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Genome-Wide Development of Polymorphic Microsatellite Markers and Association Analysis of Major Agronomic Traits in Core Germplasm Resources of Tartary Buckwheat

Tartary buckwheat (TB; Fagopyrum tataricum Gaertn.) is an important multigrain crop and medicinal plant, but functional genomics and molecular breeding research in this species have been lacking for quite some time. Here, genome-wide screening was performed to develop simple sequence repeat (SSR) ma...

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Autores principales: Hou, Siyu, Ren, Xuemei, Yang, Yang, Wang, Donghang, Du, Wei, Wang, Xinfang, Li, Hongying, Han, Yuanhuai, Liu, Longlong, Sun, Zhaoxia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8965444/
https://www.ncbi.nlm.nih.gov/pubmed/35371124
http://dx.doi.org/10.3389/fpls.2022.819008
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author Hou, Siyu
Ren, Xuemei
Yang, Yang
Wang, Donghang
Du, Wei
Wang, Xinfang
Li, Hongying
Han, Yuanhuai
Liu, Longlong
Sun, Zhaoxia
author_facet Hou, Siyu
Ren, Xuemei
Yang, Yang
Wang, Donghang
Du, Wei
Wang, Xinfang
Li, Hongying
Han, Yuanhuai
Liu, Longlong
Sun, Zhaoxia
author_sort Hou, Siyu
collection PubMed
description Tartary buckwheat (TB; Fagopyrum tataricum Gaertn.) is an important multigrain crop and medicinal plant, but functional genomics and molecular breeding research in this species have been lacking for quite some time. Here, genome-wide screening was performed to develop simple sequence repeat (SSR) markers associated with six major agronomic traits and the rutin contents of 97 core germplasm resources. A total of 40,901 SSR loci were identified; they were uniformly distributed throughout the TB genome, with a mean distance of 11 kb between loci. Based on these loci, 8,089 pairs of SSR primers were designed, and 101 primer pairs for polymorphic SSR loci were used to genotype the 97 core germplasm resources. The polymorphic SSR loci showed high genetic variation in these core germplasm resources, with an average polymorphic information content (PIC) value of 0.48. In addition, multiple SSR markers, such as SXAU8002 [100-grain weight (HGW)] and SXAU8006 [stem diameter (SD)], were found to be associated with agronomic traits in the two environments. Finally, based on gene functional annotation and homology analysis, a candidate gene, FtPinG0007685500, that may affect the node number and SD of the main stem by participating in lignin synthesis was identified. This study reports the mining of genome-wide SSR loci and the development of markers in TB, which can be used for molecular characterization of the germplasm in its gene pool. In addition, the detected markers and candidate genes could be used for marker-assisted breeding and functional gene cloning in TB.
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spelling pubmed-89654442022-03-31 Genome-Wide Development of Polymorphic Microsatellite Markers and Association Analysis of Major Agronomic Traits in Core Germplasm Resources of Tartary Buckwheat Hou, Siyu Ren, Xuemei Yang, Yang Wang, Donghang Du, Wei Wang, Xinfang Li, Hongying Han, Yuanhuai Liu, Longlong Sun, Zhaoxia Front Plant Sci Plant Science Tartary buckwheat (TB; Fagopyrum tataricum Gaertn.) is an important multigrain crop and medicinal plant, but functional genomics and molecular breeding research in this species have been lacking for quite some time. Here, genome-wide screening was performed to develop simple sequence repeat (SSR) markers associated with six major agronomic traits and the rutin contents of 97 core germplasm resources. A total of 40,901 SSR loci were identified; they were uniformly distributed throughout the TB genome, with a mean distance of 11 kb between loci. Based on these loci, 8,089 pairs of SSR primers were designed, and 101 primer pairs for polymorphic SSR loci were used to genotype the 97 core germplasm resources. The polymorphic SSR loci showed high genetic variation in these core germplasm resources, with an average polymorphic information content (PIC) value of 0.48. In addition, multiple SSR markers, such as SXAU8002 [100-grain weight (HGW)] and SXAU8006 [stem diameter (SD)], were found to be associated with agronomic traits in the two environments. Finally, based on gene functional annotation and homology analysis, a candidate gene, FtPinG0007685500, that may affect the node number and SD of the main stem by participating in lignin synthesis was identified. This study reports the mining of genome-wide SSR loci and the development of markers in TB, which can be used for molecular characterization of the germplasm in its gene pool. In addition, the detected markers and candidate genes could be used for marker-assisted breeding and functional gene cloning in TB. Frontiers Media S.A. 2022-03-15 /pmc/articles/PMC8965444/ /pubmed/35371124 http://dx.doi.org/10.3389/fpls.2022.819008 Text en Copyright © 2022 Hou, Ren, Yang, Wang, Du, Wang, Li, Han, Liu and Sun. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Hou, Siyu
Ren, Xuemei
Yang, Yang
Wang, Donghang
Du, Wei
Wang, Xinfang
Li, Hongying
Han, Yuanhuai
Liu, Longlong
Sun, Zhaoxia
Genome-Wide Development of Polymorphic Microsatellite Markers and Association Analysis of Major Agronomic Traits in Core Germplasm Resources of Tartary Buckwheat
title Genome-Wide Development of Polymorphic Microsatellite Markers and Association Analysis of Major Agronomic Traits in Core Germplasm Resources of Tartary Buckwheat
title_full Genome-Wide Development of Polymorphic Microsatellite Markers and Association Analysis of Major Agronomic Traits in Core Germplasm Resources of Tartary Buckwheat
title_fullStr Genome-Wide Development of Polymorphic Microsatellite Markers and Association Analysis of Major Agronomic Traits in Core Germplasm Resources of Tartary Buckwheat
title_full_unstemmed Genome-Wide Development of Polymorphic Microsatellite Markers and Association Analysis of Major Agronomic Traits in Core Germplasm Resources of Tartary Buckwheat
title_short Genome-Wide Development of Polymorphic Microsatellite Markers and Association Analysis of Major Agronomic Traits in Core Germplasm Resources of Tartary Buckwheat
title_sort genome-wide development of polymorphic microsatellite markers and association analysis of major agronomic traits in core germplasm resources of tartary buckwheat
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8965444/
https://www.ncbi.nlm.nih.gov/pubmed/35371124
http://dx.doi.org/10.3389/fpls.2022.819008
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