A mutation in acceptor splice site of GA3ox homolog Cla015407 gene confers a dwarf phenotype in watermelon (Citrullus lanatus L.)
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Abstract
Dwarfism is a desirable agronomic trait in watermelon. The dwarf growth habit in watermelon is controlled by a single recessive gene (dwarf; dw). Linkage analysis of 309 F2 individuals derived from inbred watermelon lines KK-6939 (viny plant) and TH-15974 (dwarf plant), positioned the dw locus at the terminal region of watermelon chromosome 9. Using the gene annotation data derived from watermelon reference genome “97103”, 25 genes were located between two flanking markers, WMSNP-0002750 and WMSNP-0002780. Only 2 out of 25 candidate genes, Cla015407 and Cla015408, are related to growth hormone and encode a protein predicted to be a gibberellin 3-beta-hydroxylase (GA3ox). Only the single nucleotide polymorphism (SNP) (G/A) at the 626th nucleotide of Cla015407 could distinguish dwarf plants from viny plants. The mutation is an acceptor splice site in intron 1 and leads to an altered splicing site at the 639th nucleotide and a 13 base pair (bp) deletion in complementary deoxyribonucleic acid (cDNA), resulting in a truncated protein in dwarf plants. Although Cla015408 encoded the same protein as Cla015407, the expression level of Cla015408 couldn’t be detected from quantitative and semi-quantitative real time polymerase chain reaction (RT-PCR). Therefore, Cla015408 couldn’t function instead of Cla015407 in dwarf plants. These results suggested that Cla015407 is the dw gene. A high throughput functional marker, Cla015407-GA, was developed and validated in various inbred lines. The functional marker is segregated with the phenotype, demonstrating that the marker has high accuracy and high value to implement in a watermelon breeding program for marker-assisted selection (MAS).
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