Development of near-isogenic line of dwarf gene Cldw-1 and transcriptome analysis in watermelon (Citrullus lanatus)

• The dwarf gene Cldw-1 was introgressed into an elite inbred line WT4 by maker assisted selection (MAS), and a near isogenic line dw-NIL1 was developed with a proportion of 98.50 % recovered to recurrent parent genome. • Cytological observations showed that the shorter cell length results in shorter internodes and dwarf phenotype, whereas an increase in cell number leads to the thicker stems in dw-NIL1. • Transcriptome analysis revealed that many auxin related DEGs may play important role in the cell size reduction which were the main factor for dwarf formation in watermelon. The dwarf structure is an important agronomic trait in watermelon, which can increase plant density and is useful for lab-saving cultivation. Cldw-1 encodes an ABCB transporter protein controlling plant height in watermelon, making it useful in dwarf breeding. However, the regulatory mechanism of Cldw-1 in dwarf formation remains unclear. In this study, a donor parent WM102 carrying the Cldw-1 gene was crossed with a recurrent parent WT4, resulting in BC 1 F 1 , BC 2 F 1 , and BC 2 F 2 populations. In each generation, the Cldw-1 co-segregating marker dCAPS3 was used for foreground selection and 108 polymorphic SSR markers were used for background selection to develop the near isogenic lines (NIL) of Cldw-1 . We ultimately obtained a dw-NIL1 in BC 2 F 2 with a proportion of recurrent parent genome (PRPG) of 98.50 % in WT4 background. Compared to WT4, the plant height, internode number, internode length and tendril length was significantly reduced in the dw-NIL1. Cytological observations indicated that the reduction in cell length lead to shorter stems, while an increase in cell number resulted in thicker stems in the dw-NIL1. Transcriptome analysis of the stems of WT4 and dw-NIL1 identified 518 differentially expressed genes (DEGs) with 392 up-regulated and 126 down-regulated. Among them, a number of DEGs were related to auxin signaling pathway, which are known to regulate plant height. Cell wall biosynthesis and modification, as well as protein modifications, were significantly enriched. These results not only provide important germplasms for dwarf breeding, but also will be helpful for better understanding the molecular mechanisms of plant height development in watermelon.