Genome‐wide scan for runs of homozygosity in the composite Montana Tropical ® beef cattle

2019 ◽  
Vol 137 (2) ◽  
pp. 155-165 ◽  
Author(s):  
Elisa Peripolli ◽  
Nedenia Bonvino Stafuzza ◽  
Sabrina Thaise Amorim ◽  
Marcos Vinícius Antunes Lemos ◽  
Laís Grigoletto ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Runs Of Homozygosity ◽  
Genome Wide ◽  
Genome Wide Scan

scholarly journals Correction to: Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Seyed Mohammad Ghoreishifar ◽  
Hossein Moradi-Shahrbabak ◽  
Mohammad Hossein Fallahi ◽  
Ali Jalil Sarghale ◽  
Mohammad Moradi-Shahrbabak ◽  
...  
Keyword(s):  
Bubalus Bubalis ◽  
River Buffalo ◽  
Runs Of Homozygosity ◽  
Inbreeding Coefficients ◽  
Genome Wide ◽  
Genome Wide Scan

scholarly journals Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Seyed Mohammad Ghoreishifar ◽  
Hossein Moradi-Shahrbabak ◽  
Mohammad Hossein Fallahi ◽  
Ali Jalil Sarghale ◽  
Mohammad Moradi-Shahrbabak ◽  
...  
Keyword(s):  
Bubalus Bubalis ◽  
River Buffalo ◽  
Runs Of Homozygosity ◽  
Inbreeding Coefficients ◽  
Genome Wide ◽  
Genome Wide Scan

scholarly journals Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods

PLoS ONE ◽  
2013 ◽  
Vol 8 (5) ◽  
pp. e64280 ◽  
Author(s):  
Yuri Tani Utsunomiya ◽  
Ana Maria Pérez O’Brien ◽  
Tad Stewart Sonstegard ◽  
Curtis Paul Van Tassell ◽  
Adriana Santana do Carmo ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Positive Selection ◽  
Recent Positive Selection ◽  
Genome Wide ◽  
Genome Wide Scan

scholarly journals Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

2017 ◽  
Vol 49 (1) ◽  
Author(s):  
Salvatore Mastrangelo ◽  
Marco Tolone ◽  
Maria T. Sardina ◽  
Gianluca Sottile ◽  
Anna M. Sutera ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Local Adaptation ◽  
Potential Candidate ◽  
Runs Of Homozygosity ◽  
Genome Wide ◽  
Genome Wide Scan

scholarly journals Genome-wide scan for runs of homozygosity identifies potential candidate regions associated with growth traits in beef cattle

2020 ◽  
Author(s):  
Guoyao Zhao ◽  
Tianliu Zhang ◽  
Yuqiang Liu ◽  
Zezhao Wang ◽  
Lei Xu ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Traits ◽  
Farm Animals ◽  
Valuable Insight ◽  
Potential Candidate ◽  
Cattle Population ◽  
Runs Of Homozygosity ◽  
Genome Wide ◽  
Candidate Regions

Abstract Background: Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of regions of the genome lead 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 growth traits in a commercial beef cattle population.Results: We identified a total of 29,271 ROH segments with an average number of 63.36 and an average length of 0.98 Mb in this commercial beef cattle population, representing ~2.53% (~63.36Mb) of the genome. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events identified across all individuals. Of these, nine regions were significantly associated with six growth phenotype traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, carcass length; P<0.01), which contain 187 candidate genes. Furthermore, we found 26 consensus ROH regions with frequencies exceeding 10%, and several of these consensus overlapped with QTLs which are associated with weight gain, calving difficulty and stillbirth. To precisely locate locus within each ROH for every studied trait, we further utilized loci-based methods for association analysis among these identified regions. Totally, we obtained 9,360 loci within ROH, and 1,631 loci displaying significant association (P<0.01) for eight traits. In addition, we found that 67 genes embedded with homozygous loci. Several identified candidate genes, including EBF2, SLC20A2, SH3BGRL2, HMGA1 and ACSL1, were related to growth traits.Conclusions: This study assessed genome-wide autozygosity pattern and inbreeding level in a commercial beef cattle population. Our study identified many candidate regions and genes with ROH for growth traits in beef cattle, which can provide important insights into investigating homozygosity across genome in other farm animals. Our findings may further be unitized to assist the design of selection mating strategy.

scholarly journals Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 524 ◽  
Author(s):  
Sangang He ◽  
Jiang Di ◽  
Bing Han ◽  
Lei Chen ◽  
Mingjun Liu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Average Length ◽  
Inbreeding Coefficient ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Genotyping Array ◽  
Genome Region ◽  
Genome Wide ◽  
Genomic Regions ◽  
Genome Wide Scan

In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.

scholarly journals Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs

2021 ◽  
Author(s):  
Xudong Wu ◽  
Ren Zhou ◽  
Wei Zhang ◽  
Bangji Cao ◽  
Jing Xia ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Runs Of Homozygosity ◽  
Genome Wide ◽  
Genome Wide Scan

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

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1425 ◽  
Author(s):  
Guoyao Zhao ◽  
Tianliu Zhang ◽  
Yuqiang Liu ◽  
Zezhao Wang ◽  
Lei Xu ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Complex Traits ◽  
Average Length ◽  
Body Height ◽  
Reproductive Traits ◽  
Valuable Insight ◽  
Runs Of Homozygosity ◽  
Genome Wide ◽  
Candidate Regions

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.

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