Co-Expression Network Analysis and Introgressive Gene Identification for Fiber Length and Strength Reveal Transcriptional Differences in 15 Cotton Chromosome Substitution Segment Lines and Their Upland and Sea Island Parents
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Evaluation and Statistical Analysis of Cotton Fiber Quality
2.2. RNA-Seq, Enrichment Analyses, and WGCNA of FL Related DEGs
2.3. RNA-Seq, Enrichment Analyses, and WGCNA of FS Related DEGs
2.4. RNA-Seq, Enrichment Analyses, and WGCNA of Fiber Quality-Related DEGs
2.5. Prediction and Enrichment Analysis of Introgressed DEGs in CSSLs
2.6. Conjoint Analyses of FQ-Related QTL and Introgressive DEGs
3. Discussion
4. Materials and Methods
4.1. Cotton Materials and Phenotypic Statistics
4.2. Plant Cultivation and Sample Collection
4.3. RNA Extraction and Library Sequencing
4.4. Transcriptome Sequencing and Data Analysis
4.5. Construction of Weight Gene Co-Expressed Network
4.6. Prediction of Introgressive DEGs in CSSLs
4.7. Combination of QTL Intervals and Introgressive DEGs in CSSLs
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Trait | QTL | G. hirsutum ID | G. barbadense ID | Non-Synonymous/Synonymous Mutation or Same Sequences |
---|---|---|---|---|
Fiber Length | qFL-C7-3 | GH_A07G1073 | GB_A07G1063 | Non-synonymous |
GH_A07G1074 | GB_A07G1064 | Non-synonymous | ||
qFL-C12-5 | GH_A12G1295 | GB_A12G1365 | Non-synonymous | |
qFL-C13-1 | GH_A13G0163 | GB_A13G0168 | Same sequences | |
qFL-C13-2 | GH_A13G0454 | GB_A13G0460 | Non-synonymous | |
GH_A13G0460 | GB_A13G0468 | Non-synonymous | ||
qFL-C14-2 | GH_D02G0665 | GB_D02G0693 | Non-synonymous | |
qFL-C14-5 | GH_D02G1983 | GB_D02G2045 | Non-synonymous | |
qFL-C15-2 | GH_D01G0849 | GB_D01G0882 | Non-synonymous | |
qFL-C17-2 | GH_D03G0331 | GB_D03G0325 | Non-synonymous | |
qFL-C21-1 | GH_D11G0612 | GB_D11G0613 | Non-synonymous | |
qFL-C21-2 | GH_D11G0693 | GB_D11G0698 | Non-synonymous | |
GH_D11G0711 | GB_D11G0717 | Synonymous | ||
qFL-C21-4 | GH_D11G2888 | GB_D11G2913 | Non-synonymous | |
Fiber Strength | qFS-C2-2 | GH_A02G1378 | GB_A02G1399 | Same sequences |
qFS-C7-4 | GH_A07G1076 | GB_A07G1066 | Non-synonymous | |
GH_A07G1078 | GB_A07G1068 | Non-synonymous | ||
qFS-C15-1 | GH_D01G0056 | GB_D01G0054 | Non-synonymous | |
GH_D01G0067 | GB_D01G0064 | Non-synonymous | ||
GH_D01G0071 | GB_D01G0068 | Non-synonymous | ||
qFS-C15-4 | GH_D01G0480 | GB_D01G0498 | Non-synonymous | |
qFS-C19-1 | GH_D05G0262 | GB_D05G0265 | Non-synonymous | |
GH_D05G0264 | GB_D05G0267 | Non-synonymous | ||
qFS-C21-1 | GH_D11G0616 | GB_D11G0417 | Non-synonymous | |
qFS-C21-5 | GH_D11G2944 | GB_D11G2973 | Non-synonymous | |
qFS-C25-1 | GH_D06G0090 | GB_D06G0111 | Non-synonymous | |
GH_D06G0098 | GB_D06G0118 | Synonymous | ||
Fiber Quality | qFL-C2-5 | GH_A02G1372 | GB_A02G1393 | Same sequences |
qFS-C7-1 | GH_A07G0378 | GB_A07G0371 | Same sequences | |
GH_A07G0380 | GB_A07G0373 | Same sequences | ||
qFS-C7-2 | GH_A07G0464 | GB_A07G0458 | Same sequences | |
qFS-C9-1 | GH_A09G1695 | GB_A09G1819 | Non-synonymous | |
qFL-C12-5 | GH_A12G1294 | GB_A12G1364 | Same sequence | |
qFS-C13-1 | GH_A13G0148 | GB_D13G0149 | Non-synonymous | |
GH_A13G0165 | GB_A13G0170 | Non-synonymous | ||
qFL-C13-2 | GH_A13G0456 | GB_A13G0463 | Same sequences | |
qFL-C15-2 | GH_D01G0853 | GB_D01G0886 | Non-synonymous | |
qFS-C14-3 | GH_D02G1927 | GB_D02G1995 | Non-synonymous | |
qFL-C14-5 | GH_D02G1984 | GB_D02G2046 | Non-synonymous | |
qFS-C19-1 | GH_D05G0268 | GB_D05G0271 | Non-synonymous | |
qFL-C19-2 | GH_D05G1491 | GB_D05G1497 | Non-synonymous | |
GH_D05G1492 | GB_D05G1498 | Synonymous | ||
qFL-C21-2 | GH_D11G0692 | GB_D11G0697 | Non-synonymous | |
GH_D11G0696 | GB_D11G0701 | Synonymous | ||
GH_D11G0701 | GB_D11G0706 | Synonymous | ||
GH_D11G0711 | GB_D11G0717 | Synonymous | ||
qFS-C21-5 | GH_D11G2942 | GB_D11G2971 | Non-synonymous | |
qFS-C25-1 | GH_D06G0090 | GB_D06G0111 | Non-synonymous |
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© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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Li, P.; Chen, Y.; Yang, R.; Sun, Z.; Ge, Q.; Xiao, X.; Yang, S.; Li, Y.; Liu, Q.; Zhang, A.; et al. Co-Expression Network Analysis and Introgressive Gene Identification for Fiber Length and Strength Reveal Transcriptional Differences in 15 Cotton Chromosome Substitution Segment Lines and Their Upland and Sea Island Parents. Plants 2024, 13, 2308. https://doi.org/10.3390/plants13162308
Li P, Chen Y, Yang R, Sun Z, Ge Q, Xiao X, Yang S, Li Y, Liu Q, Zhang A, et al. Co-Expression Network Analysis and Introgressive Gene Identification for Fiber Length and Strength Reveal Transcriptional Differences in 15 Cotton Chromosome Substitution Segment Lines and Their Upland and Sea Island Parents. Plants. 2024; 13(16):2308. https://doi.org/10.3390/plants13162308
Chicago/Turabian StyleLi, Pengtao, Yu Chen, Rui Yang, Zhihao Sun, Qun Ge, Xianghui Xiao, Shuhan Yang, Yanfang Li, Qiankun Liu, Aiming Zhang, and et al. 2024. "Co-Expression Network Analysis and Introgressive Gene Identification for Fiber Length and Strength Reveal Transcriptional Differences in 15 Cotton Chromosome Substitution Segment Lines and Their Upland and Sea Island Parents" Plants 13, no. 16: 2308. https://doi.org/10.3390/plants13162308