Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling and Genotyping Quality Control
2.2. Genome-Wide Association Studies
2.3. Selection Signature Detection Using the iHS Method
2.4. ROH Detection
3. Results
3.1. Genome-Wide Association Studies and Annotation of Candidate Genes
3.2. Selection Signatures Detected by iHS
3.3. ROH Results
3.3.1. Genomic ROH Distribution
3.3.2. Genomic Patterns of ROHs
3.3.3. The Consensus ROH Regions and the Genes Overlaping with Those Detected on the Basis of iHS
4. Discussion
4.1. Litter Size
4.2. Coat Colour
4.3. Black Middorsal Stripe
4.4. Skin Colour
4.5. Selection Signatures in YZD Goats
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/Number | Samples/Number | |
---|---|---|
Trait 1 | Trait 0 | |
Litter size/154 | More than 2 lambs/7 | 1 to 2 lambs/147 |
Coat colour/196 | Brown/10 | White/186 |
Black middorsal stripe 1/196 | Present/77 | Absent/119 |
Skin colour/205 | Pigmented/66 | Unpigmented/139 |
Trait | CHR 1 | SNP Marker | Position | p Value | Annotated Gene |
---|---|---|---|---|---|
Litter size | 11 | snp54094-scaffold824-899720 | 57366312 | 6.87 × 10−7 | Near to LRRTM4 (leucine rich repeat transmembrane neuronal 4) |
Coat colour | 12 | snp55048-scaffold842-324525 | 69164369 | 1.53 × 10−7 | LOC102187779 |
26 | snp11508-scaffold142-1990450 | 23574535 | 6.90 × 10−8 | SORCS3 (sortilin-related VPS10 domain-containing receptor 3) | |
Black dorsal stripe | 18 | snp56013-scaffold873-22716 | 14190132 | 2.43 × 10−9 | TCF25 (transcription factor 25) |
Class | ROH Number | Percent (%) | Mean Length | Genome Coverage (%) |
---|---|---|---|---|
ROH 2–4 Mb | 2882 | 64.82 | 2.59 | 0.30 |
ROH 4–8 Mb | 756 | 17.00 | 5.45 | 0.16 |
ROH 8–16 Mb | 426 | 9.58 | 10.84 | 0.18 |
>16 Mb | 382 | 8.59 | 27.92 | 0.42 |
Total | 4446 | 100 | 6.04 | 1.06 |
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Sun, X.; Niu, Q.; Jiang, J.; Wang, G.; Zhou, P.; Li, J.; Chen, C.; Liu, L.; Xu, L.; Ren, H. Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers. Genes 2023, 14, 1183. https://doi.org/10.3390/genes14061183
Sun X, Niu Q, Jiang J, Wang G, Zhou P, Li J, Chen C, Liu L, Xu L, Ren H. Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers. Genes. 2023; 14(6):1183. https://doi.org/10.3390/genes14061183
Chicago/Turabian StyleSun, Xiaoyan, Qunhao Niu, Jing Jiang, Gaofu Wang, Peng Zhou, Jie Li, Cancan Chen, Liangjia Liu, Lingyang Xu, and Hangxing Ren. 2023. "Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers" Genes 14, no. 6: 1183. https://doi.org/10.3390/genes14061183
APA StyleSun, X., Niu, Q., Jiang, J., Wang, G., Zhou, P., Li, J., Chen, C., Liu, L., Xu, L., & Ren, H. (2023). Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers. Genes, 14(6), 1183. https://doi.org/10.3390/genes14061183