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Hu Z, Yuan J, Zou R, Wang Y, Peng X, Yang X, Xie C. Identification and functional analysis of BAG gene family contributing to verticillium wilt resistance in upland cotton. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 356:112501. [PMID: 40209939 DOI: 10.1016/j.plantsci.2025.112501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 03/13/2025] [Accepted: 04/05/2025] [Indexed: 04/12/2025]
Abstract
Cotton fiber is a primary textile material and a significant economic resource globally. Verticillium dahliae, a destructive soil-borne fungal pathogen, severely impacts cotton yields. The Bcl-2-associated athanogene (BAG) protein family, functioning as molecular chaperone co-chaperones, plays a crucial role in plant stress responses. In this study, 24, 12, and 11 BAG genes were identified in upland cotton (Gossypium hirsutum), Asiatic cotton (G. arboreum), and Levant cotton (G. raimondii), respectively. The BAG gene family demonstrates relative conservation throughout cotton evolution. Conserved domain analysis revealed that BAG proteins from these species universally contain the conserved BAG domain, with some members also possessing the UBL domain and CaM-binding motifs. Virus-induced gene silencing (VIGS) was utilized to investigate gene function in upland cotton. Compared to the negative control, following V. dahliae infection, the silencing of GhBAG7.1 and GhBAG6.2 makes the plants more susceptible to infection, showing symptoms earlier. Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) analysis indicated that V. dahliae infection upregulated the expression of GhBAG7.1, GhBAG6.2, and GhBAG4.1 in upland cotton, while GhBAG4.4 expression was downregulated. Furthermore, following the silencing of the GhBAG6.2 gene, V. dahliae infection led to an initial upregulation of disease resistance-related genes (ERF1, PR5, PDF1.2, NPR1, PR1, OPR3), which was followed by a subsequent decrease in their expression. Transcriptomic analysis revealed a transient upregulation of defense-related pathways, including phenylpropanoid biosynthesis, MAPK signaling pathway, and plant-pathogen interactions, at 48- and 96-hours post-inoculation with V. dahliae. The findings provide a foundation for future research on stress-tolerant genes in cotton and offer new genetic resources for breeding disease-resistant cotton varieties.
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Affiliation(s)
- Zhijuan Hu
- The Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China; Chongqing Engineering Research Center of Specialty Crop Resources and The College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Jingjie Yuan
- The Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China; Chongqing Engineering Research Center of Specialty Crop Resources and The College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Run Zou
- The Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China; Chongqing Engineering Research Center of Specialty Crop Resources and The College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Yilan Wang
- The Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China; Chongqing Engineering Research Center of Specialty Crop Resources and The College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Xuan Peng
- The Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China; Chongqing Engineering Research Center of Specialty Crop Resources and The College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Xingyong Yang
- College of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Chengjian Xie
- The Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China; Chongqing Engineering Research Center of Specialty Crop Resources and The College of Life Science, Chongqing Normal University, Chongqing 401331, China.
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Xing B, Li P, Li Y, Cui B, Sun Z, Chen Y, Zhang S, Liu Q, Zhang A, Hao L, Du X, Liu X, Wu B, Peng R, Hu S. Integrated Transcriptomic and Metabolomic Analysis of G. hirsutum and G. barbadense Responses to Verticillium Wilt Infection. Int J Mol Sci 2024; 26:28. [PMID: 39795888 PMCID: PMC11720156 DOI: 10.3390/ijms26010028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 12/13/2024] [Accepted: 12/17/2024] [Indexed: 01/13/2025] Open
Abstract
Verticillium wilt (VW) caused by Verticillium dahliae (Vd) is a devastating fungal cotton disease characterized by high pathogenicity, widespread distribution, and frequent variation. It leads to significant losses in both the yield and quality of cotton. Identifying key non-synonymous single nucleotide polymorphism (SNP) markers and crucial genes associated with VW resistance in Gossypium hirsutum and Gossypium barbadense, and subsequently breeding new disease-resistant varieties, are essential for VW management. Here, we sequenced the transcriptome and metabolome of roots of TM-1 (G. hirsutum) and Hai7124 (G. barbadense) after 0, 1, and 2 days of V991 inoculation. Transcriptome analysis identified a total of 72,752 genes, with 5814 differentially expressed genes (DEGs) determined through multiple group comparisons. KEGG enrichment analysis revealed that the key pathways enriched by DEGs obtained from both longitudinal and transverse comparisons contained the glutathione metabolism pathway. Metabolome analysis identified 995 metabolites, and 22 differentially accumulated metabolites (DAMs), which were correlated to pathways including glutathione metabolism, degradation of valine, leucine, and isoleucine, and biosynthesis of terpenoids, alkaloids, pyridine, and piperidine. The conjoint analysis of transcriptomic and metabolomic sequencing revealed DAMs and DEGs associated with the glutathione metabolism pathway, and the key candidate gene GH_D11G2329 (glutathione S-transferase, GSTF8) potentially associated with cotton response to VW infection was selected. These findings establish a basis for investigating the mechanisms underlying the cotton plant's resistance to VW.
