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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #389393
Research Project: Genetics and Breeding of Lettuce, Spinach, Melon, and Related Species to Improve Production and Consumer-related Traits

Location: Crop Improvement and Protection Research

Title: Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm

Author
item SHI, AINONG - University Of Arkansas
item BHATTARAI, GEHENDRA - University Of Arkansas
item XIONG, HAIZHENG - University Of Arkansas
item AVILA, CARLOS - Texas A&M University
item FENG, CHUNDA - University Of Arkansas
item LIU, BO - University Of Arkansas
item JOSHI, VIJAY - Texas A&M University
item STEIN, LARRY - Texas A&M University
item Mou, Beiquan
item DU TOIT, LINDSEY - Washington State University
item CORREL, JIM - University Of Arkansas

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/9/2022
Publication Date: 3/23/2022
Citation: Shi, A., Bhattarai, G., Xiong, H., Avila, C., Feng, C., Liu, B., Joshi, V., Stein, L., Mou, B., du Toit, L., Correll, J.C. 2022. Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm. Horticulture Research. 9. Article uhac069. https://doi.org/10.1093/hr/uhac069.
DOI: https://doi.org/10.1093/hr/uhac069

Interpretive Summary: White rust (Albugo occidentalis) is one of the major yield-limiting diseases in spinach (Spinacia oleracea) production and the use of host resistance is the most efficient and environment-friendly approach to manage white rust disease. The objectives of this research were to conduct genome-wide associating study (GWAS) to identify molecular markers associated with white rust resistance and to improve selection efficiency in spinach. A GWAS panel of 346 USDA germplasm accessions was evaluated for white rust resistance and their DNA sequences were determined. Nine molecular markers, chr2_53049132, chr3_58479501, chr3_95114909, chr4_9176069, chr4_17807168, chr4_83938338, chr4_87601768, chr6_1877096, and chr6_31287118, located on chromosomes 2, 3, 4, and 6 were associated with white rust resistance in this GWAS panel. Four methods were used to test the correlation between the observed white rust resistance and the predicted performance based on the molecular markers. The results showed that using more significant molecular markers can predict the plant performance more accurately. The molecular markers and the information will help breeders to perform genome breeding through marker-assisted selection (MAS) and increase selection efficiency in spinach.

Technical Abstract: White rust (Albugo occidentalis) is one of the major yield-limiting diseases in spinach (Spinacia oleracea) production and the use of host resistance is the most efficient and environment-friendly approach to manage white rust disease. The objectives of this research were to conduct genome-wide associating study (GWAS) to identify single nucleotide polymorphism (SNP) markers associated with white rust resistance and to perform genomic prediction (GP) to estimate genomic prediction efficiency (PA) in spinach. A GWAS panel of 346 USDA germplasm accessions was phenotyped with white rust resistance and genotyped with 13,235 SNPs postulated from whole genome resequencing (WGR) technology. Nine SNPs, chr2_53049132, chr3_58479501, chr3_95114909, chr4_9176069, chr4_17807168, chr4_83938338, chr4_87601768, chr6_1877096, and chr6_31287118, located on chromosomes 2, 3, 4, and 6 were associated with white rust resistance in this GWAS panel. Four scenarios were tested for PA using Pearson’s correlation coefficient (r) between the genomic estimation breeding value (GEBV) and the observed values: (1) different ratios between the training set and testing set (fold), (2) different GP models, (3) different SNP numbers in three different SNP sets, and (4) the use of GWAS-derived significant SNP markers. Our results showed that the different folds from 2-fold to 10-fold and different GP models had similar, although not identical averaged r values in each SNP set; using more GWAS-derived significant SNP makers would increase PA with high r values up to 0.84 from this study. The SNP markers and the high PA will provide the information for breeders to perform genome breeding through marker-assisted selection (MAS) and genomic selection (GS) in spinach.