Functional analysis of a GWAS pleiotropic hotspot suggests an auxin biosynthesis gene (AhPDS1), regulating pod development in peanut (Arachis hypogaea L.).
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| Title: | Functional analysis of a GWAS pleiotropic hotspot suggests an auxin biosynthesis gene (AhPDS1), regulating pod development in peanut (Arachis hypogaea L.). |
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| Authors: | Lu, Qing1 (AUTHOR) luqing@gdaas.cn, Umer, Muhammad J.1 (AUTHOR), Liu, Hao1 (AUTHOR) liuhao@gdaas.cn, Li, Haifen1 (AUTHOR), Wang, Runfeng1 (AUTHOR), Huang, Lu1 (AUTHOR), Yu, Qianxia1 (AUTHOR), Varshney, Rajeev K.2 (AUTHOR), Pandey, Manish K.3 (AUTHOR), Hong, Yanbin1 (AUTHOR) hongyanbin@gdaas.cn, Chen, Xiaoping1 (AUTHOR) chenxiaoping@gdaas.cn |
| Source: | Plant Journal. Dec2025, Vol. 124 Issue 5, p1-17. 17p. |
| Subjects: | Genome-wide association studies, Plant hormones, Plant development, Molecular genetics, Genetics, Peanut butter, Genes, Crop improvement |
| Abstract: | SUMMARY: Peanut productivity and quality improvement rely on understanding the genetic factors influencing pod and seed size. This study aims to identify genetic factors and regulatory mechanisms influencing pod and seed size in peanuts. Herein, a genome‐wide association study (GWAS) was conducted using 390 accessions from 15 peanut growing regions to analyze pod and seed traits across multiple planting seasons. A significant phenotypic variation was observed, with broad‐sense heritability ranging from 53.6 to 85.4%. Strong correlations between pod and seed traits further suggest potential for co‐selection in breeding efforts. A pleiotropic hotspot on chromosome B06 was strongly associated with six pod and seed traits. A peanut pod size regulator AhPDS1 (PODSIZE‐1, Ahy_B06g085516) homolog of Arabidopsis thaliana YUCCA4 (AtYUC4, AT5G11320), involved in auxin biosynthesis, was selected as a candidate regulating pod and seed size. Quantitative reverse transcriptase‐polymerase chain reaction (qRT‐PCR) confirmed higher AhPDS1 expression in large pod as compared with the small pod genotypes. Subcellular localization showed AhPDS1 to be predominantly cytoplasmic, and GUS reporter assays indicated widespread expression in roots, stems, leaves, flowers, and pods, suggesting a broad functional role. Further overexpression of AhPDS1 in Arabidopsis and rice enhanced pod, seed, and grain sizes via the indole‐3‐pyruvic acid pathway in transgene lines. These findings highlight AhPDS1 as a potential target for peanut molecular breeding, offering opportunities to enhance pod size via auxin biosynthesis and support sustainable crop improvement. Significance Statement: Understanding the genetic basis of peanut pod and seed size is essential for improving yield, yet key regulators have remained elusive. By pinpointing a pleiotropic locus and validating AhPDS1 as an auxin related size regulator across species, this study fills a major knowledge gap and delivers a promising molecular target for enhancing productivity in peanut and other crops. [ABSTRACT FROM AUTHOR] |
| Copyright of Plant Journal is the property of Wiley-Blackwell 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: 190280218 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Functional analysis of a GWAS pleiotropic hotspot suggests an auxin biosynthesis gene (AhPDS1), regulating pod development in peanut (Arachis hypogaea L.). – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Lu%2C+Qing%22">Lu, Qing</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> luqing@gdaas.cn</i><br /><searchLink fieldCode="AR" term="%22Umer%2C+Muhammad+J%2E%22">Umer, Muhammad J.</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Liu%2C+Hao%22">Liu, Hao</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> liuhao@gdaas.cn</i><br /><searchLink fieldCode="AR" term="%22Li%2C+Haifen%22">Li, Haifen</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Wang%2C+Runfeng%22">Wang, Runfeng</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Huang%2C+Lu%22">Huang, Lu</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Yu%2C+Qianxia%22">Yu, Qianxia</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Varshney%2C+Rajeev+K%2E%22">Varshney, Rajeev K.</searchLink><relatesTo>2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Pandey%2C+Manish+K%2E%22">Pandey, Manish K.</searchLink><relatesTo>3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Hong%2C+Yanbin%22">Hong, Yanbin</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> hongyanbin@gdaas.cn</i><br /><searchLink fieldCode="AR" term="%22Chen%2C+Xiaoping%22">Chen, Xiaoping</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> chenxiaoping@gdaas.cn</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Plant+Journal%22">Plant Journal</searchLink>. Dec2025, Vol. 124 Issue 5, p1-17. 