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.

QTL mapping and candidate gene analysis for yield and grain weight/size in Tartary buckwheat

“…Two contrasting parents in terms of yield, grain weight and size were crossed to generate 221 recombinant inbred lines (XJ-RILs population) [ 31 ]. The maternal parent Xiaomiqiao is a Rice-Tartary type with small grains, thin and loose hull, long vegetative period and low yield, whereas the paternal parent Jinqiaomai 2 is a Tartary buckwheat type with large grains, thick and adherent hull, short vegetative period and high yield.…”

“…An ultrahigh density genetic map for the XJ-RILs population was exhibited with 4,151 bin markers comprising 122,185 SNPs in our previous study [ 31 ]. QTL mapping and the estimation of QTL effects for the tested traits were performed by the composite interval mapping (CIM) model in Windows QTL Cartographer v 2.5 software ( https://brcwebportal.cos.ncsu.edu/qtlcart/WQTLCart.htm ) with default settings.…”

“…However, up to date, very few QTLs associated with grain-related traits have been identified in Tartary buckwheat. Three major QTLs or TGW were first detected on chromosomes Ft1 and Ft4 using an RILs population in our previous study [ 31 ]. Three candidate genes significantly correlated with TGW and GW were identified on chromosomes Ft1, Ft3 and Ft4 by genome-wide association studies (GWASs) [ 32 ].…”

“…A greater understanding of genomic information and QTLs underlying grain-related traits is essential for gene discovery and marker-assisted selection in improving Tartary buckwheat yield. In this study, QTL mapping for GY, TGW, GL, GW and L/W was performed in four environments using the availability of a high-density SNP linkage map developed from the RILs population of ‘Xiaomiqiao × Jinqiaomai 2’ (XJ-RILs population) [ 31 ], and candidate genes for stable major QTLs were predicted by combining homology comparison, sequence variations and qRT‒PCR analysis between the two parents. The QTLs and candidate genes identified in this study can facilitate future molecular breeding programs to improve grain weight/size and yield in Tartary buckwheat.…”

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

“…Although genetic linkage maps of several different segregating populations have been established based on SSRs and other markers, the marker density of these maps was extremely sparse, which limited the detection of QTLs for important agronomic traits of TB ( Du et al, 2013 ; Li et al, 2017 ). Recently, a high-density TB genetic map was constructed by using the genotyping results from restriction site-associated DNA (RAD) sequencing, and several QTLs for 1,000-grain weight and hull type were found ( Shi et al, 2021 ). Although traditional linkage mapping based on segregating populations has been effective for mining important functional genes of TB, there have been few reports on the use of association analysis in natural populations to explore the genetic basis of important agronomic traits in TB.…”