Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in <i>Brassica napus</i> Revealed by Combined BSA-Seq and RNA-Seq Analysis
Rapeseed has the ability to absorb cadmium in the roots and transfer it to aboveground organs, making it a potential species for remediating soil cadmium (Cd) pollution. However, the genetic and molecular mechanisms underlying this phenomenon in rapeseed are still unclear. In this study, a ‘cadmium-...
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MDPI AG
2023-06-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/12/10163 |
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| author | Huadong Wang Jiajia Liu Juan Huang Qing Xiao Alice Hayward Fuyan Li Yingying Gong Qian Liu Miao Ma Donghui Fu Meili Xiao |
| author_facet | Huadong Wang Jiajia Liu Juan Huang Qing Xiao Alice Hayward Fuyan Li Yingying Gong Qian Liu Miao Ma Donghui Fu Meili Xiao |
| author_sort | Huadong Wang |
| collection | DOAJ |
| description | Rapeseed has the ability to absorb cadmium in the roots and transfer it to aboveground organs, making it a potential species for remediating soil cadmium (Cd) pollution. However, the genetic and molecular mechanisms underlying this phenomenon in rapeseed are still unclear. In this study, a ‘cadmium-enriched’ parent, ‘P1’, with high cadmium transport and accumulation in the shoot (cadmium root: shoot transfer ratio of 153.75%), and a low-cadmium-accumulation parent, ‘P2’, (with a cadmium transfer ratio of 48.72%) were assessed for Cd concentration using inductively coupled plasma mass spectrometry (ICP-MS). An F<sub>2</sub> genetic population was constructed by crossing ‘P1’ with ‘P2’ to map QTL intervals and underlying genes associated with cadmium enrichment. Fifty extremely cadmium-enriched F<sub>2</sub> individuals and fifty extremely low-accumulation F<sub>2</sub> individuals were selected based on cadmium content and cadmium transfer ratio and used for bulk segregant analysis (BSA) in combination with whole genome resequencing. This generated a total of 3,660,999 SNPs and 787,034 InDels between these two segregated phenotypic groups. Based on the delta SNP index (the difference in SNP frequency between the two bulked pools), nine candidate Quantitative trait loci (QTLs) from five chromosomes were identified, and four intervals were validated. RNA sequencing of ‘P1’ and ‘P2’ in response to cadmium was also performed and identified 3502 differentially expressed genes (DEGs) between ‘P1’ and ‘P2’ under Cd treatment. Finally, 32 candidate DEGs were identified within 9 significant mapping intervals, including genes encoding a glutathione S-transferase (GST), a molecular chaperone (DnaJ), and a phosphoglycerate kinase (PGK), among others. These genes are strong candidates for playing an active role in helping rapeseed cope with cadmium stress. Therefore, this study not only sheds new light on the molecular mechanisms of Cd accumulation in rapeseed but could also be useful for rapeseed breeding programs targeting this trait. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T02:21:57Z |
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| spelling | doaj.art-edf44848594647a986b24b24751e88232023-11-18T10:49:37ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-06-0124121016310.3390/ijms241210163Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in <i>Brassica napus</i> Revealed by Combined BSA-Seq and RNA-Seq AnalysisHuadong Wang0Jiajia Liu1Juan Huang2Qing Xiao3Alice Hayward4Fuyan Li5Yingying Gong6Qian Liu7Miao Ma8Donghui Fu9Meili Xiao10Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, ChinaKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, ChinaKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, ChinaGraduate School of Jiangxi Normal University, Jiangxi Normal University, Nanchang 330045, ChinaCentre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane 4072, AustraliaKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, ChinaKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, ChinaKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, ChinaKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, ChinaKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, ChinaKey Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, ChinaRapeseed has the ability to absorb cadmium in the roots and transfer it to aboveground organs, making it a potential species for remediating soil cadmium (Cd) pollution. However, the genetic and molecular mechanisms underlying this phenomenon in rapeseed are still unclear. In this study, a ‘cadmium-enriched’ parent, ‘P1’, with high cadmium transport and accumulation in the shoot (cadmium root: shoot transfer ratio of 153.75%), and a low-cadmium-accumulation parent, ‘P2’, (with a cadmium transfer ratio of 48.72%) were assessed for Cd concentration using inductively coupled plasma mass spectrometry (ICP-MS). An F<sub>2</sub> genetic population was constructed by crossing ‘P1’ with ‘P2’ to map QTL intervals and underlying genes associated with cadmium enrichment. Fifty extremely cadmium-enriched F<sub>2</sub> individuals and fifty extremely low-accumulation F<sub>2</sub> individuals were selected based on cadmium content and cadmium transfer ratio and used for bulk segregant analysis (BSA) in combination with whole genome resequencing. This generated a total of 3,660,999 SNPs and 787,034 InDels between these two segregated phenotypic groups. Based on the delta SNP index (the difference in SNP frequency between the two bulked pools), nine candidate Quantitative trait loci (QTLs) from five chromosomes were identified, and four intervals were validated. RNA sequencing of ‘P1’ and ‘P2’ in response to cadmium was also performed and identified 3502 differentially expressed genes (DEGs) between ‘P1’ and ‘P2’ under Cd treatment. Finally, 32 candidate DEGs were identified within 9 significant mapping intervals, including genes encoding a glutathione S-transferase (GST), a molecular chaperone (DnaJ), and a phosphoglycerate kinase (PGK), among others. These genes are strong candidates for playing an active role in helping rapeseed cope with cadmium stress. Therefore, this study not only sheds new light on the molecular mechanisms of Cd accumulation in rapeseed but could also be useful for rapeseed breeding programs targeting this trait.https://www.mdpi.com/1422-0067/24/12/10163cadmium accumulation<i>Brassica napus</i>bulk segregation analysiswhole genome resequencingtranscriptome |
| spellingShingle | Huadong Wang Jiajia Liu Juan Huang Qing Xiao Alice Hayward Fuyan Li Yingying Gong Qian Liu Miao Ma Donghui Fu Meili Xiao Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in <i>Brassica napus</i> Revealed by Combined BSA-Seq and RNA-Seq Analysis International Journal of Molecular Sciences cadmium accumulation <i>Brassica napus</i> bulk segregation analysis whole genome resequencing transcriptome |
| title | Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in <i>Brassica napus</i> Revealed by Combined BSA-Seq and RNA-Seq Analysis |
| title_full | Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in <i>Brassica napus</i> Revealed by Combined BSA-Seq and RNA-Seq Analysis |
| title_fullStr | Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in <i>Brassica napus</i> Revealed by Combined BSA-Seq and RNA-Seq Analysis |
| title_full_unstemmed | Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in <i>Brassica napus</i> Revealed by Combined BSA-Seq and RNA-Seq Analysis |
| title_short | Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in <i>Brassica napus</i> Revealed by Combined BSA-Seq and RNA-Seq Analysis |
| title_sort | mapping and identifying candidate genes enabling cadmium accumulation in i brassica napus i revealed by combined bsa seq and rna seq analysis |
| topic | cadmium accumulation <i>Brassica napus</i> bulk segregation analysis whole genome resequencing transcriptome |
| url | https://www.mdpi.com/1422-0067/24/12/10163 |
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