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Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing
Indicine cattle make up half of all cattle populations worldwide. Using a large genomic dataset, this study finds historic migrations and extensive introgression with domestic and wild bovine species has facilitated this species physiological adaptation to extreme environments.
- Ningbo Chen
- , Xiaoting Xia
- & Chuzhao Lei
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Article
| Open Access
Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences
Accurate haplotypes with abundant genomic variations benefit genetic research. Here, the authors accurately construct 1,874 pig haplotypes and demonstrate their applications in genome-wide association studies, prediction of breeding values and analyses of evolutionary selection.
- Xinkai Tong
- , Dong Chen
- & Lusheng Huang
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Article
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A cattle graph genome incorporating global breed diversity
Cattle reference genomes are valuable resources but are currently heavily biased towards European breeds. Here the authors integrate assemblies for African breeds into a more representative cattle graph genome capturing global breed diversity.
- A. Talenti
- , J. Powell
- & J. G. D. Prendergast
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Article
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Pig genome functional annotation enhances the biological interpretation of complex traits and human disease
Annotating functional elements of the genome helps the interpretation of genetic variation. Here, the authors compile functional genomics data for the pig genome over 14 tissues with 15 different chromatin states, integrate the data with WGS and GWAS data, and compare conservation of regulatory elements across mouse and human tissues.
- Zhangyuan Pan
- , Yuelin Yao
- & Huaijun Zhou
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Review Article
| Open Access
Combating mosquito-borne diseases using genetic control technologies
Mosquito-borne diseases pose significant global health burdens. In this review, the authors explore Wolbachia and genome engineering approaches to mosquito-borne disease population control.
- Guan-Hong Wang
- , Stephanie Gamez
- & Omar S. Akbari
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Article
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CRISPR screening of porcine sgRNA library identifies host factors associated with Japanese encephalitis virus replication
Here the authors report the construction of a genome-scale porcine CRISPR/Cas9 library, called PigGeCKO, for screening and analyses of host resistance genes and factors associated with Japanese encephalitis virus replication.
- Changzhi Zhao
- , Hailong Liu
- & Shuhong Zhao
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Article
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Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication
The comparative genomics of domesticated lineages can yield insights into the signatures of artificial selection. This study sequences 79 water buffalo genomes from 7 breeds and reveals examples of convergent domestication at the genetic level between water buffalo and cattle.
- Prasun Dutta
- , Andrea Talenti
- & James G. D. Prendergast
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Article
| Open Access
A drug-inducible sex-separation technique for insects
Sorting insects based on sex is error prone and frequently labour intensive. Here, the authors present a drug-inducible sex separation system based on sex-specific rescue from antibotic toxicity.
- Nikolay P. Kandul
- , Junru Liu
- & Omar S. Akbari
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Article
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Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle
Taurine and indicine cattle have different desirable traits making them better adapted to different climates across the world. Here, Low et al. describe a pipeline to produce haplotype-resolved, chromosome-level genomes of Angus and Brahman cattle breeds from a crossbred individual and report on comparisons of the two genomes.
- Wai Yee Low
- , Rick Tearle
- & John L. Williams
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Article
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Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology
Being man’s best friend, dogs have been bred and selected for certain morphologic traits and breed-associated behaviours. Here, Plassais et al. analyse 722 canine whole genome sequences including modern breeds, wild canids and village dogs by GWAS and search for signatures of selection.
- Jocelyn Plassais
- , Jaemin Kim
- & Elaine A. Ostrander
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Article
| Open Access
An intercross population study reveals genes associated with body size and plumage color in ducks
Ducks, one of the most common domestic fowls, originated from mallards. Here, the authors perform whole-genome sequencing of mallards, indigenous-breed ducks, and Pekin ducks, as well as 1026 ducks from a population generated by wild × domestic crosses to identify selection signals and map variants associated with body size and plumage color.
- Zhengkui Zhou
- , Ming Li
- & Yu Jiang
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Article
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Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia
There are various indigenous cattle breeds in East Asia which have a complex history. Here, the authors analyse the genomes of 49 modern breeds and eight ancient samples and identify three distinct ancestries and multiple adaptive introgressions from other bovine species.
- Ningbo Chen
- , Yudong Cai
- & Chuzhao Lei
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Article
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Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression
Domestication of wild boar populations has led to phenotypically distinct European and Asian pig breeds. Here, the authors show that Asian haplotypes that have introgressed into European pig breeds harbour genes that control economically important traits such as meat quality, development and fertility.
- Mirte Bosse
- , Hendrik-Jan Megens
- & Martien A. M. Groenen
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Contemporary and historical separation of transequatorial migration between genetically distinct seabird populations
Migratory segregation presents a hypothesized barrier to gene flow among seabirds, but its mechanisms are unclear. Rayneret al. find that migratory habitat specialization, associated with breeding asynchrony and philopatry, restricts gene flow between two seabird populations migrating across the Pacific Ocean.
- Matt J. Rayner
- , Mark E. Hauber
- & Scott A. Shaffer
Archaeological and molecular evidence for ancient chickens in Central Asia