Evaluation of non-additive genetic effects on carcass and meat quality traits in Korean Hanwoo cattle using genomic models

The traditional genetic evaluation methods generally consider additive genetic effects only and often ignore non-additive (dominance and epistasis) effects that may have contributed to genetic variation of complex traits of livestock species. The available dense single nucleotide polymorphisms (SNPs) panels offer to investigate the potential benefits of including non-additive genetic effects in the genomic evaluation models. Data from 16 971 genotyped (Illumina Bovine 50 K SNP chip) Korean Hanwoo cattle were used to estimate genetic variance components and prediction accuracy of genomic breeding values (GEBVs) for four carcass and meat quality traits: carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT) and marbling score (MS). Five different genetic models were evaluated through including additive, dominance and epistatic interactions (additive by additive, A × A; additive by dominance, A × D and dominance by dominance, D × D) successively in the models. The estimates of additive genetic variances and narrow sense heritabilities (ha2) were found similar across the evaluated models and traits except when additive interaction (A × A) was included. The dominance variance estimates relative to phenotypic variance ranged from 1.7-3.4% for CWT and MS traits, whereas, they were close to zero for EMA and BFT traits. The magnitude of A × A epistatic heritability (haa2) ranged between 14.8 and 27.7% in all traits. However, heritability estimates for A × D and D × D epistatic interactions (had2 and hdd2) were quite low compared to haa2 and were contributed only 0.0-9.7% of the total phenotypic variation. In general, broad sense heritability (hG2) estimates were almost twice (ranging between 0.54 and 0.68) the ha2 for all of the investigated traits. The inclusion of dominance effects did not improve the prediction accuracy of GEBV but improved 2.0-3.0% when epistatic effects were included in the model. More importantly, rank correlation revealed that partitioning of variance components considering dominance and epistatic effects in the model would enable to re-rank of top animals with better prediction of GEBV. The present result suggests that dominance and epistatic effects could be included in the genomic evaluation model for better estimates of variance components and more accurate prediction of GEBV for carcass and meat quality traits in Korean Hanwoo cattle.

Genetic parameters of carcass and meat quality traits in different muscles (longissimus dorsi and semimembranosus) of Hanwoo (Korean cattle)

We estimated heritability () and genetic and phenotypic correlations for carcass and meat quality traits of longissimus dorsi (LD) and semimembranosus (SM) muscles in 30-mo-old Hanwoo steers. Variance and covariance components were estimated using REML procedures under univariate and bivariate models. The mean carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS) were 428.20 ± 46.30 kg, 87.38 ± 8.54 cm2, 13.00 ± 5.14 mm, and 5.21 ± 1.56, respectively. The mean CIE reflectance of meat lightness (L*), redness (a*), and yellowness (b*) were 40.01 ± 2.73, 22.37 ± 2.18, and 10.35 ± 1.46, respectively, in LD muscles and 36.33 ± 2.44, 22.91 ± 2.43, and 10.25 ± 1.65, respectively, in SM muscles. The mean Warner-Bratzler shear force (WBSF), intramuscular fat content (IMF), water-holding capacity (WHC), and protein and ash content in LD and SM muscles were 3.84 ± 0.96 and 6.52 ± 1.21 kg, 15.91 ± 4.39 and 5.10 ± 1.94%, 62.07 ± 3.38 and 71.61 ± 2.06%, 20.01 ± 1.39 and 21.34 ± 0.89%, and 0.80 ± 0.10 and 0.93 ± 0.07, respectively. The estimates of CWT, EMA, BFT, and MS were 0.51 ± 0.13, 0.45 ± 0.13, 0.29 ± 0.09, and 0.22 ± 0.08, respectively. The estimates were moderate for meat quality traits and were 0.37 ± 0.12, 0.40 ± 0.12, 0.33 ± 0.10, 0.33 ± 0.10, 0.30 ± 0.11, and 0.24 ± 0.09 for L*, WBSF, IMF, WHC, and protein and ash content, respectively, in LD muscle; estimates from SM muscle were comparatively low (0.08 ± 0.06 to 0.25 ± 0.09). Estimates of for a* and b* were also low (0.08 ± 0.06 to 0.13 ± 0.07). Carcass weight had a moderate, positive genetic correlation with EMA (0.60 ± 0.13) and a weak correlation with MS and BFT. The genetic correlations among the 3 colorimeter variants were strong and positive within and between muscles. Intramuscular fat content had moderate to strong and negative genetic correlations with WBSF (-0.49 ± 0.18), WHC (-0.99 ± 0.01), and protein (-0.93 ± 0.04) and ash content (-0.98 ± 0.06) in LD muscle, whereas the associations were less pronounced in SM muscle. In general, CWT and EMA had low genetic and phenotypic correlations with meat quality traits, which suggests that the traits are independent and have distinct genetic contributions in each muscle. Conversely, with few exceptions, meat quality traits had genetic and phenotypic correlations with MS and BFT. In conclusion, the estimated genetic parameters for carcass and meat quality traits could be used for genetic evaluation and breeding programs in Korean Hanwoo cattle populations.

