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...
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1097534/full |
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| author | Yuting Yang Yuting Yang Wenxiang Wang Wenxiang Wang Qiong Hu Qiong Hu Harsh Raman Jia Liu Jia Liu |
| author_facet | Yuting Yang Yuting Yang Wenxiang Wang Wenxiang Wang Qiong Hu Qiong Hu Harsh Raman Jia Liu Jia Liu |
| author_sort | Yuting Yang |
| collection | DOAJ |
| 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. |
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| language | English |
| last_indexed | 2024-04-10T23:10:05Z |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-690de244ce3d4b6da019c189ee18928e2023-01-13T06:21:35ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-01-011310.3389/fpls.2022.10975341097534Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus)Yuting Yang0Yuting Yang1Wenxiang Wang2Wenxiang Wang3Qiong Hu4Qiong Hu5Harsh Raman6Jia Liu7Jia Liu8Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, ChinaShenzhen Graduate School, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, ChinaOil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, ChinaKey Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, ChinaOil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, ChinaKey Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, ChinaNew South Wales (NSW) Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, AustraliaOil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, ChinaKey Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, ChinaSpatial 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.https://www.frontiersin.org/articles/10.3389/fpls.2022.1097534/fullrapeseedpod orientationGWASRNA-seqcandidate genes |
| spellingShingle | Yuting Yang Yuting Yang Wenxiang Wang Wenxiang Wang Qiong Hu Qiong Hu Harsh Raman Jia Liu Jia Liu Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus) Frontiers in Plant Science rapeseed pod orientation GWAS RNA-seq candidate genes |
| 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 | rapeseed pod orientation GWAS RNA-seq candidate genes |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1097534/full |
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