Novel insights into genome-wide associations in<i>Bos indicus</i>reveal genetic linkages between fertility and growth

Kour, Aneet; Deb, S. M.; Nayee, Nilesh; Niranjan, S. K.; Raina, V. S.; Mukherjee, Anupama; Gupta, I. D.; Patil, Chandrashekhar S.

doi:10.1080/10495398.2021.1932520

Cited by 8 publications

(5 citation statements)

References 90 publications

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“…The ENTPD4 gene seems to be influencing both milk production [ 57 ] and fertility [ 58 ]. Another gene from this region, which seems to be involved in multiple traits, was PEBP4 which was found to simultaneously affect growth and fertility in cattle [ 59 ]. The gene SORBS3 , PPP3CC and PIWIL2 were located in a region associated with growth and wool traits in [ 60 ].…”

Section: Resultsmentioning

confidence: 99%

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Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep

Mészárosová

Mészáros

Moravčíková

et al. 2022

Animals

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This study explored the genomic diversity and selection signatures in two Slovakian national breeds, the Original Valachian and the Improved Valachian sheep. As they are an important animal genetic resource within the country, but with decreasing population size, our aim is to identify potentially valuable genomic regions. A total of 97 sheep (18 male and 79 female) from the Original Valachian, and 69 sheep (25 male and 44 female) from the Improved Valachian populations were genotyped using the GeneSeek GGP Ovine 50 K chip. The inbreeding levels were assessed with runs of homozygosity (ROH). The selection signatures within breeds were identified based on the top 1% of most homozygous regions within the breed, the so-called ROH islands. The selection signatures between breeds were assessed based on variance in linkage disequilibrium. Overall, we have identified selection signatures with quantitative trait loci (QTL) and genes pointing towards all three production purposes of the Valachian sheep, milk, meat, and wool, including their quality characteristics. Another group with apparent large importance was the various traits related to health and resistance to parasites, which is well in line with the sturdy nature of this breed.

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Section: Resultsmentioning

confidence: 99%

“…This region contained only two protein coding genes, ANK3 and CCDC6. The CCDC6 gene was of particular interest, as it was previously associated with body weight [ 59 ], but also in a gene network contributing to hypertrophy in callipyge skeletal muscle [ 90 ].…”

Section: Resultsmentioning

confidence: 99%

Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep

Mészárosová

Mészáros

Moravčíková

et al. 2022

Animals

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“…In mice, loss of the ASAP1 gene can lead to growth retardation, delayed ossification, adipocyte development, and fat depot formation reduction [ 21 ]. The SNPs related to the ASAP1 gene have also been associated with production and growth traits in cattle [ 22 , 23 ]. The CABYR gene has been widely proven to be related to sperm morphology and sperm development [ 24 , 25 ], but no research has yet shown that this gene is involved in the growth performance of animals or plants.…”

Section: Discussionmentioning

confidence: 99%

Identification of the genetic basis of the duck growth rate in multiple growth stages using genome-wide association analysis

Yang

Zeng

et al. 2023

BMC Genomics

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Background The genetic locus responsible for duck body size has been fully explained before, but the growth trait-related genetic basis is still waiting to be explored. For example, the genetic site related to growth rate, an important economic trait affecting marketing weight and feeding cost, is still unclear. Here, we performed genome wide association study (GWAS) to identify growth rate-associated genes and mutations. Result In the current study, the body weight data of 358 ducks were recorded every 10 days from hatching to 120 days of age. According to the growth curve, we evaluated the relative and absolute growth rates (RGR and AGR) of 5 stages during the early rapid growth period. GWAS results for RGRs identified 31 significant SNPs on autosomes, and these SNPs were annotated by 24 protein-coding genes. Fourteen autosomal SNPs were significantly associated with AGRs. In addition, 4 shared significant SNPs were identified as having an association with both AGR and RGR, which were Chr2: 11483045 C>T, Chr2: 13750217 G>A, Chr2: 42508231 G>A and Chr2: 43644612 C>T. Among them, Chr2: 11483045 C>T, Chr2: 42508231 G>A, and Chr2: 43644612 C>T were annotated by ASAP1, LYN and CABYR, respectively. ASAP1 and LYN have already been proven to play roles in the growth and development of other species. In addition, we genotyped every duck using the most significant SNP (Chr2: 42508231 G>A) and compared the growth rate difference among each genotype population. The results showed that the growth rates of individuals carrying the Chr2: 42508231 A allele were significantly lower than those without this allele. Moreover, the results of the Mendelian randomization (MR) analysis supported the idea that the growth rate and birth weight had a causal effect on the adult body weight, with the growth rate having a greater effect size. Conclusion In this study, 41 SNPs significantly related to growth rate were identified. In addition, we considered that the ASAP1 and LYN genes are essential candidate genes affecting the duck growth rate. The growth rate also showed the potential to be used as a reliable predictor of adult weight, providing a theoretical reference for preselection.

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“…PEBP4 (Phosphatidylethanolamine Binding Protein 4) is a member of an evolutionarily conserved family of proteins that perform important biological functions such as lipid binding and inhibition of serine proteases. According to new research, GWAS associations show genetic links between fertility and growth in cattle ( Kour et al, 2021 ). GPAT2 (Mitochondrial Glycerol-3-Phosphate Acyltransferase 2) has been linked to lipid composition because of its role in the biosynthesis of triglycerides and glycerophospholipids ( Dircks and Sul, 1997 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds

Aboul-Naga¹,

Alsamman

Allali

et al. 2022

Front. Genet.

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Heat stress caused by climatic changes is one of the most significant stresses on livestock in hot and dry areas. It has particularly adverse effects on the ability of the breed to maintain homeothermy. Developing countries are advised to protect and prepare their animal resources in the face of potential threats such as climate change. The current study was conducted in Egypt’s three hot and dry agro-ecological zones. Three local sheep breeds (Saidi, Wahati, and Barki) were studied with a total of 206 ewes. The animals were exercised under natural heat stress. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on their response to meteorological and physiological parameters. Genomic variation in these breeds was assessed using 64,756 single nucleotide polymorphic markers (SNPs). From the perspective of comparative adaptability to harsh conditions, our objective was to investigate the genomic structure that might control the adaptability of local sheep breeds to environmental stress under hot and dry conditions. In addition, indices of population structure and diversity of local breeds were examined. Measures of genetic diversity showed a significant influence of breed and location on populations. The standardized index of association (rbarD) ranged from 0.0012 (Dakhla) to 0.026 (Assuit), while for the breed, they ranged from 0.004 (Wahati) to 0.0103 (Saidi). The index of association analysis (Ia) ranged from 1.42 (Dakhla) to 35.88 (Assuit) by location and from 6.58 (Wahati) to 15.36 (Saidi) by breed. The most significant SNPs associated with heat tolerance were found in the MYO5A, PRKG1, GSTCD, and RTN1 genes (p ≤ 0.0001). MYO5A produces a protein widely distributed in the melanin-producing neural crest of the skin. Genetic association between genetic and phenotypic variations showed that OAR1_18300122.1, located in ST3GAL3, had the greatest positive effect on heat tolerance. Genome-wide association analysis identified SNPs associated with heat tolerance in the PLCB1, STEAP3, KSR2, UNC13C, PEBP4, and GPAT2 genes.

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Novel insights into genome-wide associations inBos indicusreveal genetic linkages between fertility and growth

Cited by 8 publications

References 90 publications

Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep

Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep

Identification of the genetic basis of the duck growth rate in multiple growth stages using genome-wide association analysis

Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds

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