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Affiliation(s)
- Baoguang Xing
- College of Agricultural, Tarim University, Alar 843300, China; (B.X.); (Y.L.); (B.C.); (S.Z.); (A.Z.)
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Pengtao Li
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Yanfang Li
- College of Agricultural, Tarim University, Alar 843300, China; (B.X.); (Y.L.); (B.C.); (S.Z.); (A.Z.)
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Bingkai Cui
- College of Agricultural, Tarim University, Alar 843300, China; (B.X.); (Y.L.); (B.C.); (S.Z.); (A.Z.)
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Zhihao Sun
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Yu Chen
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Shaoliang Zhang
- College of Agricultural, Tarim University, Alar 843300, China; (B.X.); (Y.L.); (B.C.); (S.Z.); (A.Z.)
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Qiankun Liu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Aiming Zhang
- College of Agricultural, Tarim University, Alar 843300, China; (B.X.); (Y.L.); (B.C.); (S.Z.); (A.Z.)
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Liuan Hao
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Xue Du
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Xiaoyan Liu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Bei Wu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Renhai Peng
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Z.S.); (Y.C.); (Q.L.); (L.H.); (X.D.); (X.L.); (B.W.)
| | - Shoulin Hu
- College of Agricultural, Tarim University, Alar 843300, China; (B.X.); (Y.L.); (B.C.); (S.Z.); (A.Z.)
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Pan P, Yao Q, Shen J, Hu L, Zhao S, Huang L, Yu G, Zhou G, Zhang J. CVW-Etr: A High-Precision Method for Estimating the Severity Level of Cotton Verticillium Wilt Disease. PLANTS (BASEL, SWITZERLAND) 2024; 13:2960. [PMID: 39519879 PMCID: PMC11548180 DOI: 10.3390/plants13212960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 10/16/2024] [Accepted: 10/21/2024] [Indexed: 11/16/2024]
Abstract
Cotton verticillium wilt significantly impacts both cotton quality and yield. Selecting disease-resistant varieties and using their resistance genes in breeding is an effective and economical control measure. Accurate severity estimation of this disease is crucial for breeding resistant cotton varieties. However, current methods fall short, slowing the breeding process. To address these challenges, this paper introduces CVW-Etr, a high-precision method for estimating the severity of cotton verticillium wilt. CVW-Etr classifies severity into six levels (L0 to L5) based on the proportion of segmented diseased leaves to lesions. Upon integrating YOLOv8-Seg with MobileSAM, CVW-Etr demonstrates excellent performance and efficiency with limited samples in complex field conditions. It incorporates the RFCBAMConv, C2f-RFCBAMConv, AWDownSample-Lite, and GSegment modules to handle blurry transitions between healthy and diseased regions and variations in angle and distance during image collection, and to optimize the model's parameter size and computational complexity. Our experimental results show that CVW-Etr effectively segments diseased leaves and lesions, achieving a mean average precision (mAP) of 92.90% and an average severity estimation accuracy of 92.92% with only 2.6M parameters and 10.1G FLOPS. Through experiments, CVW-Etr proves robust in estimating cotton verticillium wilt severity, offering valuable insights for disease-resistant cotton breeding applications.
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Affiliation(s)
- Pan Pan
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (P.P.); (Q.Y.); (J.S.); (S.Z.); (G.Z.)
