ABSTRACT
Linkage disequilibrium (LD) across the genome provides information to identify the genes and variations related to quantitative traits in genome-wide association studies (GWAS) and for the implementation of genomic selection (GS). LD can also be used to evaluate genetic diversity and population structure and reveal genomic regions affected by selection. LD structure and Ne were assessed in a set of 83 water buffaloes, comprising Azeri (AZI), Khuzestani (KHU), and Mazandarani (MAZ) breeds from Iran, Kundi (KUN) and Nili-Ravi (NIL) from Pakistan, Anatolian (ANA) buffalo from Turkey, and buffalo from Egypt (EGY). The values of corrected r 2 (defined as the correlation between two loci) of adjacent SNPs for three pooled Iranian breeds (IRI), ANA, EGY, and two pooled Pakistani breeds (PAK) populations were 0.24, 0.28, 0.27, and 0.22, respectively. The corrected r 2 between SNPs decreased with increasing physical distance from 100 Kb to 1 Mb. The LD values for IRI, ANA, EGY, and PAK populations were 0.16, 0.23, 0.24, and 0.21 for less than 100Kb, respectively, which reduced rapidly to 0.018, 0.042, 0.059, and 0.024, for a distance of 1 Mb. In all the populations, the decay rate was low for distances greater than 2Mb, up to the longest studied distance (15 Mb). The r 2 values for adjacent SNPs in unrelated samples indicated that the Affymetrix Axiom 90 K SNP genomic array was suitable for GWAS and GS in these populations. The persistency of LD phase (PLDP) between populations was assessed, and results showed that PLPD values between the populations were more than 0.9 for distances of less than 100 Kb. The Ne in the recent generations has declined to the extent that breeding plans are urgently required to ensure that these buffalo populations are not at risk of being lost. We found that results are affected by sample size, which could be partially corrected for; however, additional data should be obtained to be confident of the results.
ABSTRACT
This study was carried out to determine the effects of dietary inclusion level of canola meal (CM) on performance, organ weights and hepatic type I deiodinase gene expression in broilers. A completely randomized design with 4 levels of CM (0, 10, 20 and 30%) as a substitute for soybean meal (SBM) was utilized with 5 replicates of 9 birds each. The results showed that body weight gain (1 to 42 d) decreased linearly (P<0.01) as the inclusion of CM increased. An increase in dietary level of CM also resulted in a linear (P<0.05) increase in feed conversion ratio (1 to 42 d). Proportion of thyroids (P<0.05) and liver (P<0.01) increased linearly with increased levels of CM. A significant linear increase in right ventricular weight: total ventricular weight ratio (P<0.01) and heart weight (P<0.05) were observed by substituting CM for SBM. The concentration of plasma triiodothyronine and triiodothyronine: tetraiodothyronine ratio decreased linearly (P<0.01) with increasing level of CM. Expression of hepatic type I deiodinase gene (D1) decreased linearly (P<0.01) as inclusion level of CM in diets increased. Moreover, increasing linear (P<0.01) and quadratic responses (P<0.05) were observed in follicles number and epithelial thickness in broilers thyroids followed by increased levels of CM. In addition, increases in dietary CM inclusion led to a linear (P<0.01) increase in thyroid follicles diameters. In conclusion, the results of this study indicate that feeding increasing CM inclusions from 0 to 30% negatively affect growth performance of broiler chickens. From this study, it can also be concluded that substitution of CM for SBM adversely interferes with thyroid and liver functions and decrease D1 gene expression, likely because of higher dietary concentration of glucosinolates.
