation in upland cotton. Several studies have been conducted to elucidate the genetic basis of these traits in cotton using biparental and natural populations. In this study, by using 9,244 SNP linkage disequilibrium block (SNPLDB) loci from 315 upland cotton accessions, we carried out restricted two‐stage multilocus and multiallele genome-wide association studies (RTM‐GWASs) and identified promising haplotypes/alleles of the four stable and true major SNPLDB loci that were significantly associated with FFBN and HFFBN. Additionally, a meta-quantitative trait locus (MQTL) analysis was conducted on 274 original QTLs that were reported in 27 studies, and 40 MQTLs associated with FFBN and HFFBN were identified. Through the integration of the RTM-GWAS and meta‑QTL analyses, two stable and true major SNPLDBs (LDB_5_15144433 and LDB_16_37952328) that were distributed in the two MQTLs were identified. Ultimately, 142 genes in the two genomic regions were annotated, and three candidate genes associated with FFBN and HFFBN were identified in the genomic region (A05:14.64–15.64 Mb) via RNA-Seq and qRT‒PCR. The results of virus-induced gene silencing (VIGS) experiments indicated that GhE6 was a key gene related to HFFBN and that GhDRM1 and GhGES were important genes associated with early flowering in upland cotton. These findings will aid in the future identification of molecular markers and genetic resources for developing elite early-maturing cultivars with ideal plant characteristics. [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: 179177828 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Integrating RTM-GWAS and meta‑QTL data revealed genomic regions and candidate genes associated with the first fruit branch node and its height in upland cotton. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Su%2C+Junji%22">Su, Junji</searchLink><relatesTo>1,2</relatesTo> (AUTHOR)<i> sujj@gsau.edu.cn</i><br /><searchLink fieldCode="AR" term="%22Li%2C+Dandan%22">Li, Dandan</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Yuan%2C+Wenmin%22">Yuan, Wenmin</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Li%2C+Ying%22">Li, Ying</searchLink><relatesTo>2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Ju%2C+Jisheng%22">Ju, Jisheng</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Wang%2C+Ning%22">Wang, Ning</searchLink><relatesTo>3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Ling%2C+Pingjie%22">Ling, Pingjie</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Feng%2C+Keyun%22">Feng, Keyun</searchLink><relatesTo>3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Wang%2C+Caixiang%22">Wang, Caixiang</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> wangcaix@gsau.edu.cn</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Theoretical+%26+Applied+Genetics%22">Theoretical & Applied Genetics</searchLink>. Sep2024, Vol. 137 Issue 9, p1-18. 18p. – Name: Abstract Label: Abstract Group: Ab Data: Key message: Two genomic regions associated with FFBN and HFFBN and a potential regulatory gene (GhE6) of HFFBN were identified through the integration of RTM-GWAS and meta‑QTL analyses. Abstract The first fruit branch node (FFBN) and the height of the first fruit branch node (HFFBN) are two important traits that are related to plant architecture and early maturation in upland cotton. Several studies have been conducted to elucidate the genetic basis of these traits in cotton using biparental and natural populations. In this study, by using 9,244 SNP linkage disequilibrium block (SNPLDB) loci from 315 upland cotton accessions, we carried out restricted two‐stage multilocus and multiallele genome-wide association studies (RTM‐GWASs) and identified promising haplotypes/alleles of the four stable and true major SNPLDB loci that were significantly associated with FFBN and HFFBN. Additionally, a meta-quantitative trait locus (MQTL) analysis was conducted on 274 original QTLs that were reported in 27 studies, and 40 MQTLs associated with FFBN and HFFBN were identified. Through the integration of the RTM-GWAS and meta‑QTL analyses, two stable and true major SNPLDBs (LDB_5_15144433 and LDB_16_37952328) that were distributed in the two MQTLs were identified. Ultimately, 142 genes in the two genomic regions were annotated, and three candidate genes associated with FFBN and HFFBN were identified in the genomic region (A05:14.64–15.64 Mb) via RNA-Seq and qRT‒PCR. The results of virus-induced gene silencing (VIGS) experiments indicated that GhE6 was a key gene related to HFFBN and that GhDRM1 and GhGES were important genes associated with early flowering in upland cotton. These findings will aid in the future identification of molecular markers and genetic resources for developing elite early-maturing cultivars with ideal plant characteristics. [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/s00122-024-04703-z Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 18 StartPage: 1 Titles: – TitleFull: Integrating RTM-GWAS and meta‑QTL data revealed genomic regions and candidate genes associated with the first fruit branch node and its height in upland cotton. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Su, Junji – PersonEntity: Name: NameFull: Li, Dandan – PersonEntity: Name: NameFull: Yuan, Wenmin – PersonEntity: Name: NameFull: Li, Ying – PersonEntity: Name: NameFull: Ju, Jisheng – PersonEntity: Name: NameFull: Wang, Ning – PersonEntity: Name: NameFull: Ling, Pingjie – PersonEntity: Name: NameFull: Feng, Keyun – PersonEntity: Name: NameFull: Wang, Caixiang IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 09 Text: Sep2024 Type: published Y: 2024 Identifiers: – Type: issn-print Value: 00405752 Numbering: – Type: volume Value: 137 – Type: issue Value: 9 Titles: – TitleFull: Theoretical & Applied Genetics Type: main |
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