Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum
Upland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and producing high-quality fiber is essential for the textile industry. CCRI70 is a hybrid cotton plant harboring superior yield and fiber quality, whose recombinant inbred line (RIL) population was develope...
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Frontiers Media S.A.
2021-12-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.753755/full |
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| author | Xiao Jiang Juwu Gong Juwu Gong Jianhong Zhang Zhen Zhang Yuzhen Shi Junwen Li Aiying Liu Wankui Gong Qun Ge Xiaoying Deng Senmiao Fan Haodong Chen Zhengcheng Kuang Jingtao Pan Jincan Che Shuya Zhang Tingting Jia Renhui Wei Quanjia Chen Shoujun Wei Haihong Shang Haihong Shang Youlu Yuan Youlu Yuan Youlu Yuan |
| author_facet | Xiao Jiang Juwu Gong Juwu Gong Jianhong Zhang Zhen Zhang Yuzhen Shi Junwen Li Aiying Liu Wankui Gong Qun Ge Xiaoying Deng Senmiao Fan Haodong Chen Zhengcheng Kuang Jingtao Pan Jincan Che Shuya Zhang Tingting Jia Renhui Wei Quanjia Chen Shoujun Wei Haihong Shang Haihong Shang Youlu Yuan Youlu Yuan Youlu Yuan |
| author_sort | Xiao Jiang |
| collection | DOAJ |
| description | Upland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and producing high-quality fiber is essential for the textile industry. CCRI70 is a hybrid cotton plant harboring superior yield and fiber quality, whose recombinant inbred line (RIL) population was developed from two upland cotton varieties (sGK156 and 901-001) and were used here to investigate the source of high-quality related alleles. Based on the material of the whole population, a high-density genetic map was constructed using specific locus-amplified fragment sequencing (SLAF-seq). It contained 24,425 single nucleotide polymorphism (SNP) markers, spanning a distance of 4,850.47 centimorgans (cM) over 26 chromosomes with an average marker interval of 0.20 cM. In evaluating three fiber quality traits in nine environments to detect multiple environments stable quantitative trait loci (QTLs), we found 289 QTLs, of which 36 of them were stable QTLs and 18 were novel. Based on the transcriptome analysis for two parents and two RILs, 24,941 unique differentially expressed genes (DEGs) were identified, 473 of which were promising genes. For the fiber strength (FS) QTLs, 320 DEGs were identified, suggesting that pectin synthesis, phenylpropanoid biosynthesis, and plant hormone signaling pathways could influence FS, and several transcription factors may regulate fiber development, such as GAE6, C4H, OMT1, AFR18, EIN3, bZIP44, and GAI. Notably, the marker D13_56413025 in qFS-chr18-4 provides a potential basis for enhancing fiber quality of upland cotton via marker-assisted breeding and gene cloning of important fiber quality traits. |
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| id | doaj.art-3bfa75771f5c4b47bf29b9838930c0bf |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-22T01:33:36Z |
| publishDate | 2021-12-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-3bfa75771f5c4b47bf29b9838930c0bf2022-12-21T18:43:26ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-12-011210.3389/fpls.2021.753755753755Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutumXiao Jiang0Juwu Gong1Juwu Gong2Jianhong Zhang3Zhen Zhang4Yuzhen Shi5Junwen Li6Aiying Liu7Wankui Gong8Qun Ge9Xiaoying Deng10Senmiao Fan11Haodong Chen12Zhengcheng Kuang13Jingtao Pan14Jincan Che15Shuya Zhang16Tingting Jia17Renhui Wei18Quanjia Chen19Shoujun Wei20Haihong Shang21Haihong Shang22Youlu Yuan23Youlu Yuan24Youlu Yuan25State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaCollege of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Ürümqi, ChinaInstitute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaCotton Sciences Research Institute of Hunan, National Hybrid Cotton Research Promotion Center, Changde, ChinaCotton Sciences Research Institute of Hunan, National Hybrid Cotton Research Promotion Center, Changde, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaSchool of Agricultural Sciences, Zhengzhou University, Zhengzhou, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaCollege of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Ürümqi, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaSchool of Agricultural Sciences, Zhengzhou University, Zhengzhou, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaCollege of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Ürümqi, ChinaSchool of Agricultural Sciences, Zhengzhou University, Zhengzhou, ChinaUpland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and producing high-quality fiber is essential for the textile industry. CCRI70 is a hybrid cotton plant harboring superior yield and fiber quality, whose recombinant inbred line (RIL) population was developed from two upland cotton varieties (sGK156 and 901-001) and were used here to investigate the source of high-quality related alleles. Based on the material of the whole population, a high-density genetic map was constructed using specific locus-amplified fragment sequencing (SLAF-seq). It contained 24,425 single nucleotide polymorphism (SNP) markers, spanning a distance of 4,850.47 centimorgans (cM) over 26 chromosomes with an average marker interval of 0.20 cM. In evaluating three fiber quality traits in nine environments to detect multiple environments stable quantitative trait loci (QTLs), we found 289 QTLs, of which 36 of them were stable QTLs and 18 were novel. Based on the transcriptome analysis for two parents and two RILs, 24,941 unique differentially expressed genes (DEGs) were identified, 473 of which were promising genes. For the fiber strength (FS) QTLs, 320 DEGs were identified, suggesting that pectin synthesis, phenylpropanoid biosynthesis, and plant hormone signaling pathways could influence FS, and several transcription factors may regulate fiber development, such as GAE6, C4H, OMT1, AFR18, EIN3, bZIP44, and GAI. Notably, the marker D13_56413025 in qFS-chr18-4 provides a potential basis for enhancing fiber quality of upland cotton via marker-assisted breeding and gene cloning of important fiber quality traits.https://www.frontiersin.org/articles/10.3389/fpls.2021.753755/fullGossypium hirsutumRILfiber qualityquantitative trait lociRNA-seq |
| spellingShingle | Xiao Jiang Juwu Gong Juwu Gong Jianhong Zhang Zhen Zhang Yuzhen Shi Junwen Li Aiying Liu Wankui Gong Qun Ge Xiaoying Deng Senmiao Fan Haodong Chen Zhengcheng Kuang Jingtao Pan Jincan Che Shuya Zhang Tingting Jia Renhui Wei Quanjia Chen Shoujun Wei Haihong Shang Haihong Shang Youlu Yuan Youlu Yuan Youlu Yuan Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum Frontiers in Plant Science Gossypium hirsutum RIL fiber quality quantitative trait loci RNA-seq |
| title | Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum |
| title_full | Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum |
| title_fullStr | Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum |
| title_full_unstemmed | Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum |
| title_short | Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum |
| title_sort | quantitative trait loci and transcriptome analysis reveal genetic basis of fiber quality traits in ccri70 ril population of gossypium hirsutum |
| topic | Gossypium hirsutum RIL fiber quality quantitative trait loci RNA-seq |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.753755/full |
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