The newly sequenced mitochondrial genomes of 107 Asian swamp buffalo (Bubalus bubalis carabensis) allowed the reconstruction of the matrilineal divergence since ~900 Kya. Phylogenetic trees and Bayesian skyline plots suggest a role of the glacial periods in the demographic history of swamp buffalo. The ancestral swamp-buffalo mitogenome is dated ~232 ± 35 Kya. Two major macro-lineages diverged during the 2nd Pleistocene Glacial Period (~200–130 Kya), but most (~99%) of the current matrilines derive from only two ancestors (SA1′2 and SB) that lived around the Last Glacial Maximum (~26–19 Kya). During the late Holocene optimum (11–6 Kya) lineages differentiated further, and at least eight matrilines (SA1, SA2, SB1a, SB1b, SB2a, SB2b, SB3 and SB4) were domesticated around 7–3 Kya. Haplotype distributions support an initial domestication process in Southeast Asia, while subsequent captures of wild females probably introduced some additional rare lineages (SA3, SC, SD and SE). Dispersal of domestic buffaloes created local population bottlenecks and founder events that further differentiated haplogroup distributions. A lack of maternal gene flow between neighboring populations apparently maintained the strong phylogeography of the swamp buffalo matrilines, which is the more remarkable because of an almost complete absence of phenotypic differentiation.

With the proposed global climate change, heat tolerance is becoming increasingly important to the sustainability of livestock production systems. Results from previous studies showed that variants in the prolactin releasing hormone (PRLH) (AC_000160.1:g.11764610G>A) and superoxide dismutase 1 (SOD1) (AC_000158.1:g.3116044T>A) genes play an important role in heat tolerance in African indicine cattle. However, it is unknown whether or not the mutations are associated with heat tolerance in Chinese cattle. In this study, PCR and DNA sequencing were used to genotype two missense mutations in 725 individuals of 30 cattle breeds. Analysis results demonstrated that two classes of base substitution were detected at two loci: AC_000160.1:g.11764610G>A and AC_000158.1:g.3116044T>A or T>C respectively, with amino acid substitutions arginine to histidine and phenylalanine to isoleucine or leucine. The frequencies of the G and T alleles of the two loci gradually diminished from northern groups to southern groups of native Chinese cattle, whereas the frequencies of A and A or C alleles showed a contrary pattern, displaying a significant geographical difference across native Chinese cattle breeds. Additionally, analysis of these two loci in Chinese indigenous cattle revealed that two SNPs were significantly associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (P < 0.01), suggesting that cattle with A or C alleles were distributed in regions with higher T, RH and THI. Our results suggest that the two mutations of PRLH and SOD1 genes in Chinese cattle were associated with the heat tolerance.

SummaryStature is an important quantitative trait for cattle performance, which influences herd productivity. Previous studies have reported that an SNP (AC_000171.1:g.25015640G>T, rs109815800) in Pleomorphic adenoma gene 1 (PLAG1) on chromosome 14 (CHR14) is associated with bovine stature. To validate whether rs109815800 is associated with the body height of Chinese cattle, we carried out an association analysis using 558 adult cattle samples from seven populations. Then, 1038 samples from 38 Chinese cattle breeds were used to show the geographical distribution of this variant in China. The results showed that the Q allele (G allele) increased the height of cattle. Furthermore, the frequencies of Q allele in Chinese native breeds tend to decrease from northern China to southern China, and the frequency of Q allele in two Chinese beef cattle breeds is much higher than that in another 36 Chinese local cattle breeds. Our data suggest that the prevalence of the Q allele is correlated with latitude in China.

The aim of this study was to estimate population structure and ancestry of Qinchuan cattle by genotyping 27 individuals using the GeneSeek HD 77k BeadChip, and another 1355 cattle representing breeds distributed worldwide, which had been genotyped using the Illumina Bovine 50k BeadChip. Qinchuan cattle were characterized by a dominant Bos taurus ancestry, accompanied by a considerable proportion of Bos indicus ancestry based on principal components analysis and supervised admixture analysis. A small proportion of Bos javanicus ancestry was detected as well. A similar admixture pattern in both Qinchuan and Turkish cattle breeds reflects their similar degrees of zebu introgression. Our study presents a relatively clear view of the population structure and ancestry of Qinchuan cattle, serving to benefit our understanding of this breed and leading to better targeted conservation approaches moving forward.

