Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture–Based Systems

Machado, P C; Brito, Luiz F.; Martins, Rafaela; Pinto, L. F. B.; Silva, Marcio R.; Pedrosa, Victor Breno

doi:10.3390/ani12243526

Cited by 3 publications

(1 citation statement)

References 121 publications

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“…PRKAG2 gene serves as a marker for growth and meat quality in Qinchuan cattle (Fu et al., 2015). TIAM2 was associated with lipid metabolism and muscle tissue composition (Machado et al., 2022), while MYZO3 is a candidate gene for muscle cell differentiation (Ye et al., 2017). KIT , a classical coat color gene, plays a crucial role in melanogenesis, melanocyte migration, and proliferation.…”

Section: Discussionmentioning

confidence: 99%

Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

Ma,

Li,

et al. 2023

Food and Energy Security

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The Longnan goat (LN) is a local breed discovered during the third census of China's livestock and poultry genetic resources. In order to thoroughly comprehend the population traits, this research examined a total of 70 animals from three different goat populations, namely the LN goat, Nanjiang Brown goat (NJ), and Boer goat (Boer). Specific‐Locus Amplified Fragment Sequencing was employed to analyze genetic diversity, population structure, and selective sweep patterns. Additionally, individual DNA fingerprints were generated to provide detailed genetic profiles for each subject. A total of 643,868 single nucleotide polymorphisms (SNPs) were detected, with a majority located in intergenic and intronic regions. Genetic diversity analysis uncovered lower diversity within the LN population compared to the other two populations. The analysis of population structure unveiled significant genetic distance between LN and both NJ and Boer populations, with distinct clustering patterns observed. Moreover, genetic differentiation coefficients (FST) of 0.1019 and 0.0854 were determined between LN and Boer, as well as LN and NJ, respectively, indicating substantial genetic differentiation. Selective sweep analysis, combining FST and π ratio, identified several genes associated with growth and development, reproduction, hair color, and immunity that may serve as valuable candidates for marker‐assisted breeding. Furthermore, identification of 47,541 runs of homozygosity (ROHs) revealed non‐uniform distribution across chromosomes, with the highest frequency on chromosome 1 and the lowest on chromosome 27. Correlations between different inbreeding coefficients varied, with the highest observed between FHOM and FGRM, and the lowest between FROH >1.5Mb and FROH <500kb. A total of 46 candidate genes were annotated within high‐frequency ROH islands, primarily associated with biological processes such as reproduction, growth and development, and immunity. Finally, a DNA fingerprint, consisting of 371 highly polymorphic SNPs, was generated and presented in the form of a two‐dimensional code for convenient access. Based on the population structure analysis, LN goats have been found to have a distant genetic distance and a higher degree of differentiation from both the Boer and NJ populations. Evaluation of genetic diversity parameters and ROH analysis indicates that the LN population exhibits lower genetic diversity and shows signs of inbreeding. Our findings offer theoretical support for the identification of genetic resources within this population.

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Section: Discussionmentioning

confidence: 99%

Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

Ma,

Li,

et al. 2023

Food and Energy Security

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Impaired Detoxification of Trans, Trans‐2,4‐Decadienal, an Oxidation Product from Omega‐6 Fatty Acids, Alters Insulin Signaling, Gluconeogenesis and Promotes Microvascular Disease

Qian,

Klatt,

Bennewitz

et al. 2023

Advanced Science

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Omega‐6 fatty acids are the primary polyunsaturated fatty acids in most Western diets, while their role in diabetes remains controversial. Exposure of omega‐6 fatty acids to an oxidative environment results in the generation of a highly reactive carbonyl species known as trans, trans‐2,4‐decadienal (tt‐DDE). The timely and efficient detoxification of this metabolite, which has actions comparable to other reactive carbonyl species, such as 4‐hydroxynonenal, acrolein, acetaldehyde, and methylglyoxal, is essential for disease prevention. However, the detoxification mechanism for tt‐DDE remains elusive. In this study, the enzyme Aldh9a1b is identified as having a key role in the detoxification of tt‐DDE. Loss of Aldh9a1b increased tt‐DDE levels and resulted in an abnormal retinal vasculature and glucose intolerance in aldh9a1b−/− zebrafish. Transcriptomic and metabolomic analyses revealed that tt‐DDE and aldh9a1b deficiency in larval and adult zebrafish induced insulin resistance and impaired glucose homeostasis. Moreover, alterations in hyaloid vasculature is induced by aldh9a1b knockout or by tt‐DDE treatment can be rescued by the insulin receptor sensitizers metformin and rosiglitazone. Collectively, these results demonstrated that tt‐DDE is the substrate of Aldh9a1b which causes microvascular damage and impaired glucose metabolism through insulin resistance.

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Analysis of the genetic diversity of Ayrshire cattle in Russia. Message 2. Genome analysis based on data on the distribution of ROH patterns in Ayrshire cows

Ryabova,

Pozovnikova,

Dementieva

et al. 2023

Ecological genetics

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BACKGROUND: The analysis of ROH distribution is an important focus of genetic resource conservation programs of cattle. Characterization of ROH-islands allows to identify genetic factors affecting productivity traits of dairy cattle. AIM: was to analyze intra-breed genetic diversity and population structure of Ayrshire cattle, based on data on distribution of homozygosity patterns, as well as to identify loci associated with selection intensity and utility traits. MATERIALS AND METHODS: ROH distribution data were obtained using whole genome genotyping on Illumina BovineSNP50 (50K) DNA chips (Illumina Inc., USA). The object of the study was the DNA of Ayrshire cows (600 cows), which belonged to farms with different levels of selection and breeding work. RESULT: The results of our studies showed a generally similar level of inbredness of the analyzed Ayrshire cattle herds. The homogeneity of the population is confirmed by a large number of animals (72.83%) with FROH values between 0.10 and 0.20. Cluster analysis revealed consolidated groups of individuals, due to their ancestral origins. The discovered ROH-patterns included 268 genes, 32 of which were involved in regulation of the synthesis of protein and fat milk components. The results obtained may be used in breeding programs for Ayrshire cattle in Russia. CONCLUSIONS: The Russian population of Ayrshire cattle is distinguished by unique qualities in protein and fat milk composition and genome architecture, while maintaining genetic diversity and insignificant traces of Ayrshire cattle gene pool.

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Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture–Based Systems

Cited by 3 publications

References 121 publications

Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

Impaired Detoxification of Trans, Trans‐2,4‐Decadienal, an Oxidation Product from Omega‐6 Fatty Acids, Alters Insulin Signaling, Gluconeogenesis and Promotes Microvascular Disease

Analysis of the genetic diversity of Ayrshire cattle in Russia. Message 2. Genome analysis based on data on the distribution of ROH patterns in Ayrshire cows

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