Characterization of biological pathways associated with semen traits in the Thai multibreed dairy population

Sarakul, Mattaneeya; Elzo, Mauricio A.; Koonawootrittriron, Skorn; Suwanasopee, Thanathip; Jattawa, Danai; Laodim, Thawee

doi:10.1016/j.anireprosci.2018.09.002

Cited by 9 publications

(7 citation statements)

References 64 publications

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“…We identified variants among genesUCP2, TLE3, PAXIP1,CFAP6, DRD2, IFT140, TET,FER1l5, CCDC9, DNAJB13, TDRD with previously reported relation to functional traits like,sperm motility, spermatogenesis,capacitation and sterility [13-23]in low ejaculate rejection rate group. Similarly in high ejaculate rejection rate group genes like ADAM20, NPAS2, RYR3, DEFB124, TDRD9, TGFβ, SOX5 and SOX6 related tosperm motility, capacitation, sterility, immunotolerance of sperm, maturation of spermatozoa immune defense system of the reproductive system [24][25][26][27][28][29][30] were observed. Few genetic variants among genes likeADAM, AK7, ARID4B, CCDC9, CSMD1, DEFB124, DENND1B, DNAJB13, DRD2, FER1L5, PAX1p1, REC8, RYR3, TDRD9, TPCN1 and WDFY with previously reported relation to Male Fertility,Apoptosis, Immuno-tolerance, Sperm Motility, Capacitation and Spermatogenesis [31][32][33][34][35][36][37]were observed to be shared between both low and high ejaculate rejection rate bulls of both breeds under study.…”

Section: Discussionmentioning

confidence: 99%

Exome sequencing identifies variants associated with semen quality in Holstein Friesian and Hallikar bulls

Kunnath

Ramesha

Kataktalware

et al. 2022

Preprint

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Effective fertility of bulls is dependent on semen quality, often determined based on standard semen evaluation tests. Here we report Whole Exome Sequencing (WES) of 12 bulls from two breeds Holstien Friesian and Hallikar selected based on Ejaculate Rejection Rate (ERR). We explored the possibility of identifying genetic variants from the conserved protein coding regions of genome. A total of 10,510 SNPs and 10.236 INDELs were identified post alignment against reference genome (ARS-UCD 1.2) and were annotated using SnpEff. The number of variants with high and modifier functional impact detected were 145 and 19,122, respectively. Genetic variants common to both high and low ERR group bulls among Holstein Friesian were 08 and in Hallikar the common variants were 51. Prominent genesviz. UCP2, PANK2, GPD2, PTPRG, LARP7, EZH1, DENND1B and TDRD9 with a role in determining the semen quality were observed to be carriers of the genetic variant.

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Section: Discussionmentioning

confidence: 99%

Exome sequencing identifies variants associated with semen quality in Holstein Friesian and Hallikar bulls

Kunnath

Ramesha

Kataktalware

et al. 2022

Preprint

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“…Bull identification, collection date and time, ejaculation number, ambient temperature (in degrees Celsius), and the name of the collector were recorded during each semen collection. For a comprehensive description of these traits, please refer to Sarakul et al [ 13 ].…”

Section: Methodsmentioning

confidence: 99%

A comparison of five sets of overlapping and non-overlapping sliding windows for semen production traits in the Thai multibreed dairy population

Sarakul,

Elzo,

Koonawootrittriron

et al. 2024

Anim Biosci

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Objective: This study compared five distinct sets of biological pathways and associated genes related to semen volume (VOL), number of sperm (NS), and sperm motility (MOT) in the Thai multibreed dairy population.Methods: The phenotypic data included 13,533 VOL records, 12,773 NS records, and 12,660 MOT records from 131 bulls. The genotypic data consisted of 76,519 imputed and actual single nucleotide polymorphisms (SNPs) from 72 animals. The SNP additive genetic variances for VOL, NS, and MOT were estimated for SNP windows of one SNP (SW1), ten SNP (SW10), 30 SNP (SW30), 50 SNP (SW50), and 100 SNP (SW100) using a single-step genomic best linear unbiased prediction approach. The fixed effects in the model were contemporary group, ejaculate order, bull age, ambient temperature, and heterosis. The random effects accounted for animal additive genetic effects, permanent environment effects, and residual. The SNPs explaining at least 0.001% of the additive genetic variance in SW1, 0.01% in SW10, 0.03% in SW30, 0.05% in SW50, and 0.1% in SW100 were selected for gene identification through the NCBI database. The pathway analysis utilized genes associated with the identified SNP windows.Results: Comparison of overlapping and non-overlapping SNP windows revealed notable differences among the identified pathways and genes associated with the studied traits. Overlapping windows consistently yielded a larger number of shared biological pathways and genes than non-overlapping windows. In particular, overlapping SW30 and SW50 identified the largest number of shared pathways and genes in the Thai multibreed dairy population.Conclusion: This study yielded valuable insights into the genetic architecture of VOL, NS, and MOT. It also highlighted the importance of assessing overlapping and non-overlapping SNP windows of various sizes for their effectiveness to identify shared pathways and genes influencing multiple traits.

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“…According to the database for annotation, visualization and integrated discovery (DAVI D), SSH2 is involved in the regulation of the actin cytoskeleton pathway and in several other molecular and biological functions such as the regulation of actin polymerization or depolymerization and DNA binding. In previous studies, SSH2 was associated with somatic cell score and semen traits in cattle [84,85]. Bouwman et al [42] identified several SNP on BTA19 associated with cattle stature, including rs132693733 (19:21339030), rs109018020 (19:23816722) and rs137732346 (19:25980624).…”

Section: Multi-breed Gwas For Conformation Traits and Functional Annomentioning

confidence: 96%

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

et al. 2020

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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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Characterization of biological pathways associated with semen traits in the Thai multibreed dairy population

Cited by 9 publications

References 64 publications

Exome sequencing identifies variants associated with semen quality in Holstein Friesian and Hallikar bulls

Exome sequencing identifies variants associated with semen quality in Holstein Friesian and Hallikar bulls

A comparison of five sets of overlapping and non-overlapping sliding windows for semen production traits in the Thai multibreed dairy population

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

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