- National Agriculture Science Data Center, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; (L.H.); (G.Y.)
| | - Qiong Yao
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (P.P.); (Q.Y.); (J.S.); (S.Z.); (G.Z.)
- National Agriculture Science Data Center, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; (L.H.); (G.Y.)
- Agricultural College, Henan University, Kaifeng 475004, China
| | - Jiawei Shen
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (P.P.); (Q.Y.); (J.S.); (S.Z.); (G.Z.)
- National Agriculture Science Data Center, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; (L.H.); (G.Y.)
| | - Lin Hu
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (P.P.); (Q.Y.); (J.S.); (S.Z.); (G.Z.)
- National Agriculture Science Data Center, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; (L.H.); (G.Y.)
| | - Sijian Zhao
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (P.P.); (Q.Y.); (J.S.); (S.Z.); (G.Z.)
| | - Longyu Huang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; (L.H.); (G.Y.)
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Guoping Yu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; (L.H.); (G.Y.)
- China National Rice Research Institute, Hangzhou 311401, China
| | - Guomin Zhou
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (P.P.); (Q.Y.); (J.S.); (S.Z.); (G.Z.)
- National Agriculture Science Data Center, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; (L.H.); (G.Y.)
- Nanjing Institute of Agricultural Mechanization, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Jianhua Zhang
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (P.P.); (Q.Y.); (J.S.); (S.Z.); (G.Z.)
- National Agriculture Science Data Center, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; (L.H.); (G.Y.)
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Xu J, Zhou T, Wang P, Wang Y, Yang Y, Pu Y, Chen Q, Sun G. The GhEB1C gene mediates resistance of cotton to Verticillium wilt. PLANTA 2024; 260:110. [PMID: 39352582 DOI: 10.1007/s00425-024-04524-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 08/31/2024] [Indexed: 10/27/2024]
Abstract
MAIN CONCLUSION The GhEB1C gene of the EB1 protein family functions as microtubule end-binding protein and may be involved in the regulation of microtubule-related pathways to enhance resistance to Verticillium wilt. The expression of GhEB1C is induced by SA, also contributing to Verticillium wilt resistance. Cotton, as a crucial cash and oil crop, faces a significant threat from Verticillium wilt, a soil-borne disease induced by Verticillium dahliae, severely impacting cotton growth and development. Investigating genes associated with resistance to Verticillium wilt is paramount. We identified and performed a phylogenetic analysis on members of the EB1 family associated with Verticillium wilt in this work. GhEB1C was discovered by transcriptome screening and was studied for its function in cotton defense against V. dahliae. The RT-qPCR analysis revealed significant expression of the GhEB1C gene in cotton leaves. Subsequent localization analysis using transient expression demonstrated cytoplasmic localization of GhEB1C. VIGS experiments indicated that silencing of the GhEB1C gene significantly increased susceptibility of cotton to V. dahliae. Comparative RNA-seq analysis showed that GhEB1C silenced plants exhibited altered microtubule-associated protein pathways and flavonogen-associated pathways, suggesting a role for GhEB1C in defense mechanisms. Overexpression of tobacco resulted in enhanced resistance to V. dahliae as compared to wild-type plants. Furthermore, our investigation into the relationship between the GhEB1C gene and plant disease resistance hormones salicylic axid (SA) and jasmonic acid (JA) revealed the involvement of GhEB1C in the regulation of the SA pathway. In conclusion, our findings demonstrate that GhEB1C plays a crucial role in conferring immunity to cotton against Verticillium wilt, providing valuable insights for further research on plant adaptability to pathogen invasion.
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Affiliation(s)
- Jianglin Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Ting Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - YongQiang Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Yejun Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yuanchun Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Institute of Western Agriculture, the Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Quanjia Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China.