Genetic Diversity and Phylogenetic Analysis of South-East Asian Duck Populations Based on the mtDNA D-loop Sequences

The maternally inherited mitochondrial DNA (mtDNA) D–loop region is widely used for exploring genetic relationships and for investigating the origin of various animal species. Currently, domestic ducks play an important role in animal protein supply. In this study, partial mtDNA D–loop sequences were obtained from 145 samples belonging to six South-East Asian duck populations and commercial duck population. All these populations were closely related to the mallard duck (Anas platyrhynchos), as indicated by their mean overall genetic distance. Sixteen nucleotide substitutions were identified in sequence analyses allowing the distinction of 28 haplotypes. Around 42.76% of the duck sequences were classified as Hap_02, which completely matched with Anas platyrhynchos duck species. The neighbor-joining phylogenetic tree also revealed that South-East Asian duck populations were closely related to Anas platyrhynchos. Network profiles were also traced using the 28 haplotypes. Overall, results showed that those duck populations D-loop haplotypes were shared between several duck breeds from Korea and Bangladesh sub continental regions. Therefore, these results confirmed that South-East Asian domestic duck populations have been domesticated from Anas platyrhynchos duck as the maternal origins.

Genetic diversity and maternal origin of Bangladeshi chicken

Local domestic chicken populations are of paramount importance as a source of protein in developing countries. Bangladesh possesses a large number of native chicken populations which display a broad range of phenotypes well adapted to the extreme wet and hot environments of this region. This and the fact that wild jungle fowls (JFs) are still available in some regions of the country, it urges to study the present genetic diversity and relationships between Bangladeshi autochthonous chicken populations. Here, we report the results of the mitochondrial DNA (mtDNA) sequence polymorphisms analyses to assess the genetic diversity and possible maternal origin of Bangladeshi indigenous chickens. A 648-bp fragment of mtDNA control region (D-loop) was analyzed in 96 samples from four different chicken populations and one red JF population. Sequence analysis revealed 39 variable sites that defined 25 haplotypes. Estimates of haplotype and nucleotide diversities ranged from 0.745 to 0.901 and from 0.011 to 0.016, respectively. The pairwise differences between populations ranged from 0.091 to 1.459 while most of the PhiST (ΦST) values were significant. Furthermore, AMOVA analysis revealed 89.16 % of the total genetic diversity was accounted for within population variation, indicating little genetic differentiation among the studied populations. The median network analysis from haplotypes of Bangladeshi chickens illustrated five distinct mitochondrial haplogroups (A, D, E, F and I). Individuals from all Bangladeshi chicken populations were represented in the major clades D and E; those maternal origins are presumed to be from Indian Subcontinent and Southeast Asian countries, more particularly from South China, Vietnam, Myanmar and Thailand. Further, phylogenetic analysis between indigenous chicken populations and sub-species of red JFs showed G. g. gallus and G. g. spadiceus shared with almost all haplogroups and had major influence than G. g. murghi in the origin of indigenous chicken of Bangladesh. These results suggest that Bangladeshi indigenous chickens still have abundant genetic diversity and have originated from multiple maternal lineages, and further conservation efforts are warranted to maintain the diversity.

Amides from Streptomyces hygroscopicus and their antimicrobial activity [corrected]

Three amides, N-salicyloyl-2-aminopropan-1,3-diol (1) and 1-acetyl-N-salicyloyl-2-aminopropan-3-ol (2) including a natural product, N-salicyloyl-2-aminopropan-1-ol (3) were isolated from an ethyl acetate extract of the culture filtrate of Streptomyces hygroscopicus [corrected] The structures of these compounds were unambiguously established by interpretation of their spectral data including, a series of 1D and 2D-NMR and MS analyses. Compounds 1-3 showed significant antibacterial activity against a wide range of Gram positive and Gram negative bacteria.