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. 2022 Jun 14;12(12):1546.
doi: 10.3390/ani12121546.

Runs of Homozygosity and Quantitative Trait Locus/Association for Semen Parameters in Selected Chinese and South African Beef Cattle

Mamokoma Cathrine Modiba  1   2 , Khathutshelo Agree Nephawe  3 , Jun Wang  1   2 , Nompilo Hlongwane  4 , Khanyisile Hadebe  4 , Wenfa Lu  1   2 , Bohani Mtileni  3
Affiliations

Runs of Homozygosity and Quantitative Trait Locus/Association for Semen Parameters in Selected Chinese and South African Beef Cattle

Mamokoma Cathrine Modiba et al. Animals (Basel). .

Abstract

In this study, runs of homozygosity (ROH) and quantitative trait locus/association (QTL) for semen parameters in selected Chinese and South African beef cattle breed were estimated. The computed results showed 7516 ROH were observed between classes 0−5 Mb with no ROH observed in classes >40 Mb. Distribution of ROH showed high level of genomic coverage for ANG, NGU, CSI, and BEL breeds. Approximately 13 genomic regions with QTL were controlling sperm motility, sperm concentration, semen volume, sperm count, sperm head abnormalities, sperm tail abnormalities, sperm integrity, and percentage of abnormal sperm traits. Nine candidate genes, CDF9, MARCH1, WDR19, SLOICI, ST7, DOP1B, CFAF9, INHBA, and ADAMTS1, were suggested to be associated with above mentioned QTL traits. The results for inbreeding coefficient showed moderate correlation between FROH vs FHOM at 0.603 and high correlation between FROH 0−5 Mb 0.929, and lowest correlation for 0−>40 Mb 0.400. This study suggested recent inbreeding in CSI, BEL, ANG, BON, SIM, and NGU breeds. Furthermore, it highlighted varied inbreeding levels and identified QTL for semen traits and genes of association. These results can assist in implementation of genetic improvement strategies for bulls and provide awareness and proper guidelines in developing breeding programs.

Keywords: ROH; inbreeding coefficient; quantitative trait locus/association and breeds.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Classification of ROH were estimated per breed; each ROH length category and average per breed, represented from left to the right: Belgian Blue (BEL), Chinese Simmentaler (CSI), Bonsmara (BON), Nguni (NGU), South African Simmentaler (SIM), and Angus (ANG). All Breeds had the highest ROH between 0–5 Mb with the NGU and AGN showing the highest ROH 0–5 Mb on chromosomes 5, 6, 11, and 14 for SIM, and chromosomes 5, 7, and 14 for BON, respectively, in South African breeds.
Figure 2
Figure 2
Number of ROH per chromosomes for Chinese CSI and BEL with significant ROH observed on chromosomes 5, 6, 11, and 14 for both breeds.
Figure 3
Figure 3
Number runs of homozygosity per chromosomes for South Africa BON, NGU, SIM, and ANG with significant ROH observed on chromosomes 1, 2, 3, 4, 5, 6, 7, 11, and 14, with NGU and ANG showing the most significant chromosome coverage.
Figure 4
Figure 4
Manhattan plot for SNPs in ROH from the top to bottom (A) BEL, (B) CSI, and (C) BON, with BTA 14 having the most significant SNP in ROH for the three breeds. Manhattan plot for SNPs in ROH from the top to bottom (D) NGU, (E) ANG, and (F) SIM, with ANG having the most significant SNP in ROH on BTA 1,3, 5,7,13,14, and 20 compared to SIM and breeds.3.3. QTL and Identification of Candidate Genes within Runs of Homozygosity.
Figure 4
Figure 4
Manhattan plot for SNPs in ROH from the top to bottom (A) BEL, (B) CSI, and (C) BON, with BTA 14 having the most significant SNP in ROH for the three breeds. Manhattan plot for SNPs in ROH from the top to bottom (D) NGU, (E) ANG, and (F) SIM, with ANG having the most significant SNP in ROH on BTA 1,3, 5,7,13,14, and 20 compared to SIM and breeds.3.3. QTL and Identification of Candidate Genes within Runs of Homozygosity.
Figure 5
Figure 5
Inbreeding coefficient at a genomic level for all six breeds.
See this image and copyright information in PMC

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