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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
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.
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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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