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Paratuberculosis is a chronic disease of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). It occurs worldwide and causes a significant loss in the animal production industry. There is no cure for MAP infection and vaccination is problematic. Identification of genetics of susceptibility could be a useful adjunct for programs that focus on management, testing and culling of diseased animals. A case-control, genome-wide association study (GWAS) was conducted using Holstein and Jersey cattle in a combined analysis in order to identify markers and chromosomal regions associated with susceptibility to MAP infection across-breed. A mixed-model method (GRAMMAR-GC) implemented in the GenABEL R package and a Bayes C analysis implemented in GenSel software were used as alternative approaches to conduct GWAS analysis focused on single SNPs and chromosomal segments, respectively. After conducting quality control, 22 406 SNPs from 2157 individuals were available for the GRAMMAR-GC (Bayes C) analysis and 45 640 SNPs from 2199 individuals were available for the Bayes C analysis. One SNP located on BTA27 (8·6 Mb) was identified as moderately associated (P < 5 × 10-5, FDR = 0·44) in the GRAMMAR-GC analysis of the combined breed data. Nine 1 Mb windows located on BTA 2, 3 (3 windows), 6, 8, 25, 27 and 29 each explained ≥1% of the total proportion of genetic variance in the Bayes C analysis. In an analysis ignoring differences in linkage phase, two moderately significantly associated SNPs were identified; ARS-BFGL-NGS-19381 on BTA23 (32 Mb) and Hapmap40994-BTA-46361 on BTA19 (61 Mb). New common genomic regions and candidate genes have been identified from the across-breed analysis that might be involved in the immune response and susceptibility to MAP infection.

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The target area of this study was the South Sinai region, 200 km North East of Cairo, located at 29°35′30″N 32°42′20″E and extends about 50 km in length with approximately 20 km depth. Data were collected during year 2012-2013 as a part of the improving livestock in Sinai Program funded by Desert Research Center, Ministry of Agriculture, Egypt. A total of 125 owners (25 owners from 5 locations) was involved in a specific questionnaire sheet covering all possible livestock diversity and distribution, their productive and reproductive performance, flock and pasture management, phenotype characterization and internal parasites information. The five studied locations were Wadi-Sudr, Wadi-Abousouria, El-Bagha, El-Rena We El-Nhyat and Sadat. Results of such survey study showed that livestock population in South Sinai is mainly contributed by goats (58%), followed by sheep (38%) and the least was camels (2%), cattle (1%) and buffaloes (1%). One commercial farm of 2000 head of broilers was contributed 60% of poultry in the target studied area, followed by local (Baladi) chicken (25%), ducks (10%) and least was barbeque (5%). Average number of goats, contributing to the flock structure is greater than that of sheep, the ratio being 2.2:1. The amount of goat milk is about 0.2-0.6 kg per day. Chemical analysis of goat milk as % was 12.89 total solid, 4.16 fat and 3.54 protein. Camels are generally used for milk and meat production. It could be concluded that livestock production system of the target area depend on small ruminants and camels production. Grazing area was not sufficient for small ruminants and camels feeding requirements. Sheep had a higher percentage of infection of internal parasites than goats in the studied area.

A dynamic flock model (DFM) of intensive Barki sheep production system in Matrouh Governorate is presented. The model studies the complexity of the reproduction management systems of three lambing in two years and the productive efficiency and financial return. The data for three production cycles were collected during 2006-2009 from a Barki flock of the Sustainable Development Center for Matrouh Resources, Desert Research Center, Ministry of Agriculture. The flock size was started by 367 yearling ewes, all joined for first time in September, 2006 with 30 fertile rams in matting groups. According to the first meeting result, the ewes divided into two batches. First batch including the pregnant ewes and other including non pregnant ewes. Productive traits studied were lambing %, weaning %, twining %, mortality % from birth to weaning%, number of ewe joined, number of ewe lambing, number of lambs born, number of lambs weaned and replacement rate of yearling ewes. Financial indicators considered for each production cycle were gross output of flock product (lambs sold, wool, manure and culling animals) and gross margin. Input/output data of both batch's productivity and financial were analyzed at each phase corresponded to the characterization of the each batch flock. The results showed that The overall average of lambing %, weaning %, twining % and mortality from birth to weaning% were 86%, 98%,5% and 9%, respectively. The differences of gross margin ranged between-32625 LE in first cycle to 21748 LE in third cycle. The gross output of lambs, wool, manure and culling animals in first production cycle was about 87%, 2%, 11% and 0%, respectively of the total gross output. While, in second production cycle was 71%, 2%, 9% and 18%, respectively and in third production cycle was 67%, 2%, 11% and 21%, respectively. It could be concluded that productive studied traits were better than investigated by other research paper, except that weaning %, which led to less sold lambs, which effected on financial return. Finally, could be investigated that intensification Barki sheep production system in Matrouh governorate was not satisfied income, because the gross margin contributed-23%, 8% and 12% for three studied production cycles, respectively.