Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb

Abstract

Meat quality data can only be obtained after slaughter when selection decisions about the live animal are already too late. Carcass estimated breeding values present major precision problems due to low accuracy, and by the time an informed decision on the genetic merit for meat quality is made, the animal is already dead. We report for the first time, a targeted next-generation sequencing (NGS) of single nucleotide polymorphisms (SNP) of lipid metabolism genes in Tattykeel Australian White (TAW) sheep of the MARGRA lamb brand, utilizing an innovative and minimally invasive muscle biopsy sampling technique for directly quantifying the genetic worth of live lambs for health-beneficial omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA), intramuscular fat (IMF), and fat melting point (FMP). NGS of stearoyl-CoA desaturase (SCD), fatty acid binding protein-4 (FABP4), and fatty acid synthase (FASN) genes identified functional SNP with unique DNA marker signatures for TAW genetics. The SCD g.23881050T>C locus was significantly associated with IMF, C22:6n-3, and C22:5n-3; FASN g.12323864A>G locus with FMP, C18:3n-3, C18:1n-9, C18:0, C16:0, MUFA, and FABP4 g.62829478A>T locus with IMF. These add new knowledge, precision, and reliability in directly making early and informed decisions on live sheep selection and breeding for health-beneficial n-3 LC-PUFA, FMP, IMF and superior meat-eating quality at the farmgate level. The findings provide evidence that significant associations exist between SNP of lipid metabolism genes and n-3 LC-PUFA, IMF, and FMP, thus underpinning potential marker-assisted selection for meat-eating quality traits in TAW lambs.

Towards Sustainable Sources of Omega-3 Long-Chain Polyunsaturated Fatty Acids in Northern Australian Tropical Crossbred Beef Steers through Single Nucleotide Polymorphisms in Lipogenic Genes for Meat Eating Quality

“…The SCD genotype was reported to explain only 4% of the MUFA composition in Japanese Black cattle [37], and 5% in MUFA and 4% oleic acid variation, respectively, in Wagyu × Limousin cattle [38]. The significant correlations between EPA, DPA, and DHA with at least 16 SCD SNP observed in this study corroborate the findings of a previous study in sheep that recorded significant correlations between two SCD SNP and ω3 long-chain PUFA [32]. The three ω3 long-chain PUFA are synthesized from alpha-linolenic acid through the activity of ∆6 desaturase and ∆5 desaturase among other enzymes, but not ∆9 desaturase since ALA already has a double bond between C9 and C10 [83,84].…”

“…The procedures were carried out as described previously [32] with slight modifications on the gene amplification conditions. The target genes were amplified using the primer sequences presented in Table S1 and the gel image of the amplification products is presented in Supplementary Figure S1.…”

“…For instance, associations were reported between the growth hormone g.253 locus SNP with C14:0, C16:1, and C18:0 concentrations in Japanese Black cattle [28]; multiple autosomal SNP loci with C14:0, C16:0, and C18:0 concentrations in Nellore bulls [29]; the diacylglycerol O-acyltransferase 1 gene SNP K232A and c.947 of µ-calpain gene with IMF in meat of five beef cattle breeds in Sweden [30]; and multiple SNP in the hormone-sensitive lipase gene with IMF of the Qinchuan and Nanyang cattle [31]. Furthermore, the stearoyl-CoA desaturase (SCD) g.23881050T>C locus was significantly associated with IMF, C22:6ω-3, and C22:5ω-3, fatty acid binding protein 4 (FABP4) g.62829478A>T locus with IMF and fatty acid synthase (FASN) g.12323864A>G locus with C18:3ω-3, C18:1ω-9, C18:0, and C16:0 concentrations in Tattykeel Australian White lamb [32].…”

“…Meat quality measurements are often attained after slaughter making it difficult to predict meat quality in living animals [44,45]. Pewan et al (2021) demonstrated that a combination of laboratory-based IMF, FMP, and fatty acid analyses of samples obtained through a minimally invasive biopsy sampling and next-generation sequencing of polymorphisms in lipid metabolism genes is a suitable method to directly quantify the genetic worth of live animals for IMF and fatty acid composition. Therefore, this study aimed to identify targeted SNP in lipid metabolism related genes of tropically adapted crossbred beef cattle of northern Australia and determine associations with loin eye muscle fat characteristics.…”

Genetics and nutrition impacts on herd productivity in the Northern Australian beef cattle production cycle

“…Whole genome sequencing to target specific genes associated with meat quality characteristics ( Pewan et al. 2021a ; ( Pewan et al., 2021b ) ( Pewan et al., 2020a ); ( Pewan et al., 2020b ) are needed to further develop tropical cattle breeds with superior genes more suited to the North Australian beef industry ( Mwangi et al. 2019 ).…”