Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals, SNP Genotyping, and Quality Control
2.2. Imputation, Lift-Over, and Annotation
2.3. Variance Component Estimation of Genome Regions
2.4. Exon-Specific Association Test (ESAS)
2.5. Favorable and Unfavorable Haplotypes
2.6. Genomic Prediction
2.7. Prediction of Damaging Causal Mutations and Structure
3. Results
3.1. Genome Partitioning of Genetic Variation
3.2. Identification of Candidate Causal Variants
3.3. Explanatory Power of Candidate SNPs
3.4. Favorable and Unfavorable Homozygous Haplotypes
3.5. Effects of Causal Variants on Protein Structure
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Trait | Chr:Pos | Allele | RefSNPID | Gene | SNPeffect | SE | p-Value |
---|---|---|---|---|---|---|---|
CW | 4:4857791 | A/G | rs210475204 | COBL | 6.507 | 1.09 | 2.195 × 10−9 |
4:9502576 | C/T | rs445255852 | LRRD1 | 6.653 | 1.24 | 7.130 × 10−8 | |
4:9875221 | G/A | rs379759182 | RBM48 | 4.342 | 0.89 | 9.806 × 10−7 | |
4:7208133 | C/T | rs516634298 | ABCA13 | 3.780 | 0.79 | 1.666 × 10−6 | |
6:37403795 | T/C | rs109696064 | LCORL | 13.712 | 1.49 | 3.011 × 10−20 | |
6:37343379 | G/T | rs109570900 | NCAPG | 11.838 | 1.43 | 9.919 × 10−17 | |
6:36630884 | T/C | rs383697460 | PKD2 | 15.613 | 2.83 | 3.458 × 10−8 | |
6:58146321 | G/A | rs797342426 | Hypothetical | 14.673 | 2.68 | 4.520 × 10−8 | |
6:36880429 | C/T | rs716537943 | IBSP | 7.977 | 1.52 | 1.490 × 10−7 | |
6:36028197 | G/A | rs383620650 | FAM13A | 8.228 | 1.59 | 2.346 × 10−7 | |
6:37237698 | T/C | rs210785796 | FAM184B | −4.537 | 0.88 | 2.626 × 10−7 | |
14:19524263 | T/C | rs449968016 | PRKDC | 16.417 | 1.27 | 4.337 × 10−38 | |
14:30393332 | C/A | rs109953090 | DNAJC5B | 10.964 | 1.10 | 2.686 × 10−23 | |
14:30518533 | T/C | rs381116984 | CRH | 10.866 | 1.10 | 5.889 × 10−23 | |
14:33878123 | A/G | rs464130691 | NCOA2 | 10.022 | 1.34 | 8.765 × 10−14 | |
14:16328530 | A/G | rs471616366 | Hypothetical | 10.655 | 1.47 | 4.335 × 10−13 | |
14:16641005 | C/T | rs211636635 | TBC1D31 | 10.450 | 1.47 | 1.045 × 10−12 | |
14:16698021 | G/T | rs208131933 | TBC1D31 | 10.450 | 1.47 | 1.045 × 10−12 | |
14:19984551 | A/G | rs109071668 | PPDPFL | 4.505 | 0.69 | 7.512 × 10−11 | |
14:9051405 | A/T | rs209264955 | HHLA1 | 5.423 | 0.84 | 8.386 × 10−11 | |
14:19372860 | T/C | rs210839501 | SPIDR | 3.949 | 0.66 | 2.213 × 10−9 | |
14:21195722 | G/T | rs380004533 | ST18 | −4.275 | 0.75 | 9.922 × 10−9 | |
14:26475692 | A/G | rs381829093 | CHD7 | −4.136 | 0.73 | 1.314 × 10−8 | |
14:31303419 | G/A | rs109820067 | CSPP1 | −3.879 | 0.70 | 2.738 × 10−8 | |
14:43787543 | A/G | rs380389290 | Hypothetical | 5.905 | 1.07 | 3.557 × 10−8 | |
14:9111310 | T/C | rs209285140 | OC90 | 4.037 | 0.73 | 3.609 × 10−8 | |
14:9111217 | A/G | rs210209375 | OC90 | 4.036 | 0.73 | 3.659 × 10−8 | |
14:16590597 | T/C | rs207540257 | FAM83A | 6.487 | 1.18 | 3.713 × 10−8 | |
