Morphological study in Azeri and Khuzestani buffaloes of Iran

In order to evaluate and compare the properties of type traits in Khuzestani and Azeri river buffaloes, 148 and 336 Khuzestani and Azeri buffaloes were used, respectively. Animals were evaluated for traits such as Height at Withers, Body depth, Body length, Heart girth, Hip width, Pin width and Hip to Pin length. The averages for these traits in Khuzestani breed were 145.2±6.63, 78.27±5.43, 140.5±10.05, 208.87±13.75, 57±4.44, 25.29±3.03 and 44±2.97 cm and in Azeri breed were 138.93±6.39, 76.4±5.61, 136.22±10.05, 184±13.66, 54.96±4.85, 26.43±3.94 and 43.8±3.44 cm, respectively. The effect of breed on height at withers, heart girth and hip width was quite significant (P<0.001) and values for these traits in Khuzestani breed was higher than Azeri. The effect of parity number for all studied traits was significant (P<0.001), except for the heart girth. Heifers had the lowest values among different age groups and differences in this group increased with increasing age and parity. Also, the effects of province as a factor for climate and culture circumstances on studied traits was quite significant (P<0.001), except for the heart girth and hip to Pin length. Buffaloes in Guilan province had lowest and buffaloes in Khuzestan and Kermanshah provinces had the highest values

The Evolution of Meganucleases Genome Engineering Tools: an overview

Human beings today have been able to pursue goals with non-random changes in the genome of living organisms. This is the process of genetic engineering or genome editing, which involves replacing, inserting, or deleting an arbitrary genomic sequence using an artificial restriction enzyme capable of cleaving a specific part of the genome. The ability to manipulate and modify genes and functional studies as well as awareness of the molecular basis of diseases and the development of new and targeted therapies with these techniques have been created. To date, different techniques have now been developed with the ability to edit targeted genomics including Zinc-finger nucleases (ZFNs), Transcription activator-like effector nucleases (TALEN) and Clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR associated protein 9 (Cas9) (CRISPR/Cas9). The fusing of a zinc-finger DNA-binding domain to a DNA-cleavage domain produces artificial restriction enzymes known as Zinc-finger nucleases (ZFNs). Zinc finger domains can be designed to target a specific DNA sequence which causes ZFNs to target unique sequences in complex genomes. TALENs are made by fusing a TAL effector DNA-binding domain to a DNA cleavage domain to cut DNA strands at specific locations. CRISPR/Cas9 is a bacterial immune system against viruses in which the Cas9 nucleus connects with a single-strand guide to a complementary target sequence and makes changes. In this study, we will review the evolution and various aspects of each one over time.</jats:p

A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds

Abstract Background Identification of genomic regions that have been targets of selection may shed light on the genetic history of livestock populations and help to identify variation controlling commercially important phenotypes. The Azeri and Kuzestani buffalos are the most common indigenous Iranian breeds which have been subjected to divergent selection and are well adapted to completely different regions. Examining the genetic structure of these populations may identify genomic regions associated with adaptation to the different environments and production goals. Results A set of 385 water buffalo samples from Azeri (N = 262) and Khuzestani (N = 123) breeds were genotyped using the Axiom® Buffalo Genotyping 90 K Array. The unbiased fixation index method (FST) was used to detect signatures of selection. In total, 13 regions with outlier FST values (0.1%) were identified. Annotation of these regions using the UMD3.1 Bos taurus Genome Assembly was performed to find putative candidate genes and QTLs within the selected regions. Putative candidate genes identified include FBXO9, NDFIP1, ACTR3, ARHGAP26, SERPINF2, BOLA-DRB3, BOLA-DQB, CLN8, and MYOM2. Conclusions Candidate genes identified in regions potentially under selection were associated with physiological pathways including milk production, cytoskeleton organization, growth, metabolic function, apoptosis and domestication-related changes include immune and nervous system development. The QTL identified are involved in economically important traits in buffalo related to milk composition, udder structure, somatic cell count, meat quality, and carcass and body weight

Additional file 1: of A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds

Least-square means and standard deviations of some morphometric and body size traits in Iranian Azeri and Khuzestani water buffalo breeds. (DOCX 19 kb

Additional file 12: of A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds

FST output file. (XLS 9242 kb

Additional file 10: of A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds

Genes included in selected regions (Biomart input & output). (XLS 105 kb

Additional file 13: of A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds

Windowed FST output file. (XLS 6816 kb

Additional file 1: of A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds

Least-square means and standard deviations of some morphometric and body size traits in Iranian Azeri and Khuzestani water buffalo breeds. (DOCX 19 kb

Additional file 8: of A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds

Genome wide distribution of iHS from Khuzestani buffalo breed values. (TXT 2864 kb

Additional file 6: of A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds

Genome wide distribution of iHS and XP-EHH plot. (PDF 349 kb