Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton
Upland cotton is an important allotetraploid crop that provides both natural fiber for the textile industry and edible vegetable oil for the food or feed industry. To better understand the genetic mechanism that regulates the biosynthesis of storage oil in cottonseed, we identified the genes harbore...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-01-01
|
| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022001295 |
| _version_ | 1797978195774930944 |
|---|---|
| author | Juwu Gong Yan Peng Jiwen Yu Wenfeng Pei Zhen Zhang Daoran Fan Linjie Liu Xianghui Xiao Ruixian Liu Quanwei Lu Pengtao Li Haihong Shang Yuzhen Shi Junwen Li Qun Ge Aiying Liu Xiaoying Deng Senmiao Fan Jingtao Pan Quanjia Chen Youlu Yuan Wankui Gong |
| author_facet | Juwu Gong Yan Peng Jiwen Yu Wenfeng Pei Zhen Zhang Daoran Fan Linjie Liu Xianghui Xiao Ruixian Liu Quanwei Lu Pengtao Li Haihong Shang Yuzhen Shi Junwen Li Qun Ge Aiying Liu Xiaoying Deng Senmiao Fan Jingtao Pan Quanjia Chen Youlu Yuan Wankui Gong |
| author_sort | Juwu Gong |
| collection | DOAJ |
| description | Upland cotton is an important allotetraploid crop that provides both natural fiber for the textile industry and edible vegetable oil for the food or feed industry. To better understand the genetic mechanism that regulates the biosynthesis of storage oil in cottonseed, we identified the genes harbored in the major quantitative trait loci/nucleotides (QTLs/QTNs) of kernel oil content (KOC) in cottonseed via both multiple linkage analyses and genome-wide association studies (GWAS). In ‘CCRI70′ RILs, six stable QTLs were simultaneously identified by linkage analysis of CHIP and SLAF-seq strategies. In ‘0-153′ RILs, eight stable QTLs were detected by consensus linkage analysis integrating multiple strategies. In the natural panel, thirteen and eight loci were associated across multiple environments with two algorithms of GWAS. Within the confidence interval of a major common QTL on chromosome 3, six genes were identified as participating in the interaction network highly correlated with cottonseed KOC. Further observations of gene differential expression showed that four of the genes, LtnD, PGK, LPLAT1, and PAH2, formed hub genes and two of them, FER and RAV1, formed the key genes in the interaction network. Sequence variations in the coding regions of LtnD, FER, PGK, LPLAT1, and PAH2 genes may support their regulatory effects on oil accumulation in mature cottonseed. Taken together, clustering of the hub genes in the lipid biosynthesis interaction network provides new insights to understanding the mechanism of fatty acid biosynthesis and TAG assembly and to further genetic improvement projects for the KOC in cottonseeds. |
| first_indexed | 2024-04-11T05:19:07Z |
| format | Article |
| id | doaj.art-08997f0cfaee4ae0b2d7a09d9206148a |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:19:07Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-08997f0cfaee4ae0b2d7a09d9206148a2022-12-24T04:52:04ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012018411859Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cottonJuwu Gong0Yan Peng1Jiwen Yu2Wenfeng Pei3Zhen Zhang4Daoran Fan5Linjie Liu6Xianghui Xiao7Ruixian Liu8Quanwei Lu9Pengtao Li10Haihong Shang11Yuzhen Shi12Junwen Li13Qun Ge14Aiying Liu15Xiaoying Deng16Senmiao Fan17Jingtao Pan18Quanjia Chen19Youlu Yuan20Wankui Gong21State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, ChinaThird Division of the Xinjiang Production and Construction Corps Agricultural Research Institute, Tumushuke, Xijiang 843900, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, ChinaCollege of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, ChinaCollege of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, ChinaEngineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China; Corresponding authors.State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Corresponding authors.State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Corresponding authors.Upland cotton is an important allotetraploid crop that provides both natural fiber for the textile industry and edible vegetable oil for the food or feed industry. To better understand the genetic mechanism that regulates the biosynthesis of storage oil in cottonseed, we identified the genes harbored in the major quantitative trait loci/nucleotides (QTLs/QTNs) of kernel oil content (KOC) in cottonseed via both multiple linkage analyses and genome-wide association studies (GWAS). In ‘CCRI70′ RILs, six stable QTLs were simultaneously identified by linkage analysis of CHIP and SLAF-seq strategies. In ‘0-153′ RILs, eight stable QTLs were detected by consensus linkage analysis integrating multiple strategies. In the natural panel, thirteen and eight loci were associated across multiple environments with two algorithms of GWAS. Within the confidence interval of a major common QTL on chromosome 3, six genes were identified as participating in the interaction network highly correlated with cottonseed KOC. Further observations of gene differential expression showed that four of the genes, LtnD, PGK, LPLAT1, and PAH2, formed hub genes and two of them, FER and RAV1, formed the key genes in the interaction network. Sequence variations in the coding regions of LtnD, FER, PGK, LPLAT1, and PAH2 genes may support their regulatory effects on oil accumulation in mature cottonseed. Taken together, clustering of the hub genes in the lipid biosynthesis interaction network provides new insights to understanding the mechanism of fatty acid biosynthesis and TAG assembly and to further genetic improvement projects for the KOC in cottonseeds.http://www.sciencedirect.com/science/article/pii/S2001037022001295Hub geneGene clusterInteraction networkKernel oil contentQuantitative trait lociUpland cotton |
| spellingShingle | Juwu Gong Yan Peng Jiwen Yu Wenfeng Pei Zhen Zhang Daoran Fan Linjie Liu Xianghui Xiao Ruixian Liu Quanwei Lu Pengtao Li Haihong Shang Yuzhen Shi Junwen Li Qun Ge Aiying Liu Xiaoying Deng Senmiao Fan Jingtao Pan Quanjia Chen Youlu Yuan Wankui Gong Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton Computational and Structural Biotechnology Journal Hub gene Gene cluster Interaction network Kernel oil content Quantitative trait loci Upland cotton |
| title | Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton |
| title_full | Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton |
| title_fullStr | Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton |
| title_full_unstemmed | Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton |
| title_short | Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton |
| title_sort | linkage and association analyses reveal that hub genes in energy flow and lipid biosynthesis pathways form a cluster in upland cotton |
| topic | Hub gene Gene cluster Interaction network Kernel oil content Quantitative trait loci Upland cotton |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022001295 |
| work_keys_str_mv | AT juwugong linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT yanpeng linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT jiwenyu linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT wenfengpei linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT zhenzhang linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT daoranfan linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT linjieliu linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT xianghuixiao linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT ruixianliu linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT quanweilu linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT pengtaoli linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT haihongshang linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT yuzhenshi linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT junwenli linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT qunge linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT aiyingliu linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT xiaoyingdeng linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT senmiaofan linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT jingtaopan linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT quanjiachen linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT youluyuan linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton AT wankuigong linkageandassociationanalysesrevealthathubgenesinenergyflowandlipidbiosynthesispathwaysformaclusterinuplandcotton |