Cargando…
A potential candidate gene associated with the angles of the ear leaf and the second leaf above the ear leaf in maize
BACKGROUND: Leaf angle is a key trait for maize plant architecture that plays a significant role in its morphological development, and ultimately impacting maize grain yield. Although many studies have been conducted on the association and localization of genes regulating leaf angle in maize, most o...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10625212/ https://www.ncbi.nlm.nih.gov/pubmed/37924003 http://dx.doi.org/10.1186/s12870-023-04553-9 |
_version_ | 1785131082678534144 |
---|---|
author | Kuang, Tianhui Hu, Can Shaw, Ranjan Kumar Zhang, Yudong Fan, Jun Bi, Yaqi Jiang, Fuyan Guo, Ruijia Fan, Xingming |
author_facet | Kuang, Tianhui Hu, Can Shaw, Ranjan Kumar Zhang, Yudong Fan, Jun Bi, Yaqi Jiang, Fuyan Guo, Ruijia Fan, Xingming |
author_sort | Kuang, Tianhui |
collection | PubMed |
description | BACKGROUND: Leaf angle is a key trait for maize plant architecture that plays a significant role in its morphological development, and ultimately impacting maize grain yield. Although many studies have been conducted on the association and localization of genes regulating leaf angle in maize, most of the candidate genes identified are associated with the regulation of ligule-ear development and phytohormone pathways, and only a few candidate genes have been reported to enhance the mechanical strength of leaf midrib and vascular tissues. RESULTS: To address this gap, we conducted a genome-wide association study (GWAS) using the leaf angle phenotype and genotyping-by-sequencing data generated from three recombinant inbred line (RIL) populations of maize. Through GWAS analysis, we identified 156 SNPs significantly associated with the leaf angle trait and detected a total of 68 candidate genes located within 10 kb upstream and downstream of these individual SNPs. Among these candidate genes, Zm00001d045408, located on chromosome 9 emerged as a key gene controlling the angles of both the ear leaf and the second leaf above the ear leaf. Notably, this new gene’s homolog in Arabidopsis promotes cell division and vascular tissue development. Further analysis revealed that a SNP transversion (G/T) at 7.536 kb downstream of the candidate gene Zm00001d045408 may have caused a reduction in leaf angles of the ear and the second leaf above the ear leaf. Our analysis of the 10 kb region downstream of this candidate gene revealed a 4.337 kb solo long-terminal reverse transcription transposon (solo LTR), located 3.112 kb downstream of Zm00001d045408, with the SNP located 87 bp upstream of the solo LTR. CONCLUSIONS: In summary, we have identified a novel candidate gene, Zm00001d045408 and a solo LTR that are associated with the angles of both the ear leaf and the second leaf above the ear leaf. The future research holds great potential in exploring the precise role of newly identified candidate gene in leaf angle regulation. Functional characterization of this gene can help in gaining deeper insights into the complex genetic pathways underlying maize plant architecture. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04553-9. |
format | Online Article Text |
id | pubmed-10625212 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-106252122023-11-05 A potential candidate gene associated with the angles of the ear leaf and the second leaf above the ear leaf in maize Kuang, Tianhui Hu, Can Shaw, Ranjan Kumar Zhang, Yudong Fan, Jun Bi, Yaqi Jiang, Fuyan Guo, Ruijia Fan, Xingming BMC Plant Biol Research BACKGROUND: Leaf angle is a key trait for maize plant architecture that plays a significant role in its morphological development, and ultimately impacting maize grain yield. Although many studies have been conducted on the association and localization of genes regulating leaf angle in maize, most of the candidate genes identified are associated with the regulation of ligule-ear development and phytohormone pathways, and only a few candidate genes have been reported to enhance the mechanical strength of leaf midrib and vascular tissues. RESULTS: To address this gap, we conducted a genome-wide association study (GWAS) using the leaf angle phenotype and genotyping-by-sequencing data generated from three recombinant inbred line (RIL) populations of maize. Through GWAS analysis, we identified 156 SNPs significantly associated with the leaf angle trait and detected a total of 68 candidate genes located within 10 kb upstream and downstream of these individual SNPs. Among these candidate genes, Zm00001d045408, located on chromosome 9 emerged as a key gene controlling the angles of both the ear leaf and the second leaf above the ear leaf. Notably, this new gene’s homolog in Arabidopsis promotes cell division and vascular tissue development. Further analysis revealed that a SNP transversion (G/T) at 7.536 kb downstream of the candidate gene Zm00001d045408 may have caused a reduction in leaf angles of the ear and the second leaf above the ear leaf. Our analysis of the 10 kb region downstream of this candidate gene revealed a 4.337 kb solo long-terminal reverse transcription transposon (solo LTR), located 3.112 kb downstream of Zm00001d045408, with the SNP located 87 bp upstream of the solo LTR. CONCLUSIONS: In summary, we have identified a novel candidate gene, Zm00001d045408 and a solo LTR that are associated with the angles of both the ear leaf and the second leaf above the ear leaf. The future research holds great potential in exploring the precise role of newly identified candidate gene in leaf angle regulation. Functional characterization of this gene can help in gaining deeper insights into the complex genetic pathways underlying maize plant architecture. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04553-9. BioMed Central 2023-11-04 /pmc/articles/PMC10625212/ /pubmed/37924003 http://dx.doi.org/10.1186/s12870-023-04553-9 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Kuang, Tianhui Hu, Can Shaw, Ranjan Kumar Zhang, Yudong Fan, Jun Bi, Yaqi Jiang, Fuyan Guo, Ruijia Fan, Xingming A potential candidate gene associated with the angles of the ear leaf and the second leaf above the ear leaf in maize |
title | A potential candidate gene associated with the angles of the ear leaf and the second leaf above the ear leaf in maize |
title_full | A potential candidate gene associated with the angles of the ear leaf and the second leaf above the ear leaf in maize |
title_fullStr | A potential candidate gene associated with the angles of the ear leaf and the second leaf above the ear leaf in maize |
title_full_unstemmed | A potential candidate gene associated with the angles of the ear leaf and the second leaf above the ear leaf in maize |
title_short | A potential candidate gene associated with the angles of the ear leaf and the second leaf above the ear leaf in maize |
title_sort | potential candidate gene associated with the angles of the ear leaf and the second leaf above the ear leaf in maize |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10625212/ https://www.ncbi.nlm.nih.gov/pubmed/37924003 http://dx.doi.org/10.1186/s12870-023-04553-9 |
work_keys_str_mv | AT kuangtianhui apotentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT hucan apotentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT shawranjankumar apotentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT zhangyudong apotentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT fanjun apotentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT biyaqi apotentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT jiangfuyan apotentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT guoruijia apotentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT fanxingming apotentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT kuangtianhui potentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT hucan potentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT shawranjankumar potentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT zhangyudong potentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT fanjun potentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT biyaqi potentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT jiangfuyan potentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT guoruijia potentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize AT fanxingming potentialcandidategeneassociatedwiththeanglesoftheearleafandthesecondleafabovetheearleafinmaize |