Genetic markers as a basis for the excellence of carcass quality traits in the Latvian dark-headed sheep breed.

The project aims to develop a panel of genetic markers associated with carcass quality characteristics in Latvian Dark-Head (LT; Latvijas tumšgalve) sheep, contributing to sustainable rural development and the conservation of natural resources. The project involves selecting lambs for feeding trials, grouping animals by carcass-trait quality, and identifying genetic markers for these traits using the OvineSNP50 chip sequencing methodology. Predictive modelling and biostatistical methods will validate the markers. Throughout the project, young researchers will develop new skills, with results published in scientific journals and presented at conferences. The UL will register the acquired scientific knowledge to safeguard intellectual property rights. Additionally, a unique biological sample collection and data platform will be established to support future research. The current project will help establish a new direction in livestock genetic research at UL, expand collaboration, and attract new partners from the Baltic States. This will promote comprehensive research in sheep genetic selection and support the integration of genetic technologies into practical sheep breeding programs in Latvia.

This proposal supports the need for sustainable use of native animal genetic resources in sheep farming. By conducting comprehensive research to enhance understanding of the genetic factors influencing animal-to-animal variations on favourable carcass composition traits, we aim to develop a cost-effective and rapid tool for genetic selection that can be used to analyze live lambs. This initiative aims to enhance marker-assisted selection (MAS) in sheep breeding, supporting sustainable livestock practices and conserving biodiversity. The project supports a knowledge-intensive bioeconomy by making local sheep breeds more productive and of higher quality. This is in line with Latvia's Smart Specialisation Strategy (RIS3).

By 2050, agricultural productivity needs to go up by 70% in order to feed a growing population [1]. We are at a critical juncture where food systems must balance the need for sufficient, healthy, and affordable food with the need to preserve ecosystems essential to life [1]. Therefore, the use of natural resources for livestock production is a significant source of environmental stress. To solve this problem, new technologies are needed to increase production while ensuring environmental sustainability. The goal is to produce food more economically and more efficiently from an environmental perspective than current practices.

Latvia and the other Baltic countries have a long history of raising sheep, which is an important part of their farming industry. However, unlike many other European countries that use genetic technologies to assess breeding values, sheep breeding programmes in this region have traditionally relied on phenotypic data to select production traits. This is primarily due to the lack of performance-specific genetic markers for local sheep breeds, including the native LT sheep. However, breeders and sheepfarmers in Latvia recognise the benefits of genetic selection. They are increasingly open to implementing these technologies into practical breeding programs as they meet their goals of increasing productivity and efficiency (https://www.laaa.lv).

In addition to management methods that optimise productivity, it is important to select more genetically efficient sheep. Efficient animals, that require fewer natural resources are more environmentally friendly and economically viable [2]. Thus, there is a need to develop innovative approaches to optimise the use of existing genetic variation both within and between animal populations.

Marker-assisted selection (MAS) is a valuable tool for identifying desirable traits, such as carcass composition, by leveraging the relationship between DNA regions and quantitative trait loci (QTL) within breeds [3]. Although the SheepQTLdb (December 2023) contains limited QTL data for sheep, analysing single-nucleotide polymorphisms (SNPs) in local breeds shows promise for selective breeding [4]. The period from weaning to six months is critical for lamb growth, offering an opportunity to identify animals for breeding or meat production [5].

MAS can be used to select crossbred offspring with optimal genetic profiles and estimated breeding values (EBVs) or to predict the productive potential of lambs already born [6,7 ].

Genome-wide association studies (GWAS) have pinpointed quantitative trait loci (QTL) for carcass composition, encompassing bone density, across various chromosomes in Coopworth, Scottish Blackface, British Texel, Charollais, and Suffolk breeds. Therefore, genetic variants within specific QTL regions associated with productive sheep traits can be used as genetic markers for MAS in sheep breeding. Currently, two commercial DNA tests (LoinMax and MyoMax) target genetic variants in the Carwell and myostatin genes for this purpose [8,9].

The current project involves conducting a sequencing study of the sheep genome of sheep breeds raised in Latvia using the OvineSNP50 chip from Illumina, which covers 54,977 single nucleotide polymorphisms (SNPs). This will provide detailed genetic data for in-depth analysis of the genetic background of these breeds. Although carcass composition traits are not commonly included in sheep breeding programs due to the complexity and cost of measurement, their importance for profitability is growing. Genomic approaches offer significant advantages, including reduced reliance on costly phenotyping, the ability to select breeding stock at an early age via DNA sampling, and faster genetic gains [10].