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Jiao W, Song B, Pan H, Liu X. Influences of Salt Stress on Cotton Metabolism and Its Consequential Effects on the Development and Fecundity of Aphis gossypii Glover. INSECTS 2024; 15:713. [PMID: 39336681 PMCID: PMC11432358 DOI: 10.3390/insects15090713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 09/15/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024]
Abstract
The degree of global soil salinization is gradually deepening, which will inevitably affect agricultural ecology. It has been found that salt stress induces the resistance of host plants to phytophagous pests. However, little is known about the effects of salt-stressed cotton plants on the fitness of cotton aphids (Aphis gossypii Glover). In this study, we investigated the differences between cotton metabolomes under mild (75 mM NaCl) and moderate (150 mM NaCl) salinity conditions and their effects on the fitness of cotton aphids. The results showed that 49 metabolites exhibited significant upregulation, while 86 metabolites were downregulated, with the increasing NaCl concentration. The duration of nymphal aphids under 150 mM NaCl significantly extended to 6.31 days when compared with the control (0 mM NaCl, 4.10 days). Meanwhile, the longevity of adult aphids decreased significantly under 75 and 150 mM NaCl, with an average of 10.38 days (0 mM NaCl) reduced to 8.55 and 4.89 days, respectively. Additionally, the total reproduction number of single females decreased from 31.31 (0 mM NaCl) to 21.13 (75 mM NaCl) and 10.75 (150 mM NaCl), whereas the survival rate of aphids decreased from 81.25% (0 mM NaCl) to 56.25% (75 mM NaCl) and 34.38% (150 mM NaCl) on the 12th day. These results support the hypothesis that plants growing under salt stress are better defended against herbivores. Furthermore, 49 differential metabolites were found to be negatively correlated with the longevity and fecundity of adult aphids, while 86 different metabolites showed the opposite trend. These results provide insights into the occurrence and control of cotton aphids amidst the escalating issue of secondary salinization.
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Affiliation(s)
- Wangquan Jiao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
- National Plant Protection Scientific Observation and Experiment Station of Korla, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Bingmei Song
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
- National Plant Protection Scientific Observation and Experiment Station of Korla, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Hongsheng Pan
- National Plant Protection Scientific Observation and Experiment Station of Korla, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Xiaoning Liu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
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Adegbola RO, Ponvert ND, Brown JK. Genetic Variability Among U.S.-Sentinel Cotton Plot Cotton Leafroll Dwarf Virus and Globally Available Reference Isolates Based on ORF0 Diversity. PLANT DISEASE 2024; 108:1799-1811. [PMID: 38277653 DOI: 10.1094/pdis-02-23-0243-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
The aphid-transmitted polerovirus, cotton leafroll dwarf virus (CLRDV), first characterized from symptomatic cotton plants in South America, has been identified in commercial cotton plantings in the United States. Here, the CLRDV intraspecific diversity was investigated by comparative sequence analysis of the most divergent CLRDV coding region, ORF0/P0. Bayesian analysis of ORF0 sequences for U.S. and reference populations resolved three well-supported sister clades comprising one U.S. and two South American lineages. Principal component analysis (PCA) identified seven statistically supported intraspecific populations. The Bayesian phylogeny and PCA dendrogram-inferred relationships were congruent. Population analysis of ORF0 sequences indicated most lineages have evolved under negative selection, albeit certain sites/isolates evolved under positive selection. Both U.S. and South American isolates exhibited extensive ORF0 diversity. At least two U.S. invasion foci were associated with their founder populations in Alabama-Georgia and eastern Texas. The Alabama-Georgia founder is implicated as the source of recent widespread expansion and establishment of secondary disease foci throughout the southeastern-central United States. Based on the geographically restricted distribution, spread of another extant Texas population appeared impeded by a population bottleneck. Extant CLRDV isolates represent several putative introductions potentially associated with catastrophic weather events dispersing viruliferous cotton aphids of unknown origin(s).
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Affiliation(s)
| | | | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721
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Sreedasyam A, Lovell JT, Mamidi S, Khanal S, Jenkins JW, Plott C, Bryan KB, Li Z, Shu S, Carlson J, Goodstein D, De Santiago L, Kirkbride RC, Calleja S, Campbell T, Koebernick JC, Dever JK, Scheffler JA, Pauli D, Jenkins JN, McCarty JC, Williams M, Boston L, Webber J, Udall JA, Chen ZJ, Bourland F, Stiller WN, Saski CA, Grimwood J, Chee PW, Jones DC, Schmutz J. Genome resources for three modern cotton lines guide future breeding efforts. NATURE PLANTS 2024; 10:1039-1051. [PMID: 38816498 PMCID: PMC11208153 DOI: 10.1038/s41477-024-01713-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/27/2024] [Indexed: 06/01/2024]
Abstract
Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars ('UGA230', 'UA48' and 'CSX8308') and updating the 'TM-1' cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from 'Pima' cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.
