In this study, we aimed to elucidate the origin of domestic chickens and their evolutionary history over the course of their domestication. We conducted a large-scale genetic study using mitochondrial DNA D-loop sequences and 28 microsatellite DNA markers to investigate the diversity of 298 wild progenitor red junglefowl (Gallus gallus) across two subspecies (G. g. gallusandG. g. spadiceus) from 12 populations and 138 chickens from 10 chicken breeds indigenous to Thailand. Twenty-nine D-loop sequence haplotypes were newly identified: 14 and 17 for Thai indigenous chickens and red junglefowl, respectively. Bayesian clustering analysis with microsatellite markers also revealed high genetic diversity in the red junglefowl populations. These results suggest that the ancestral populations of Thai indigenous chickens were large, and that a part of the red junglefowl population gene pool was not involved in the domestication process. In addition, some haplogroups that are distributed in other countries of Southeast Asia were not observed in either the red junglefowls or the indigenous chickens examined in the present study, suggesting that chicken domestication occurred independently across multiple regions in Southeast Asia.

The objective of this study was to estimate variance components and genetic parameters for lactation milk yield (LY), lactation length (LL), average milk yield per day (YD), initial milk yield (IY), peak milk yield (PY), days to peak (DP) and parameters (ln(a) and c) of the modified incomplete gamma function (MIG) in an Ethiopian multibreed dairy cattle population. The dataset was composed of 5,507 lactation records collected from 1,639 cows in three locations (Bako, Debre Zeit and Holetta) in Ethiopia from 1977 to 2010. Parameters for MIG were obtained from regression analysis of monthly test-day milk data on days in milk. The cows were purebred (Bos indicus) Boran (B) and Horro (H) and their crosses with different fractions of Friesian (F), Jersey (J) and Simmental (S). There were 23 breed groups (B, H, and their crossbreds with F, J, and S) in the population. Fixed and mixed models were used to analyse the data. The fixed model considered herd-year-season, parity and breed group as fixed effects, and residual as random. The single and two-traits mixed animal repeatability models, considered the fixed effects of herd-year-season and parity subclasses, breed as a function of cow H, F, J, and S breed fractions and general heterosis as a function of heterozygosity, and the random additive animal, permanent environment, and residual effects. For the analysis of LY, LL was added as a fixed covariate to all models. Variance components and genetic parameters were estimated using average information restricted maximum likelihood procedures. The results indicated that all traits were affected (p<0.001) by the considered fixed effects. High grade B×F cows (3/16B 13/16F) had the highest least squares means (LSM) for LY (2,490±178.9 kg), IY (10.5±0.8 kg), PY (12.7±0.9 kg), YD (7.6±0.55 kg) and LL (361.4±31.2 d), while B cows had the lowest LSM values for these traits. The LSM of LY, IY, YD, and PY tended to increase from the first to the fifth parity. Single-trait analyses yielded low heritability (0.03±0.03 and 0.08±0.02) and repeatability (0.14±0.01 to 0.24±0.02) estimates for LL, DP and parameter c. Medium heritability (0.21±0.03 to 0.33±0.04) and repeatability (0.27±0.02 to 0.53±0.01) estimates were obtained for LY, IY, PY, YD and ln(a). Genetic correlations between LY, IY, PY, YD, ln(a), and LL ranged from 0.59 to 0.99. Spearman's rank correlations between sire estimated breeding values for LY, LL, IY, PY, YD, ln(a) and c were positive (0.67 to 0.99, p<0.001). These results suggested that selection for IY, PY, YD, or LY would genetically improve lactation milk yield in this Ethiopian dairy cattle population.

A genome-wide association study was performed for milk yield per lactation (MY), initial yield (IY), peak yield (PY), persistency (PS) and age at first calving (AFC) in a Thai multibreed dairy cattle population. The dataset contained 1305 first-lactation cows raised on 188 farms located in Central, Northeastern and Southern Thailand. Cows were genotyped with GeneSeek Genomic Profiler low-density bead chips (8810 single nucleotide polymorphism [SNP]; n = 1255) and with high-density bead chips (76,883 SNP; n = 50). The single SNP association analyses utilized 8096 SNPs in common between the low and high density GeneSeek chips. The mixed model contained the fixed effects of contemporary group, fraction of non-Holstein breeds, age at first calving and gene content, and the random effects of animal and residual. Computations were done with the QXPAK.5 software. The number of SNPs associated with MY, IY, PY, PS and AFC at the significant threshold level of p < 0.00001 were 75, 102, 145, 74 and 24, respectively. Of the 366 SNP markers significantly associated with the studied traits, 54 (14.75%) were associated with two traits and 312 (85.25%) with only one trait, and all but one of the 54 SNPs associated with two traits affected MY and lactation characteristics. Genetic improvement of Thai dairy cows for lactation characteristics, milk yield and age at first calving could be aided by selecting animals with the SNP markers found to be highly associated with genes influencing these traits