Identification of genomic regions related to age at first calving and first calving interval in water buffalo using single‐step GBLUP

Neto, Francisco Ribeiro de Araujo; Takada, Luciana; Santos, Daniel Jordan de Abreu; Aspilcueta-Borquis, Rusbel Raúl; Cardoso, Diércles Francisco; Nascimento, André Vieira do; Leão, Karen Martins; Oliveira, Henrique Nunes de; Tonhati, Humberto

doi:10.1111/rda.13811

Cited by 16 publications

(6 citation statements)

References 34 publications

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“…These genes were previously reported to be F I G U R E 1 Genome-wide distribution of selection signatures in native Turkish and cosmopolitan cattle breeds by integrated haplotype score (iHS; the red line indicates the threshold of top 0.1% SNPs in each breed). associated with Evans syndrome (TTP2) and economically important traits such as meat yield (DIAPH3 and METTL21C), meat quality (ZNF24 and ZNF397) as well as the first calving interval (ZSCAN30) in numerous mammalian species (Damon et al, 2012;de Araujo Neto et al, 2020;Jerez-Timaure et al, 2019;Lee et al, 2017;Lim et al, 2013;Stepensky et al, 2015). Indeed, as reby Demir et al (2021) native Turkish cattle breeds cannot compete with cosmopolitan cattle breeds in terms of economically important traits, while they are Similarly, some strong selection signatures were also detected by different approaches in previous studies.…”

Section: Discussionmentioning

confidence: 98%

Genome‐wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye

Demir,

Moravčíková,

Kaya

et al. 2023

Animal Genetics

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Via long‐term natural and artificial selection pressure, homozygosity may extend across the genome, leaving genomic patterns called selection signatures. This study is the first attempt to assess genome‐wide selection signatures in six native Turkish and two cosmopolitan cattle breeds by 211.119 bi‐allelic SNPs recovered using the double digest restriction associated DNA sequencing method. The integrated haplotype score (iHS) statistic was utilised to reveal selection signatures within populations, whereas the cross‐population extended haplotype homozygosity (XP‐EHH) and fixation index (FST) approaches were preferred to reveal differently fixed genomic regions between native Turkish and cosmopolitan cattle breeds. Selection signatures in 142 genomic regions containing 305 genes were detected within eight cattle breeds by iHS statistics. The XP‐EHH and FST approaches revealed that 197 and 114 SNPs were under selection pressure, respectively, which overlapped with 144 and 190 genes, respectively. A total of 18 genes were detected by at least two approaches. Six genes related to disease resistance (TTP2), meat yield (DIAPH3 and METTL21C), meat quality (ZNF24 and ZNF397) and first calving interval (ZSCAN30) turned out to be differently fixed between native Turkish and cosmopolitan cattle breeds, as they were identified by both XP‐EHH and FST approaches. In addition, the iHS approach revealed that eight genes associated with visual modality (LSGN), olfaction (MOXD2, OR4C1F and OR4C1F), and immune response (TRBV3‐1 and CLDN10) were under selection pressure in both native and cosmopolitan cattle breeds. Owing to their being significantly related to survival traits, these regions may have played a key role in cattle genome evolution. Future studies utilising denser genetic data are required to obtain deeper knowledge on effects of natural and artificial selection in Anatolian cattle breeds. © 2023 Stichting International Foundation for Animal Genetics.

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Section: Discussionmentioning

confidence: 98%

Genome‐wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye

Demir,

Moravčíková,

Kaya

et al. 2023

Animal Genetics

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“…Another region on chromosome 3 contains DAPK1 (death-associated protein kinase 1), CTSL (cathepsin L), and FBP2 (fructose bisphophatase 2) genes, which are involved in various metabolic processes such as immunity and milk production ( Vineeth et al, 2019 ; Guan et al, 2020 ). The KCNF1 (potassium voltage-gated channel modifier subfamily F member 1) gene on chromosome 12 has been previously reported to be associated with fertility traits in buffaloes ( de Araujo Neto et al, 2020 ). Another candidate region spanning 280 kb on chromosome 1, which was detected by both approaches, contains PDE9A gene (phosphodiesterase 9A).…”

