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

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.

Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes

“…Wood formation distinguishes woody from herbaceous plants, and represents a major metabolic sink for woody plants [ 17 ]. Several polymorphic SSR markers identified within genes associated with woody trait were helpful for marker-assisted breeding [ 17 , 20 , 21 ]. Lignin is the main component of secondary cell walls, and is essential for wood formation [ 22 , 23 ].…”

Genome-Wide Development of Polymorphic Microsatellite Markers and Genetic Diversity Analysis for the Halophyte Suaeda aralocaspica (Amaranthaceae)

“…Therefore, it can be inferred that SSRs we abundant in the whole genome of S. aralocaspica. Dinucleotide and trinucleotide repe were the most common SSRs in the genome of S. aralocaspica, similar to Tartary buckwh [30]. However, there is a difference in abundance between the two, as dinucleotide repe were the most common in Tartary buckwheat (63.95%), whereas trinucleotide repe were more common in S. aralocaspica (75.74%).…”

Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum

“…Several SSR markers have been developed and used to characterise the genetic diversity of common [ 60 , 61 , 62 , 63 ] and Tartary buckwheat [ 38 , 64 , 65 ]. Importantly, Hou et al [ 27 ] developed a large set of SSR markers through genome-wide screening and used them for genetic diversity analysis and marker-trait association to identify genomic regions associated with important agronomic traits in Tartary buckwheat. In our study, 25 SSR markers selected from the above studies were used to investigate the genetic diversity and structure of a large global collection of common and Tartary buckwheat.…”

“…Compared to other DNA-based markers, SSRs are best suited for characterising genetic diversity due to their high reproducibility, abundance, codominance, and multi-allelic inheritance [ 26 ]. In addition, Hou et al [ 27 ] have demonstrated the great utility of combining SSRs and agro-morphological markers in identifying genomic regions controlling important agronomic traits in Tartary buckwheat.…”