Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut
The cultivated peanut (<i>Arachis hypogaea</i> L.) is an important oilseed crop worldwide, and fatty acid composition is a major determinant of peanut oil quality. In the present study, we conducted a genome-wide association study (GWAS) for nine fatty acid traits using the whole genome...
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MDPI AG
2023-12-01
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| Online Access: | https://www.mdpi.com/2223-7747/13/1/16 |
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| author | Juan Wang Haoning Chen Yuan Li Dachuan Shi Wenjiao Wang Caixia Yan Mei Yuan Quanxi Sun Jing Chen Yifei Mou Chunjuan Qu Shihua Shan |
| author_facet | Juan Wang Haoning Chen Yuan Li Dachuan Shi Wenjiao Wang Caixia Yan Mei Yuan Quanxi Sun Jing Chen Yifei Mou Chunjuan Qu Shihua Shan |
| author_sort | Juan Wang |
| collection | DOAJ |
| description | The cultivated peanut (<i>Arachis hypogaea</i> L.) is an important oilseed crop worldwide, and fatty acid composition is a major determinant of peanut oil quality. In the present study, we conducted a genome-wide association study (GWAS) for nine fatty acid traits using the whole genome sequences of 160 representative Chinese peanut landraces and identified 6-1195 significant SNPs for different fatty acid contents. Particularly for oleic acid and linoleic acid, two peak SNP clusters on Arahy.09 and Arahy.19 were found to contain the majority of the significant SNPs associated with these two fatty acids. Additionally, a significant proportion of the candidate genes identified on Arahy.09 overlap with those identified in early studies, among which three candidate genes are of special interest. One possesses a significant missense SNP and encodes a known candidate gene <i>FAD2A</i>. The second gene is the gene closest to the most significant SNP for linoleic acid. It codes for an MYB protein that has been demonstrated to impact fatty acid biosynthesis in <i>Arabidopsis</i>. The third gene harbors a missense SNP and encodes a JmjC domain-containing protein. The significant phenotypic difference in the oleic acid/linoleic acid between the genotypes at the first and third candidate genes was further confirmed with PARMS analysis. In addition, we have also identified different candidate genes (i.e., <i>Arahy.ZV39IJ</i>, <i>Arahy.F9E3EA</i>, <i>Arahy.X9ZZC1,</i> and <i>Arahy.Z0ELT9</i>) for the remaining fatty acids. Our findings can help us gain a better understanding of the genetic foundation of peanut fatty acid contents and may hold great potential for enhancing peanut quality in the future. |
| first_indexed | 2024-03-08T14:58:57Z |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-08T14:58:57Z |
| publishDate | 2023-12-01 |
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| series | Plants |
| spelling | doaj.art-08af29cff88b46b48dc09ef11a3fba192024-01-10T15:05:55ZengMDPI AGPlants2223-77472023-12-011311610.3390/plants13010016Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the PeanutJuan Wang0Haoning Chen1Yuan Li2Dachuan Shi3Wenjiao Wang4Caixia Yan5Mei Yuan6Quanxi Sun7Jing Chen8Yifei Mou9Chunjuan Qu10Shihua Shan11Shandong Peanut Research Institute, Qingdao 266100, ChinaShandong Peanut Research Institute, Qingdao 266100, ChinaNational Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 22100 Lund, SwedenQingdao Academy of Agricultural Sciences, Qingdao 266100, ChinaQingdao Academy of Agricultural Sciences, Qingdao 266100, ChinaShandong Peanut Research Institute, Qingdao 266100, ChinaShandong Peanut Research Institute, Qingdao 266100, ChinaShandong Peanut Research Institute, Qingdao 266100, ChinaShandong Peanut Research Institute, Qingdao 266100, ChinaShandong Peanut Research Institute, Qingdao 266100, ChinaShandong Peanut Research Institute, Qingdao 266100, ChinaShandong Peanut Research Institute, Qingdao 266100, ChinaThe cultivated peanut (<i>Arachis hypogaea</i> L.) is an important oilseed crop worldwide, and fatty acid composition is a major determinant of peanut oil quality. In the present study, we conducted a genome-wide association study (GWAS) for nine fatty acid traits using the whole genome sequences of 160 representative Chinese peanut landraces and identified 6-1195 significant SNPs for different fatty acid contents. Particularly for oleic acid and linoleic acid, two peak SNP clusters on Arahy.09 and Arahy.19 were found to contain the majority of the significant SNPs associated with these two fatty acids. Additionally, a significant proportion of the candidate genes identified on Arahy.09 overlap with those identified in early studies, among which three candidate genes are of special interest. One possesses a significant missense SNP and encodes a known candidate gene <i>FAD2A</i>. The second gene is the gene closest to the most significant SNP for linoleic acid. It codes for an MYB protein that has been demonstrated to impact fatty acid biosynthesis in <i>Arabidopsis</i>. The third gene harbors a missense SNP and encodes a JmjC domain-containing protein. The significant phenotypic difference in the oleic acid/linoleic acid between the genotypes at the first and third candidate genes was further confirmed with PARMS analysis. In addition, we have also identified different candidate genes (i.e., <i>Arahy.ZV39IJ</i>, <i>Arahy.F9E3EA</i>, <i>Arahy.X9ZZC1,</i> and <i>Arahy.Z0ELT9</i>) for the remaining fatty acids. Our findings can help us gain a better understanding of the genetic foundation of peanut fatty acid contents and may hold great potential for enhancing peanut quality in the future.https://www.mdpi.com/2223-7747/13/1/16peanut oilfatty acidsGC-MSGWASPARMS |
| spellingShingle | Juan Wang Haoning Chen Yuan Li Dachuan Shi Wenjiao Wang Caixia Yan Mei Yuan Quanxi Sun Jing Chen Yifei Mou Chunjuan Qu Shihua Shan Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut Plants peanut oil fatty acids GC-MS GWAS PARMS |
| title | Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut |
| title_full | Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut |
| title_fullStr | Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut |
| title_full_unstemmed | Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut |
| title_short | Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut |
| title_sort | identification of quantitative trait nucleotides and development of diagnostic markers for nine fatty acids in the peanut |
| topic | peanut oil fatty acids GC-MS GWAS PARMS |
| url | https://www.mdpi.com/2223-7747/13/1/16 |
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