Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

Abstract Background Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. Results We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher’s exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. Conclusions Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.

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

Animals ◽

10.3390/ani10081425 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1425 ◽

Cited By ~ 1

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

10.21203/rs.3.rs-17425/v1 ◽

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.

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

Animals ◽

10.3390/ani10030524 ◽

2020 ◽

Vol 10 (3) ◽

pp. 524 ◽

Cited By ~ 3

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.

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Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes in Three Pig Breeds

Animals ◽

10.3390/ani9080518 ◽

2019 ◽

Vol 9 (8) ◽

pp. 518 ◽

Cited By ~ 11

Author(s):

Xie ◽

Shi ◽

Liu ◽

Deng ◽

Wang ◽

...

Keyword(s):

Candidate Genes ◽

Target Genes ◽

Average Length ◽

Reproductive Traits ◽

Genomic Region ◽

Inbreeding Coefficient ◽

Runs Of Homozygosity ◽

Pig Breeds ◽

Yorkshire Pigs ◽

The Difference

Runs of homozygosity (ROH) are contiguous homozygous genotype segments in the genome that are present in an individual since the identical haplotypes are inherited from each parent. The aim of this study was to investigate the frequency and distribution of ROH in the genomes of Landrace, Songliao black and Yorkshire pigs. We calculated two types of genome inbreeding coefficients and their correlation, including the inbreeding coefficient based on ROH (FROH) and the inbreeding coefficient based on the difference between the observed and expected number of homozygous genotypes (FHOM). Furthermore, we identified candidate genes in the genomic region most associated with ROH. We identified 21,312 ROH in total. The average number of ROH per individual was 32.99 ± 0.38 and the average length of ROH was 6.40 ± 0.070 Mb in the three breeds. The FROH results showed that Yorkshire pigs exhibited the highest level of inbreeding (0.092 ± 0.0015) and that Landrace pigs exhibited the lowest level of inbreeding (0.073 ± 0.0047). The average correlation between FROH and FHOM was high (0.94) within three breeds. The length of ROH provides insight into the inbreeding history of these three pig breeds. In this study, Songliao black pigs presented a higher frequency and average length of long ROH (>40 Mb) compared with those of Landrace and Yorkshire pigs, which indicated greater inbreeding in recent times. Genes related to reproductive traits (GATM, SPATA46, HSD17B7, VANGL2, DAXX, CPEB1), meat quality traits (NR1I3, APOA2, USF1) and energy conversion (NDUFS2) were identified within genomic regions with a high frequency of ROH. These genes could be used as target genes for further marker-assisted selection and genome selection.

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Identification of Candidate Genomic Regions for Chicken Egg Production Traits Based on Genome Wide Association Study

10.21203/rs.3.rs-148037/v1 ◽

2021 ◽

Author(s):

Xiurong Zhao ◽

Changsheng Nie ◽

Jinxin Zhang ◽

Xinghua Li ◽

Tao Zhu ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Egg Production ◽

Genome Wide Association Study ◽

Reproductive Traits ◽

Genome Wide Association ◽

Production Traits ◽

Genome Wide ◽

Chicken Breeds ◽

Genomic Regions

Abstract Background: Since the domestication of chicken, various chicken breeds have been developed for food production, entertainment, and so on. Compared to indigenous chicken breeds which generally do not show elite production performance, commercial breeds or lines are selected intensely for meat or egg production. In the present study, in order to understand the molecular mechanisms underlying the dramatic egg yielding differences between commercial egg-type chickens and indigenous chickens, we performed a genome-wide association study (GWAS) in a mixed linear model. Results: We obtained 148 single nucleotide polymorphisms (SNPs) associated with egg production traits or reproductive traits (57 significantly, 91 suggestively). Among them, 18 SNPs overlapped with previously reported quantitative trait loci (QTL), including 13 for egg production and 5 for reproductive traits. Three SNPs were significantly associated with multiple egg production traits, such as egg number, age at first egg, and egg production rate in chickens. Furthermore, we identified 32 candidate genes based on the function of the screened genes. These genes were found to be mainly involved in regulating hormones, playing a role in the formation, growth, and development of follicles, and in the development of the reproductive system. Some genes such as NELL2, KITLG, GHRHR, NCOA1, ITPR1, GAMT, and CAMK4 deserve our attention and further study since they have been reported to be closely related to reproductive traits. In addition, the most significant genomic region obtained in this study was located at 48.61-48.84Mb on GGA5. In this region, we have repeatedly annotated four genes, in which YY1 and WDR25 have been shown to be related to oocytes and reproductive tissues, respectively, which implies that this region may be a candidate region underlying egg production traits. Conclusion: Our study utilized the genomic information from various chicken breeds or populations differed in egg production to understand the molecular genetic mechanisms involved in reproduction traits. We identified a series of SNPs, candidate genes, or genomic regions that associated with reproductive traits, which could help us in developing egg production in chickens.

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Candidate genes for production traits in Nelore beef cattle

Genetics and Molecular Research ◽

10.4238/2012.september.19.1 ◽

2012 ◽

Vol 11 (4) ◽

pp. 4138-4144 ◽

Cited By ~ 5

Author(s):

P.C. Tizioto ◽

S.L. Meirelles ◽

R.R. Tulio ◽

A.N. Rosa ◽

M.M. Alencar ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Production Traits

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Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

Genes ◽

10.3390/genes10110938 ◽

2019 ◽

Vol 10 (11) ◽

pp. 938 ◽

Cited By ~ 4

Author(s):

Islam ◽

Li ◽

Liu ◽

Berihulay ◽

Abied ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Positive Selection ◽

Candidate Genes ◽

Runs Of Homozygosity ◽

Selection Signatures ◽

Effective Population ◽

Signature Of Selection ◽

Genomic Regions ◽

Insight Into

: Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.

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Mapping genomic regions for reproductive traits in beef cattle: Inclusion of the X chromosome

Reproduction in Domestic Animals ◽

10.1111/rda.13810 ◽

2020 ◽

Vol 55 (11) ◽

pp. 1650-1654 ◽

Cited By ~ 1

Author(s):

Iara Del Pilar Solar Diaz ◽

Gregório Miguel Ferreira de Camargo ◽

Valdecy Aparecida Rocha da Cruz ◽

Isis da Costa Hermisdorff ◽

Caio Victor Damasceno Carvalho ◽

...

Keyword(s):

Beef Cattle ◽

X Chromosome ◽

Reproductive Traits ◽

Genomic Regions

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Candidate genes for male and female reproductive traits in Canchim beef cattle

Journal of Animal Science and Biotechnology ◽

10.1186/s40104-017-0199-8 ◽

2017 ◽

Vol 8 (1) ◽

Cited By ~ 13

Author(s):

Marcos Eli Buzanskas ◽

Daniela do Amaral Grossi ◽

Ricardo Vieira Ventura ◽

Flavio Schramm Schenkel ◽

Tatiane Cristina Seleguim Chud ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Reproductive Traits ◽

Male And Female ◽

Female Reproductive Traits

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Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs

Genes ◽

10.3390/genes11050577 ◽

2020 ◽

Vol 11 (5) ◽

pp. 577

Author(s):

Huiwen Zhan ◽

Saixian Zhang ◽

Kaili Zhang ◽

Xia Peng ◽

Shengsong Xie ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Population Size ◽

Effective Population Size ◽

Average Length ◽

The Other ◽

Runs Of Homozygosity ◽

Effective Population ◽

Inbreeding Coefficients ◽

Genome Wide ◽

Genomic Regions

Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.

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