Fine mapping of QTL and identification of candidate genes responsible for tuberous stem formation in Kohlrabi (Brassica oleracea var. gongylodes L.)

Abstract

Tuberous stem is a key determinant of yield and quality in kohlrabi, and it is a prime target of artificial selection for breeding and domestication. To dissect the genetic basis of tuberization, a previously identified major QTL, REnBo2 on chromosome C03 was fine mapped to a 42.8-kb interval using the recombinant populations of three different backcross generations derived from the double haploid lines of kohlrabi and broccoli. Three genes namely Bol012972, Bol012973 and Bol012974 encoding a CBL-interacting protein kinase 6 (CIPK6), fatty acid desaturase 6 (FAD6) and WRKY transcription factor 32 (WRKY32), respectively, were annotated in the fine-mapped interval in Brassica oleracea reference genomes. FAD6 is unlikely to be the responsible gene due to its function as a fatty acid desaturase. Based on the gene structure and expression analyses of the remaining two candidates along with our previously conducted transcriptome and endogenous phytohormone profiles, Bol012972 (CIPK6) was identified as a promising candidate for REnBo2. Since the knockdown mutant of CIPK6 was known to exhibits swollen hypocotyls in Arabidopsis, we speculate that CIPK6 may regulate kohlrabi tuber development through regulating the auxin levels. The result will provide a foundation to elucidate the genetic mechanism for tuber formation in kohlrabi and other Brassica crops.