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Demography as a confounding factor to explain highly diverged loci between cultivated and wild rice

Published online by Cambridge University Press:  05 February 2024

Jinggong Xiang-Yu ,
Zhili Gu ,
Haipeng Li Open the ORCID record for Haipeng Li [Opens in a new window]  and
Bao-Rong Lu
Jinggong Xiang-Yu
Affiliation:
CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao Road 6699, Jinan 250118, China
Zhili Gu
Affiliation:
CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
Haipeng Li*
Affiliation:
CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao Road 6699, Jinan 250118, China
Bao-Rong Lu*
Affiliation:
Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, School of Life Sciences, Fudan University, Songhu Road 2005, Shanghai 200438 China
*
Corresponding authors: Haipeng Li and Bao-Rong Lu; Email: lihaipeng@sinh.ac.cn; brlu@fudan.edu.cn
Corresponding authors: Haipeng Li and Bao-Rong Lu; Email: lihaipeng@sinh.ac.cn; brlu@fudan.edu.cn
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Abstract

The domestication of rice increases the divergence between cultivated rice and its wild progenitor because of artificial selection. However, it remains unknown whether highly diverged loci in rice can be explained by neutral demographic scenarios alone. In this study, we genotyped 45 InDels (insertion/deletion) in two subspecies of Asian cultivated rice (Oryza sativa ssp. japonica and Oryza sativa ssp. indica) and their wild progenitor (O. rufipogon/O. nivara). Among them, 17 loci are highly diverged (FST > 0.4) between rice cultivars and their ancestor. We performed coalescent-based simulations on neutral demographic scenarios and found that neutral demography alone could explain the polymorphic profiles on those highly diverged loci between cultivated and wild rice. Therefore, more signatures of selection should be considered when detecting artificial selection in rice.

Keywords

artificial selectionFSTneutral demographyrice
Type
Research Article
Information
Plant Genetic Resources , Volume 22 , Issue 1 , February 2024 , pp. 45 - 49
Copyright
Copyright © The Author(s), 2024. Published by Cambridge University Press on behalf of National Institute of Agricultural Botany

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Footnotes

*

These authors contributed equally to this study.

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