Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Mar 15:13:819008.
doi: 10.3389/fpls.2022.819008. eCollection 2022.

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

Siyu Hou  1   2 , Xuemei Ren  1   2 , Yang Yang  1   2 , Donghang Wang  1 , Wei Du  1 , Xinfang Wang  1 , Hongying Li  1   2 , Yuanhuai Han  1   2 , Longlong Liu  3 , Zhaoxia Sun  1   2
Affiliations

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

Siyu Hou et al. Front Plant Sci. .

Abstract

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.

Keywords: Tartary buckwheat; agronomic traits; association study; core germplasm; genome-wide SSR marker development.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Proportions of different types of simple sequence repeat (SSR) units in the Tartary buckwheat (TB) genome. Each pie chart represents the SSR loci with different repeat units in the genome.
FIGURE 2
FIGURE 2
The chromosomal distribution of the 101 SSR markers used in this study.
FIGURE 3
FIGURE 3
Population structure and relationship analysis of 97 core TB germplasm resources. (A) Distribution of ΔK at different K-values. (B) Population structure of 97 core TB germplasm resources inferred by genotyping 101 SSR markers (K = 2). Not all names of the accessions are displayed. (C) Neighbor-joining cluster diagram of TB resources based on SSR markers. (D) Affinity within the population and the proportion of different levels of kinship.
FIGURE 4
FIGURE 4
Venn diagram of associated sites based on a general linear model.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Agrama H. A., Eizenga G. C., Yan W. (2007). Association mapping of yield and its components in rice cultivars. Mol. Breeding. 19 341–356. 10.1007/s11032-006-9066-6 - DOI
    1. Beier S., Thiel T., Münch T., Scholz U., Mascher M. (2017). MISA-web: a web server for microsatellite prediction. Bioinformatics. 33 2583–2585. 10.1093/bioinformatics/btx198 - DOI - PMC - PubMed
    1. Bradbury P. J., Zhang Z. W., Kroon D. E., Casstevens T. M., Ramdoss Y., Buckler E. S. (2007). TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 23 2633–2635. 10.1093/bioinformatics/btm308 - DOI - PubMed
    1. Breseghello F. (2006). Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172 1165–1177. 10.1534/genetics.105.044586 - DOI - PMC - PubMed
    1. Brunori A., Baviello G., Corrado Z., Gianluca C., Gergő S., Végvári G. (2010). The use of Fagopyrum tataricum gaertn. whole flour to confer preventive contents of rutin to some traditional tuscany biscuits. Annals of the University Dunarea de Jos of Galati. Fascicle VI Food Technol. 34 148–151.

LinkOut - more resources