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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Publications at this Location » Publication #344836
Research Project: Introgression of Novel Resistant Genes and Development of Integrated Production Systems for Managing Reniform Nematodes in Cotton

Location: Crop Genetics Research

Title: Genome-wide association study of Gossypium arboreum resistance to reniform nematode

Author
item LI, RUIJUAN - Uc Davis Medical Center
item Erpelding, John
item Stetina, Salliana - Sally

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/26/2018
Publication Date: 8/3/2018
Publication URL: http://handle.nal.usda.gov/10113/6082536
Citation: Li, R., Erpelding, J.E., Stetina, S.R. 2018. Genome-wide association study of Gossypium arboreum resistance to reniform nematode. BioMed Central (BMC) Genetics. 19:52. https://doi.org/10.1186/s12863-018-0662-3.
DOI: https://doi.org/10.1186/s12863-018-0662-3

Interpretive Summary: Reniform nematode is a microscopic worm that is commonly found in the soils of the southeastern United Sates. This is the main cotton producing region of the United States and no upland cotton varieties are available that are resistant to the nematode. The nematode will damage the cotton plant by feeding on the roots, which results in less cotton being produce by the plant. Presently, farmers have to rely on pesticides to reduce nematode damage, but this increases production cost and has human health and environmental concerns. Sources of resistance are needed to more effectively control the nematode. The United States plant germplasm system maintains a collection of Asiatic cotton varieties that are an important source of resistance genes. However, these Asiatic cotton varieties have half the number of chromosomes as upland cotton varieties, which makes it difficult to transfer the resistance to upland cotton varieties. To improve the ability of transferring resistance, a study was conducted to determine the location of resistance genes on the chromosomes of resistant Asiatic cotton varieties. The response to nematode infection was evaluated for 246 Asiatic cotton varieties and these varieties were also evaluated with 7,220 DNA markers. By analyzing these data, 15 DNA markers were found to be associated with genes for nematode resistance and these markers were located in 12 regions on 8 chromosomes. These data indicated that Asiatic cotton varieties are a rich source of nematode resistance genes and that the varieties have multiple genes for resistance. The data from this study can be used to identify DNA markers linked to the resistance genes that can be used to track the transfer of resistance to upland cotton to identify plants with the resistance genes in order to more quickly develop resistant varieties.

Technical Abstract: Background: Reniform nematode (Rotylenchulus reniformis) is a serious root pathogen of upland cotton (Gossypium hirsutum) in the United States due to the lack of resistant cultivars. In contrast, the G. arboreum germplasm collection is an important source of resistance that can aid in the management of the disease. To understand the genetic basis of reniform nematode resistance from G. arboreum, a genome-wide association study was performed using 246 G. arboreum germplasm accessions and 7,220 single nucleotide polymorphic (SNP) sequence markers generated from genotyping-by-sequencing. Results: Fifteen SNPs representing 12 genomic loci distributed over eight chromosomes were shown to be significantly associated with reniform nematode resistance. Major alleles for 14 SNPs were identified as the allele associated with reniform nematode resistance. From these loci, 366 genes containing or physically close to the markers 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, redox reaction, and cell wall modification that may have a role in the expression of resistance. Conclusions: The identification of multiple genomic loci associated with reniform nematode resistance would indicate the G. arboreum germplasm collection is an important resource of novel resistance genes for cotton improvement. The significantly associated markers identified from this study can serve as important tools in the molecular breeding of upland cotton with improved reniform nematode resistance derived from G. arboreum. Additionally, determining the genetic structure and functional analysis of reniform nematode resistance candidate genes will contribute to the understanding of the molecular mechanisms of resistance, which will aid in the pyramiding of multiple resistance genes.