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Zhao N, Guo A, Wang W, Li B, Wang M, Zhou Z, Jiang K, Aierxi A, Wang B, Adjibolosoo D, Xia Z, Li H, Cui Y, Kong J, Hua J. GbPP2C80 Interacts with GbWAKL14 to Negatively Co-Regulate Resistance to Fusarium and Verticillium wilt via MPK3 and ROS Signaling in Sea Island Cotton. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2309785. [PMID: 38889299 DOI: 10.1002/advs.202309785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/21/2024] [Indexed: 06/20/2024]
Abstract
Fusarium wilt (FW) is widespread in global cotton production, but the mechanism underlying FW resistance in superior-fiber-quality Sea Island cotton is unclear. This study reveals that FW resistance has been the target of genetic improvement of Sea Island cotton in China since the 2010s. The key nonsynonymous single nucleotide polymorphism (SNP, T/C) of gene Gbar_D03G001670 encoding protein phosphatase 2C 80 (PP2C80) results in an amino acid shift (L/S), which is significantly associated with FW resistance of Sea Island cotton. Silencing GbPP2C80 increases FW resistance in Sea Island cotton, whereas overexpressing GbPP2C80 reduces FW resistance in Arabidopsis. GbPP2C80 and GbWAKL14 exist synergistically in Sea Island cotton accessions with haplotype forms "susceptible-susceptible" (TA) and "resistant-resistant" (CC), and interact with each other. CRISPR/Cas9-mediated knockout of GbWAKL14 enhances FW and Verticillium wilt (VW) resistance in upland cotton and overexpression of GbWAKL14 and GbPP2C80 weakens FW and VW resistance in Arabidopsis. GbPP2C80 and GbWAKL14 respond to FW and VW by modulating reactive oxygen species (ROS) content via affecting MPK3 expression. In summary, two tandem genes on chromosome D03, GbPP2C80, and GbWAKL14, functions as cooperative negative regulators in cotton wilt disease defense, providing novel genetic resources and molecular markers for the development of resistant cotton cultivars.
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Affiliation(s)
- Nan Zhao
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Anhui Guo
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Weiran Wang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
| | - Bin Li
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Meng Wang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
| | - Zixin Zhou
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
| | - Kaiyun Jiang
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Alifu Aierxi
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
| | - Baoliang Wang
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Daniel Adjibolosoo
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhanghao Xia
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huijing Li
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yanan Cui
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
| | - Jinping Hua
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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Zhang J, Zhu Y, Wheeler T, Dever JK. Development and validation of allele-specific PCR-based SNP typing in a gene on chromosome D03 conferring resistance to Fusarium wilt race 4 in Upland cotton (Gossypium hirsutum). Mol Genet Genomics 2023; 298:1579-1589. [PMID: 37923792 DOI: 10.1007/s00438-023-02079-1] [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: 07/08/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
Upland cotton (Gossypium hirsutum) is the most important fiber crop for the global textile industry. Fusarium oxysporum f. sp. vasinfectum (FOV) is one of the most destructive soil-borne fungal pathogens in cotton. Among eight pathogenic races and other strains, FOV race 4 (FOV4) is the most virulent race in US cotton production. A single nucleotide polymorphism (SNP) in a glutamate receptor-like gene (GhGLR4.8) on chromosome D03 was previously identified and validated to confer resistance to FOV race 7, and targeted genome sequencing demonstrated that it was also associated with resistance to FOV4. The objective of this study was to develop an easy and convenient PCR-based marker assay. To target the resistance SNP, a forward primer for the SNP with a mismatch in the 3rd position was designed for both the resistance (R) and susceptibility (S) alleles, respectively, with addition of 20-mer T7 promoter primer to the 5' end of the forward primer for the R allele. The two forward primers, in combination with each of five common reverse primers, were targeted to amplify amplicons of 50-260 bp in size with R and S alleles differing in 20 bp. Results showed that each of three common reverse primers in combination with the two forward primers produced polymorphic markers between R and S plants that were consistent with the targeted genome sequencing results. The polymorphism was distinctly resolved using both polyacrylamide and agarose gel electrophoreses. In addition, a sequence comparative analysis between the resistance gene and homologous sequences in sequenced tetraploid and diploid A and D genome species showed that none of the species possessed the resistance gene allele, suggesting its recent origin from a natural point mutation. The allele-specific PCR-based SNP typing method based on a three-primer combination provides a fast and convenient marker-assisted selection method to search and select for FOV4-resistant Upland cotton.
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Affiliation(s)
- Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Yi Zhu
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Terry Wheeler
- Texas A&M AgriLife Research, 1102 E. Drew Street, Lubbock, TX, 79403, USA
| | - Jane K Dever
- Texas A&M AgriLife Research, 1102 E. Drew Street, Lubbock, TX, 79403, USA
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Zhang J, Zhu Y, Wheeler T, Dever JK, Hake K. Targeted development of diagnostic SNP markers for resistance to Fusarium wilt race 4 in Upland cotton (Gossypium hirsutum). Mol Genet Genomics 2023; 298:895-903. [PMID: 37120777 DOI: 10.1007/s00438-023-02024-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/08/2023] [Indexed: 05/01/2023]
Abstract
Fusarium wilt caused by the soil-borne fungus Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) has become one of the most important emerging diseases in US cotton production. Numerous QTLs have been reported for resistance to FOV; however, no major FOV4-resistance QTL or gene has been identified and used in breeding Upland cotton (Gossypium hirsutum) for FOV4 resistance. In this study, a panel of 223 Chinese Upland cotton accessions was evaluated for FOV4 resistance based on seedling mortality rate (MR) and stem and root vascular discoloration (SVD and RVD). SNP markers were developed based on targeted genome sequencing using AgriPlex Genomics. The chromosome region at 2.130-2.292 Mb on D03 was significantly correlated with both SVD and RVD but not with MR. Based on the two most significant SNP markers, accessions homozygous for AA or TT SNP genotype averaged significantly lower SVD (0.88 vs. 2.54) and RVD (1.46 vs. 3.02) than those homozygous for CC or GG SNP genotype. The results suggested that a gene or genes within the region conferred resistance to vascular discoloration caused by FOV4. The Chinese Upland accessions had 37.22% homozygous AA or TT SNP genotype and 11.66% heterozygous AC or TG SNP genotype, while 32 US elite public breeding lines all had the CC or GG SNP genotype. Among 463 obsolete US Upland accessions, only 0.86% possessed the AA or TT SNP genotype. This study, for the first time, has developed diagnostic SNPs for marker-assisted selection and identified FOV4-resistant Upland germplasms with the SNPs.
