Analysis of evolutionary relationships provides new clues to the origins of weedy rice

Abstract Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR)...

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Autores principales: Bing Han, Xiaoding Ma, Di Cui, Yanjie Wang, Leiyue Geng, Guilan Cao, Hui Zhang, Hee‐Jong Koh, Longzhi Han
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Publicado: Wiley 2020
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Acceso en línea:https://doaj.org/article/b05cab57c5b647ee84c10abd7864a66b
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spelling oai:doaj.org-article:b05cab57c5b647ee84c10abd7864a66b2021-11-04T13:06:09ZAnalysis of evolutionary relationships provides new clues to the origins of weedy rice2045-775810.1002/ece3.5948https://doaj.org/article/b05cab57c5b647ee84c10abd7864a66b2020-01-01T00:00:00Zhttps://doi.org/10.1002/ece3.5948https://doaj.org/toc/2045-7758Abstract Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR), improved rice (IR) cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that WR populations have the highest level of genetic diversity (He = 0.8386) and can be divided into two groups (japonica‐type and indica‐type). The japonica‐type WR accessions from Heilongjiang province (HLJ), Jilin province (JL), Liaoning province (LN), and NX provinces clustered with the landraces grown in these same provinces. The indica‐types from Jiangsu province (JS) also clustered with the indica‐type landraces from JS province. Comparative transcriptome analysis of WR‚ IR and LR from HLJ, JL, and LN provinces showed that the WR still clustered with the LR, and that the IR lines comprise a single population. Thirty‐two differentially expressed genes were shared by the IR and LR groups as well as between the IR and WR groups. Using Gene ontology (GO) analysis, we identified 19 shared GO terms in the IR and LR groups as well as between the IR and WR groups. Our results suggest that WR populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN provinces suggests that IR populations have become a end point in the evolution of WR, which provides a new perspective for the study of WR origins and lays a solid foundation for rice breeding.Bing HanXiaoding MaDi CuiYanjie WangLeiyue GengGuilan CaoHui ZhangHee‐Jong KohLongzhi HanWileyarticlecomparative transcriptome analysisgenetic diversityhaplotype analysisweedy riceEcologyQH540-549.5ENEcology and Evolution, Vol 10, Iss 2, Pp 891-900 (2020)
institution DOAJ
collection DOAJ
language EN
topic comparative transcriptome analysis
genetic diversity
haplotype analysis
weedy rice
Ecology
QH540-549.5
spellingShingle comparative transcriptome analysis
genetic diversity
haplotype analysis
weedy rice
Ecology
QH540-549.5
Bing Han
Xiaoding Ma
Di Cui
Yanjie Wang
Leiyue Geng
Guilan Cao
Hui Zhang
Hee‐Jong Koh
Longzhi Han
Analysis of evolutionary relationships provides new clues to the origins of weedy rice
description Abstract Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR), improved rice (IR) cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that WR populations have the highest level of genetic diversity (He = 0.8386) and can be divided into two groups (japonica‐type and indica‐type). The japonica‐type WR accessions from Heilongjiang province (HLJ), Jilin province (JL), Liaoning province (LN), and NX provinces clustered with the landraces grown in these same provinces. The indica‐types from Jiangsu province (JS) also clustered with the indica‐type landraces from JS province. Comparative transcriptome analysis of WR‚ IR and LR from HLJ, JL, and LN provinces showed that the WR still clustered with the LR, and that the IR lines comprise a single population. Thirty‐two differentially expressed genes were shared by the IR and LR groups as well as between the IR and WR groups. Using Gene ontology (GO) analysis, we identified 19 shared GO terms in the IR and LR groups as well as between the IR and WR groups. Our results suggest that WR populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN provinces suggests that IR populations have become a end point in the evolution of WR, which provides a new perspective for the study of WR origins and lays a solid foundation for rice breeding.
format article
author Bing Han
Xiaoding Ma
Di Cui
Yanjie Wang
Leiyue Geng
Guilan Cao
Hui Zhang
Hee‐Jong Koh
Longzhi Han
author_facet Bing Han
Xiaoding Ma
Di Cui
Yanjie Wang
Leiyue Geng
Guilan Cao
Hui Zhang
Hee‐Jong Koh
Longzhi Han
author_sort Bing Han
title Analysis of evolutionary relationships provides new clues to the origins of weedy rice
title_short Analysis of evolutionary relationships provides new clues to the origins of weedy rice
title_full Analysis of evolutionary relationships provides new clues to the origins of weedy rice
title_fullStr Analysis of evolutionary relationships provides new clues to the origins of weedy rice
title_full_unstemmed Analysis of evolutionary relationships provides new clues to the origins of weedy rice
title_sort analysis of evolutionary relationships provides new clues to the origins of weedy rice
publisher Wiley
publishDate 2020
url https://doaj.org/article/b05cab57c5b647ee84c10abd7864a66b
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