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

Siyu Hou; Siyu Hou; Xuemei Ren; Xuemei Ren; Yang Yang; Yang Yang; Donghang Wang; Wei Du; Xinfang Wang; Hongying Li; Hongying Li; Yuanhuai Han; Yuanhuai Han; Longlong Liu; Zhaoxia Sun; Zhaoxia Sun

doi:10.3389/fpls.2022.819008

Frontiers in Plant Science (Mar 2022)

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

Siyu Hou,
Siyu Hou,
Xuemei Ren,
Xuemei Ren,
Yang Yang,
Yang Yang,
Donghang Wang,
Wei Du,
Xinfang Wang,
Hongying Li,
Hongying Li,
Yuanhuai Han,
Yuanhuai Han,
Longlong Liu,
Zhaoxia Sun,
Zhaoxia Sun

Affiliations

Siyu Hou: College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
Siyu Hou: Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, China
Xuemei Ren: College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
Xuemei Ren: Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, China
Yang Yang: College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
Yang Yang: Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, China
Donghang Wang: College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
Wei Du: College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
Xinfang Wang: College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
Hongying Li: College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
Hongying Li: Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, China
Yuanhuai Han: College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
Yuanhuai Han: Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, China
Longlong Liu: Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
Zhaoxia Sun: College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
Zhaoxia Sun: Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, China

DOI: https://doi.org/10.3389/fpls.2022.819008
Journal volume & issue: Vol. 13

Abstract

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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.

Published in Frontiers in Plant Science

ISSN: 1664-462X (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Agriculture: Plant culture
Website: https://www.frontiersin.org/journals/plant-science

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