Quantitative trait loci analysis of lateral shoot growth in tomato

• In tomato, seventeen additive QTLs for lateral branch development were identified.
• One epistatic (QTL × QTL) interaction was detected for LS10 on chr. 1 and 12.
• QTLs for days to flowering time were co-located with lateral shoot development on chr.1.
• Lateral shoot development was regulated by additive, epistatic and pleiotropic QTLs.

Branching is an important agronomic trait to determine plant architecture and fruit yield. In tomato, the regulatory mechanisms of shoot branching patterns have been studied mainly in mutants defective in meristem identity. Little is known about quantitative trait loci (QTLs) and their genetic interaction (epistasis) in lateral shoot development. Here, the genetic control of lateral bud outgrowth initiation and subsequent lateral bud development into branches were investigated. We used a BC1F7 population developed from Solanum lycopersicum (SL) and its close wild relative Solanum pimpinellifolium (SP) to measure the number of leaves on primary shoot (LN), the proportion of nodes with lateral buds (LS0) and lateral branches longer than 5 cm (LS5) and 10 cm (LS10) on main axis, the proportion of nodes with secondary lateral branches longer than 1 cm (LSLS1) on primary lateral branches, and the lengths of the longest primary and secondary lateral branches (LLSL1 and LLSL2, respectively). Composite interval mapping detected 17 additive QTLs; those for LS5, LS10, and LLSL1 clustered near C2_At5g49480 or LEATPACb on chromosome 1 and LEOH361 on chromosome 4. One epistatic (QTL × QTL) interaction was identified for LS10 QTLs on chromosomes 1 and 12, where recombinant-type alleles increased lateral bud development into primary lateral branches. We analyzed further the QTLs clustered on chromosome 1 using two BC3F4 populations containing introgression region from the SP, which revealed the co-location of QTLs for lateral shoot development and days to flowering time. These results suggest that lateral shoot development is regulated by some additive and epistatic QTLs, some of which possibly exhibit a pleiotropic effect on flowering time.