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

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 Wannan Black pigs

Animal Bioscience ◽

10.5713/ab.20.0679 ◽

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

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

Journal of Animal Breeding and Genetics ◽

10.1111/jbg.12428 ◽

2019 ◽

Vol 137 (2) ◽

pp. 155-165 ◽

Cited By ~ 3

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

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138. GENOME-WIDE LINKAGE SCAN FOR FAMILIAL DIZYGOTIC TWINNING

Reproduction Fertility and Development ◽

10.1071/srb10abs138 ◽

2010 ◽

Vol 22 (9) ◽

pp. 56

Author(s):

J. N. Painter ◽

G. Willemsen ◽

D. R. Nyholt ◽

C. Hoekstra ◽

D. Duffy ◽

...

Keyword(s):

Candidate Genes ◽

Complex Trait ◽

Potential Candidate ◽

Chromosome 2 ◽

Family Work ◽

Linkage Analyses ◽

Genome Wide ◽

A Genome ◽

The Usa ◽

Genetic And Environmental Factors

The tendency to conceive dizygotic (DZ) twins is a complex trait influenced by genetic and environmental factors. To search for new candidate loci for twinning we have conducted a genome-wide linkage scan in 525 families using microsatellite and single nucleotide polymorphism (SNP) marker panels. Non-parametric linkage analyses including 523 families containing a total of 1115 mothers of DZ twins (MODZT) from Australia and New Zealand (ANZ) and The Netherlands (NL) produced four linkage peaks above the threshold for suggestive linkage, including a highly suggestive peak at the extreme telomeric end of chromosome 6 with an exponential (exp)LOD score of 2.813 (P = 0.0002). Since the DZ twinning rate increases steeply with maternal age independent of genetic effects, we also investigated linkage including only families where at least one MODZT gave birth to her first set of twins before the age of 30. These analyses produced a maximum expLOD score of 2.718 (p = 0.0002), largely due to linkage signal from the ANZ cohort, however, ordered subset analyses indicated this result is most likely a chance finding in the combined dataset. Linkage analyses were also performed for two large DZ twinning families from the USA, one of which produced a peak on chromosome 2 in the region of two potential candidate genes. Sequencing of FSHR and FIGLA, along with INHBB in MODZTs from two large NL families with family-specific linkage peaks directly over this gene, revealed a potentially functional variant in the 5’ untranslated region of FSHR that segregated with the DZ twinning phenotype in the UT family. Work is continuing screening candidate genes. Our data provide further evidence for complex inheritance of familial DZ twinning.

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A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

BMC Genomics ◽

10.1186/s12864-020-07170-0 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Sèyi Fridaïus Ulrich Vanvanhossou ◽

Carsten Scheper ◽

Luc Hippolyte Dossa ◽

Tong Yin ◽

Kerstin Brügemann ◽

...

Keyword(s):

Immune Response ◽

Candidate Genes ◽

Feed Efficiency ◽

Morphological Traits ◽

Carcass Traits ◽

Potential Candidate ◽

Adaptive Traits ◽

Morphometric Traits ◽

Indigenous Cattle ◽

Genome Wide

Abstract Background Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. Results SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). Conclusions Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

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