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Affiliation(s)
- Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- DOE Joint Genome Institute, Berkeley, CA, USA.
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sameer Khanal
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Jerry W Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Christopher Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kempton B Bryan
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Zhigang Li
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | | | | | | | - Luis De Santiago
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ryan C Kirkbride
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | | | - Todd Campbell
- USDA-ARS, Coastal Plains Soil Water and Plant Research Center, Florence, SC, USA
| | - Jenny C Koebernick
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Jane K Dever
- Texas A&M AgriLife Research, Lubbock, TX, USA
- Pee Dee Research and Education Center, Clemson University, Florence, SC, USA
| | | | - Duke Pauli
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Johnie N Jenkins
- USDA-ARS, Genetics and Sustainable Agriculture Research Unit, Mississippi State, MS, USA
| | - Jack C McCarty
- USDA-ARS, Genetics and Sustainable Agriculture Research Unit, Mississippi State, MS, USA
| | - Melissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - LoriBeth Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Joshua A Udall
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Fred Bourland
- Northeast Research and Extension Center (NEREC), University of Arkansas, Keiser, AR, USA
| | - Warwick N Stiller
- CSIRO Agriculture and Food Cotton Research Unit, Narrabri, New South Wales, Australia
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Peng W Chee
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Don C Jones
- Agriculture and Environmental Research Cotton Incorporated, Cary, NC, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- DOE Joint Genome Institute, Berkeley, CA, USA.
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8
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Wilson IW, Moncuquet P, Yuan Y, Soliveres M, Li Z, Stiller W, Zhu QH. Genetic Mapping and Characterization of Verticillium Wilt Resistance in a Recombinant Inbred Population of Upland Cotton. Int J Mol Sci 2024; 25:2439. [PMID: 38397116 PMCID: PMC10889826 DOI: 10.3390/ijms25042439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Verticillium wilt (VW) is an important and widespread disease of cotton and once established is long-lived and difficult to manage. In Australia, the non-defoliating pathotype of Verticillium dahliae is the most common, and extremely virulent. Breeding cotton varieties with increased VW resistance is the most economical and effective method of controlling this disease and is greatly aided by understanding the genetics of resistance. This study aimed to investigate VW resistance in 240 F7 recombinant inbred lines (RIL) derived from a cross between MCU-5, which has good resistance, and Siokra 1-4, which is susceptible. Using a controlled environment bioassay, we found that resistance based on plant survival or shoot biomass was complex but with major contributions from chromosomes D03 and D09, with genomic prediction analysis estimating a prediction accuracy of 0.73 based on survival scores compared to 0.36 for shoot biomass. Transcriptome analysis of MCU-5 and Siokra 1-4 roots uninfected or infected with V. dahliae revealed that the two cultivars displayed very different root transcriptomes and responded differently to V. dahliae infection. Ninety-nine differentially expressed genes were located in the two mapped resistance regions and so are potential candidates for further identifying the genes responsible for VW resistance.
