Location: Crop Improvement and Protection Research
Title: Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasmAuthor
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SHI, AINONG - University Of Arkansas |
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BHATTARAI, GEHENDRA - University Of Arkansas |
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XIONG, HAIZHENG - University Of Arkansas |
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AVILA, CARLOS - Texas A&M University |
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FENG, CHUNDA - University Of Arkansas |
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LIU, BO - University Of Arkansas |
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JOSHI, VIJAY - Texas A&M University |
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STEIN, LARRY - Texas A&M University |
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Mou, Beiquan |
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DU TOIT, LINDSEY - Washington State University |
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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. |