Comprehensive selection signature analyses in dairy cattle exploiting purebred and crossbred genomic data

Nayak, Sonali Sonejita; Panigrahi, Manjit; Rajawat, Divya; Ghildiyal, Kanika; Sharma, Anurodh; Parida, Subhashree; Bhushan, Bharat; Mishra, B. P.; Dutt, Triveni

doi:10.1007/s00335-023-10021-4

Cited by 10 publications

(2 citation statements)

References 65 publications

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“…Notably, two significant SNPs we identified, annotated to the OPTC and Neurofascin ( NFASC ) genes by HWAS-H, also reside on BTA 16, thus providing some validation of our findings with the previous study. Furthermore, KCNIP4 has been positively linked to traits related to milk production and adaptability via selection signature analysis in dairy cattle [ 24 ]. The gene link to adaptation can be used for sustainable agriculture practices, such as enhancing cattle resilience to changing climates and potentially reducing stress-related methane emissions.…”

Section: Discussionmentioning

confidence: 99%

Exploring the Interplay between the Hologenome and Complex Traits in Bovine and Porcine Animals Using Genome-Wide Association Analysis

Qadri,

Lai,

Zhao

et al. 2024

IJMS

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Genome-wide association studies (GWAS) significantly enhance our ability to identify trait-associated genomic variants by considering the host genome. Moreover, the hologenome refers to the host organism’s collective genetic material and its associated microbiome. In this study, we utilized the hologenome framework, called Hologenome-wide association studies (HWAS), to dissect the architecture of complex traits, including milk yield, methane emissions, rumen physiology in cattle, and gut microbial composition in pigs. We employed four statistical models: (1) GWAS, (2) Microbial GWAS (M-GWAS), (3) HWAS-CG (hologenome interaction estimated using COvariance between Random Effects Genome-based restricted maximum likelihood (CORE-GREML)), and (4) HWAS-H (hologenome interaction estimated using the Hadamard product method). We applied Bonferroni correction to interpret the significant associations in the complex traits. The GWAS and M-GWAS detected one and sixteen significant SNPs for milk yield traits, respectively, whereas the HWAS-CG and HWAS-H each identified eight SNPs. Moreover, HWAS-CG revealed four, and the remaining models identified three SNPs each for methane emissions traits. The GWAS and HWAS-CG detected one and three SNPs for rumen physiology traits, respectively. For the pigs’ gut microbial composition traits, the GWAS, M-GWAS, HWAS-CG, and HWAS-H identified 14, 16, 13, and 12 SNPs, respectively. We further explored these associations through SNP annotation and by analyzing biological processes and functional pathways. Additionally, we integrated our GWA results with expression quantitative trait locus (eQTL) data using transcriptome-wide association studies (TWAS) and summary-based Mendelian randomization (SMR) methods for a more comprehensive understanding of SNP-trait associations. Our study revealed hologenomic variability in agriculturally important traits, enhancing our understanding of host-microbiome interactions.

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Section: Discussionmentioning

confidence: 99%

Exploring the Interplay between the Hologenome and Complex Traits in Bovine and Porcine Animals Using Genome-Wide Association Analysis

Qadri,

Lai,

Zhao

et al. 2024

IJMS

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“…Recently, such methods as quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS) (Bekele et al, 2023;Chen S.Y. et al, 2023;Teng et al, 2023), targeted RNA sequencing (RNA-seq) (Fang et al, 2020;Ahmad et al, 2021) and detecting signatures of selection in genomes (Rajawat et al, 2022;Nayak et al, 2023;Persichilli et al, 2023) have been widely applied to identify the genes and mutations directly affecting milk yield and milk composition (Khatkar et al, 2004;Weller, Ron, 2011;Lopdell, 2023).…”

Section: Introductionmentioning

confidence: 99%

Association of three single nucleotide polymorphisms in the <i>LPIN1</i> gene with milk production traits in cows of the Yaroslavl breed

Igoshin,

Mishakova,

Aitnazarov

et al. 2024

Vestn. VOGiS

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Lipin-1 is a member of the evolutionarily conserved family of proteins and is expressed predominantly in adipose tissue and skeletal muscle. On the one hand, lipin-1 is an enzyme that catalyzes the dephosphorylation of phosphatidic acid to diacylglycerol (DAG) and thus participates in the metabolic pathways of biosynthesis of storage lipids in the cell, membrane phospholipids, and intracellular signaling molecules. On the other hand, lipin-1 is able to be transported from the cytoplasm to the nucleus and is a coactivator of lipid metabolism gene transcription. It was shown, using the analysis of single nucleotide polymorphism (SNP) associations, that the lipin-1 coding gene (LPIN1) is a promising candidate gene for milk production traits in Holstein and Brown Swiss cows. However, it is unclear how much of its effect depends on the breed. The Yaroslavl dairy cattle breed was created in the 18–19 centuries in Russia by breeding northern Great Russian cattle, which were short and poor productive, but well adapted to local climatic conditions and bad food base. It was shown by whole genome genotyping and sequencing that the Yaroslavl breed has unique genetics compared to Russian and other cattle breeds. The aim of the study was to assess the frequency of alleles and genotypes of three SNPs in the LPIN1 gene and to study the association of these SNPs with milk production traits in Yaroslavl cows. Blood samples from 142 cows of the Yaroslavl breed were obtained from two farms in the Yaroslavl region. Genotyping of SNPs was carried out by polymerase chain reaction-restriction fragment length polymorphism method. Associations of SNPs with 305-day milk yield, fat yield, fat percentages, protein yield, and protein percentages were studied from the first to the fourth lactation. Statistical tests were carried out using a mixed linear model, taking into account the relationship between individuals. We identified three SNPs – rs110871255, rs207681322 and rs109039955 with a frequency of a rare allele of 0.042–0.261 in Yaroslavl cows. SNP rs110871255 was associated with fat yield during the third and fourth lactations. SNP rs207681322 was associated with milk yield for the second, third and fourth lactations, as well as protein yield for the third lactation. Thus, we identified significant associations of SNPs rs207681322 and rs110871255 in the LPIN1 gene with a number of milk production traits during several lactations in Yaroslavl cows.

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Genomic patterns of selection in morphometric traits across diverse Indian cattle breeds

Rajawat,

Nayak,

Jain

et al. 2024

Mamm Genome

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Comprehensive selection signature analyses in dairy cattle exploiting purebred and crossbred genomic data

Cited by 10 publications

References 65 publications

Exploring the Interplay between the Hologenome and Complex Traits in Bovine and Porcine Animals Using Genome-Wide Association Analysis

Exploring the Interplay between the Hologenome and Complex Traits in Bovine and Porcine Animals Using Genome-Wide Association Analysis

Association of three single nucleotide polymorphisms in the <i>LPIN1</i> gene with milk production traits in cows of the Yaroslavl breed

Genomic patterns of selection in morphometric traits across diverse Indian cattle breeds

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