17p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Genome-wide+association+studies%22">Genome-wide association studies</searchLink><br /><searchLink fieldCode="DE" term="%22Plant+hormones%22">Plant hormones</searchLink><br /><searchLink fieldCode="DE" term="%22Plant+development%22">Plant development</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+genetics%22">Molecular genetics</searchLink><br /><searchLink fieldCode="DE" term="%22Genetics%22">Genetics</searchLink><br /><searchLink fieldCode="DE" term="%22Peanut+butter%22">Peanut butter</searchLink><br /><searchLink fieldCode="DE" term="%22Genes%22">Genes</searchLink><br /><searchLink fieldCode="DE" term="%22Crop+improvement%22">Crop improvement</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: SUMMARY: Peanut productivity and quality improvement rely on understanding the genetic factors influencing pod and seed size. This study aims to identify genetic factors and regulatory mechanisms influencing pod and seed size in peanuts. Herein, a genome‐wide association study (GWAS) was conducted using 390 accessions from 15 peanut growing regions to analyze pod and seed traits across multiple planting seasons. A significant phenotypic variation was observed, with broad‐sense heritability ranging from 53.6 to 85.4%. Strong correlations between pod and seed traits further suggest potential for co‐selection in breeding efforts. A pleiotropic hotspot on chromosome B06 was strongly associated with six pod and seed traits. A peanut pod size regulator AhPDS1 (PODSIZE‐1, Ahy_B06g085516) homolog of Arabidopsis thaliana YUCCA4 (AtYUC4, AT5G11320), involved in auxin biosynthesis, was selected as a candidate regulating pod and seed size. Quantitative reverse transcriptase‐polymerase chain reaction (qRT‐PCR) confirmed higher AhPDS1 expression in large pod as compared with the small pod genotypes. Subcellular localization showed AhPDS1 to be predominantly cytoplasmic, and GUS reporter assays indicated widespread expression in roots, stems, leaves, flowers, and pods, suggesting a broad functional role. Further overexpression of AhPDS1 in Arabidopsis and rice enhanced pod, seed, and grain sizes via the indole‐3‐pyruvic acid pathway in transgene lines. These findings highlight AhPDS1 as a potential target for peanut molecular breeding, offering opportunities to enhance pod size via auxin biosynthesis and support sustainable crop improvement. Significance Statement: Understanding the genetic basis of peanut pod and seed size is essential for improving yield, yet key regulators have remained elusive. By pinpointing a pleiotropic locus and validating AhPDS1 as an auxin related size regulator across species, this study fills a major knowledge gap and delivers a promising molecular target for enhancing productivity in peanut and other crops. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Plant Journal is the property of Wiley-Blackwell 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: 10.1111/tpj.70608 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 17 StartPage: 1 Subjects: – SubjectFull: Genome-wide association studies Type: general – SubjectFull: Plant hormones Type: general – SubjectFull: Plant development Type: general – SubjectFull: Molecular genetics Type: general – SubjectFull: Genetics Type: general – SubjectFull: Peanut butter Type: general – SubjectFull: Genes Type: general – SubjectFull: Crop improvement Type: general Titles: – TitleFull: Functional analysis of a GWAS pleiotropic hotspot suggests an auxin biosynthesis gene (AhPDS1), regulating pod development in peanut (Arachis hypogaea L.). Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Lu, Qing – PersonEntity: Name: NameFull: Umer, Muhammad J. – PersonEntity: Name: NameFull: Liu, Hao – PersonEntity: Name: NameFull: Li, Haifen – PersonEntity: Name: NameFull: Wang, Runfeng – PersonEntity: Name: NameFull: Huang, Lu – PersonEntity: Name: NameFull: Yu, Qianxia – PersonEntity: Name: NameFull: Varshney, Rajeev K. – PersonEntity: Name: NameFull: Pandey, Manish K. – PersonEntity: Name: NameFull: Hong, Yanbin – PersonEntity: Name: NameFull: Chen, Xiaoping IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 12 Text: Dec2025 Type: published Y: 2025 Identifiers: – Type: issn-print Value: 09607412 Numbering: – Type: volume Value: 124 – Type: issue Value: 5 Titles: – TitleFull: Plant Journal Type: main |
| ResultId | 1 |
