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ARS Home » Southeast Area » Griffin, Georgia » Plant Genetic Resources Conservation Unit » Research » Publications at this Location » Publication #389805
Research Project: Conservation, Characterization, Evaluation, and Distribution of Grain, Oilseed, Vegetable, Subtropical and Tropical Legume, and Warm Season Grass Genetic Resources and Associated Information

Location: Plant Genetic Resources Conservation Unit

Title: Genome-Wide Association Study and Genomic Selection for Sting Nematode Resistance in Peanut Using the USDA Public Data

Author
item RAVELOMBOLA, WALTRAM - Texas A&M Agrilife
item CASON, JOHN - Texas A&M Agrilife
item Tallury, Shyamalrau - Shyam
item MANLEY, AURORA - Texas A&M Agrilife
item PHAM, HANH - Texas A&M Agrilife

Submitted to: Journal of Crop Improvement
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2022
Publication Date: 6/22/2022
Citation: Ravelombola, W., Cason, J., Tallury, S.P., Manley, A., Pham, H. 2022. Genome-Wide Association Study and Genomic Selection for Sting Nematode Resistance in Peanut Using the USDA Public Data. Journal of Crop Improvement. p.1-18. https://doi.org/10.1080/15427528.2022.2087127.
DOI: https://doi.org/10.1080/15427528.2022.2087127

Interpretive Summary: In the US, peanut crop is valued at $1.28 billion annually. The sting nematode is a pathogen that can significantly reduce peanut yields. The pathogen causes plant stunting, yellowing of leaves, and severely damages the root system leading to total yield loss. Chemical control protects the crop from the nematode damage but leads to environmental concerns and increased production costs. Use of nematode resistant peanut cultivars is the most affordable and sustainable option to controlling sting nematode. A total of 775 USDA peanut accessions were tested for sting nematode resistance in field conditions and 630 were recorded as resistant. Modern DNA techniques were used to identify genes responsible for sting nematode resistance in these accessions. These findings can be used to develop sting nematode resistant peanut cultivars.

Technical Abstract: Cultivated peanut (Arachis hypogaea L.) is valued at $1.28 billion annually in the USA. The sting nematode, Belonolaimus longicaudatus, is an ectoparasitic pathogen that can devastate peanut production. Breeding for resistance to this pathogen is one of the most affordable ways to limit its damaging effects on peanut. The use of molecular tools can further accelerate the development of sting nematoderesistant cultivars. The objectives of this study were to identify single-nucleotide polymorphism (SNP) markers associated with sting nematode resistance in peanuts using publicly available datasets and to assess the accuracy of genomic selection in predicting the resistance to sting nematode. SNP discovery was conducted using a genome-wide association study (GWAS) in a peanut panel consisting of 775 USDA accessions, which were phenotyped for sting nematode resistance. GWAS was conducted using 13,306 filtered SNPs, run in TASSEL with three different statistical models. Results showed that (1) a total of 9, 13, 18, 2, and 4 SNPs, respectively, were found to be associated with sting nematode resistance using the singlemarker regression, generalized linear model (PCA), generalized linear model (Q), and mixed linear model (PCA), and mixed linear model (Q), respectively; (2) two SNPs overlapped among the models; and (3) genomic selection was higher when the SNPs from GWAS were used to fit the model. To the best of our knowledge, this is the first report on SNP markers associated with and genomic selection for sting nematode resistance in peanuts. These results can be used to develop a molecular breeding strategy to select for sting nematode resistance in peanuts.