The Uruguayan Creole cattle population (N = 600) is located in a native habitat in south-east Uruguay. We analyzed its genetic diversity and compared it to other populations of American Creole cattle. A random sample of 64 animals was genotyped for a set of 17 microsatellite loci, and the D-loop hyper-variable region of mtDNA was sequenced for 28 calves of the same generation. We identified an average of 5.59 alleles per locus, with expected heterozygosities between 0.466 and 0.850 and an expected mean heterozygosity of 0.664. The polymorphic information content ranged from 0.360 to 0.820, and the global FIS index was 0.037. The D-loop analysis revealed three haplotypes (UY1, UY2 and UY3), belonging to the European matriline group, with a haplotype diversity of 0.532. The history of the population, changes in the effective population size, bottlenecks, and genetic drift are possible causes of the genetic variability patterns that we detected.

Transcriptome deep sequencing is a powerful tool for exploring the genetic architecture of complex traits. Gene expression patterns may explain a high degree of the observed phenotypic differences in histochemical and metabolic parameters related to meat quality among different muscles. In this study, we sequenced by RNA-Seq the whole transcriptome of nine lamb muscles: Semimembranosus (SM), Semitendinosus (ST), Cranial gluteobiceps, Gluteus medius (GM), Rectus femoris, Supraspinatus (SS), Longissimus lumborum (LL), Adductor and Psoas major. Significant gene expression differences were detected between almost all pairwise comparisons, being more pronounced between SS and ST, SM and LL, and ST and GM. These differences can be explained in terms of ATPase and glycolytic activities, muscle fiber typing and oxidative score, clustering muscles as fast glycolytic, intermediate or slow oxidative. ST showed up-regulation of gene pathways related to carbohydrate metabolism, energy generation and protein turnover as expected from a fast white muscle. SS showed myosin isoforms typical of slow muscles and high expression of genes related to calcium homeostasis and vascularization. SM, LL and GM showed in general intermediate gene expression patterns. Several novel transcripts were detected, mostly related to muscle contraction and structure, oxidative metabolism, lipid metabolism and protein phosphorylation. Expression profiles were consistent with previous histochemical and metabolic characterization of these muscles. Up-regulation of ion transport genes may account for significant differences in water holding capacity. High expression of genes related to cell adhesion, cytoskeleton organization, extracellular matrix components and protein phosphorylation may be related to meat yellowness and lower tenderness scores. Differential expression of genes related to glycolytic activity and lactic acid generation among fast, intermediate and slow muscles may explain the detected final meat pH differences. These results reveal new candidate genes associated with lamb meat quality, and give a deeper insight into the genetic architecture of these complex traits.

Rarámuri Criollo (RC) cattle have been raised by the isolated Tarahumara communities of Chihuahua, Mexico, for nearly 500 years, mostly under natural selection and minimal management. RC cattle were introduced to the United States Department of Agriculture-Agricultural Research Service Jornada Experimental Range (RCJER) in 2005 to begin evaluations of beef production performance and their adaptation to the harsh ecological and climatic conditions of the Northern Chihuahuan Desert. While this research unveiled crucial information on their phenotypic plasticity and adaptation, the genetic diversity and structure of the RCJER population remains poorly understood. This study analyzed the genetic diversity, population structure, ancestral composition, and selection signatures of the RCJER herd using a ~64 K SNP array. The RCJER herd exhibits moderate genetic diversity and low population stratification with no evident clustering, suggesting a shared genetic background among different subfamilies. Admixture analysis revealed the RCJER herd represents a distinctive genetic pool within the Criollo cattle breeds, with significant Iberian ancestry. Selection signatures identified candidate genes and quantitative trait loci (QTL) for traits associated with milk composition, growth, meat and carcass, reproduction, metabolic homeostasis, health, and coat color. The RCJER population represents a distinctive genetic resource adapted to harsh environmental conditions while maintaining productive and reproductive attributes. These findings are crucial to ensuring the long-term genetic conservation of the RCJER and their strategic expansion into locally adapted beef production systems in the USA.