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Badass Chinese sheep quickly evolved adaptations to extreme plateau and desert environments—New study


TibetanSheep_Crienglish

Native Chinese sheep breeds, one of which is seen here grazing on the Tibetan Plateau, are serving as a climate change bellwether (photo credit: CRIENGLISH.com).

To paraphrase Luigi Guarino in his new and lively Science Blog series for the Crop Trust, with food demand estimated to increase by anywhere from 50–70% by 2050 (read Guarino for why the great spread in estimations), and with climate change bearing down upon us, manifested in more unpredictable and extreme climates, crop breeders will have to work faster and smarter, using all the tools at their disposal, to keep the world fed. And they will need all the diversity they can get their hands on. That’s the raw material of crop improvement, Guarino reminds us.

The same goes for livestock improvement, only, unlike the case for crop varieties, we have no similar genebanks storing the diversity of animals that would allow us to pull out of the freezer a whole goat or camel, say, the breed of which had disappeared from the world’s fields. Once gone, these animals are gone for good.

That’s one of the reasons that livestock genetics is such an important area of study. The world is losing its diverse livestock breeds at a rapid clip (estimated by the Food and Agriculture Organization of the United Nations at an average loss of two breeds every week). If we want to understand the genetics underlying the ability of some animals to withstand great heat or cold, or to resist some diseases, or to thrive on scarce water or poor fodder, we need to be conducting those investigations today, while we still have a diversity of farm animals to investigate. And most of those diverse animals are being raised in developing countries.

Among the scientists focusing on the developing world’s remaining rich farmyard diversity is Han Jianlin, who is based in Beijing. Jianlin is a livestock geneticist on joint appointment at the International Livestock Research Institute (ILRI) and the Chinese Academy of Agricultural Sciences (CAAS)-ILRI Joint Laboratory on Livestock and Forage Genetic Resources (JLLFGR), which is housed in CAAS’ Institute of Animal Science. Jianlin is one of 22 Chinese authors of a new paper published in the scientific journal Molecular Biology and Evolution (7 Jul 2016, advance access).

In this paper, the authors say, ‘Through comparisons of the genomes of sheep from extreme environments with those from contrasting environments, we aimed to identify the candidate genes, functional Gene Ontology (GO) categories and signaling pathways responsible for the rapid adaptations (i.e., over thousands of years) of sheep to plateau and desert environments. Additionally, to elucidate the evolutionary history of Chinese native sheep, a comprehensive analysis of the genomic diversity, population structure and demographic history of these animals was performed based on genomic data.’

The findings in a nutshell

  • Comparisons of the whole genomes of native sheep from extreme environments and contrasting reference conditions revealed a variety of novel genes, important pathways and GO categories associated with local adaptations of sheep in plateau and desert environments
  • These results advance our understanding of the genetic mechanisms underlying the rapid adaptations of sheep and other livestock species, particularly small ruminants, to survive in similar extreme environments
  • The genomic data generated in this study will serve as a valuable resource for genomics-assisted breeding to develop new tolerant sheep breeds in the face of global climate change

***
As ILRI livestock geneticist Olivier Hanotte explains:

This study illustrates how uniquely and rapidly domesticated animals can adapt to new environments. This is key to their survival and success. This remarkable adaptation is made possible only by the great genetic diversity found within and between breeds. We have a responsibility to catalogue that diversity, to annotate it and to understand it.

This is why ILRI and its partners are shaping a new initiative to be led by the countries possessing the greatest livestock diversity. This project, dubbed the 10,000 Livestock Genome, aims to create a virtual livestock diversity biobank to catalogue and annotate, to better understand and use, the developing world’s wealth of animal genetic resources.

Those interested in supporting the 10K Livestock Genome project should contact Steve Kemp, leader of ILRI’s Animal Biosciences program (and see the program’s blog site) and LiveGene and related initiatives (s.kemp [at] cgiar.org).

***

The following extracts (some emphases added) from the paper exclude scientific references readers will find in the journal paper.

From the abstract
‘Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication.

Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8–9 kya [thousand years ago]) migration and differentiation.

‘Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ~5× for 75 samples and ~42× for two samples.

‘Comparative genomic analyses among sheep in contrasting environments, i.e., plateau (>4,000 m above sea level) versus lowland (<100 m), high-altitude region (>1,500 m) versus low-altitude region (<1,300 m), desert (<10 mm average annual precipitation) versus highly humid region (>600 mm), and arid zone (<400 mm) versus humid zone (>400 mm), detected a novel set of candidate genes as well as pathways and GO [Gene Ontology] categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. Additionally, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified.

This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change.

From the introduction
‘. . . [I]t is important to understand the genetic basis of well-adapted local livestock breeds in extreme environments to develop appropriate breeding programs under scenarios of future climate change. After domestication in the Fertile Crescent approximately 8,000–9,000 years ago, sheep (Ovis aries) spread and became adapted to a wide range of agroecological conditions, especially those distributed on plateaus or in desert regions, which are sensitive to climate change.

Thus, these animals provide an excellent model to gain novel insights into genetic mechanisms underlying the rapid adaptations of livestock to extreme environments within a short period of time.

