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Sweet sorghum [ Sorghum bicolor (L.) Moench] accumulates large amounts of sugars in the stem parenchyma and can be used to manufacture sucrose and alcohol. Soluble acid invertase (SAI) plays an important role in sucrose accumulation in the sweet sorghum stem. Characterization of SAI genes and development of functional markers are important for marker-assisted selection in breeding programs. Here, the full-length genomic DNA sequence of a SAI gene ( SAI- 1) was cloned by in silico cloning and experimentally validated. The SAI- 1 gene comprises three exons and two introns, totaling 4,966 bp, with an open reading frame of 2,025 bp encoding a polypeptide of 674 amino acids. The protein encoded by SAI- 1 (molecular weight 73.4 kDa) contains a glycosyl hydrolase family 32 conserved domain, which catalyzes the hydrolysis of sucrose. Four allelic variants at the SAI- 1 locus, SAI- 1a, SAI- 1b, SAI- 1c and SAI- 1d (GenBank accession nos. JX535515, JX535516, JX535517 and JX535518), were identified in 165 sweet sorghum cultivars. A co-dominant marker, SBX1, was developed to discriminate these variants. The mean Brix value from cultivars with a 141-bp ( SAI- 1c) PCR product was higher than in cultivars with a 136-bp ( SAI- 1b) product, and the mean Brix value from cultivars with a 136-bp ( SAI- 1b) product was significantly higher than those with a 132-bp ( SAI- 1a) product. The results showed that a domain of ATTGA repeat sequences in the second intron might be an important regulatory site, and that the functional marker SBX1 was closely related to the Brix value, and could therefore be used in sweet sorghum breeding programs. [ABSTRACT FROM AUTHOR]