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Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study

BACKGROUND: Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Here, we performed a genome-wide association study (GWAS) on POD activity using an association population consisted with 207 wheat wo...

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Autores principales: Zhou, Zhengfu, Guan, Huiyue, Liu, Congcong, Zhang, Ziwei, Geng, Shenghui, Qin, Maomao, Li, Wenxu, Shi, Xia, Dai, Ziju, Lei, Zhensheng, Wu, Zhengqing, Tian, Baoming, Hou, Jinna
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8579651/
https://www.ncbi.nlm.nih.gov/pubmed/34758752
http://dx.doi.org/10.1186/s12870-021-03299-6
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author Zhou, Zhengfu
Guan, Huiyue
Liu, Congcong
Zhang, Ziwei
Geng, Shenghui
Qin, Maomao
Li, Wenxu
Shi, Xia
Dai, Ziju
Lei, Zhensheng
Wu, Zhengqing
Tian, Baoming
Hou, Jinna
author_facet Zhou, Zhengfu
Guan, Huiyue
Liu, Congcong
Zhang, Ziwei
Geng, Shenghui
Qin, Maomao
Li, Wenxu
Shi, Xia
Dai, Ziju
Lei, Zhensheng
Wu, Zhengqing
Tian, Baoming
Hou, Jinna
author_sort Zhou, Zhengfu
collection PubMed
description BACKGROUND: Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Here, we performed a genome-wide association study (GWAS) on POD activity using an association population consisted with 207 wheat world-wide collected varieties. Our study also provide basis for the genetic improvement of flour color-based quality in wheat. RESULTS: Twenty quantitative trait loci (QTLs) were detected associated with POD activity, explaining 5.59–12.67% of phenotypic variation. Superior alleles were positively correlated with POD activity. In addition, two SNPs were successfully developed to KASP (Kompetitive Allele-Specific PCR) markers. Two POD genes, TraesCS2B02G615700 and TraesCS2D02G583000, were aligned near the QTLs flanking genomic regions, but only TraesCS2D02G583000 displayed significant divergent expression levels (P < 0.001) between high and low POD activity varieties in the investigated association population. Therefore, it was deduced to be a candidate gene. The expression level of TraesCS2D02G583000 was assigned as a phenotype for expression GWAS (eGWAS) to screen regulatory elements. In total, 505 significant SNPs on 20 chromosomes (excluding 4D) were detected, and 9 of them located within 1 Mb interval of TraesCS2D02G583000. CONCLUSIONS: To identify genetic loci affecting POD activity in wheat grain, we conducted GWAS on POD activity and the candidate gene TraesCS2D02G583000 expression. Finally, 20 QTLs were detected for POD activity, whereas two QTLs associated SNPs were converted to KASP markers that could be used for marker-assisted breeding. Both cis- and trans-acting elements were revealed by eGWAS of TraesCS2D02G583000 expression. The present study provides genetic loci for improving POD activity across wide genetic backgrounds and largely improved the selection efficiency for breeding in wheat. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-021-03299-6.
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spelling pubmed-85796512021-11-10 Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study Zhou, Zhengfu Guan, Huiyue Liu, Congcong Zhang, Ziwei Geng, Shenghui Qin, Maomao Li, Wenxu Shi, Xia Dai, Ziju Lei, Zhensheng Wu, Zhengqing Tian, Baoming Hou, Jinna BMC Plant Biol Research BACKGROUND: Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Here, we performed a genome-wide association study (GWAS) on POD activity using an association population consisted with 207 wheat world-wide collected varieties. Our study also provide basis for the genetic improvement of flour color-based quality in wheat. RESULTS: Twenty quantitative trait loci (QTLs) were detected associated with POD activity, explaining 5.59–12.67% of phenotypic variation. Superior alleles were positively correlated with POD activity. In addition, two SNPs were successfully developed to KASP (Kompetitive Allele-Specific PCR) markers. Two POD genes, TraesCS2B02G615700 and TraesCS2D02G583000, were aligned near the QTLs flanking genomic regions, but only TraesCS2D02G583000 displayed significant divergent expression levels (P < 0.001) between high and low POD activity varieties in the investigated association population. Therefore, it was deduced to be a candidate gene. The expression level of TraesCS2D02G583000 was assigned as a phenotype for expression GWAS (eGWAS) to screen regulatory elements. In total, 505 significant SNPs on 20 chromosomes (excluding 4D) were detected, and 9 of them located within 1 Mb interval of TraesCS2D02G583000. CONCLUSIONS: To identify genetic loci affecting POD activity in wheat grain, we conducted GWAS on POD activity and the candidate gene TraesCS2D02G583000 expression. Finally, 20 QTLs were detected for POD activity, whereas two QTLs associated SNPs were converted to KASP markers that could be used for marker-assisted breeding. Both cis- and trans-acting elements were revealed by eGWAS of TraesCS2D02G583000 expression. The present study provides genetic loci for improving POD activity across wide genetic backgrounds and largely improved the selection efficiency for breeding in wheat. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-021-03299-6. BioMed Central 2021-11-10 /pmc/articles/PMC8579651/ /pubmed/34758752 http://dx.doi.org/10.1186/s12870-021-03299-6 Text en © The Author(s) 2021 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/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Zhou, Zhengfu
Guan, Huiyue
Liu, Congcong
Zhang, Ziwei
Geng, Shenghui
Qin, Maomao
Li, Wenxu
Shi, Xia
Dai, Ziju
Lei, Zhensheng
Wu, Zhengqing
Tian, Baoming
Hou, Jinna
Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study
title Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study
title_full Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study
title_fullStr Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study
title_full_unstemmed Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study
title_short Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study
title_sort identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8579651/
https://www.ncbi.nlm.nih.gov/pubmed/34758752
http://dx.doi.org/10.1186/s12870-021-03299-6
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