Numerous studies have been conducted to investigate genetic diversity, origins and domestication of donkey using autosomal microsatellites and the mitochondrial genome, whereas the male-specific region of the Y chromosome of modern donkeys is largely uncharacterized. In the current study, 14 published equine Y chromosome-specific microsatellites (Y-STR) were investigated in 395 male donkey samples from China, Egypt, Spain and Peru using fluorescent labeled microsatellite markers. The results showed that seven Y-STRs-EcaYP9, EcaYM2, EcaYE2, EcaYE3, EcaYNO1, EcaYNO2 and EcaYNO4-were male specific and polymorphic, showing two to eight alleles in the donkeys studied. A total of 21 haplotypes corresponding to three haplogroups were identified, indicating three independent patrilines in domestic donkey. These markers are useful for the study the Y-chromosome diversity and population genetics of donkeys in Africa, Europe, South America and China.

With the introduction of various subjects, such as clinical epidemiology and evidence-based medicine, the qualities and levels of Traditional Chinese Herbal Medicine (TCHM) in China improved substantially, and the processes of internationalization of Traditional Chinese Medicine (TCM) are further accelerated. Since, a variety of drug products in China have been approved for marketing in other countries, and approximately 10 products have submitted the IND application to FDA of United States, of which various Chinese herbal preparations such as compound Danshen dripping pills, Xingling granules, and HMPL-004 have been approved to be investigated in phase III clinical trials. In general, multi-center studies of TCHM are increasing with years, but most of the studies are performed in some certain country, and the actual international multi-center clinical trials are very rare. Number of SCI literatures on multi-center clinical trials of TCHM that published in the recent decade also showed increasing tendency with years, despite the evident reduction in the past 2 years due to the influence of COVID-19 pandemic. Of the multi-center clinical trials of TCHM that performed by mainland China and other oversees regions, except for Taiwan, China, nearly 70% were focused on classic Chinese medicinal formulae and Chinese patent medicine, while the other 30% were on dietary supplements and plant extracts. Facing the future, the “human experience” has attracted close attentions from researchers throughout the world. Effectively utilizing the historic “human experience” is an important method to vitalize potential of original scientific and technological resources of TCHM. Performing multi-center clinical trials with high qualities is still an essential method for TCHM in accessing the mainstream medicine market. In addition, it is also required to further improve the evaluation techniques and methods that not only meet the international standards but also meet the characteristics of TCHM. Furthermore, we should also focus on the TCHM specific clinical values and scientific reports.

Recent transcriptomic analysis of the bovine Y chromosome revealed abundant presence of multi-copy protein coding gene families on the male-specific region of the Y chromosome (MSY). Copy number variations (CNVs) of several MSY genes are closely related to semen quality and male reproduction in cattle. However, the CNVs of MSY genes in water buffalo are largely unknown. Therefore, this study aimed to investigate the CNVs of HSFY and ZNF280BY of 298 buffaloes from 17 populations distributed in China, Vietnam and Laos using quantitative PCR. Our results revealed that the median copy numbers of the HSFY and ZNF280BY genes were 47 (ranging from 20 to 145) and 269 (ranging from 73 to 974) respectively. In conclusion, this study indicated that HSFY and ZNF280BY showed abundant CNVs within swamp buffalo populations.

The swamp buffalo (Bubalus carabanensis) is mainly bred for meat, transport and rice cultivation in China and Southeast Asian countries. In the current study, we investigated the genetic diversity, maternal origin and phylogenetic relationship of swamp buffalo by analyzing 1,786 mitochondrial cytochrome b (cytb) sequences from China, Vietnam, Laos, Thailand, India and Bangladesh. Our results indicated that the swamp buffalo can be divided into two major lineages (SA and SB with the sublineages) and three rare lineages (SC, SD and SE), which showed strong geographic differentiation. The SA1 lineage represented a major domestication event, which involved population expansion. Regions III and V showed higher haplotype diversity than the other regions, indicating that the regions of Southwest China and IndoChina are potential domestication centers for the swamp buffalo. In addition, the swamp buffalo showed a closer phylogenetic relationship to tamaraw. In conclusion, our findings revealed a high level of genetic diversity and the phylogenetic pattern of the swamp buffalo.