The genetic bases of demographic changes and artificial selection underlying domestication are of great interest in evolutionary biology. Here we perform whole-genome sequencing of multiple grey wolves, Chinese indigenous dogs and dogs of diverse breeds. Demographic analysis show that the split between wolves and Chinese indigenous dogs occurred 32,000 years ago and that the subsequent bottlenecks were mild. Therefore, dogs may have been under human selection over a much longer time than previously concluded, based on molecular data, perhaps by initially scavenging with humans. Population genetic analysis identifies a list of genes under positive selection during domestication, which overlaps extensively with the corresponding list of positively selected genes in humans. Parallel evolution is most apparent in genes for digestion and metabolism, neurological process and cancer. Our study, for the first time, draws together humans and dogs in their recent genomic evolution.

Coat color in dog breeds is an excellent character for revealing the power of artificial selection, as it is extremely diverse and likely the result of recent domestication. Coat color is generated by melanocytes, which synthesize pheomelanin (a red or yellow pigment) or eumelanin (a black or brown pigment) through the pigment type-switching pathway, and is regulated by three genes in dogs: MC1R (melanocortin receptor 1), CBD103 (β-defensin 103), and ASIP (agouti-signaling protein precursor). The genotypes of these three gene loci in dog breeds are associated with coat color pattern. Here, we resequenced these three gene loci in two Kunming dog populations and analyzed these sequences using population genetic approaches to identify evolutionary patterns that have occurred at these loci during the recent domestication and breeding of the Kunming dog. The analysis showed that MC1R undergoes balancing selection in both Kunming dog populations, and that the Fst value for MC1R indicates significant genetic differentiation across the two populations. In contrast, similar results were not observed for CBD103 or ASIP. These results suggest that high heterozygosity and allelic differences at the MC1R locus may explain both the mixed color coat, of yellow and black, and the difference in coat colors in both Kunming dog populations.

The Kunming dog is the first and only working dog breed from China to be recognized worldwide. As a domestic working dog, its excellent working performance has been well established; however, its normal reproductive parameters are not well understood. Therefore, this study was conducted to document the main reproductive parameters of this purebred working dog in field breeding conditions. Data on 1004 heats (753 with mating) from 203 bitches between 2008 to 2014, were collected and analyzed. The pregnancy rate and whelping rate was 79.42% and 75.30%, respectively. Finally, for 567 litters (4298 puppies), the mean litter size was 7.19 ± 0.12 puppies (range 1-15). The mean gestation period and birth weight were approximately 61.64 ± 0.10 days and 407.25 ± 1.21 g. The mean sex ratio was 1.03 males to 1.00 female. Estrus occurred throughout the year with no significant differences between seasons and months (P > 0.05), which confirms that Kunming dogs are non-seasonal breeders; births occurred in every month of the year. Pregnant bitches exhibited significantly longer inter-estrus intervals than non-pregnant bitches (220.85 ± 2.05 vs. 180.19 ± 2.94 days, P < 0.05). Bitch parity influenced litter size, and the gestation length and birth weight of the puppies were negatively affected by litter size. This study helps elucidate the reproductive potential of this breed and provides reference values for reproductive performance in the Kunming dog.

Low temperature at the booting stage in rice (Oryza sativa L.) can cause male sterility, resulting in yield losses. A set of chromosome segment substitution lines derived from the varieties Sasanishiki (cold-tolerant, ssp. japonica) and Habataki (cold-susceptible, ssp. indica) was used for analysis across two natural, low-temperature environments to study the genetic basis for cold tolerance at the booting stage. Spikelet fertility was used as the evaluation index for cold tolerance identification. Eight quantitative trait loci (QTLs) for cold tolerance were detected, two of which were located on chromosomes 3 (qCTSF3.1 and qCTSF3.2), and the others on chromosomes 4 (qCTSF4), 5 (qCTSF5), 6 (qCTSF6), 7 (qCTSF7), 8 (qCTSF8) and 9 (qCTSF9). The phenotypic variation explained by each QTL ranged from 5.4% to 25.3%. Of the eight QTLs, six (qCTSF3.2, qCTSF5, qCTSF6, qCTSF7, qCTSF8, qCTSF9) were repeatedly detected in two environments. QTLs qCTSF3.1, qCTSF7 and qCTSF9 overlapped with previously reported QTLs. All tolerant alleles for all QTLs were contributed by Sasanishiki.