Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds

Saravanan, K.A.; Panigrahi, Manjit; Kumar, Harshit; Parida, Subhashree; Bhushan, Bharat; Gaur, Gyanendra Kumar; Dutt, Triveni; Mishra, Bishnu Prasad; Singh, Ranvir

doi:10.1016/j.ygeno.2021.02.009

Cited by 60 publications

(62 citation statements)

References 65 publications

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“…In this study, we aimed to investigate genomic evidence of selection signatures in Shanghai Holstein cattle using GGRS data. Two complementary approaches were applied for the detection of selection signatures in the studied population, i.e., the ROH and iHS methods, which should boost the accuracy of detection and eliminate unknown bias [ 26 – 28 ]. Overall, 101 and 18 candidate regions under selection were detected by the iHS approach and ROH estimation, respectively.…”

Section: Discussionmentioning

confidence: 99%

“…Saravanan et al (2021) implemented two complementary approaches viz. iHS and ROH to detect selection signatures for intra-population analyses in Indian cattle [ 28 ]. Pemberton et al (2012) reported that the frequencies of ROH across the genome are correlated with signals of recent positive selection [ 39 ].…”

Section: Discussionmentioning

confidence: 99%

“…Many studies have found that there is a strong time-lagged effect of these female fertility disorders on longevity traits [ 59 ]. Genomic scans for selection signatures revealed that ARFGEF1 is a hallmark gene for milk yield in cattle [ 28 , 60 ].…”

Section: Discussionmentioning

confidence: 99%

“…GOLGA4 was found to be associated with milk yield in many dairy populations [ 69 ]. ITGA9 was identified in a large number of studies on the signature of selection and environmental adaptation to exposure to thermal stress in cattle [ 28 , 70 – 72 ]. According to the study of Makina et al (2015), ADIPOR2 , which is related to reproductive performance, was identified by detecting signatures of selection within and between six cattle breeds in South Africa [ 73 ].…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

et al. 2021

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Background Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behaviour, appearance, and important economic traits of Shanghai Holstein cattle. In particular, the longevity of the Shanghai Holstein cattle population is generally short, approximately the 2nd to 3rd lactation. In this study, two complementary approaches, integrated haplotype score (iHS) and runs of homozygosity (ROH), were applied for the detection of selection signatures within the genome using genotyping by genome-reduced sequence data from 1092 cows. Results In total, 101 significant iHS genomic regions containing selection signatures encompassing a total of 256 candidate genes were detected. There were 27 significant |iHS| genomic regions with a mean |iHS| score > 2. The average number of ROH per individual was 42.15 ± 25.47, with an average size of 2.95 Mb. The length of 78 % of the detected ROH was within the range of 1–2 MB and 2–4 MB, and 99 % were shorter than 8 Mb. A total of 168 genes were detected in 18 ROH islands (top 1 %) across 16 autosomes, in which each SNP showed a percentage of occurrence > 30 %. There were 160 and 167 genes associated with the 52 candidate regions within health-related QTL intervals and 59 candidate regions within reproduction-related QTL intervals, respectively. Annotation of the regions harbouring clustered |iHS| signals and candidate regions for ROH revealed a panel of interesting candidate genes associated with adaptation and economic traits, such as IL22RA1, CALHM3, ITGA9, NDUFB3, RGS3, SOD2, SNRPA1, ST3GAL4, ALAD, EXOSC10, and MASP2. In a further step, a total of 1472 SNPs in 256 genes were matched with 352 cis-eQTLs in 21 tissues and 27 trans-eQTLs in 6 tissues. For SNPs located in candidate regions for ROH, a total of 108 cis-eQTLs in 13 tissues and 4 trans-eQTLs were found for 1092 SNPs. Eighty-one eGenes were significantly expressed in at least one tissue relevant to a trait (P value < 0.05) and matched the 256 genes detected by iHS. For the 168 significant genes detected by ROH, 47 gene-tissue pairs were significantly associated with at least one of the 37 traits. Conclusions We provide a comprehensive overview of selection signatures in Shanghai Holstein cattle genomes by combining iHS and ROH. Our study provides a list of genes associated with immunity, reproduction and adaptation. For functional annotation, the cGTEx resource was used to interpret SNP-trait associations. The results may facilitate the identification of genes relevant to important economic traits and can help us better understand the biological processes and mechanisms affected by strong ongoing natural or artificial selection in livestock populations.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

et al. 2021

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“…Functional analyses of list candidate genes showed a DNA polymerase epsilon ( POLE ) gene potentially associated with reproductive traits [ 73 ]; they might be implicated in milk yield regulation by performing certain biological functions [ 74 ], while our findings suggest that POLE is associated with the bone quality trait.…”

Section: Discussionmentioning

confidence: 96%

Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle

Abdalla

Nazar

et al. 2021

Animals

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Feet and leg conformation traits are considered one of the most important economical traits in dairy cattle and have a great impact on the profitability of milk production. Therefore, identifying the single nucleotide polymorphisms (SNPs), genes and pathways analysis associated with these traits might contribute to the genomic selection and long-term plan selection for dairy cattle. We conducted genome-wide association studies (GWASs) using the fixed and random model circulating probability unification (FarmCPU) method to identify SNPs associated with bone quality, heel depth, rear leg side view and rear leg rear view of Chinese Holstein cows. Phenotypic measurements were collected from 1000 individuals of Chinese Holstein cattle and the GeneSeek Genomic Profiler Bovine 100 K SNP chip was utilized for individual genotyping. After quality control, 984 individual cows and 84,906 SNPs remained for GWAS work; as a result, we identified 20 significant SNPs after Bonferroni correction. Several candidate genes were identified within distances of 200 kb upstream or downstream to the significant SNPs, including ADIPOR2, INPP4A, DNMT3A, ALDH1A2, PCDH7, XKR4 and CADPS. Further bioinformatics analyses showed 34 gene ontology terms and two signaling pathways were significantly enriched (p ≤ 0.05). Many terms and pathways are related to biological quality, metabolism and development processes; these identified SNPs and genes could provide useful information about the genetic architecture of feet and leg traits, thus improving the longevity and productivity of Chinese Holstein dairy cattle.

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Chlamydia abortus OmcB protein is essential for adhesion to host cells

Liang

Liu

et al. 2021

J Basic Microbiol

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Chlamydia abortus (C. abortus) is one of the most important zoonotic pathogens, causing a number of serious diseases. The adhesion of C. abortus to host cells is the first and crucial step in the process of infection. Outer membrane protein 2 (OmcB) is the second most abundant outer membrane protein. It has been shown to be an important adhesin of Chlamydia trachomatis and Chlamydia pneumoniae. In the present study, the OmcB gene of C. abortus was cloned and expressed in Escherichia coli, and the recombinant OmcB protein with His-tag was used to prepare polyclonal antibodies. Infectivity inhibition assays carried out with C. abortus in the presence of recombinant OmcB showed a considerable reduction (∼50%) in infectivity. Using anti-OmcB serum in infectivity inhibition assays resulted in a 30% reduction in infectivity. Anti-OmcB serum and recombinant OmcB protein in infection inhibition assays showed that OmcB is a surface-exposed protein that functions as an adhesin. The constructed deletion variant of the OmcB motif for infection inhibition assays showed that the first XBBXBX motif of the C. abortus OmcB protein is essential for binding to host cells.

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Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds

Cited by 60 publications

References 65 publications

Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle

Chlamydia abortus OmcB protein is essential for adhesion to host cells

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