We used data collected on 48,739 cows from 1982 to 2013 from Foka farm in the Isfahan province of Iran to assess the reasons for culling in Iranian Holstein dairy cattle in the context of breeding values of economic traits, and also to study the relationship between longevity and production traits. Estimation of (co)variance components and genetic parameters for studied traits including MY, FY, herd life (HL) and length of production life (LPL) was by AI-REML algorithm in WOMBAT software. The results showed that 27.11% of cows were culled voluntarily under the farmers’ command. The number and reasons for culling animals varied considerably over the years. Also, the results showed that involuntarily culled animals were valuable with significantly higher breeding values for MY and FY (P < .0001) than those of voluntarily culled individuals. The estimates of heritability for longevity traits (HL and LPL) were low (0.11 and 0.09), but their genetic correlation with production traits were high and positive (0.63–0.70). Our results suggest that some opportunity may exist for genetic improvements in fat and milk yield in Iranian Holsteins.

The purpose of the current study was to examine transcriptomic-based profiling of differentially expressed innate immune genes between indigenous and commercial chickens. In order to compare the transcriptome profiles of the different chicken breeds, we extracted RNA from blood samples of the Isfahan indigenous chicken (as indigenous) and Ross broiler chicken (as commercial) breeds. RNA-Seq yielded totals of 36,763,939 and 31,545,002 reads for the indigenous and commercial breeds, respectively, with clean reads then aligned to the chicken reference genome (Galgal5). Overall, 1327 genes were significantly differentially expressed, of which 1013 genes were upregulated in the commercial versus the indigenous breed, while 314 were more highly expressed in the indigenous birds. Furthermore, our results demonstrated that the SPARC, ATP6V0D2, IL4I1, SMPDL3A, ADAM7, TMCC3, ULK2, MYO6, THG1L and IRG1 genes were the most significantly expressed genes in the commercial birds and the PAPPA, DUSP1, PSMD12, LHX8, IL8, TRPM2, GDAP1L1, FAM161A, ABCC2 and ASAH2 genes were the most significant in the indigenous chickens. Of notable finding in this study was that the high-level gene expressions of heat-shock proteins (HSPs) in the indigenous breeds could serve as a guideline for future genetic improvement. This study identified genes with breed-specific expression, and comparative transcriptome analysis helped understanding of the differences in underlying genetic mechanisms between commercial and local breeds. Therefore, the current results can be used to identify candidate genes for further breed improvement.