Genetics and genomics of reproductive disorders in Canadian Holstein cattle

Guarini, A.R.; Lourenço, Daniela; Brito, Luiz F.; Sargolzaei, Mehdi; Baes, C.F.; Miglior, F.; Misztal, I.; Schenkel, F.S.

doi:10.3168/jds.2018-15038

Cited by 50 publications

(50 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…We also found two genes (CTNNBIP1 and NMNAT1) to be related to reproductive efficiency. CTNNBIP1 has been previously reported to be related to prenatal death in Nordic Red [64] and retained placenta in Canadian Holstein dairy cows [65]. NMNAT1 was found to affect age at first calving in Nellore cattle [66], and this gene was also implicated in influencing the female reproductive efficiency in cattle [67].…”

Section: Discussionmentioning

confidence: 91%

Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

Zhao

Zhang

Liu

et al. 2020

Animals

View full text Add to dashboard Cite

Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of ROH leading to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with important traits in Chinese Wagyu beef cattle. We identified a total of 29,271 ROH segments from 462 animals. Within each animal, an average number of ROH was 63.36 while an average length was 62.19 Mb. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events across all individuals. Of these, nine regions containing 154 candidate genes, were significantly associated with six traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, and carcass length; p < 0.01). Moreover, we found 26 consensus ROH regions with frequencies exceeding 10%, and several regions overlapped with QTLs, which are associated with body weight, calving ease, and stillbirth. Among them, we observed 41 candidate genes, including BCKDHB, MAB21L1, SLC2A13, FGFR3, FGFRL1, CPLX1, CTNNA1, CORT, CTNNBIP1, and NMNAT1, which have been previously reported to be related to body conformation, meat quality, susceptibility, and reproductive traits. In summary, we assessed genome-wide autozygosity patterns and inbreeding levels in Chinese Wagyu beef cattle. Our study identified many candidate regions and genes overlapped with ROH for several important traits, which could be unitized to assist the design of a selection mating strategy in beef cattle.

show abstract

Section: Discussionmentioning

confidence: 91%

Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

Zhao

Zhang

Liu

et al. 2020

Animals

View full text Add to dashboard Cite

show abstract

“…The WssGBLUP has been successfully applied to several genomic prediction studies (Zhang et al, 2016;Lourenco et al, 2017;Guarini et al, 2019). However, to our best knowledge, there are no reports evaluating the prediction ability of WssGBLUP in crossbred animals, especially in F1 populations.…”

Section: Introductionmentioning

confidence: 99%

Comparing Alternative Single-Step GBLUP Approaches and Training Population Designs for Genomic Evaluation of Crossbred Animals

et al. 2020

View full text Add to dashboard Cite

As crossbreeding is extensively used in some livestock species, we aimed to evaluate the performance of single-step GBLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) methods to predict Genomic Estimated Breeding Values (GEBVs) of crossbred animals. Different training population scenarios were evaluated: (SC1) ssGBLUP based on a single-trait model considering purebred and crossbred animals in a joint training population; (SC2) ssGBLUP based on a multiple-trait model to enable considering phenotypes recorded in purebred and crossbred training animals as different traits; (SC3) WssGBLUP based on a single-trait model considering purebred and crossbred animals jointly in the training population (both populations were used for SNP weights' estimation); (SC4) WssGBLUP based on a single-trait model considering only purebred animals in the training population (crossbred population only used for SNP weights' estimation); (SC5) WssGBLUP based on a single-trait model and the training population characterized by purebred animals (purebred population used for SNP weights' estimation). A complex trait was simulated assuming alternative genetic architectures. Different scaling factors to blend the inverse of the genomic (G −1 ) and pedigree (A −1 22 ) relationship matrices were also tested. The predictive performance of each scenario was evaluated based on the validation accuracy and regression coefficient. The genetic correlations across simulated populations in the different scenarios ranged from moderate to high (0.71-0.99). The scenario mimicking a completely polygenic trait (h 2 QTL = 0) yielded the lowest validation accuracy (0.12; for SC3 and SC4). The simulated scenarios assuming 4,500 QTLs affecting the trait and h 2 QTL = h 2 resulted in the greatest GEBV accuracies (0.47; for SC1 and SC2). The regression coefficients ranged from 0.28 (for SC3 assuming polygenic effect) to 1.27 (for SC2 considering 4,500 QTLs). In general, SC3 and SC5 resulted in inflated GEBVs, whereas other scenarios yielded deflated GEBVs. The scaling factors used to combine G −1 and A −1 22 had a small influence on the validation accuracies, but a greater effect on the regression coefficients. Due to the complexity of multiple-trait models Alvarenga et al. ssGBLUP Approaches for Crossbred Evaluation and WssGBLUP analyses, and a similar predictive performance across the methods evaluated, SC1 is recommended for genomic evaluation in crossbred populations with similar genetic structures [moderate-to-high (0.71-0.99) genetic correlations between purebred and crossbred populations].

show abstract

“…PIK3R1 , ITK and TMEM173 were identified as potential positional candidate genes associated with infection of Mycobacterium avium subspecies paratuberculosis in cattle [ 40 – 42 ]. A study reported that the MTSS1 was related to metritis in cattle [ 43 ]. Guangxi Zhuang Autonomous Region undergoes characteristic subtropical monsoon climate with hot and humid summers and dry and mild winters, which provides an environment for the spread of disease.…”

Section: Discussionmentioning

confidence: 99%

Selection signatures of Fuzhong Buffalo based on whole-genome sequences

et al. 2020

View full text Add to dashboard Cite

Background Fuzhong buffalo, a native breed of Guangxi Zhuang Autonomous Region, is traditionally used as a draft animal to provide farm power in the rice cultivation. In addition, the Fuzhong buffalo also prepared for the bullfighting festival organized by the locals. The detection of the selective signatures in its genome can help in elucidating the selection mechanisms in its stamina and muscle development of a draft animal. Results In this study, we analyzed 27 whole genomes of buffalo (including 15 Fuzhong buffalo genomes and 12 published buffalo genomes from Upper Yangtze region). The ZHp, ZFst, π-Ratio, and XP-EHH statistics were used to identify the candidate signatures of positive selection in Fuzhong buffalo. Our results detected a set of candidate genes involving in the pathways and GO terms associated with the response to exercise (e.g., ALDOA, STAT3, AKT2, EIF4E2, CACNA2D2, TCF4, CDH2), immunity (e.g., PTPN22, NKX2-3, PIK3R1, ITK, TMEM173), nervous system (e.g., PTPN21, ROBO1, HOMER1, MAGI2, SLC1A3, NRG3, SNAP47, CTNNA2, ADGRL3). In addition, we also identified several genes related to production and growth traits (e.g., PHLPP1, PRKN, MACF1, UCN3, RALGAPA1, PHKB, PKD1L). Our results depicted several pathways, GO terms, and candidate genes to be associated with response to exercise, immunity, nervous system, and growth traits. Conclusions The selective sweep analysis of the Fuzhong buffalo demonstrated positive selection pressure on potential target genes involved in behavior, immunity, and growth traits, etc. Our findings provided a valuable resource for future research on buffalo breeding and an insight into the mechanisms of artificial selection.

show abstract

Genetics and genomics of reproductive disorders in Canadian Holstein cattle

Cited by 50 publications

References 66 publications

Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

Comparing Alternative Single-Step GBLUP Approaches and Training Population Designs for Genomic Evaluation of Crossbred Animals

Selection signatures of Fuzhong Buffalo based on whole-genome sequences

Contact Info

Product

Resources

About