Agricultural development trends are leading to increased genetic uniformity in livestock, with endangered breeds being lost and inbreeding rising in commercial populations. Much genetic diversity is being lost through breed replacement and crossbreeding [11]. Local sheep breeds in the Baltic region possess unique adaptive traits, such as disease resistance, climatic tolerance, and efficient use of low-quality feed [12,13]. However, there is limited scientific, economic, and genetic evaluation of these breeds in different environments. In the future, their genetic diversity may prove essential due to changing livestock production conditions.

Therefore, the primary focus of this study is the native Latvian Dark-Head (LT) sheep breed, which constitutes about 23% of Latvia's total sheep population and 70% of purebred sheep, making it the only locally bred sheep breed in the country. Developed between 1927 and 1937 through crossbreeding Oxford Down and Shropshire sheep with local coarse-wooled sheep, the LT breed is known for its good productivity, lamb survival, and milk production. It exhibits traits such as fast growth and a long, vast body, which correlates positively with back muscle development.

LT sheep meat has been found to have a favourable amino acid profile and taste, though further improvements in carcass quality and muscle and fat layers are needed [14]. Previous studies (Project of the Ministry of Agriculture of Latvia, 2013-2018) on Latvian meat breeds showed that Suffolk lambs had the highest growth rate (over 450 g/day), like Charolais and Ile-de-France breeds, reaching 45-50 kg live weight by 4-5 months.

Our study aims to identify a panel of genetic markers linked to productive carcass characteristics in other meat sheep breeds in Latvia, such as Ile de France, Charolais, Texel, Suffolk, Dorper, and Oxford Down. This panel will then be introduced into the Latvian Dark-Head breed through marker-assisted selection (MAS), providing a novel approach to improving productive traits without the need for crossbreeding with outside genetic material.

Currently, no genetic parameters for performance and carcass composition quality traits are available for LT sheep breeds as well as for other native breeds in the Baltic region. The physiological determinants of quality of carcass composition traits or putative biomarkers used to analyze animal-to-animal variation in live lambs could be used as a cost-effective and rapid tool for genetic selection or management decisions.

Originality and innovative aspects of the research: The research aims to develop a practical methodology for predicting carcass quality traits using genetic markers obtained from the blood of live lambs.

In addition, the project is expected to enhance sustainability and efficiency in sheep farming across the Baltic region, as the goal of current study is also to increase cooperation between the Baltic countries and attract new partners to promote comprehensive research into sheep farming practices in the region. By working collaboratively and sharing our findings, we can advance sheep breeding and promote the conservation of local sheep breeds.

The proposed research is classified as industrial research. This research focuses on developing new genetic markers to improve sheep farming efficiency, integrating scientific innovation with practical applications for sustainable livestock management and breeding programmes.

The research content incorporates a gender dimension. The project does not directly involve human subjects; however, its outcomes may indirectly affect the livelihoods of sheep farmers, especially women who are frequently engaged in sheep husbandry in Latvia. To promote equitable benefits, the team will effectively communicate research findings to all stakeholders, including women farmers.

The action will incorporate interdisciplinary aspects. To achieve the project goal, expertise in molecular biology, genetics, agriculture, and biotechnology will be combined with access to lamb samples, including blood and carcass quality data from feeding trials. We can use animals with predictable performance related to the main economic pathways (carcass composition traits) for further marker-assisted selection. In this way, synergies between the two topics will be ensured; a pilot study (LZP No. lzp-2021/1-0489, (2022-2024)) successfully implemented by UL and the current postdoctoral proposal. This continuation of research is essential due to previous valuable insights into genetic markers linked to meat productivity. The new project aims to further livestock genetic research at LU and address gaps in sheep genetics in Latvia.

Objective 1. Characterise carcass composition parameters for meat quality in lambs after feeding trial I; assess the post-fat cohort with the highest, average, and lowest characteristics.

Objective 2. Scan the genetic background of Latvian sheep breeds' DNA.

Objective 3. Analyse associations between carcass characteristics and genetic background, developing a genetic marker panel for carcass composition traits.

Objective 4. Validate the genetic marker panel using predictive modelling in a secondary animal collection after the second-year feeding trial.

Objective 5. Create a data platform to provide access to sheep genetics and carcass composition data.