Identification of a major QTL for root thickness in diploid wild sweetpotato (Ipomoea trifida) using QTL-seq

Ipomoea trifida, the closest relative of sweetpotato, does not generally form storage roots, but some lines develop thick roots similar to the storage roots of the sweetpotato. Revealing the molecular mechanism of thick root development in I. trifida would help us understand the evolution of storage roots in the sweetpotato. In this study, we conducted a mapping method for quantitative trait loci (QTLs) known as QTL-seq, which is a kind of next-generation sequencing-based bulk segregant analysis. We performed QTL-seq using a backcross population (BC1F1) derived from two I. trifida lines: Mx23Hm, which does not show root-thickening; and 0431-1, which produces thick roots. The aim was to identify the QTL region involved in thick root development. As a result, a major QTL for root thickness (qRT1) was detected in the 2.94-8.71 Mb region of chr06 of Itr_r2.2, in both pot and field experiments. Six DNA markers were designed for qRT1 using InDels on chr06. Genotyping each BC1F1 individual based on these DNA markers agreed well with the SNP-Index of QTL-seq. Moreover, most individuals with 0431-1-type alleles of qRT1 developed thicker roots than individuals without 0431-1-type alleles of qRT1 in the BC2F2 population. The results of this study implied that qRT1 was an important QTL for regulating root thickness in I. trifida.