High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice

Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes fro...

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Autores principales: Fei Li, Zhenyun Han, Weihua Qiao, Junrui Wang, Yue Song, Yongxia Cui, Jiaqi Li, Jinyue Ge, Danjing Lou, Weiya Fan, Danting Li, Baoxuan Nong, Zongqiong Zhang, Yunlian Cheng, Lifang Zhang, Xiaoming Zheng, Qingwen Yang
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Publicado: Frontiers Media S.A. 2021
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Acceso en línea:https://doaj.org/article/8926d1a9315f4aeab5b74208678e1713
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spelling oai:doaj.org-article:8926d1a9315f4aeab5b74208678e17132021-11-19T05:19:10ZHigh-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice1664-462X10.3389/fpls.2021.775051https://doaj.org/article/8926d1a9315f4aeab5b74208678e17132021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fpls.2021.775051/fullhttps://doaj.org/toc/1664-462XGenes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F2 population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.Fei LiZhenyun HanWeihua QiaoJunrui WangJunrui WangYue SongYongxia CuiYongxia CuiJiaqi LiJiaqi LiJinyue GeDanjing LouWeiya FanDanting LiBaoxuan NongZongqiong ZhangYunlian ChengLifang ZhangXiaoming ZhengQingwen YangFrontiers Media S.A.articleweedy ricegenetic mapQTL mappingreference genomecomparative genomicsPlant cultureSB1-1110ENFrontiers in Plant Science, Vol 12 (2021)
institution DOAJ
collection DOAJ
language EN
topic weedy rice
genetic map
QTL mapping
reference genome
comparative genomics
Plant culture
SB1-1110
spellingShingle weedy rice
genetic map
QTL mapping
reference genome
comparative genomics
Plant culture
SB1-1110
Fei Li
Zhenyun Han
Weihua Qiao
Junrui Wang
Junrui Wang
Yue Song
Yongxia Cui
Yongxia Cui
Jiaqi Li
Jiaqi Li
Jinyue Ge
Danjing Lou
Weiya Fan
Danting Li
Baoxuan Nong
Zongqiong Zhang
Yunlian Cheng
Lifang Zhang
Xiaoming Zheng
Qingwen Yang
High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice
description Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F2 population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.
format article
author Fei Li
Zhenyun Han
Weihua Qiao
Junrui Wang
Junrui Wang
Yue Song
Yongxia Cui
Yongxia Cui
Jiaqi Li
Jiaqi Li
Jinyue Ge
Danjing Lou
Weiya Fan
Danting Li
Baoxuan Nong
Zongqiong Zhang
Yunlian Cheng
Lifang Zhang
Xiaoming Zheng
Qingwen Yang
author_facet Fei Li
Zhenyun Han
Weihua Qiao
Junrui Wang
Junrui Wang
Yue Song
Yongxia Cui
Yongxia Cui
Jiaqi Li
Jiaqi Li
Jinyue Ge
Danjing Lou
Weiya Fan
Danting Li
Baoxuan Nong
Zongqiong Zhang
Yunlian Cheng
Lifang Zhang
Xiaoming Zheng
Qingwen Yang
author_sort Fei Li
title High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice
title_short High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice
title_full High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice
title_fullStr High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice
title_full_unstemmed High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice
title_sort high-quality genomes and high-density genetic map facilitate the identification of genes from a weedy rice
publisher Frontiers Media S.A.
publishDate 2021
url https://doaj.org/article/8926d1a9315f4aeab5b74208678e1713
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