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Affiliation(s)
- Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Yi Zhu
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Terry Wheeler
- Texas A&M AgriLife Research, 1102 E. Drew Street, Lubbock, TX, 79403, USA
| | - Jane K Dever
- Texas A&M AgriLife Research, 1102 E. Drew Street, Lubbock, TX, 79403, USA
| | - Kater Hake
- Cotton Incorporated, 6399 Weston Parkway, Cary, NC, 27513, USA
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Lu Q, Yu X, Wang H, Yu Z, Zhang X, Zhao Y. Construction of ultra-high-density genetic linkage map of a sorghum-sudangrass hybrid using whole genome resequencing. PLoS One 2022; 17:e0278153. [PMID: 36445892 PMCID: PMC9707794 DOI: 10.1371/journal.pone.0278153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
The sorghum-sudangrass hybrid is a vital annual gramineous herbage. Few reports exist on its ultra-high-density genetic map. In this study, we sought to create an ultra-high-density genetic linkage map for this hybrid to strengthen its functional genomics research and genetic breeding. We used 150 sorghum-sudangrass hybrid F2 individuals and their parents (scattered ear sorghum and red hull sudangrass) for high-throughput sequencing on the basis of whole genome resequencing. In total, 1,180.66 Gb of data were collected. After identification, filtration for integrity, and partial segregation, over 5,656 single nucleotide polymorphism markers of high quality were detected. An ultra-high-density genetic linkage map was constructed using these data. The markers covered approximately 2,192.84 cM of the map with average marker intervals of 0.39 cM. The length ranged from 115.39 cM to 264.04 cM for the 10 linkage groups. Currently, this represents the first genetic linkage map of this size, number of molecular markers, density, and coverage for sorghum-sudangrass hybrid. The findings of this study provide valuable genome-level information on species evolution and comparative genomics analysis and lay the foundation for further research on quantitative trait loci fine mapping and gene cloning and marker-assisted breeding of important traits in sorghum-sudangrass hybrids.
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Affiliation(s)
- Qianqian Lu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xiaoxia Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Huiting Wang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Zhuo Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- * E-mail:
| | - Xia Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Yaqi Zhao
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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Zhu Y, Thyssen GN, Abdelraheem A, Teng Z, Fang DD, Jenkins JN, McCarty JC, Wedegaertner T, Hake K, Zhang J. A GWAS identified a major QTL for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a MAGIC population of Upland cotton and a meta-analysis of QTLs for Fusarium wilt resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2297-2312. [PMID: 35577933 DOI: 10.1007/s00122-022-04113-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 04/20/2022] [Indexed: 05/16/2023]
Abstract
A major QTL conferring resistance to Fusarium wilt race 4 in a narrow region of chromosome D02 was identified in a MAGIC population of 550 RILs of Upland cotton. Numerous studies have been conducted to investigate the genetic basis of Fusarium wilt (FW, caused by Fusarium oxysporum f. sp. vasinfectum, FOV) resistance using bi-parental and association mapping populations in cotton. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs), together with their 11 Upland cotton (Gossypium hirsutum) parents, was used to identify QTLs for FOV race 4 (FOV4) resistance. Among the parents, Acala Ultima, M-240 RNR, and Stoneville 474 were the most resistant, while Deltapine Acala 90, Coker 315, and Stoneville 825 were the most susceptible. Twenty-two MAGIC lines were consistently resistant to FOV4. Through a genome-wide association study (GWAS) based on 473,516 polymorphic SNPs, a major FOV4 resistance QTL within a narrow region on chromosomes D02 was detected, allowing identification of 14 candidate genes. Additionally, a meta-analysis of 133 published FW resistance QTLs showed a D subgenome and individual chromosome bias and no correlation between homeologous chromosome pairs. This study represents the first GWAS study using a largest genetic population and the most comprehensive meta-analysis for FW resistance in cotton. The results illustrated that 550 lines were not enough for high resolution mapping to pinpoint a candidate gene, and experimental errors in phenotyping cotton for FW resistance further compromised the accuracy and precision in QTL localization and identification of candidate genes. This study identified FOV4-resistant parents and MAGIC lines, and the first major QTL for FOV4 resistance in Upland cotton, providing useful information for developing FOV4-resistant cultivars and further genomic studies towards identification of causal genes for FOV4 resistance in cotton.
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Affiliation(s)
- Yi Zhu
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Gregory N Thyssen
- Cotton Fiber Bioscience and Cotton Chemistry and Utilization Research Units, USDA-ARS-SRRC, New Orleans, LA, USA
| | - Abdelraheem Abdelraheem
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Zonghua Teng
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, USA
| | - Johnie N Jenkins
- Crop Science Research Laboratory, USDA-ARS, Mississippi State, MS, USA
| | - Jack C McCarty
- Crop Science Research Laboratory, USDA-ARS, Mississippi State, MS, USA
| | | | | | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
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