Inference of Admixture Origins in Indigenous African Cattle.

Present-day African cattle retain a unique genetic profile composed of a mixture of the Bos taurus and Bos indicus populations introduced into the continent at different time periods. However, details of the admixture history and the exact origins of the source populations remain obscure. Here, we infer the source of admixture in the earliest domestic cattle in Africa, African taurine. We detect a significant contribution (up to ∼20%) from a basal taurine lineage, which might represent the now-extinct African aurochs. In addition, we show that the indicine ancestry of African cattle, although most closely related to so-far sampled North Indian indicine breeds, has a small amount of additional genetic affinity to Southeast Asian indicine breeds. Our findings support the hypothesis of aurochs introgression into African taurine and generate a novel hypothesis that the origin of indicine ancestry in Africa might be different indicine populations than the ones found in North India today

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

Background CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV. Results Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs. Conclusion For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments

Author Correction: Mitonuclear incompatibility as a hidden driver behind the genome ancestry of African admixed cattle

The original article contained minor errors in Figs. 1 and 3 which have both since been corrected

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

BackgroundCNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV.ResultsHere, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs.ConclusionFor some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments

Correction to: Population diferentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

Following publication of the original article [1], the authors reported that the following missing authors from the authorship list: • Endashaw Terefe • Gurja Belay • Abdulfatai Tijjani • Jian-Lin Han • Olivier Hanotte The corrected authorship list and the updated ‘Authors’ contributions’ and ‘Acknowledgements’ declarations are provided in this Correction article. The original article [1] has been updated

High level of complexity and global diversity of the 3q29 locus revealed by optical mapping and long-read sequencing.

BACKGROUND: High sequence identity between segmental duplications (SDs) can facilitate copy number variants (CNVs) via non-allelic homologous recombination (NAHR). These CNVs are one of the fundamental causes of genomic disorders such as the 3q29 deletion syndrome (del3q29S). There are 21 protein-coding genes lost or gained as a result of such recurrent 1.6-Mbp deletions or duplications, respectively, in the 3q29 locus. While NAHR plays a role in CNV occurrence, the factors that increase the risk of NAHR at this particular locus are not well understood. METHODS: We employed an optical genome mapping technique to characterize the 3q29 locus in 161 unaffected individuals, 16 probands with del3q29S and their parents, and 2 probands with the 3q29 duplication syndrome (dup3q29S). Long-read sequencing-based haplotype resolved de novo assemblies from 44 unaffected individuals, and 1 trio was used for orthogonal validation of haplotypes and deletion breakpoints. RESULTS: In total, we discovered 34 haplotypes, of which 19 were novel haplotypes. Among these 19 novel haplotypes, 18 were detected in unaffected individuals, while 1 novel haplotype was detected on the parent-of-origin chromosome of a proband with the del3q29S. Phased assemblies from 44 unaffected individuals enabled the orthogonal validation of 20 haplotypes. In 89% (16/18) of the probands, breakpoints were confined to paralogous copies of a 20-kbp segment within the 3q29 SDs. In one del3q29S proband, the breakpoint was confined to a 374-bp region using long-read sequencing. Furthermore, we categorized del3q29S cases into three classes and dup3q29S cases into two classes based on breakpoints. Finally, we found no evidence of inversions in parent-of-origin chromosomes. CONCLUSIONS: We have generated the most comprehensive haplotype map for the 3q29 locus using unaffected individuals, probands with del3q29S or dup3q29S, and available parents, and also determined the deletion breakpoint to be within a 374-bp region in one proband with del3q29S. These results should provide a better understanding of the underlying genetic architecture that contributes to the etiology of del3q29S and dup3q29S

Identification of potential biomarkers for diagnosis of pancreatic and biliary tract cancers by sequencing of serum microRNAs