14:16590776 | T/C | rs380808409 | FAM83A | 6.487 | 1.18 | 3.713 × 10−8 | |
14:9111232 | G/A | rs207841625 | OC90 | 3.968 | 0.72 | 4.009 × 10−8 | |
14:16609068 | T/A | rs210725961 | FAM83A | 6.441 | 1.18 | 4.470 × 10−8 | |
14:24756697 | T/C | rs136157938 | SDCBP | −3.559 | 0.66 | 5.573 × 10−8 | |
14:30837447 | C/T | rs109134892 | MYBL1 | −3.230 | 0.67 | 1.567 × 10−6 | |
BFT | 2:107160304 | G/T | rs109446852 | ZFAND2B | 0.799 | 0.11 | 1.840 × 10−12 |
2:107114443 | A/G | rs383795443 | SLC23A3 | 0.768 | 0.12 | 2.549 × 10−11 | |
EMA | 14:19524263 | T/C | rs449968016 | PRKDC | 1.644 | 0.30 | 4.617 × 10−8 |
MS | 3:19028381 | G/A | rs210416891 | MRPL9 | 0.251 | 0.05 | 1.408 × 10−6 |
19:7310638 | G/C | rs799291287 | ANKFN1 | −0.234 | 0.05 | 9.683 × 10−7 | |
22:11849704 | G/C | rs799031002 | ACVR2B | 0.298 | 0.05 | 1.567 × 10−8 |
Trait | CHROM | RefSNPID | Gene | %V(g) | %V(p) |
---|---|---|---|---|---|
CW | BTA4 | rs210475204 | COBL | 1.634 | 0.005 |
BTA6 | rs109696064 | LCORL | 4.495 | 0.014 | |
BTA14 | rs449968016 | PRKDC | 8.470 | 0.026 | |
BFT | BTA2 | rs109446852 | ZFAND2B | 2.075 | 0.006 |
EMA | BTA14 | rs449968016 | PRKDC | 1.728 | 0.005 |
MS | BTA3 | rs210416891 | MRPL9 | 1.104 | 0.004 |
BTA19 | rs799291287 | ANKFN1 | 0.566 | 0.002 | |
BTA22 | rs799031002 | ACVR2B | 1.187 | 0.004 |
Trait | Protein | HGVS | Predicted Classification 1 | Damaging Score 2 | Sensitivity | Specificity |
---|---|---|---|---|---|---|
CW | COBL | p.Arg660Gln | No damage | 0.007 | 0.96 | 0.75 |
LCORL | p.Glu485Lys | Unknown | Unknown | Unknown | Unknown | |
PRKDC | p.Ala895Thr | Probably damaging | 0.988 | 0.73 | 0.96 | |
BFT | ZFAND2B | p.Leu117Arg | No damage | 0.000 | 1.00 | 0.00 |
EMA | PRKDC | p.Ala895Thr | Probably damaging | 0.988 | 0.73 | 0.96 |
MS | MRPL9 | p.Thr226Ala | Probably damaging | 0.998 | 0.27 | 0.99 |
ANKFN1 | p.Leu174Val | Probably damaging | 0.961 | 0.78 | 0.95 | |
ACVR2B | p.Thr395Ser | Possibly damaging | 0.734 | 0.85 | 0.92 |
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Lee, D.J.; Kim, Y.; Dinh, P.T.N.; Chung, Y.; Lee, D.; Kim, Y.; Lee, S.H.; Choi, I.; Lee, S.H. Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding. Genes 2023, 14, 1839. https://doi.org/10.3390/genes14101839
Lee DJ, Kim Y, Dinh PTN, Chung Y, Lee D, Kim Y, Lee SH, Choi I, Lee SH. Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding. Genes. 2023; 14(10):1839. https://doi.org/10.3390/genes14101839
Chicago/Turabian StyleLee, Dong Jae, Yoonsik Kim, Phuong Thanh N. Dinh, Yoonji Chung, Dooho Lee, Yeongkuk Kim, Soo Hyun Lee, Inchul Choi, and Seung Hwan Lee. 2023. "Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding" Genes 14, no. 10: 1839. https://doi.org/10.3390/genes14101839
APA StyleLee, D. J., Kim, Y., Dinh, P. T. N., Chung, Y., Lee, D., Kim, Y., Lee, S. H., Choi, I., & Lee, S. H. (2023). Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding. Genes, 14(10), 1839. https://doi.org/10.3390/genes14101839