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

Abstract

Background: Grain weight/size influences not only grain yield (GY) but also nutritional and appearance quality and consumer preference in Tartary buckwheat. The identification of quantitative trait loci (QTLs)/genes for grain weight/size is an important objective of Tartary buckwheat genetic research and breeding programs.

Results: Herein, we mapped the QTLs for GY, 1000-grain weight (TGW), grain length (GL), grain width (GW) and grain length-width ratio (L/W) in four environments using 221 recombinant inbred lines (XJ-RILs) derived from a cross of 'Xiaomiqiao × Jinqiaomai 2'. In total, 32 QTLs, including 7 for GY, 5 for TGW, 6 for GL, 11 for GW and 3 for L/W, were detected and distributed in 24 genomic regions. Two QTL clusters, qClu-1-3 and qClu-1-5, located on chromosome Ft1, were revealed to harbour 7 stable major QTLs for GY (qGY1.2), TGW (qTGW1.2), GL (qGL1.1 and qGL1.4), GW (qGW1.7 and qGW1.10) and L/W (qL/W1.2) repeatedly detected in three and above environments. A total of 59 homologues of 27 known plant grain weight/size genes were found within the physical intervals of qClu-1-3 and qClu-1-5. Six homologues, FtBRI1, FtAGB1, FtTGW6, FtMADS1, FtMKK4 and FtANT, were identified with both non-synonymous SNP/InDel variations and significantly differential expression levels between the two parents, which may play important roles in Tatary buckwheat grain weight/size control and were chosen as core candidate genes for further investigation.

Conclusions: Two stable major QTL clusters related to grain weight/size and six potential key candidate genes were identified by homology comparison, SNP/InDel variations and qRT‒qPCR analysis between the two parents. Our research provides valuable information for improving grain weight/size and yield in Tartary buckwheat breeding.

Keywords: Candidate gene; Grain weight/size; QTL; SNP/InDel variation; Tartary buckwheat; Yield.

Fig. 1

The distribution of the QTLs for grain yield (GY), 1000-grain weight (TGW), grain length (GL), grain width (GW), grain length–width ratio (L/W) and QTL clusters detected in the XJ-RILs population derived from the cross of ‘Xiaomiqiao × Jinqiaomai 2’ in four environments. The red, green, blue, black, cyan and magenta lines represent QTLs for GL, L/W, GW, GY, TGW and QTLs clusters, respectively. The horizon lines indicate the peak position, and the vertical lines indicate the confidence interval of QTLs. The interval of the vertical filled rectangle represents the minimal and maximal peak positions of QTLs repeatedly detected in different environments, and the number in brackets gives the number of environments in which the QTL detected

Fig. 2

The expression of the seven homologues of grain weight/size genes in the parental lines Xiaomiqiao and Jinqiaomai 2