Theoretical and Applied Genetics

, Volume 126, Issue 11, pp 2897–2906 | Cite as

Gene discovery and functional marker development for fragrance in sorghum (Sorghum bicolor (L.) Moench)

  • Chutintorn Yundaeng
  • Prakit SomtaEmail author
  • Sithichoke Tangphatsornruang
  • Sugunya Wongpornchai
  • Peerasak Srinives
Original Paper


Key message

Sequence analysis and genetic mapping revealed that a 1,444 bp deletion causes a premature stop codon in SbBADH2 of sorghum IS19912. The non-function of SbBADH2 is responsible for fragrance in sorghum IS19912.


2-acetyl-1-pyrroline (2AP) is a potent volatile compound causing fragrance in several plants and foods. Seeds of some varieties of rice, sorghum and soybean possess fragrance. The genes responsible for fragrance in rice and soybean are orthologs that correspond to betaine aldehyde dehydrogenase 2 (BADH2). Genotypes harboring fragrance in rice and soybean contain a premature stop codon in BADH2 which impairs the synthesis of full length functional BADH2 protein leading to the accumulation of 2AP. In this study, we reported an association between the BADH2 gene and fragrance in sorghum. An F2 population of 187 plants developed from a cross between KU630 (non-fragrant) and IS19912 (fragrant) was used. Leaves of F2 and F3 progenies were evaluated for fragrance by organoleptic test, while seeds of F2 plants were analyzed for 2AP. The tests consistently showed that the fragrance is controlled by a single recessive gene. Gene expression analysis of SbBADH1 and SbBADH2 in leaves of KU630 and IS19912 at various stages revealed that SbBADH1 and SbBADH2 were expressed in both accessions. Sequence comparison between KU630 and IS19912 revealed a continuous 1,444 bp deletion encompassing exon 12 to 15 of SbBADH2 in IS19912 which introduces a frameshift mutation and thus causes a premature stop codon. An indel marker was developed to detect polymorphism in SbBADH2. Bulk segregant and QTL analyses confirmed the association between SbBADH2 and fragrance.


Sorghum Premature Stop Codon Single Recessive Gene Full Genomic Sequence Length BADH2 Gene 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This research was supported by the Royal Golden Jubilee Ph.D. Scholarship co-funded by the Thailand Research Fund (TRF) and Kasetsart University to P. