Selection signatures of Qinchuan cattle based on whole-genome sequences

Wang, Sihu; Raza, Sayed Haidar Abbas; Zhang, Ke; Mei, Chugang; Alamoudi, Muna O.; Aloufi, Bandar Hamad; Alshammari, Ahmed Mohajja; Liu, Zan

doi:10.1080/10495398.2022.2033252

Cited by 8 publications

(5 citation statements)

References 53 publications

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“…Other interesting genes near topmost differentiated genomic regions between DSN and Holstein are CCNDBP1 on BTA 10, a candidate for skeletal myogenesis ( Huang et al, 2016 ); UNC13C on BTA 10 a candidate for feed efficiency ( Freua et al, 2016 ); EMB on BTA 20 a candidate for mammary gland tissue development ( Butty et al, 2017 ); NIPBL on BTA 20 a candidate for growth ( de Simoni Gouveia et al, 2017 ; Wang et al, 2022 ) and previously detected as positively selected in German Holstein in the study between DSN and German Holstein using Illumina BovineSNP50 Beadchip ( Naderi et al, 2020 ); and ALS2CL , LRRC2 , and TDGF1 on BTA 22, which are candidates for milk production ( Ibeagha-Awemu et al, 2016 ) and fertility ( Wei et al, 2017 ; Tríbulo et al, 2018 ), and previously detected in highly differentiated regions between recent populations of Dutch Frisian and Holstein ( Hulsegge et al, 2022 ). In the region on BTA 22, the gene LTF (lactotransferrin) was found which is a major iron-binding protein in milk and body secretions of bovine ( Rejman et al, 1989 ; Pierce et al, 1991 ) with an antimicrobial activity ( Bellamy et al, 1992 ).…”

Section: Discussionmentioning

confidence: 99%

Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing

et al. 2023

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German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (FST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (FHom) and genomic inbreeding (FRoH) through runs of homozygosity (RoHs). Region-wide FST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The FHom and FRoH values in DSN were among the lowest. Regions with high FST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. FST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.

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Section: Discussionmentioning

confidence: 99%

Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing

et al. 2023

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“…The previously identified missense mutation in the PRKAG3 gene was the 7th highest-scoring pCADD SNP, while the highest scoring variant was a synonymous variant located in the ring finger protein 25 ( RNF25) gene. This gene encodes a ligase that partly controls naked cuticle 2 (NKD2) degradation in humans [ 38 ], which has been suggested to have a role in muscle development [ 41 ] . Although RNF25 may have a role in muscle pH, the more likely candidate causative gene for the association with muscle pH identified in this region is PRKAG3 .…”

Section: Discussionmentioning

confidence: 99%

A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines

et al. 2023

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Background Genome-wide association studies (GWAS) aim at identifying genomic regions involved in phenotype expression, but identifying causative variants is difficult. Pig Combined Annotation Dependent Depletion (pCADD) scores provide a measure of the predicted consequences of genetic variants. Incorporating pCADD into the GWAS pipeline may help their identification. Our objective was to identify genomic regions associated with loin depth and muscle pH, and identify regions of interest for fine-mapping and further experimental work. Genotypes for ~ 40,000 single nucleotide morphisms (SNPs) were used to perform GWAS for these two traits, using de-regressed breeding values (dEBV) for 329,964 pigs from four commercial lines. Imputed sequence data was used to identify SNPs in strong ($$\ge$$ ≥ 0.80) linkage disequilibrium with lead GWAS SNPs with the highest pCADD scores. Results Fifteen distinct regions were associated with loin depth and one with loin pH at genome-wide significance. Regions on chromosomes 1, 2, 5, 7, and 16, explained between 0.06 and 3.55% of the additive genetic variance and were strongly associated with loin depth. Only a small part of the additive genetic variance in muscle pH was attributed to SNPs. The results of our pCADD analysis suggests that high-scoring pCADD variants are enriched for missense mutations. Two close but distinct regions on SSC1 were associated with loin depth, and pCADD identified the previously identified missense variant within the MC4R gene for one of the lines. For loin pH, pCADD identified a synonymous variant in the RNF25 gene (SSC15) as the most likely candidate for the muscle pH association. The missense mutation in the PRKAG3 gene known to affect glycogen content was not prioritised by pCADD for loin pH. Conclusions For loin depth, we identified several strong candidate regions for further statistical fine-mapping that are supported in the literature, and two novel regions. For loin muscle pH, we identified one previously identified associated region. We found mixed evidence for the utility of pCADD as an extension of heuristic fine-mapping. The next step is to perform more sophisticated fine-mapping and expression quantitative trait loci (eQTL) analysis, and then interrogate candidate variants in vitro by perturbation-CRISPR assays.

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“…The gene NIBPL was linked to the DNA repair process (i.e, recovery from damage caused by the UV component of sun light in mammals) [32]. Also, the NIPBL gene is a candidate gene for growth traits for cattle [33]. Other candidate genes, ILR7 and LIFR, have been identified to contribute to immune response [34][35][36].…”

Section: Signatures Of Selectionmentioning

confidence: 99%

Selective signatures in composite MONTANA TROPICAL beef cattle reveal potential genomic regions for tropical adaptation

Santos,

Eler,

Oliveira

et al. 2024

PLoS ONE

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Genomic regions related to tropical adaptability are of paramount importance for animal breeding nowadays, especially in the context of global climate change. Moreover, understanding the genomic architecture of these regions may be very relevant for aiding breeding programs in choosing the best selection scheme for tropical adaptation and/or implementing a crossbreeding scheme. The composite MONTANA TROPICAL® population was developed by crossing cattle of four different biological types to improve production in harsh environments. Pedigree and genotype data (51962 SNPs) from 3215 MONTANA TROPICAL® cattle were used to i) characterize the population structure; ii) identify signatures of selection with complementary approaches, i.e. Integrated Haplotype Score (iHS) and Runs of Homozygosity (ROH); and iii) understand genes and traits related to each selected region. The population structure based on principal components had a weak relationship with the genetic contribution of the different biological types. Clustering analyses (ADMIXTURE) showed different clusters according to the number of generations within the composite population. Considering results of both selection signatures approaches, we identified only one consensus region on chromosome 20 (35399405–40329703 bp). Genes in this region are related to immune function, regulation of epithelial cell differentiation, and cell response to ionizing radiation. This region harbors the slick locus which is related to slick hair and epidermis anatomy, both of which are related to heat stress adaptation. Also, QTLs in this region were related to feed intake, milk yield, mastitis, reproduction, and slick hair coat. The signatures of selection detected here arose in a few generations after crossbreeding between contrasting breeds. Therefore, it shows how important this genomic region may be for these animals to thrive in tropical conditions. Further investigations on sequencing this region can identify candidate genes for animal breeding and/or gene editing to tackle the challenges of climate change.

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Selection signatures of Qinchuan cattle based on whole-genome sequences

Cited by 8 publications

References 53 publications

Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing

Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing

A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines

Selective signatures in composite MONTANA TROPICAL beef cattle reveal potential genomic regions for tropical adaptation

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