Genome-wide association study and genomic selection for sting nematode resistance in peanut using the USDA public data

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 nematode-resistant 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 single-marker 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.

KEYWORDS:

• Cultivated peanut
• GS
• GWAS
• SNP
• sting nematode

Acknowledgments

This work was in part supported by the USDA National Institute of Food and Agriculture Hatch project accession number 1025956, the National Peanut Board and Texas Peanut Producers Board. We are grateful to the USDA for conducting the phenotypic evaluation and to the National Ag Library and PeanutBase for the availability of the genotypic data.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/15427528.2022.2087127

Additional information

Funding

This work was supported by the USDA NIFA Hatch [1025956]; Texas Peanut Board and National Peanut Board.