Runs of Homozygosity and Quantitative Trait Locus/Association for Semen Parameters in Selected Chinese and South African Beef Cattle
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sampling, Genotyping and Quality Control
2.2. Estimation of Runs of Homozygosity (ROH)
2.3. QTL and Genomic Regions in ROH
2.4. Classification of Runs and Inbreeding Co-Efficient
3. Results
3.1. Distribution of Runs of Homozygosity (ROH)
3.2. The proportion of SNPs in ROH
3.3. Inbreeding Coefficient FROH vs. FHOM and ROH Regions
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Acknowledgments
Conflicts of Interest
References
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Breeds | Start SNP | End SNP | Start Position | End Position | BTA | nSNP |
---|---|---|---|---|---|---|
SIM | BovineHD0600010649 | BovineHD0600010935 | 38474338 | 39921321 | 6 | 258 |
SIM | BovineHD0600010973 | ARS-BFGL-NGS-99026 | 40064733 | 72930338 | 6 | 1491 |
CSI | BovineHD1400006792 | BovineHD1400006937 | 23394002 | 23917569 | 14 | 60 |
CSI | BTB-01143619 | BovineHD1400007578 | 26196375 | 26302589 | 14 | 21 |
CSI | BovineHD4100004545 | BovineHD0600010837 | 38290032 | 39418286 | 6 | 183 |
BON | BovineHD1400006736 | BovineHD1400006801 | 23240328 | 23407192 | 14 | 55 |
BON | BovineHD1400007096 | BovineHD1400007272 | 24448641 | 25069487 | 14 | 107 |
BON | ARS-BFGL-NGS 100816 | BovineHD0500032567 | 111909943 | 112748475 | 5 | 39 |
BEL | BovineHD1400001029 | BovineHD0300021345 | 7162753 | 73321455 | 3 | 43 |
BEL | BTA-107777 | BovineHD0300022023 | 73921609 | 75752848 | 3 | 77 |
BEL | BovineHD0500024941 | BovineHD0500026993 | 87870382 | 95025828 | 5 | 295 |
BEL | BovineHD1400006790 | BovineHD1400007272 | 233392546 | 25069487 | 14 | 265 |
BEL | BovineHD1400007377 | BovineHD1400007531 | 25607730 | 26108646 | 14 | 117 |
BEL | BovineHD0400019201 | BovineHD0400019430 | 6990155 | 70569432 | 4 | 17 |
ANG | BovineHD0100044669 | Hapmap23088-BTA-151194 | 153400885 | 154349918 | 1 | 47 |
ANG | BovineHD1300018328 | BovineHD1300018406 | 64228423 | 64621429 | 13 | 10 |
ANG | BovineHD1400006790 | BovineHD1400006916 | 23392546 | 23831754 | 14 | 31 |
ANG | BovineHD1400007051 | BovineHD1400007272 | 24315353 | 25069487 | 14 | 55 |
ANG | BovineHD1400007366 | BovineHD1400007408 | 25480962 | 25583674 | 14 | 31 |
ANG | BovineHD1400007518 | BovineHD1400007583 | 26051609 | 26938603 | 14 | 49 |
ANG | BovineHD1400007694 | BovineHD1400024442 | 26700286 | 26938603 | 14 | 52 |
ANG | BovineHD2000001713 | BovineHD2000001840 | 5497761 | 5839847 | 20 | 81 |
ANG | BovineHD0300015826 | BovineHD0300015865 | 52418548 | 52539507 | 3 | 32 |
ANG | BovineHD0500030711 | BovineHD0500030764 | 106905471 | 106988256 | 5 | 47 |
ANG | BovineHD0700027123 | BovineHD0700027253 | 92797461 | 93307177 | 7 | 53 |
Breed | QTL TRAIT | BTA | Gene |
---|---|---|---|
SIM | Sperm motility, Sperm head abnormalities (SPHAB) and Sperm tail abnormalities | 6 | WD repeat domain 19 (WDR 19) |
Semen volume, sperm motility and sperm count | 6 | MARCHF1 membrane associated ring-CH-type finger 1 (MARCH1) | |
CSI | Sperm motility, Sperm head abnormalities (SPHAB) and Sperm tail abnormalities (SPTAB) | 6 | WD repeat domain 19 (WDR 19) |
BON | Sperm motility (SPMOT) | 5 | WD repeat domain 19 (WDR 19) |
Sperm motility (SPMOT) | 5 | Solute carrier organic anion transporter family member 1C1 (SLCOICI) | |
BEL | Sperm motility (SPMOT) | 5 | Solute carrier organic anion transporter family member 1C1 (SLCO1C1) WD repeat domain 19 (WDR 19) |
Sperm count and sperm motility | 4 | suppression of tumorigenicity 7 (ST7) inhibin subunit beta A (INHBA) | |
ANG | Sperm motility and sperm count | 1 | DOP1 leucine zipper like protein B (DOP1B) |
Sperm concentration | 1 | 1 cilia and flagella associated protein 91 CFAP9 | |
Sperm motility | 1 | crystallin zeta like 1 (CRYZL1) ADAM metallopeptidase with thrombospondin type 1 motif 1 (ADAMTS1) | |
Percentage normal sperm | 13 | - | |
Sperm motility | 3 | - | |
Sperm acrosome integrity rate, sperm motility and sperm count. | 7 | growth differentiation factor 9 GDF9 |
Classes | Froh_Class_0 | Froh_Class_5 | Froh_Class_10 | Froh_Class_20 | Froh |
---|---|---|---|---|---|
Froh_Class_5 | 0.929 | ||||
Froh_Class_10 | 0.711 | 0.864 | |||
Froh_Class_20 | 0.567 | 0.743 | 0.881 | ||
Froh_Class_40 | 0.400 | 0.527 | 0.599 | 0.665 | |
Fhom | 0.603 |
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Modiba, M.C.; Nephawe, K.A.; Wang, J.; Hlongwane, N.; Hadebe, K.; Lu, W.; Mtileni, B. Runs of Homozygosity and Quantitative Trait Locus/Association for Semen Parameters in Selected Chinese and South African Beef Cattle. Animals 2022, 12, 1546. https://doi.org/10.3390/ani12121546
Modiba MC, Nephawe KA, Wang J, Hlongwane N, Hadebe K, Lu W, Mtileni B. Runs of Homozygosity and Quantitative Trait Locus/Association for Semen Parameters in Selected Chinese and South African Beef Cattle. Animals. 2022; 12(12):1546. https://doi.org/10.3390/ani12121546
Chicago/Turabian StyleModiba, Mamokoma Cathrine, Khathutshelo Agree Nephawe, Jun Wang, Nompilo Hlongwane, Khanyisile Hadebe, Wenfa Lu, and Bohani Mtileni. 2022. "Runs of Homozygosity and Quantitative Trait Locus/Association for Semen Parameters in Selected Chinese and South African Beef Cattle" Animals 12, no. 12: 1546. https://doi.org/10.3390/ani12121546