The aim of this study was to investigate the effect of single nucleotide polymorphisms (SNPs) of the melanogenesis associated transcription factor (MITF) and dopachrome tautomerase (DCT) genes on plumage coloration in Asian native duck breeds. MITF encodes a protein for microphthalmia-associated transcription factor, which regulates the development and function of melanocytes for pigmentation of skin, hair, and eyes. Among the tyrosinase-related family genes, DCT is a pigment cell-specific gene that plays important roles in the melanin synthesis pathway and the expression of skin, feather, and retina color. Five Asian duck varieties (black Korean native, white Korean native, commercial Peking, Nageswari, and Bangladeshi Deshi white ducks) were investigated to examine the polymorphisms associated with plumage colors. Among previously identified SNPs, three synonymous SNPs and one indel of MITF and nine SNPs in exon regions of DCT were genotyped. The allele frequencies for SNPs of the black and white plumage color populations were estimated and Fisher's exact test was conducted to assess the association between the allele frequencies of these two populations. Two synonymous SNPs (c.114T>G and c.147T>C) and a 14-bp indel (GCTGCAAAC AGATG) in intron 7 of MITF were significantly associated with the black- and white-colored breeds (pG (p.His313Arg)] in DCT, was highly significantly associated (pG) was significantly associated (p<0.05) with black and white color plumage in the studied duck populations. The results of this study provide a basis for further investigations of the associations between polymorphisms and plumage color phenotypes in Asian duck breeds.

Understanding the genetic basis of locally adapted indigenous cattle populations is essential to design appropriate strategies and programs for their genetic improvement and conservation. Here, we report genetic diversity measures, population differentiation, and structure of 218 animals sampled from six indicine cattle populations of Bangladesh. Animals were genotyped with Illumina Bovine SNP50K BeadChip along with genotyped data of 505 individuals included from 19 zebu and taurine breeds worldwide. The principal component analysis (PCA) showed clear geographic separation between taurine and indicine lineages where Bangladeshi indigenous cattle clustered with South Asian zebu populations. However, overlapped clusters in PCA, heterozygosity estimates, and Neighbor-Joining phylogenetic tree analysis revealed weak genetic differentiation among the indigenous cattle populations of Bangladesh. The admixture analysis at K = 5 and 9 suggests distinct genetic structure of the studied populations along with 1 to 4% of taurine ancestry. The effective population size suggested a limited pool of ancestors particularly for Sahiwal and North Bengal Grey cattle. In conclusion, these findings shed insights into the genetic architecture of six indigenous cattle populations of Bangladesh for the first time and suggested as distinct gene pools without potential admixture with zebu or taurine populations.

We estimated heritability (h²) 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 h² 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 h² 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 h² 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.

Objective: The objectives of this study were to investigate the genetic diversity, population structure and relatedness among the five chicken populations of Bangladesh using microsatellite markers.Methods: A total of 161 individuals representing 5 chicken populations (non-descript Deshi [ND], naked neck [NN], hilly [HI], Aseel [AS], and red jungle fowl [JF]) were included in this study to investigate genetic diversity measures, population structure, genetic distance and phylogenetic relationships. Genotyping was performed using 16 selected polymorphic microsatellite markers distributed across 10 chromosomes.Results: The average observed and expected heterozygosity, mean number of alleles and polymorphic information content were found to be 0.67±0.01, 0.70±0.01, 10.7 and 0.748, respectively in the studied populations. The estimated overall fixation index across the loci (F), heterozygote deficiency within (FIS) and among (FIT) chicken populations were 0.04±0.02, 0.05 and 0.16, respectively. Analysis of molecular variance analysis revealed 88.07% of the total genetic diversity was accounted for within population variation and the rest 11.93% was incurred with population differentiation (FST). The highest pairwise genetic distance (0.154) was found between ND and AS while the lowest distance was between JF and AS (0.084). Structure analysis depicted that the studied samples can be categorized into four distinct types or varieties (ΔK = 3.74) such as ND, NN, and HI where AS and JF clustered together as an admixed population. The Neighbor-Joining phylogenetic tree and discriminant analysis of principal component also showed close relatedness among three chicken varieties namely AS, HI, and JF.Conclusion: The results reflected that indigenous chicken of Bangladesh still possess rich genetic diversity but weak differentiation among the studied populations. This finding provides some important insight on genetic diversity measures that could support the designing and implementing of future breeding plans for indigenous chickens of Bangladesh.

Previous studies demonstrated that polymorphisms in the μ-calpain (CAPN1) and calpastatin (CAST) genes had significant effects on meat tenderness in different cattle populations. The aim of this study was to validate the potential association of seven single nucleotide polymorphisms (SNPs) harbored in these two candidate genes with meat tenderness in the Longissimus thoracis (LT) and Semimembranosus (SM) muscles. A total of 1000 animals were genotyped using TaqMan SNP genotyping arrays, and the meat tenderness of two muscle (LT and SM at 7 days post-slaughter) was assessed based on Warner-Bratzler WBSF (WBSF) testing. We observed significant associations of the CAPN1:c.580T>C, CAPN1:c.658T>C and CAST:c.1985G>C polymorphisms (p < 0.05) with the WBSF values in the LT and SM muscles. Additive effects of the C allele in CAPN1:c.580T>C and CAST:c.1985G>C were associated with an increase of 0.16 and 0.15 kg, and 0.08 and 0.26 kg WBSF in the LT and SM, respectively; CAPN1:c.658T>C had negative effects on the WBSFs. Furthermore, six reconstructed haplotypes demonstrated significant associations with WBSF values (p < 0.05). In conclusion, the significant associations identified between the SNPs in CAPN1, CAST and WBSF values could be utilized in marker-assisted selection programs in order to improve the beef tenderness of Hanwoo cattle.

Molecular characterization and A1/A2 genotyping of casein beta gene in zebu and crossbred cattle of Bangladesh | Mohammad Hasanuzzaman Pabitra, Tanvir Mohammad Maruf, Sabrina Islam Mony, Rashik Ebnat, Md. Rashedul Hoque, Mohammad Shamsul Alam Bhuiyan | Agricultural Journals