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Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

BACKGROUND: Since its development and wide adoption in China, hybrid rice has reached the yield plateau for more than three decades. To understand the genetic basis of heterosis in rice and accelerate hybrid rice breeding, the yield performances of the elite rice hybrid, Quan-you-si-miao (QYSM) were...

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Autores principales: Zhang, Fan, Zhang, Conghe, Zhao, Xiuqin, Zhu, Shuangbing, Chen, Kai, Zhou, Guixiang, Wu, Zhichao, Li, Min, Zheng, Tianqing, Wang, Wensheng, Yan, Zhi, Fei, Qinyong, Li, Zhikang, Chen, Jinjie, Xu, Jianlong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526777/
https://www.ncbi.nlm.nih.gov/pubmed/36181551
http://dx.doi.org/10.1186/s12284-022-00595-z
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author Zhang, Fan
Zhang, Conghe
Zhao, Xiuqin
Zhu, Shuangbing
Chen, Kai
Zhou, Guixiang
Wu, Zhichao
Li, Min
Zheng, Tianqing
Wang, Wensheng
Yan, Zhi
Fei, Qinyong
Li, Zhikang
Chen, Jinjie
Xu, Jianlong
author_facet Zhang, Fan
Zhang, Conghe
Zhao, Xiuqin
Zhu, Shuangbing
Chen, Kai
Zhou, Guixiang
Wu, Zhichao
Li, Min
Zheng, Tianqing
Wang, Wensheng
Yan, Zhi
Fei, Qinyong
Li, Zhikang
Chen, Jinjie
Xu, Jianlong
author_sort Zhang, Fan
collection PubMed
description BACKGROUND: Since its development and wide adoption in China, hybrid rice has reached the yield plateau for more than three decades. To understand the genetic basis of heterosis in rice and accelerate hybrid rice breeding, the yield performances of the elite rice hybrid, Quan-you-si-miao (QYSM) were genetically dissected by whole-genome sequencing, large-scale phenotyping of 1061 recombined inbred lines (RILs) and 1061 backcross F(1) (BCF(1)) hybrids derived from QYSM’s parents across three environments and gene-based analyses. RESULTS: Genome-wide scanning of 13,847 segregating genes between the parents and linkage mapping based on 855 bins across the rice genome and phenotyping experiments across three environments resulted in identification of large numbers of genes, 639 main-effect QTLs (M-QTLs) and 2736 epistatic QTLs with significant additive or heterotic effects on the trait performances of the combined population consisting of RILs and BCF(1) hybrids, most of which were environment-specific. The 324 M-QTLs affecting yield components included 32.7% additive QTLs, 38.0% over-dominant or dominant ones with strong and positive effects and 29.3% under-dominant or incomplete recessive ones with significant negative heterotic effects. 63.6% of 1403 genes with allelic introgression from subspecies japonica/Geng in the parents of QYSM may have contributed significantly to the enhanced yield performance of QYSM. CONCLUSIONS: The parents of QYSM and related rice hybrids in China carry disproportionally more additive and under-dominant genes/QTLs affecting yield traits. Further focus in indica/Xian rice breeding should shift back to improving inbred varieties, while breaking yield ceiling of Xian hybrids can be achieved by one or combinations of the three strategies: (1) by pyramiding favorable alleles of additive genes, (2) by eliminating or minimizing under-dominant loci, and (3) by pyramiding overdominant/dominant genes polymorphic, particularly those underlying inter-subspecific heterosis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12284-022-00595-z.
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spelling pubmed-95267772022-10-28 Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations Zhang, Fan Zhang, Conghe Zhao, Xiuqin Zhu, Shuangbing Chen, Kai Zhou, Guixiang Wu, Zhichao Li, Min Zheng, Tianqing Wang, Wensheng Yan, Zhi Fei, Qinyong Li, Zhikang Chen, Jinjie Xu, Jianlong Rice (N Y) Research BACKGROUND: Since its development and wide adoption in China, hybrid rice has reached the yield plateau for more than three decades. To understand the genetic basis of heterosis in rice and accelerate hybrid rice breeding, the yield performances of the elite rice hybrid, Quan-you-si-miao (QYSM) were genetically dissected by whole-genome sequencing, large-scale phenotyping of 1061 recombined inbred lines (RILs) and 1061 backcross F(1) (BCF(1)) hybrids derived from QYSM’s parents across three environments and gene-based analyses. RESULTS: Genome-wide scanning of 13,847 segregating genes between the parents and linkage mapping based on 855 bins across the rice genome and phenotyping experiments across three environments resulted in identification of large numbers of genes, 639 main-effect QTLs (M-QTLs) and 2736 epistatic QTLs with significant additive or heterotic effects on the trait performances of the combined population consisting of RILs and BCF(1) hybrids, most of which were environment-specific. The 324 M-QTLs affecting yield components included 32.7% additive QTLs, 38.0% over-dominant or dominant ones with strong and positive effects and 29.3% under-dominant or incomplete recessive ones with significant negative heterotic effects. 63.6% of 1403 genes with allelic introgression from subspecies japonica/Geng in the parents of QYSM may have contributed significantly to the enhanced yield performance of QYSM. CONCLUSIONS: The parents of QYSM and related rice hybrids in China carry disproportionally more additive and under-dominant genes/QTLs affecting yield traits. Further focus in indica/Xian rice breeding should shift back to improving inbred varieties, while breaking yield ceiling of Xian hybrids can be achieved by one or combinations of the three strategies: (1) by pyramiding favorable alleles of additive genes, (2) by eliminating or minimizing under-dominant loci, and (3) by pyramiding overdominant/dominant genes polymorphic, particularly those underlying inter-subspecific heterosis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12284-022-00595-z. Springer US 2022-10-01 /pmc/articles/PMC9526777/ /pubmed/36181551 http://dx.doi.org/10.1186/s12284-022-00595-z Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research
Zhang, Fan
Zhang, Conghe
Zhao, Xiuqin
Zhu, Shuangbing
Chen, Kai
Zhou, Guixiang
Wu, Zhichao
Li, Min
Zheng, Tianqing
Wang, Wensheng
Yan, Zhi
Fei, Qinyong
Li, Zhikang
Chen, Jinjie
Xu, Jianlong
Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations
title Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations
title_full Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations
title_fullStr Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations
title_full_unstemmed Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations
title_short Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations
title_sort genomic architecture of yield performance of an elite rice hybrid revealed by its derived recombinant inbred line and their backcross hybrid populations
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526777/
https://www.ncbi.nlm.nih.gov/pubmed/36181551
http://dx.doi.org/10.1186/s12284-022-00595-z
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