Background Pancreatic and biliary tract cancer (PC and BTC, respectively) are difficult to diagnose because of their clinical characteristics; however, recent studies suggest that serum microRNAs (miRNAs) might be the key to developing more efficient diagnostic methods for these cancers. Methods We analysed the genome-wide expression of serum miRNAs in PC and BTC patients to identify novel biomarker candidates using high-throughput sequencing and experimentally validated miRNAs on clinical samples. Results Statistical and classification analysis of the serum miRNA-expression profiles of 55 patient samples showed distinguishable patterns between cancer patients and healthy controls; however, we were unable to distinguish the two cancers. We found that three of the highest performing miRNAs were capable of distinguishing cancer patients from controls, with an accuracy of 92.7%. Additionally, dysregulation of these three cancer-specific miRNAs was demonstrated in an independent sample group by quantitative reverse transcription polymerase chain reaction. Conclusions These results suggested three candidate serum miRNAs (mir-744-5p, mir-409-3p, and mir-128-3p) as potential biomarkers for PC and BTC diagnosis.This work was supported by the Post-Genome Technology Development Program. (No. 10040174; Multiple biomarker development through validation of useful markers generated by next-generation bio-data-based genome research) funded by the Ministry of Trade, Industry, and Energy (MOTIE, Korea). The funders had no role in study design, data collection, analysis and interpretation of data, or in the writing of the manuscript

The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Cattle pastoralism plays a central role in human livelihood in Africa. However, the genetic history of its success remains unknown. Here, through whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine × indicine cattle admixture event dated to circa 750–1,050 yr ago, which has shaped the genome of today’s cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune-, heat-tolerance- and reproduction-related genes. Moreover, we identify one highly divergent locus in African taurine cattle, which is putatively linked to trypanotolerance and present in crossbred cattle living in trypanosomosis-infested areas. Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism

Pengaruh Kualitas Produk, Harga, Dan Saluran Distribusi Terhadap Loyalitas Pelanggan Majalah Swa Melalui Variabel Kepuasan Pelanggan (Studi Kasus Pada Pelanggan Majalah Swa Di DKI Jakarta)

Customer loyalty is a goal that has to be achieved by a company. To be able to get loyal customers, SWA magazine needs to pay attention on the factors that influence customers\u27 loyalty. Moreover, business and economy themed magazines are mushrooming, leading to the opportunity for the readers to move from one magazine to another.This research aimed to ascertain the effect of product quality, price, and distribution channel on customer loyalty of SWA magazine in Jakarta through customer satisfaction variable both simultaneously and partially. The hypothesis was there was an effect of product quality, price, and distribution channel on customer loyalty of SWA magazine in Jakarta through customer satisfaction variable both simultaneously and partially. The type of this research was explanatory research with 97 respondents with multi stage sampling technique through questionnaire and interview. The data was analyzed using linear regression method with the assistance of SPSS 16.0.The result of this research showed that product quality, price and distribution channel variables had significant and positive effect partially on customer satisfaction. Product quality variable did not have partially significant effect on customer loyalty. Price and distribution channel variables had partially significant and positive effect on customer loyalty. Product quality and price variables had simultaneously positive and significant effect on customer satisfaction while distribution channel had simultaneously negative effect on customer satisfaction. Simultaneously, product quality, price, and distribution channel variables had positive effect and not significant effect on customer loyalty. Partially, customer satisfaction had positive and significant effect on customer loyalty.Based on the result of this research, a conclusion was drawn that customers\u27 perception on product quality, price, and distribution channel was good. Customers\u27 satisfaction and loyalty of SWA magazine were also good. The company was suggested to improving the product quality, adjusting the price and boosting the distribution channel of SWA magazine in accordance with customers\u27 needs and expectation, so that, customers can feel the satisfaction and decided to be loyal customers

The genome landscape of indigenous African cattle

Background: The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems. Results: We analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds. We find the highest genetic diversity among African zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. In particular, we identify signatures of selection including genes and/ or pathways controlling anemia and feeding behavior in the trypanotolerant N’Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in zebu breeds. Conclusions: Our findings unravel at the genome-wide level, the unique adaptive diversity of African cattle while emphasizing the opportunities for sustainable improvement of livestock productivity on the continent