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

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 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 genes associated with local adaptation in Valle del Belice sheep

Genetics Selection Evolution ◽

10.1186/s12711-017-0360-z ◽

2017 ◽

Vol 49 (1) ◽

Cited By ~ 35

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

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

BMC Genomics ◽

10.1186/s12864-021-07992-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Guoyao Zhao ◽

Yuqiang Liu ◽

Qunhao Niu ◽

Xu Zheng ◽

Tianliu Zhang ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Average Length ◽

Snp Array ◽

Reproductive Traits ◽

Farm Animals ◽

Production Traits ◽

Runs Of Homozygosity ◽

Exact Test ◽

Genomic Regions

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 Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽

10.3390/ani11010192 ◽

2021 ◽

Vol 11 (1) ◽

pp. 192

Author(s):

Xinghai Duan ◽

Bingxing An ◽

Lili Du ◽

Tianpeng Chang ◽

Mang Liang ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Growth Curve ◽

Growth And Development ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Coefficient Of Determination ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

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Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep

Genetics Selection Evolution ◽

10.1186/s12711-021-00649-8 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Bingru Zhao ◽

Hanpeng Luo ◽

Xixia Huang ◽

Chen Wei ◽

Jiang Di ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Genetic Improvement ◽

Genome Wide Association Study ◽

Growth Traits ◽

Fibre Diameter ◽

Single Step ◽

Genome Wide Association ◽

Six Traits ◽

Genome Wide

Abstract Background Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). Results Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from − 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. Conclusions Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.

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Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

Scientific Reports ◽

10.1038/s41598-021-85921-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Raju Bheemanahalli ◽

Montana Knight ◽

Cherryl Quinones ◽

Colleen J. Doherty ◽

S. V. Krishna Jagadish

Keyword(s):

Grain Size ◽

Candidate Genes ◽

Gene Network ◽

Genome Wide Association ◽

Potential Candidate ◽

Genetic Loci ◽

Stay Green ◽

Yield And Quality ◽

Genome Wide ◽

Wide Range

AbstractHigh night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

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Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

Scientific Reports ◽

10.1038/s41598-021-91373-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lili Du ◽

Tianpeng Chang ◽

Bingxing An ◽

Mang Liang ◽

Xinghai Duan ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Molecular Mechanism ◽

Meat Quality ◽

Relevant Literature ◽

Transcriptome Profiling ◽

Water Holding Capacity ◽

Potential Candidate ◽

Protein Protein Interaction ◽

Water Holding

AbstractWater holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

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