‘In recent years, to characterize adaptive genetic variations, whole-genome sequencing studies have been performed on a wide range of organisms that live in harsh or extreme environments. Studies conducted on livestock are limited, although they include work on adaptations to high altitudes in yak, Tibetan mastiff and Tibetan chicken, hot and arid environments in goat and sheep, severe desert conditions in domestic Bactrian camel and subarctic cold environments in Yakutian horse.

However, to our knowledge, no study has characterized the rapid genetic adaptations of livestock to various extreme environments based on whole-genome sequences.

‘Out of the dispersal center in the Mongolian region, Chinese native sheep breeds only have diverged for several thousands of years . . . . In the present study, we sequenced the whole genomes of 77 sheep (Ovis aries) including those from habitats in extreme (or harsh) environments: Tibetan areas on the Qinghai-Tibetan Plateau (>4,000 m above sea level), high-altitude region (>1,500 m), Taklimakan Desert region (<10 mm average annual precipitation), and arid zone (<400 mm average annual precipitation). The set of samples represented 21 native breeds of different genetic and geographic origins in China.’

From the conclusions
‘In conclusion, comparisons of the whole genomes of native sheep from extreme environments and contrasting reference conditions revealed a variety of novel genes, important pathways and GO categories associated with local adaptations of sheep in plateau and desert environments. Specifically, the candidate genes, pathways and GO terms were functionally related to hypoxia responses in the plateau environment, water reabsorption in the desert environment, and energy metabolism and body size in both environments.

‘These results advance our understanding of the genetic mechanisms underlying the rapid adaptations of sheep and other livestock species, particularly small ruminants, to survive in similar extreme environments. The population genomic analyses of 77 Chinese native sheep and three wild species provided new insights into sheep domestication, evolution and demographic history. In particular, we found strong genomic evidence for the partitioning of Chinese native sheep into three genetic groups (Qinghai-Tibetan, Yunnan-Kweichow and Northern and Eastern Chinese breeds) as well as for their divergence and gene flow. We also detected climate-driven population size fluctuations of ancestral sheep population over the past million years. The genomic data generated in this study will serve as a valuable resource for genomics-assisted breeding to develop new tolerant sheep breeds in the face of global climate change.’

Acknowledgments
This work was financially supported by the External Cooperation Program of Chinese Academy of Sciences, the International S&T Cooperation Program of China, the Breakthrough Project of Strategic Priority Program of the Chinese Academy of Sciences, the National High Technology Research and Development Program of China, the National Transgenic Breeding Project of China, the Taishan Scholars Program of Shandong Province and grants from the National Natural Science Foundation of China.

Han Jianlin leads genetics work at the CAAS-ILRI Joint Laboratory for Livestock and Forage Genetic Resources, located within the CAAS Institute of Animal Sciences, in Beijing, China. Jianlin’s research is conducted under ILRI’s Animal Biosciences program and within the multi-institutional CGIAR Research Program on Livestock and Fish.

More information
Read the whole science paper
Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments, by Ji Yang, Wen-Rong Li, Feng-Hua Lv,, San-Gang He,, Shi-Lin Tian, Wei-Feng Peng, Ya-Wei Sun, Yong-Xin Zhao, Xiao-Long Tu, Min Zhang, Xing-Long Xie, Yu-Tao Wang, Jin-Quan Li, Yong-Gang Liu, Zhi-Qiang Shen, Feng Wang, Guang-Jian Liu, Hong-Feng Lu, Juha Kantanen, Jian-Lin Han (ILRI), Meng-Hua Li and Ming-Jun Liu, in Molecular Biology and Evolution, 7 Jul 2016 (advance access).

Read about an earlier ILRI co-authored paper on sheep genetics
DNA analysis of Asian sheep reveals unique diversity crucial to contemporary food and climate concerns, 1 Sep 2015 (ILRI News blog); Sheep genomics: ‘Sheep—A very long yarn’—Financial Times, 8 Sep 2015 (ILRI Clippings blog). Read the earlier scientific paper itself: Mitogenomic meta-analysis identifies two phases of migration in the history of eastern Eurasian sheep, by Feng-Hua Lv, Wei-Feng Peng, Ji Yang, Yong-Xin Zhao, Wen-Rong Li, Ming-Jun Liu, Yue-Hui Ma, Qian-Jun Zhao, Guang-Li Yang, Feng Wang, Jin-Quan Li, Yong-Gang Liu, Zhi-Qiang Shen, Sheng-Guo Zhao, EEr Hehua, Neena A Gorkhali, SM Farhad Vahidi, Muhammad Muladno, Arifa N Naqvi, Jonna Tabell, Terhi Iso-Touru, Michael W Bruford, Juha Kantanen, Jian-Lin Han (ILRI/JLLFGR) and Meng-Hua Li, in Molecular Biology and Evolution, 16 Jun 2015.

Learn more about the ILRI-CAAS Joint Laboratory for Livestock and Forage Genetic Resources, in Beijing.

Read more from ILRI about safeguarding livestock diversity.

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