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.

Shedrach Benjamin Pewan,Richard Crawford Edmunds,Oyelola Abdulwasiu Adegboye,Felista Waithira Mwangi,Roger Huerlimann,Michelle Lauren Elizabeth Henry,Robert Tumwesigye Kinobe,Benjamin William Behrens Holman,John Roger Otto,Alyssa Maree Budd,Aduli Enoch Othniel Malau-Aduli

doi:10.3390/foods10102288

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.

Highlights

Eating quality is the single largest determinant of consumer acceptability and satisfaction with meat products
The top 10 rams and 200 ewes were selected and mated to generate 150 progeny whose muscle biopsy samples were laboratory tested for n-3 LC-PUFA, intramuscular fat (IMF), fat melting point (FMP), and genomic DNA sequenced at 10 months of age prior to being finished at a commercial feedlot
At the fatty acid binding protein-4 (FABP4) g.62829478A>G single nucleotide polymorphisms (SNP) locus, only IMF variation tended towards significance between the genotypes (p < 0.06). It is well-established that DNA-based inheritance enables the transmission of selected phenotypes across generations either without changes in the DNA sequence through epigenetic inheritance [31] or through functional mutations involving changes in only one base pair

Summary

Introduction

Eating quality is the single largest determinant of consumer acceptability and satisfaction with meat products. Attempts to predict IMF [6,7,8], intramuscular connective tissue [9], composition and quality characteristics [10], tenderness, ultimate pH, and IMF content [11,12,13] from near infra-red based regression equations were characterized by low accuracy, inconsistency, and divergence between calibration and validation data. Such inaccuracies lead to lamb inefficiencies and an estimated annual value-chain wastage costs of $130 million to the Australian beef industry [5]. The use of conventional laboratory-based fat extraction, ‘slip point’ and gas chromatography methods still remain the most accurate techniques for measuring IMF, FMP, and n-3 LC-PUFA, and for predicting consumer acceptance of beef and sheep meat [19]

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