Mapping QTLs for 1000-grain weight and genes controlling hull type using SNP marker in Tartary buckwheat (Fagopyrum tataricum)

Abstract

Background: Tartary buckwheat (Fagopyrum tataricum), an important pseudocereal crop, has high economic value due to its nutritional and medicinal properties. However, dehulling of Tartary buckwheat is difficult owing to its thick and tough hull, which has greatly limited the development of the Tartary buckwheat processing industry. The construction of high-resolution genetic maps serves as a basis for identifying quantitative trait loci (QTLs) and qualitative trait genes for agronomic traits. In this study, a recombinant inbred lines (XJ-RILs) population derived from a cross between the easily dehulled Rice-Tartary type and Tartary buckwheat type was genotyped using restriction site-associated DNA (RAD) sequencing to construct a high-density SNP genetic map. Furthermore, QTLs for 1000-grain weight (TGW) and genes controlling hull type were mapped in multiple environments.

Results: In total, 4151 bin markers comprising 122,185 SNPs were used to construct the genetic linkage map. The map consisted of 8 linkage groups and covered 1444.15 cM, with an average distance of 0.35 cM between adjacent bin markers. Nine QTLs for TGW were detected and distributed on four loci on chromosome 1 and 4. A major locus detected in all three trials was mapped in 38.2-39.8 cM region on chromosome 1, with an LOD score of 18.1-37.0, and explained for 23.6-47.5% of the phenotypic variation. The genes controlling hull type were mapped to chromosome 1 between marker Block330 and Block331, which was closely followed by the major locus for TGW. The expression levels of the seven candidate genes controlling hull type present in the region between Block330 and Block336 was low during grain development, and no significant difference was observed between the parental lines. Six non-synonymous coding SNPs were found between the two parents in the region.

Conclusions: We constructed a high-density SNP genetic map for the first time in Tartary buckwheat. The mapped major loci controlling TGW and hull type will be valuable for gene cloning and revealing the mechanism underlying grain development and easy dehulling, and marker-assisted selection in Tartary buckwheat.

Keywords: 1000-grain wight; Genetic map; Hull type; QTLs mapping; RAD sequencing; Tartary buckwheat.

Fig. 1

High-density genetic map of the XJ-RILs population derived from the cross of ‘Xiaomiqiao × Jinqiaomai 2’ constructed by bin markers

Fig. 2

Collinearity between the genetic map derived from the XJ-RILs population derived from the cross of ‘Xiaomiqiao × Jinqiaomai 2’ and the reference genome (Pinku1). In each plot, the genetic position of the 8 linkage groups from the XJ-RILs population map is on the x-axis, and the physical positions of the 8 Tartary buckwheat chromosomes is on the y-axis

Fig. 3

Grain samples of female (Xiaomiqiao) and male (Jinqiaomai 2)

Fig. 4

Frequency distribution of TGW in the XJ-RILs population derived from the cross of ‘Xiaomiqiao × Jinqiaomai 2’ under three field trials. The black and white arrows the values for the parents Xiaomiqiao and Jinqiaomai 2, respectively

Fig. 5

Locations of genes controlling hull type and identified QTLs for TGW in the XJ-RILs population derived from the cross of ‘Xiaomiqiao × Jinqiaomai 2’ under multiple environments. The markers marked in purple were phenotype markers of hull type from F₈ and F₉-RILs in two environments. TGW, 1000-grain weight. The red horizon lines indicated the peak position, and the red vertical lines indicated the confidence interval of QTLs

Fig. 6

Expression patterns of candidate genes controlling hull type in Xiaomiqiao and Jinqiaomai 2