Genome-wide association study of Gossypium arboreum resistance to reniform nematode
Abstract
Background: Reniform nematode (Rotylenchulus reniformis) has emerged as one of the most destructive root pathogens of upland cotton (Gossypium hirsutum) in the United States. Management of R. reniformis has been hindered by the lack of resistant G. hirsutum cultivars; however, resistance has been frequently identified in germplasm accessions from the G. arboreum collection. To determine the genetic basis of reniform nematode resistance, a genome-wide association study (GWAS) was performed using 246 G. arboreum germplasm accessions that were genotyped with 7220 single nucleotide polymorphic (SNP) sequence markers generated from genotyping-by-sequencing. Results: Fifteen SNPs representing 12 genomic loci distributed over eight chromosomes showed association with reniform nematode resistance. For 14 SNPs, major alleles were shown to be associated with resistance. From the 15 significantly associated SNPs, 146 genes containing or physically close to these loci were identified as putative reniform nematode resistance candidate genes. These genes are involved in a broad range of biological pathways, including plant innate immunity, transcriptional regulation, and redox reaction that may have a role in the expression of resistance. Eighteen of these genes corresponded to differentially expressed genes identified from G. hirsutum in response to reniform nematode infection. Conclusions: The identification of multiple genomic loci associated withmore »
- Authors:
-
[2];
- Univ. of California, Davis, CA (United States). Dept. of Plant Biology
- US Dept. of Agriculture (USDA)., Stoneville, MS (United States). Crop Genetics Research Unit
- Publication Date:
- Research Org.:
- Oak Ridge Associated Univ., Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE; USDA-ARS
- OSTI Identifier:
- 1626783
- Grant/Contract Number:
- AC05-06OR23100; 6066–22000-074-00D
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Genetics (Online)
- Additional Journal Information:
- Journal Name: BMC Genetics (Online); Journal Volume: 19; Journal Issue: 1; Journal ID: ISSN 1471-2156
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- Genetics & Heredity; Cotton; Genome-wide association study; Genotyping-by-sequencing; Germplasm; Cotton, Genome-wide association study, Genotyping-by-sequencing, Germplasm, Gossypium arboreum; Host-plant resistance; reniform nematode; Single nucleotide polymorphism
Citation Formats
Li, Ruijuan, Erpelding, John E., and Stetina, Salliana R. Genome-wide association study of Gossypium arboreum resistance to reniform nematode. United States: N. p., 2018.
Web. doi:10.1186/s12863-018-0662-3.
Li, Ruijuan, Erpelding, John E., & Stetina, Salliana R. Genome-wide association study of Gossypium arboreum resistance to reniform nematode. United States. https://doi.org/10.1186/s12863-018-0662-3
Li, Ruijuan, Erpelding, John E., and Stetina, Salliana R. Fri .
"Genome-wide association study of Gossypium arboreum resistance to reniform nematode". United States. https://doi.org/10.1186/s12863-018-0662-3. https://www.osti.gov/servlets/purl/1626783.
@article{osti_1626783,
title = {Genome-wide association study of Gossypium arboreum resistance to reniform nematode},
author = {Li, Ruijuan and Erpelding, John E. and Stetina, Salliana R.},
abstractNote = {Background: Reniform nematode (Rotylenchulus reniformis) has emerged as one of the most destructive root pathogens of upland cotton (Gossypium hirsutum) in the United States. Management of R. reniformis has been hindered by the lack of resistant G. hirsutum cultivars; however, resistance has been frequently identified in germplasm accessions from the G. arboreum collection. To determine the genetic basis of reniform nematode resistance, a genome-wide association study (GWAS) was performed using 246 G. arboreum germplasm accessions that were genotyped with 7220 single nucleotide polymorphic (SNP) sequence markers generated from genotyping-by-sequencing. Results: Fifteen SNPs representing 12 genomic loci distributed over eight chromosomes showed association with reniform nematode resistance. For 14 SNPs, major alleles were shown to be associated with resistance. From the 15 significantly associated SNPs, 146 genes containing or physically close to these loci were identified as putative reniform nematode resistance candidate genes. These genes are involved in a broad range of biological pathways, including plant innate immunity, transcriptional regulation, and redox reaction that may have a role in the expression of resistance. Eighteen of these genes corresponded to differentially expressed genes identified from G. hirsutum in response to reniform nematode infection. Conclusions: The identification of multiple genomic loci associated with reniform nematode resistance would indicate that the G. arboreum collection is a significant resource of novel resistance genes. The significantly associated markers identified from this GWAS can be used for the development of molecular tools for breeding improved reniform nematode resistant upland cotton with resistance introgressed from G. arboreum. Additionally, a greater understanding of the molecular mechanisms of reniform nematode resistance can be determined through genetic structure and functional analyses of candidate genes, which will aid in the pyramiding of multiple resistance genes.},
doi = {10.1186/s12863-018-0662-3},
journal = {BMC Genetics (Online)},
number = 1,
volume = 19,
place = {United States},
year = {Fri Aug 03 00:00:00 EDT 2018},
month = {Fri Aug 03 00:00:00 EDT 2018}
}
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Figures / Tables:
Fig. 1: Frequency distribution of female index (FI) values for the 246 Gossypium arboreum germplasm accessions. FI = (average number of female reniform nematode on an accession per gram of root tissue / average number of female reniform nematode on the susceptible Gossypium hirsutum control genotype PI 529251 per grammore »
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