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Affiliation(s)
- Iain W. Wilson
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia
| | | | - Yuman Yuan
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia
| | - Melanie Soliveres
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia
| | - Zitong Li
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia
| | - Warwick Stiller
- CSIRO Agriculture and Food, Locked Bag 59, Narrabri, NSW 2390, Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia
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9
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Zhu Y, Zhao M, Li T, Wang L, Liao C, Liu D, Zhang H, Zhao Y, Liu L, Ge X, Li B. Interactions between Verticillium dahliae and cotton: pathogenic mechanism and cotton resistance mechanism to Verticillium wilt. FRONTIERS IN PLANT SCIENCE 2023; 14:1174281. [PMID: 37152175 PMCID: PMC10161258 DOI: 10.3389/fpls.2023.1174281] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/28/2023] [Indexed: 05/09/2023]
Abstract
Cotton is widely grown in many countries around the world due to the huge economic value of the total natural fiber. Verticillium wilt, caused by the soil-borne pathogen Verticillium dahliae, is the most devastating disease that led to extensive yield losses and fiber quality reduction in cotton crops. Developing resistant cotton varieties through genetic engineering is an effective, economical, and durable strategy to control Verticillium wilt. However, there are few resistance gene resources in the currently planted cotton varieties, which has brought great challenges and difficulties for breeding through genetic engineering. Further revealing the molecular mechanism between V. dahliae and cotton interaction is crucial to discovering genes related to disease resistance. In this review, we elaborated on the pathogenic mechanism of V. dahliae and the resistance mechanism of cotton to Verticillium wilt. V. dahliae has evolved complex mechanisms to achieve pathogenicity in cotton, mainly including five aspects: (1) germination and growth of microsclerotia; (2) infection and successful colonization; (3) adaptation to the nutrient-deficient environment and competition of nutrients; (4) suppression and manipulation of cotton immune responses; (5) rapid reproduction and secretion of toxins. Cotton has evolved multiple physiological and biochemical responses to cope with V. dahliae infection, including modification of tissue structures, accumulation of antifungal substances, homeostasis of reactive oxygen species (ROS), induction of Ca2+ signaling, the mitogen-activated protein kinase (MAPK) cascades, hormone signaling, and PAMPs/effectors-triggered immune response (PTI/ETI). This review will provide an important reference for the breeding of new cotton germplasm resistant to Verticillium wilt through genetic engineering.
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Affiliation(s)
- Yutao Zhu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
- *Correspondence: Yutao Zhu, ; Bingbing Li,
| | - Mei Zhao
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Taotao Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Lianzhe Wang
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Chunli Liao
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Dongxiao Liu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Huamin Zhang
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Yanpeng Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lisen Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bingbing Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
- *Correspondence: Yutao Zhu, ; Bingbing Li,
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10
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Conaty WC, Broughton KJ, Egan LM, Li X, Li Z, Liu S, Llewellyn DJ, MacMillan CP, Moncuquet P, Rolland V, Ross B, Sargent D, Zhu QH, Pettolino FA, Stiller WN. Cotton Breeding in Australia: Meeting the Challenges of the 21st Century. FRONTIERS IN PLANT SCIENCE 2022; 13:904131. [PMID: 35646011 PMCID: PMC9136452 DOI: 10.3389/fpls.2022.904131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
The Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program is the sole breeding effort for cotton in Australia, developing high performing cultivars for the local industry which is worth∼AU$3 billion per annum. The program is supported by Cotton Breeding Australia, a Joint Venture between CSIRO and the program's commercial partner, Cotton Seed Distributors Ltd. (CSD). While the Australian industry is the focus, CSIRO cultivars have global impact in North America, South America, and Europe. The program is unique compared with many other public and commercial breeding programs because it focuses on diverse and integrated research with commercial outcomes. It represents the full research pipeline, supporting extensive long-term fundamental molecular research; native and genetically modified (GM) trait development; germplasm enhancement focused on yield and fiber quality improvements; integration of third-party GM traits; all culminating in the release of new commercial cultivars. This review presents evidence of past breeding successes and outlines current breeding efforts, in the areas of yield and fiber quality improvement, as well as the development of germplasm that is resistant to pests, diseases and abiotic stressors. The success of the program is based on the development of superior germplasm largely through field phenotyping, together with strong commercial partnerships with CSD and Bayer CropScience. These relationships assist in having a shared focus and ensuring commercial impact is maintained, while also providing access to markets, traits, and technology. The historical successes, current foci and future requirements of the CSIRO cotton breeding program have been used to develop a framework designed to augment our breeding system for the future. This will focus on utilizing emerging technologies from the genome to phenome, as well as a panomics approach with data management and integration to develop, test and incorporate new technologies into a breeding program. In addition to streamlining the breeding pipeline for increased genetic gain, this technology will increase the speed of trait and marker identification for use in genome editing, genomic selection and molecular assisted breeding, ultimately producing novel germplasm that will meet the coming challenges of the 21st Century.
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Affiliation(s)
| | | | - Lucy M. Egan
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
| | - Xiaoqing Li
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Zitong Li
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Shiming Liu
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
| | | | | | | | | | - Brett Ross
- Cotton Seed Distributors Ltd., Wee Waa, NSW, Australia
| | - Demi Sargent
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Canberra, ACT, Australia
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