Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep

Hernández-Montiel, Wilber; Martínez-Núñez, Mario Alberto; Ramón-Ugalde, Julio P.; Román-Ponce, Sergio Iván; Calderón-Chagoya, René; Zamora-Bustillos, Roberto

doi:10.3390/ani10030434

Cited by 47 publications

(31 citation statements)

References 102 publications

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“…Whether this predominant hypermethylation is directly related to or part of several complex mechanisms toward the success of fertilization remains to be studied. Of particular interest for pigs, being a polytocous species, was the hypomethylation found in CLSTN2 , which is a candidate gene for litter size, as determined in sheep using GWAS [ 71 ].…”

Section: Discussionmentioning

confidence: 99%

Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model

Pértille

Álvarez‐Rodríguez

Silva

et al. 2021

IJMS

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A combined Genotyping By Sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) protocol was used to identify—in parallel—genetic variation (Genomic-Wide Association Studies (GWAS) and epigenetic differences of Differentially Methylated Regions (DMR) in the genome of spermatozoa from the porcine animal model. Breeding boars with good semen quality (n = 11) and specific and well-documented differences in fertility (farrowing rate, FR) and prolificacy (litter size, LS) (n = 7) in artificial insemination programs, using combined FR and LS, were categorized as High Fertile (HF, n = 4) or Low Fertile (LF, n = 3), and boars with Unknown Fertility (UF, n = 4) were tested for eventual epigenetical similarity with those fertility-proven. We identified 165,944 Single Nucleotide Polymorphisms (SNPs) that explained 14–15% of variance among selection lines. Between HF and LF individuals (n = 7, 4 HF and 3 LF), we identified 169 SNPs with p ≤ 0.00015, which explained 58% of the variance. For the epigenetic analyses, we considered fertility and period of ejaculate collection (late-summer and mid-autumn). Approximately three times more DMRs were observed in HF than in LF boars across these periods. Interestingly, UF boars were clearly clustered with one of the other HF or LF groups. The highest differences in DMRs between HF and LF experimental groups across the pig genome were located in the chr 3, 9, 13, and 16, with most DMRs being hypermethylated in LF boars. In both HF and LF boars, DMRs were mostly hypermethylated in late-summer compared to mid-autumn. Three overlaps were detected between SNPs (p ≤ 0.0005, n = 1318) and CpG sites within DMRs. In conclusion, fertility levels in breeding males including FR and LS can be discerned using methylome analyses. The findings in this biomedical animal model ought to be applied besides sire selection for andrological diagnosis of idiopathic sub/infertility.

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Section: Discussionmentioning

confidence: 99%

Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model

Pértille

Álvarez‐Rodríguez

Silva

et al. 2021

IJMS

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“…A recent study in pigs reported that intramuscular adipocytes showed dose-dependent serotonin stimulation, which then resulted in decreased fat accumulation in mature adipocytes ( Tada et al, 2020 ). A GWAS in sheep linked a SNP close to htr1e with internal fat content ( Hernández-Montiel et al, 2020 ). In Yan Yellow cattle, RNA-seq analysis revealed a positive role for another serotonin receptor, htr2a , in adipogenesis ( Yun et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus mykiss

et al. 2021

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One of the top priorities of the aquaculture industry is the genetic improvement of economically important traits in fish, such as those related to processing and quality. However, the accuracy of genetic evaluations has been hindered by a lack of data on such traits from a sufficiently large population of animals. The objectives of this study were thus threefold: (i) to estimate genetic parameters of growth-, yield-, and quality-related traits in rainbow trout (Oncorhynchus mykiss) using three different phenotyping technologies [invasive and non-invasive: microwave-based, digital image analysis, and magnetic resonance imaging (MRI)], (ii) to detect quantitative trait loci (QTLs) associated with these traits, and (iii) to identify candidate genes present within these QTL regions. Our study collected data from 1,379 fish on growth, yield-related traits (body weight, condition coefficient, head yield, carcass yield, headless gutted carcass yield), and quality-related traits (total fat, percentage of fat in subcutaneous adipose tissue, percentage of fat in flesh, flesh colour); genotypic data were then obtained for all fish using the 57K SNP Axiom® Trout Genotyping array. Heritability estimates for most of the 14 traits examined were moderate to strong, varying from 0.12 to 0.67. Most traits were clearly polygenic, but our genome-wide association studies (GWASs) identified two genomic regions on chromosome 8 that explained up to 10% of the genetic variance (cumulative effects of two QTLs) for several traits (weight, condition coefficient, subcutaneous and total fat content, carcass and headless gutted carcass yields). For flesh colour traits, six QTLs explained 1–4% of the genetic variance. Within these regions, we identified several genes (htr1, gnpat, ephx1, bcmo1, and cyp2x) that have been implicated in adipogenesis or carotenoid metabolism, and thus represent good candidates for further functional validation. Finally, of the three techniques used for phenotyping, MRI demonstrated particular promise for measurements of fat content and distribution, while the digital image analysis-based approach was very useful in quantifying colour-related traits. This work provides new insights that may aid the development of commercial breeding programmes in rainbow trout, specifically with regard to the genetic improvement of yield and flesh-quality traits as well as the use of invasive and/or non-invasive technologies to predict such traits.

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“…Similarly, in this study, the Protein processing in endoplasmic reticulum (oas04141) KEGG term was identified as a pathway associated with protein metabolism. Both Ovarian steroidogenesis and protein digestion and absorption KEGG pathways have recently been reported in a GWAS study as pathways affecting prolificacy in sheep [ 62 ]. Many signaling KEGG pathways were identified and some of them were related to reproductive processes.…”

Section: Discussionmentioning

confidence: 99%

“…cGMP) to support the oocyte development, metabolism, and hemostasis [ 79 ]. Many genomics, transcriptomics, and proteomics studies reported many pathways related to both cell adhesion and gap junction process as pathways which has vital roles in prolificacy [ 49 , 62 , 77 , 80 , 81 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep

et al. 2021

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Litter size is one of the most important economic traits in sheep. Identification of gene variants that are associated with the prolificacy rate is an important step in breeding program success and profitability of the farm. So, to identify genetic mechanisms underlying the variation in litter size in Iranian Baluchi sheep, a two-step genome-wide association study (GWAS) was performed. GWAS was conducted using genotype data from 91 Baluchi sheep. Estimated breeding values (EBVs) for litter size calculated for 3848 ewes and then used as the response variable. Besides, a pathway analysis using GO and KEGG databases were applied as a complementary approach. A total of three single nucleotide polymorphisms (SNPs) associated with litter size were identified, one each on OAR2, OAR10, and OAR25. The SNP on OAR2 is located within a novel putative candidate gene, Neurotrophic receptor tyrosine kinase 2. This gene product works as a receptor which is essential for follicular assembly, early follicular growth, and oocyte survival. The SNP on OAR25 is located within RAB4A which is involved in blood vessel formation and proliferation through angiogenesis. The SNP on OAR10 was not associated with any gene in the 1Mb span. Moreover, gene-set analysis using the KEGG database identified several pathways, such as Ovarian steroidogenesis, Steroid hormone biosynthesis, Calcium signaling pathway, and Chemokine signaling. Also, pathway analysis using the GO database revealed several functional terms, such as cellular carbohydrate metabolic, biological adhesion, cell adhesion, cell junction, and cell-cell adherens junction, among others. This is the first study that reports the NTRK2 gene affecting litter size in sheep and our study of this gene functions showed that this gene could be a good candidate for further analysis.

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Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep

Cited by 47 publications

References 102 publications

Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model

Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model

Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus mykiss

Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep

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