Section: Discussionmentioning

confidence: 99%

Comparative Signatures of Selection Analyses Identify Loci Under Positive Selection in the Murrah Buffalo of India

et al. 2021

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India is home to a large and diverse buffalo population. The Murrah breed of North India is known for its milk production, and it has been used in breeding programs in several countries. Selection signature analysis yield valuable information about how the natural and artificial selective pressures have shaped the genomic landscape of modern-day livestock species. Genotype information was generated on six buffalo breeds of India, namely, Murrah, Bhadawari, Mehsana, Pandharpuri, Surti, and Toda using ddRAD sequencing protocol. Initially, the genotypes were used to carry out population diversity and structure analysis among the six breeds, followed by pair-wise comparisons of Murrah with the other five breeds through XP-EHH and FST methodologies to identify regions under selection in Murrah. Admixture results showed significant levels of Murrah inheritance in all the breeds except Pandharpuri. The selection signature analysis revealed six regions in Murrah, which were identified in more than one pair-wise comparison through both XP-EHH and FST analyses. The significant regions overlapped with QTLs for milk production, immunity, and body development traits. Genes present in these regions included SLC37A1, PDE9A, PPBP, CXCL6, RASSF6, AFM, AFP, ALB, ANKRD17, CNTNAP2, GPC5, MYLK3, and GPT2. These genes emerged as candidates for future polymorphism studies of adaptability and performance traits in buffaloes. The results also suggested ddRAD sequencing as a useful cost-effective alternative for whole-genome sequencing to carry out diversity analysis and discover selection signatures in Indian buffalo breeds.

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“…On BTA25, the mitogen-activated protein kinase 3 (MAPK3), septin 14 (SEPTIN14), and poly(A) polymerase beta (PAPOLB) were found to regulate ovulation in mice [118], spermatogenesis in humans [119], and spermatogenesis in mice [120], respectively. Other suggestive candidate genes included the synaptophysin like 1 (SYPL1) on BTA4 contributing to sperm maturation in sheep [121], multiple EGF like domains 11 (MEGF11) on BTA10 associated with lifetime productivity in pigs [122], fucosyltransferase 8 (FUT8) on BTA10 differentially expressed between matured oocytes from older and younger women [123], myelin transcription factor 1 (MYT1) on BTA13 involved in reduced fertility of anovular dairy cows [124], Rho guanine nucleotide exchange factor 3 (ARHGEF3) on BTA22 associated with number of piglets weaned [125], monoglyceride lipase (MGLL) on BTA22 influencing metabolism of endocannabinoids in bovine endometrium [126], NEDD4 like E3 ubiquitin protein ligase (NEDD4L) on BTA24 associated with AFC in buffaloes [127], and BCL2 apoptosis regulator (BCL2) on BTA24 influencing oocyte and early embryo survival in humans [128].…”

Section: Qtl and Candidate Genes Found For Sire Traitsmentioning

confidence: 99%

Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes

et al. 2022

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Background Genetic progress for fertility and reproduction traits in dairy cattle has been limited due to the low heritability of most indicator traits. Moreover, most of the quantitative trait loci (QTL) and candidate genes associated with these traits remain unknown. In this study, we used 5.6 million imputed DNA sequence variants (single nucleotide polymorphisms, SNPs) for genome-wide association studies (GWAS) of 18 fertility and reproduction traits in Holstein cattle. Aiming to identify pleiotropic variants and increase detection power, multiple-trait analyses were performed using a method to efficiently combine the estimated SNP effects of single-trait GWAS based on a chi-square statistic. Results There were 87, 72, and 84 significant SNPs identified for heifer, cow, and sire traits, respectively, which showed a wide and distinct distribution across the genome, suggesting that they have relatively distinct polygenic nature. The biological functions of immune response and fatty acid metabolism were significantly enriched for the 184 and 124 positional candidate genes identified for heifer and cow traits, respectively. No known biological function was significantly enriched for the 147 positional candidate genes found for sire traits. The most important chromosomes that had three or more significant QTL identified are BTA22 and BTA23 for heifer traits, BTA8 and BTA17 for cow traits, and BTA4, BTA7, BTA17, BTA22, BTA25, and BTA28 for sire traits. Several novel and biologically important positional candidate genes were strongly suggested for heifer (SOD2, WTAP, DLEC1, PFKFB4, TRIM27, HECW1, DNAH17, and ADAM3A), cow (ANXA1, PCSK5, SPESP1, and JMJD1C), and sire (ELMO1, CFAP70, SOX30, DGCR8, SEPTIN14, PAPOLB, JMJD1C, and NELL2) traits. Conclusions These findings contribute to better understand the underlying biological mechanisms of fertility and reproduction traits measured in heifers, cows, and sires, which may contribute to improve genomic evaluation for these traits in dairy cattle.

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Identification of genomic regions related to age at first calving and first calving interval in water buffalo using single‐step GBLUP

Cited by 16 publications

References 34 publications

Genome‐wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye

Genome‐wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye

Comparative Signatures of Selection Analyses Identify Loci Under Positive Selection in the Murrah Buffalo of India

Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes

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