Cargando…
Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus)
Spatial distribution and orientation of pods on the main raceme (stem) and branches could affect rapeseed yield. However, genomic regions underlying the pod orientation were not described in Brassica species. Here, we determined the extent of genetic variation in pod orientation, described as the an...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9880488/ https://www.ncbi.nlm.nih.gov/pubmed/36714779 http://dx.doi.org/10.3389/fpls.2022.1097534 |
_version_ | 1784878923260100608 |
---|---|
author | Yang, Yuting Wang, Wenxiang Hu, Qiong Raman, Harsh Liu, Jia |
author_facet | Yang, Yuting Wang, Wenxiang Hu, Qiong Raman, Harsh Liu, Jia |
author_sort | Yang, Yuting |
collection | PubMed |
description | Spatial distribution and orientation of pods on the main raceme (stem) and branches could affect rapeseed yield. However, genomic regions underlying the pod orientation were not described in Brassica species. Here, we determined the extent of genetic variation in pod orientation, described as the angles of pedicel on raceme (APR) and angles of the pod on pedicel (APP) among 136 rapeseed accessions grown across three environments of the upper, middle and lower Yangtze River in China. The APR ranged from 59° to 109°, while the APP varied from 142° to 178°. Statistical analysis showed that phenotypic variation was due to genotypic (G) and environmental (E) effects. Using the genome-wide association analysis (GWAS) approach, two QTLs for APR (qBnAPR.A02 and qBnAPR.C02) and two for APP (qBnAPP.A05 and qBnAPP.C05), having minor to moderate allelic effects (4.30% to 19.47%) were identified. RNA-seq analysis revealed 606 differentially expressed genes (DEGs) in two rapeseed accessions representing the extreme phenotypes for pod orientation and different alleles at the QTLs of APR. Three DEGs (BnLAZY4.A02, BnSAUR32.A02, and BnSAUR32.C02) were identified as the most likely candidates responsible for variation in pod orientation (APR). This study elucidates the genomic regions and putative candidate genes underlying pod orientation in B. napus. |
format | Online Article Text |
id | pubmed-9880488 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-98804882023-01-28 Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus) Yang, Yuting Wang, Wenxiang Hu, Qiong Raman, Harsh Liu, Jia Front Plant Sci Plant Science Spatial distribution and orientation of pods on the main raceme (stem) and branches could affect rapeseed yield. However, genomic regions underlying the pod orientation were not described in Brassica species. Here, we determined the extent of genetic variation in pod orientation, described as the angles of pedicel on raceme (APR) and angles of the pod on pedicel (APP) among 136 rapeseed accessions grown across three environments of the upper, middle and lower Yangtze River in China. The APR ranged from 59° to 109°, while the APP varied from 142° to 178°. Statistical analysis showed that phenotypic variation was due to genotypic (G) and environmental (E) effects. Using the genome-wide association analysis (GWAS) approach, two QTLs for APR (qBnAPR.A02 and qBnAPR.C02) and two for APP (qBnAPP.A05 and qBnAPP.C05), having minor to moderate allelic effects (4.30% to 19.47%) were identified. RNA-seq analysis revealed 606 differentially expressed genes (DEGs) in two rapeseed accessions representing the extreme phenotypes for pod orientation and different alleles at the QTLs of APR. Three DEGs (BnLAZY4.A02, BnSAUR32.A02, and BnSAUR32.C02) were identified as the most likely candidates responsible for variation in pod orientation (APR). This study elucidates the genomic regions and putative candidate genes underlying pod orientation in B. napus. Frontiers Media S.A. 2023-01-13 /pmc/articles/PMC9880488/ /pubmed/36714779 http://dx.doi.org/10.3389/fpls.2022.1097534 Text en Copyright © 2023 Yang, Wang, Hu, Raman and Liu https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Yang, Yuting Wang, Wenxiang Hu, Qiong Raman, Harsh Liu, Jia Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus) |
title | Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus) |
title_full | Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus) |
title_fullStr | Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus) |
title_full_unstemmed | Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus) |
title_short | Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus) |
title_sort | genome-wide association and rna-seq analyses identify loci for pod orientation in rapeseed (brassica napus) |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9880488/ https://www.ncbi.nlm.nih.gov/pubmed/36714779 http://dx.doi.org/10.3389/fpls.2022.1097534 |
work_keys_str_mv | AT yangyuting genomewideassociationandrnaseqanalysesidentifylociforpodorientationinrapeseedbrassicanapus AT wangwenxiang genomewideassociationandrnaseqanalysesidentifylociforpodorientationinrapeseedbrassicanapus AT huqiong genomewideassociationandrnaseqanalysesidentifylociforpodorientationinrapeseedbrassicanapus AT ramanharsh genomewideassociationandrnaseqanalysesidentifylociforpodorientationinrapeseedbrassicanapus AT liujia genomewideassociationandrnaseqanalysesidentifylociforpodorientationinrapeseedbrassicanapus |