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Kumar P, Khanal S, Da Silva M, Singh R, Davis RF, Nichols RL, Chee PW. Transcriptome analysis of a nematode resistant and susceptible upland cotton line at two critical stages of Meloidogyne incognita infection and development. PLoS One 2019; 14:e0221328. [PMID: 31504059 PMCID: PMC6736245 DOI: 10.1371/journal.pone.0221328] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 08/06/2019] [Indexed: 11/18/2022] Open
Abstract
Host plant resistance is the most practical approach to control the Southern root-knot nematode (Meloidogyne incognita; RKN), which has emerged as one of the most serious economic pests of Upland cotton (Gossypium hirsutum L.). Previous QTL analyses have identified a resistance locus on chromosome 11 (qMi-C11) affecting galling and another locus on chromosome-14 (qMi-C14) affecting egg production. Although these two QTL regions were fine mapped and candidate genes identified, expression profiling of genes would assist in further narrowing the list of candidate genes in the QTL regions. We applied the comparative transcriptomic approach to compare expression profiles of genes between RKN susceptible and resistance genotypes at an early stage of RKN development that coincides with the establishment of a feeding site and at the late stage of RKN development that coincides with RKN egg production. Sequencing of cDNA libraries produced over 315 million reads of which 240 million reads (76%) were mapped on to the Gossypium hirsutum genome. A total of 3,789 differentially expressed genes (DEGs) were identified which were further grouped into four clusters based on their expression profiles. A large number of DEGs were found to be down regulated in the susceptible genotype at the late stage of RKN development whereas several genes were up regulated in the resistant genotype. Key enriched categories included transcription factor activity, defense response, response to phyto-hormones, cell wall organization, and protein serine/threonine kinase activity. Our results also show that the DEGs in the resistant genotype at qMi-C11 and qMi-C14 loci displayed higher expression of defense response, detoxification and callose deposition genes, than the DEGs in the susceptible genotype.
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Affiliation(s)
- Pawan Kumar
- Dept. of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States of America
| | - Sameer Khanal
- Dept. of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States of America
| | - Mychele Da Silva
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States of America
| | - Rippy Singh
- Dept. of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States of America
| | - Richard F. Davis
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States of America
- USDA-ARS, Crop Protection and Management Research Unit, Tifton, GA, United States of America
- * E-mail: (RFD);(PWC)
| | | | - Peng W. Chee
- Dept. of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States of America
- * E-mail: (RFD);(PWC)
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Wubben MJ, Thyssen GN, Callahan FE, Fang DD, Deng DD, McCarty JC, Li P, Islam MS, Jenkins JN. A novel variant of Gh_D02G0276 is required for root-knot nematode resistance on chromosome 14 (D02) in Upland cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1425-1434. [PMID: 30741320 DOI: 10.1007/s00122-019-03289-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/12/2019] [Indexed: 05/24/2023]
Abstract
MAGIC population sequencing and virus-induced gene silencing identify Gh_D02G0276 as a novel root-knot nematode resistance gene on chromosome 14 in Upland cotton. The southern root-knot nematode [RKN; Meloidogyne incognita (Kofoid & White)] remains the primary yield-limiting biotic stress to Upland cotton (Gossypium hirsutum L.) throughout the southeastern USA. While useful genetic markers have been developed for two major RKN resistance loci on chromosomes 11 (A11) and 14 (D02), these markers are not completely effective because the causative genes have not been identified. Here, we sequenced 550 recombinant inbred lines (RILs) from a multi-parent advanced generation intercross (MAGIC) population to identify five RILs that had informative recombinations near the D02-RKN resistance locus. The RKN resistance phenotypes of these five RILs narrowed the D02-RKN locus to a 30-kb region with four candidate genes. We conducted virus-induced gene silencing (VIGS) on each of these genes and found that Gh_D02G0276 was required for suppression of RKN egg production conferred by the Chr. D02 resistance gene. The resistant lines all possessed an allele of Gh_D02G0276 that showed non-synonymous mutations and was prematurely truncated. Furthermore, a Gh_D02G0276-specific marker for the resistance allele variant was able to identify RKN-resistant germplasm from a collection of 367 cotton accessions. The Gh_D02G0276 peptide shares similarity with domesticated hAT-like transposases with additional novel N- and C-terminal domains that resemble the target of known RKN effector molecules and a prokaryotic motif, respectively. The truncation in the resistance allele results in a loss of a plant nuclear gene-specific C-terminal motif, potentially rendering this domain antigenic due to its high homology with bacterial proteins. The conclusive identification of this RKN resistance gene opens new avenues for understanding plant resistance mechanisms to RKN as well as opportunities to develop more efficient marker-assisted selection in cotton breeding programs.
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Affiliation(s)
- Martin J Wubben
- Crop Science Research Laboratory, Genetics and Precision Agriculture Research Unit, USDA-ARS, 150 Twelve Lane, Mississippi State, MS, 39762, USA.
| | - Gregory N Thyssen
- Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, USDA-ARS, New Orleans, LA, USA
- Southern Regional Research Center, Cotton Chemistry and Utilization Research Unit, USDA-ARS, New Orleans, LA, USA
| | - Franklin E Callahan
- Crop Science Research Laboratory, Genetics and Precision Agriculture Research Unit, USDA-ARS, 150 Twelve Lane, Mississippi State, MS, 39762, USA
| | - David D Fang
- Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, USDA-ARS, New Orleans, LA, USA
| | - Dewayne D Deng
- Crop Science Research Laboratory, Genetics and Precision Agriculture Research Unit, USDA-ARS, 150 Twelve Lane, Mississippi State, MS, 39762, USA
| | - Jack C McCarty
- Crop Science Research Laboratory, Genetics and Precision Agriculture Research Unit, USDA-ARS, 150 Twelve Lane, Mississippi State, MS, 39762, USA
| | - Ping Li
- Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, USDA-ARS, New Orleans, LA, USA
| | | | - Johnie N Jenkins
- Crop Science Research Laboratory, Genetics and Precision Agriculture Research Unit, USDA-ARS, 150 Twelve Lane, Mississippi State, MS, 39762, USA
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