Signatures of selection reveal candidate genes involved in production traits in Chinese crossbred buffaloes

Identification of selection signature is important for a better understanding of genetic mechanisms that affect phenotypic differentiation in livestock. However, the genome-wide selection responses have not been investigated for the production traits of Chinese crossbred buffaloes. In this study, an SNP data set of 133 buffaloes (Chinese crossbred buffalo, n = 45; Chinese local swamp buffalo, n = 88) was collected from the Dryad Digital Repository database (https://datadryad.org/stash/). Population genetics analysis showed that these buffaloes were divided into the following 2 groups: crossbred buffalo and swamp buffalo. The crossbred group had higher genetic diversity than the swamp group. Using 3 complementary statistical methods (integrated haplotype score, cross population extended haplotype homozygosity, and composite likelihood ratio), a total of 31 candidate selection regions were identified in the Chinese crossbred population. Here, within these candidate regions, 25 genes were under the putative selection. Among them, several candidate genes were reported to be associated with production traits. In addition, we identified 13 selection regions that overlapped with bovine QTLs that were mainly involved in milk production and composition traits. These results can provide useful insights regarding the selection response for production traits of Chinese crossbred buffalo, as identified candidate genes influence production performance.

Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk production traits in Chinese buffalo breeds

The water buffalo is an important dual-purpose livestock that is widespread throughout central and southern China. However, there has been no characterization of the population genetics of Chinese buffalo. Using an Axiom buffalo genotyping array (Thermo Fisher Scientific, Wilmington, DE), we analyzed the genetic diversity, linkage disequilibrium pattern, and signature of selection in 176 Chinese buffaloes from 13 breeds. A total of 35,547 SNP passed quality control and were used for further analyses. Population genetic analysis revealed a clear separation between swamp and river types. Ten Chinese indigenous breeds were clustered into the swamp group, the Murrah and Nili-Ravi breeds were clustered into the river group, and the crossbred breed was closer to the river group. Genetic diversity analysis showed that the swamp group had a lower average expected heterozygosity. Linkage disequilibrium decay distance was much shorter in the swamp group compared with the river group, with an average square of correlation coefficient value of 0.2 of approximately 50 kb. Analysis of runs of homozygosity indicated extensive remote and recent inbreeding within swamp and river groups, respectively. Moreover, one genomic region under selection was detected between the river and swamp groups. Our findings contribute to our understanding of the characterization of population genetics in Chinese buffaloes, which in turn may be used in buffalo breeding programs.

The role of the killer cell immunoglobulin-like receptor (KIR) "missing self" model in unrelated donor HSCT: a meta-analysis

Some studies have found that donor-recipient killer cell immunoglobulin g-like receptor (KIRs) ligand compatibility or incompatibility influences the prognosis of hematopoietic stem cell transplantation between unrelated individuals, although the conclusions of these studies are controversial. We performed a meta-analysis concerning unrelated donor transplantation with donor-recipient KIRs compatible or incompatible. A higher 5-year overall survival rate (odds ratio [OR] = 1.93, 95% confidence interval [CI] = 1.03 to 3.61, P = .04) was found in KIR-mismatched transplantations; however, no difference was observed in the incidence of grade 2 to 4 acute graft-vs-host disease (OR = 0.94, 95% CI = 0.71 to 1.24, P = .64), 5-year relapse rate (OR = 1.05, CI = 0.75 to 1.47, P = .77), or transplantation/treatment-related mortality (OR = 0.61, CI = 0.15 to 2.51, P = .50). Our meta-analysis confirmed that incompatibility in KIR ligands favors 5-year overall survival rate but has no effect on the incidence of grade 2 to 4 acute graft-vs-host disease, relapse, or transplantation/treatment-related mortality.

Cloning and sequencing of the rDNA gene family of the water buffalo (Bubalus bubalis)

The rDNA genes coding for ribosomal RNA in animals are complicated repeat sequences with high GC content. We amplified water buffalo rDNA gene sequences with the long and accurate (LA) PCR method, using LA Taq DNA polymerase and GC buffer, based on bioinformatic analysis of related organisms. The rDNA genes were found to consist of 9016 nucleotides, including three rRNA genes and two internal transcribed spacers (ITS), which we named 18S rRNA, ITS1, 5.8S rRNA, ITS2 and 28S rRNA. We tested and optimized conditions for cloning these complicated rDNA sequences, including specific rules of primer design, improvements in the reaction system, and selection of the DNA polymerase.