Long-range linkage disequilibrium in French beef cattle breeds

Background Linkage disequilibrium (LD) is a key parameter to study the history of populations and to identify and fine map quantitative trait loci (QTL) and it has been studied for many years in animal populations. The advent of new genotyping technologies has allowed whole-genome LD studies in most cattle populations. However, to date, long-range LD (LRLD) between distant variants on the genome has not been investigated in detail in cattle. Here, we present the first comprehensive study of LRLD in French beef cattle by analysing data on 672 Charolais (CHA), 462 Limousine (LIM) and 326 Blonde d’Aquitaine (BLA) individuals that were genotyped on the Illumina BovineHD Beadchip. Furthermore, whole-genome LD and haplotype block structure were analysed in these three breeds. Results We computed linkage disequilibrium (r2) values for 5.9, 5.6 and 6.0 billion pairs of SNPs on the 29 autosomes of CHA, LIM and BLA, respectively. Mean r2 values drop to less than 0.1 for distances between SNPs greater than 120 kb. However, for the first time, we detected the existence of LRLD in the three main French beef breeds. In total, 598, 266, and 795 LRLD events (r2 ≥ 0.6) were detected in CHA, LIM and BLA, respectively. Each breed had predominantly population-specific LRLD interactions, although shared LRLD events occurred in a number of regions (55 LRLD events were shared between two breeds and nine between the three breeds). Examples of possible functional gene interactions and QTL co-location were observed with some of these LRLD events, which suggests epistatic selection. Conclusions We identified long-range linkage disequilibrium for the first time in French beef cattle populations. Epistatic selection may be the main source of the observed LRLD events, but other forces may also be involved. LRLD information should be accounted for in genome-wide association studies.

Selecting sorting centres to avoid long distance transport of weaned beef calves

The transport of weaned calves from cow–calf producers to fatteners is a general concern for the young bull industry due to its documented negative impact on the welfare, health and performance of the animals. These transfers are often managed by intermediaries who transport weaned calves to sorting centres, where they are grouped into batches before being sent to fattening units. In this study, we present an algorithm to limiting these transfer distances by appropriately selecting the sorting centre through which they must go. We tested the effectiveness of this algorithm on historical data from a French beef producer organization managing 136,892 transfers using 13 sorting centres. The results show a decrease in the transfer distances compared to the historical record, especially for the calves travelling over long distances (− 76 km, i.e. 18% on average for the 33% longest transfers). Moreover, the distribution of calves between the sorting centres proposed by the algorithm reveals differences in their efficiency in minimizing transfer distances. In addition to its usefulness as a management tool for the daily transport of cattle, this algorithm provides prospects for improving the management of the sorting centres themselves.

Effects of crossing of domestic breed with beef breeds on the quality of meat in PR China and Republic of Serbia

This paper presents the results of crossing Domestic Spotted breed with beef cattle breeds in the People's Republic of China and the Republic of Serbia. China is a big country of beef production and consumption. In 2012, beef production in China was 5,540,000 tons, which accounted for 9.7% of the global beef production, ranking the third in the world. The main sources of China?s beef are from crossbreeding cattle (native breed crossbred with foreign beef cattle). Simmental cattle are the most-widely used beef cattle in China?s improved beef cattle. China has cultivated its own Simmental after over 40 years? crossbreeding and improvement. China?s consumers mainly have three demands for beef quality as follows: expensive beef produced from Wagyu crossbreed with better marbling; lean beef from Simmental, Charolais and Limousin crossbreeds, top parts supplied to hotels while common parts to supermarkets; veal from cow calves. Chinese researchers are carrying out researches which are centered on marbling beef, lean beef and veal on complete techniques of good breed, feeding management, slaughter and cutting and carcass classification. At present, researchers have lively interest in functional genomics of meat quality traits of cattle, they expect to use these methods to study meat quality traits and then improve the meat quality. Improved cattle breeds universally utilized in China are mainly Simmental followed by Charolais, Limousin, Wagyu and Angus. Other three cattle breeds including Belgian blue cattle, Piedmontese and Gelbvien have ever been applied, however, rarely used in present beef cattle production. Republic of Serbia has in the future to quickly and efficiently provide adequate quantities of top quality meat. One of the ways to increase the yield and quality of the meat is crossing of Domestic spotted cattle of lower production traits with French beef cattle breeds. Beef production in the EU is adapted to the consumer taste. Meat must have a light red colour, equally suffused with fat and with pronounced sensory characteristics such as tenderness, juiciness, flavour and aroma. The results on the quality of meat of F1 generation crosses (Domestic Spotted breed with French beef cattle breeds Charolais and Limousine) indicate that by industrial crossing beef, meat-packing and organoleptic characteristics of meat can be improved.