Genomic selection using a subset of SNPs identified by genome-wide association analysis for disease resistance traits in aquaculture species

Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.

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Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection

Frontiers in Plant Science ◽

10.3389/fpls.2018.00343 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 9

Author(s):

Michel S. McElroy ◽

Alberto J. R. Navarro ◽

Guiliana Mustiga ◽

Conrad Stack ◽

Salvador Gezan ◽

...

Keyword(s):

Genomic Selection ◽

Association Analysis ◽

Theobroma Cacao ◽

Genome Wide Association ◽

Genome Wide Association Analysis ◽

Genome Wide

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Genome wide association analysis for bacterial kidney disease resistance in a commercial North American Atlantic salmon (Salmo salar) population using a 50 K SNP panel

Aquaculture ◽

10.1016/j.aquaculture.2018.06.014 ◽

2018 ◽

Vol 495 ◽

pp. 465-471 ◽

Cited By ~ 6

Author(s):

Melissa K. Holborn ◽

Keng P. Ang ◽

J.A.K. Elliott ◽

Frank Powell ◽

Elizabeth G. Boulding

Keyword(s):

Disease Resistance ◽

Kidney Disease ◽

Atlantic Salmon ◽

Association Analysis ◽

Salmo Salar ◽

Genome Wide Association ◽

Genome Wide Association Analysis ◽

Bacterial Kidney Disease ◽

Genome Wide ◽

Snp Panel

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Faculty Opinions recommendation of Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1083881.536824 ◽

2007 ◽

Cited By ~ 1

Author(s):

Terri Beaty

Keyword(s):

Type 2 Diabetes ◽

Association Analysis ◽

Genome Wide Association ◽

Genome Wide Association Analysis ◽

Genome Wide

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Faculty Opinions recommendation of Alpha-T-catenin (CTNNA3) gene was identified as a risk variant for toluene diisocyanate-induced asthma by genome-wide association analysis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1157877.619129 ◽

2009 ◽

Author(s):

Francine Kauffmann ◽

Lidwien Smit

Keyword(s):

Association Analysis ◽

Toluene Diisocyanate ◽

Genome Wide Association ◽

Risk Variant ◽

Genome Wide Association Analysis ◽

Genome Wide

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A Caution in Association of ABO Blood Group with COVID-19

Global Clinical and Translational Research ◽

10.36316/02.0031 ◽

2020 ◽

Cited By ~ 2

Keyword(s):

Gene Cluster ◽

Clinical Outcomes ◽

Blood Group ◽

Association Analysis ◽

Blood Type ◽

Genome Wide Association ◽

Chromosome 3 ◽

Abo Blood Group ◽

Genome Wide Association Analysis ◽

Genome Wide

A comment on Zhao J, Yang Y, Huang H, Li D, Gu D, Lu X, et al. Association of ABO blood group and Covid19 susceptability. medRxiv [PREPRINT]. 2020; https://doi.org/10.1101/2020.03.11.20031096. Zeng X, Fan H, Lu D, Huang F, Meng X, Li Z, et al. Association between ABO blood group and clinical outcomes of Covid19. medRxiv[PREPRINT].2020; https://doi.org/10.1101/2020.04.15.20063107. Zietz M, Tatonetti N. Testing the association between blood type and COVID-19 infection, intubation, and death medRxiv [PREPRINT]. 2020; https://doi.org/10.1101/2020.04.08.20058073. Ellinghaus D, Degenhardt F, Bujanda L, al. e. The ABO blood group and a chromosome 3 gene cluster associate with SRAS-CoV2 respitarory failure in an Italy-Spain genome-wide association analysis. medRxiv. 2020; https://doi.org/10.1101/2020.05.31.20114991.

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