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Genomic decoding of breeding history to guide breeding-by-design in rice
Deciphering the intrinsic molecular logic of empirical crop breeding from a genomic perspective is a decisive prerequisite for breeding-by-design (BbD), but remains not well established. Here, we decoded the historical features of past rice breeding by phenotyping and haplotyping 546 accessions cove...
Autores principales: | , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10089590/ https://www.ncbi.nlm.nih.gov/pubmed/37056426 http://dx.doi.org/10.1093/nsr/nwad029 |
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author | Chen, Zhuo Bu, Qingyun Liu, Guifu Wang, Maoqing Wang, Hongru Liu, Huazhao Li, Xiufeng Li, Hong Fang, Jun Liang, Yan Teng, Zhenfeng Kang, Sai Yu, Hong Cheng, Zhukuan Xue, Yongbiao Liang, Chengzhi Tang, Jiuyou Li, Jiayang Chu, Chengcai |
author_facet | Chen, Zhuo Bu, Qingyun Liu, Guifu Wang, Maoqing Wang, Hongru Liu, Huazhao Li, Xiufeng Li, Hong Fang, Jun Liang, Yan Teng, Zhenfeng Kang, Sai Yu, Hong Cheng, Zhukuan Xue, Yongbiao Liang, Chengzhi Tang, Jiuyou Li, Jiayang Chu, Chengcai |
author_sort | Chen, Zhuo |
collection | PubMed |
description | Deciphering the intrinsic molecular logic of empirical crop breeding from a genomic perspective is a decisive prerequisite for breeding-by-design (BbD), but remains not well established. Here, we decoded the historical features of past rice breeding by phenotyping and haplotyping 546 accessions covering the majority of cultivars bred in the history of Northeast China (NEC). We revealed that three groups founded the genetic diversities in NEC rice with distinct evolution patterns and traced and verified the breeding footprints to known or genome-wide association study (GWAS)-detected quantitative trait loci (QTLs), or introgressions from indica sub-species with chronological changes in allele frequencies. Then we summarized a rice breeding trend/principle in NEC, and combined with the successful example in breeding and application of Zhongkefa5 to demonstrate the guiding value of our conclusion for BbD in practice. Our study provides a paradigm for decoding the breeding history of a specific crop to guide BbD, which may have implications in different crop breeding. |
format | Online Article Text |
id | pubmed-10089590 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-100895902023-04-12 Genomic decoding of breeding history to guide breeding-by-design in rice Chen, Zhuo Bu, Qingyun Liu, Guifu Wang, Maoqing Wang, Hongru Liu, Huazhao Li, Xiufeng Li, Hong Fang, Jun Liang, Yan Teng, Zhenfeng Kang, Sai Yu, Hong Cheng, Zhukuan Xue, Yongbiao Liang, Chengzhi Tang, Jiuyou Li, Jiayang Chu, Chengcai Natl Sci Rev Research Article Deciphering the intrinsic molecular logic of empirical crop breeding from a genomic perspective is a decisive prerequisite for breeding-by-design (BbD), but remains not well established. Here, we decoded the historical features of past rice breeding by phenotyping and haplotyping 546 accessions covering the majority of cultivars bred in the history of Northeast China (NEC). We revealed that three groups founded the genetic diversities in NEC rice with distinct evolution patterns and traced and verified the breeding footprints to known or genome-wide association study (GWAS)-detected quantitative trait loci (QTLs), or introgressions from indica sub-species with chronological changes in allele frequencies. Then we summarized a rice breeding trend/principle in NEC, and combined with the successful example in breeding and application of Zhongkefa5 to demonstrate the guiding value of our conclusion for BbD in practice. Our study provides a paradigm for decoding the breeding history of a specific crop to guide BbD, which may have implications in different crop breeding. Oxford University Press 2023-02-09 /pmc/articles/PMC10089590/ /pubmed/37056426 http://dx.doi.org/10.1093/nsr/nwad029 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Chen, Zhuo Bu, Qingyun Liu, Guifu Wang, Maoqing Wang, Hongru Liu, Huazhao Li, Xiufeng Li, Hong Fang, Jun Liang, Yan Teng, Zhenfeng Kang, Sai Yu, Hong Cheng, Zhukuan Xue, Yongbiao Liang, Chengzhi Tang, Jiuyou Li, Jiayang Chu, Chengcai Genomic decoding of breeding history to guide breeding-by-design in rice |
title | Genomic decoding of breeding history to guide breeding-by-design in rice |
title_full | Genomic decoding of breeding history to guide breeding-by-design in rice |
title_fullStr | Genomic decoding of breeding history to guide breeding-by-design in rice |
title_full_unstemmed | Genomic decoding of breeding history to guide breeding-by-design in rice |
title_short | Genomic decoding of breeding history to guide breeding-by-design in rice |
title_sort | genomic decoding of breeding history to guide breeding-by-design in rice |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10089590/ https://www.ncbi.nlm.nih.gov/pubmed/37056426 http://dx.doi.org/10.1093/nsr/nwad029 |
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