Using Linear Discriminant Analysis to Characterize Novel Single Nucleotide Polymorphisms and Expression Profile Changes in Genes of Three Breeds of Rabbit (<i>Oryctolagus cuniculus</i>)

Ateya, Ahmed; Hendam, Basma M.; Radwan, Hend; Elfadl, Eman A. Abo; Al‐Sharif, Mona

doi:10.30802/aalas-cm-20-000103

Cited by 3 publications

(1 citation statement)

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“…Nucleotide sequence variation for the MC4R gene between the two breeds, as well as between the breeds and reference sequences available in GenBank (HF970577.1), confirmed all five identified SNPs. The identification of some SNPs specific to each breed is probably related to the founder effect associated with origin, history, evolution, and genetic constituents of each breed (Carneiro et al, 2011;Ateya et al, 2021).…”

Section: Resultsmentioning

confidence: 99%

MC4R gene polymorphisms for classification of growth efficiency and carcass measurements in two rabbit breeds in Egypt

Radwan¹,

Ateya²,

Elfad³

et al. 2023

SA J. An. Sci.

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Melanocortin 4 receptor (MC4R), a protein derived from the MC4R gene, is involved in feed intake, metabolism control, and body weight regulation in humans. The purpose of this research was to explore MC4R polymorphisms alongside metabolic marker changes and their relationship with growth and carcass measurements in rabbits. Using synthetic line V (V-line) and Baladi Black rabbit breeds (60 rabbits per breed), blood samples were collected for DNA extraction and biochemical analysis. The polymerase chain reaction (PCR) product of MC4R (493 bp) revealed five nonsynonymous single nucleotide polymorphisms (SNPs; submitted to GenBank with accession numbers gb|MT832144|, gb|MT832145|, and gb|MT832146|). Four SNPs were characteristic of the V-line breed, and one was characteristic of the Baladi Black. For classification of the defined SNP-dependent groups within and between breeds, a discriminant analysis model correctly classified a percentage of cases with the following predictor variables: 90.8% for body weight at 5–14 weeks of age; 85% for feed consumption, daily feed intake, and feed conversion ratio; and 93.3% for carcass measurements (for which hind part weight, liver weight, and liver percentage were the best predictors in both breeds). There were significant differences between and within V-line and Baladi Black breeds in agreement with metabolic biochemical marker profiles and the defined SNPs. The identified SNPs in the MC4R gene and profile of the investigated metabolic biomarkers could be used as candidates and reference for the effective characterization of the two rabbit breeds. This study could therefore facilitate the introduction of markerassisted selection for growth performance characteristics in rabbits.

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Section: Resultsmentioning

confidence: 99%

MC4R gene polymorphisms for classification of growth efficiency and carcass measurements in two rabbit breeds in Egypt

Radwan¹,

Ateya²,

Elfad³

et al. 2023

SA J. An. Sci.

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Association of single nucleotide polymorphisms in Neuropeptide Y (NPY) and Phosphoglycerate Mutase 2 (PGAM2) genes with growth traits in rabbits

Helal,

Ahmed,

Ragab

et al. 2024

Trop Anim Health Prod

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Genetic improvement of local rabbit breeds using modern approaches such as marker-assisted selection requires accurate and precise information about marker‒trait associations in animals with different genetic backgrounds. Therefore, this study was designed to estimate the association between two mutations located in the Neuropeptide Y (NPY, g.1778G > C) and Phosphoglycerate Mutase 2 (PGAM2, c.195 C > T) genes in New Zealand White (NZW), Baladi (BR), and V-line rabbits. The first mutation was genotyped using high-resolution melting, and the second mutation was genotyped using the PCR-RFLP method. The results revealed significant associations between the NPY mutation and body weight at 10 (V-line) and 12 weeks of age (NZW, BR, and V-line), body weight gain (BWG) from 10 to 12 weeks of age (BR), BWG from 6 to 12 weeks of age (NZW, BR, and V-line), average daily gain (NZW, BR, and V-line, and BR), growth rate (GR) from 8 to10 weeks (V-line), 10 to 12 weeks (BR), and GR from 6 to 12 weeks of age (BR, and V-line). The PGAM2 mutation was associated with body weight at 10 (V-line) and 12 (NZW, and V-line) weeks of age, with significant positive additive effects at 12 weeks of age in all breeds, and was associated with BWG from 8 to 10 and 10 to 12 in BR, and BWG from 6 to 12 weeks of age (NZW, and BR), and average daily gain (NZW, and BR), and was associated with GR form 8 to 10 weeks (BR), from10 to 12 weeks (BR, and V-line) and from 6 to 12 weeks (BR). The results highlighted the importance of the two mutations in growth development, and the possibility of considering them as candidate genes for late growth in rabbits.

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Efficiency of leptin gene polymorphisms in the evaluation of the growth performance and carcass measurements of v-line and Baladi black rabbits

et al. 2023

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This study investigated the association between both polymorphisms and metabolic marker changes of the leptin gene, and body weight, weight gain, carcass traits, feed intake, and feed conversion ratio. Blood samples were collected from 60 V-line and 60 Baladi Black rabbits for DNA extraction and biochemical analysis. DNA sequencing of leptin (202-bp) revealed four non-synonymous single nucleotide polymorphism (SNPs) that characterized a number of V-line rabbits. Statistical analysis revealed that the identified SNPs were associated with rabbit growth and carcass measurements (p < 0.05). A discriminant analysis model showed a high classification percentage for the identified SNPs within and between breeds using body weight at 5-14 weeks of age (91.7%), slaughter traits (91.6%), feed intake, daily feed intake, and feed conversion ratio (76.7%). This study reveals that leptin gene could be a candidate for growth traits in rabbits enabling the development of marker-assisted selection (MAS) in different rabbit breeds.

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Using Linear Discriminant Analysis to Characterize Novel Single Nucleotide Polymorphisms and Expression Profile Changes in Genes of Three Breeds of Rabbit (Oryctolagus cuniculus)

Cited by 3 publications

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MC4R gene polymorphisms for classification of growth efficiency and carcass measurements in two rabbit breeds in Egypt

MC4R gene polymorphisms for classification of growth efficiency and carcass measurements in two rabbit breeds in Egypt

Association of single nucleotide polymorphisms in Neuropeptide Y (NPY) and Phosphoglycerate Mutase 2 (PGAM2) genes with growth traits in rabbits

Efficiency of leptin gene polymorphisms in the evaluation of the growth performance and carcass measurements of v-line and Baladi black rabbits

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