RNA sampling time on postmortem avian carcasses in the wild

Shao, Ziying, Hou, Xian, Chen, Yangkang, Lin, Zhenzhen and Zhan, Xiangjiang 2023. RNA sampling time on postmortem avian carcasses in the wild. Wildlife Biology: A journal for wildlife science 2023 (6) , e01157. 10.1002/wlb3.01157

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Abstract

Genetic sampling, especially high‐quality RNA from wild avian populations, is challenging in wildlife biology due to rapid RNA degradation. Although carcasses could be a potential RNA source, the optimal postmortem sampling time on the avian carcasses under field conditions remains unclear. Here, we carried out a field experiment on the Qinghai‐Tibet Plateau (QTP) and evaluated the relationship between PMI and RNA degradation in three tissue types (muscle, brain, and liver) of the domestic chicken Gallus gallus domesticus carcasses. In the muscle and brain tissues, we found that the RNA Integrity Number (RIN) of samples collected within 60 h postmortem was more than 7.0, suggesting a high RNA extract quality. The following RNA‐seq experiment demonstrated that gene expression profiles of the samples collected within 36 h postmortem were comparable to those of fresh samples (i.e. 0 h), with a low percentage of differentially expressed genes (< 3.0%) observed between samples at 0 and 36 h postmortem. However, in the liver tissue, RNA samples already degraded at 12 h postmortem, showing low RIN values (< 7.0), different gene expression profiles from fresh samples, and a high percentage of differentially expressed genes (15.6%). Therefore, our study suggests that samples from muscle and brain tissues collected within 36 h postmortem are qualified for RNA‐seq analyses. In contrast, only the fresh RNA samples from liver tissue are qualified. Our study provides a practicable and efficient sampling strategy for the transcriptome study on avian populations under extreme environment such as the QTP.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Biosciences
Additional Information:	License information from Publisher: LICENSE 1: URL: http://creativecommons.org/licenses/by/3.0/
Publisher:	Nordic Society Oikos
ISSN:	0909-6396
Date of First Compliant Deposit:	2 October 2023
Date of Acceptance:	10 August 2023
Last Modified:	04 Dec 2023 14:38
URI:	https://orca.cardiff.ac.uk/id/eprint/162880

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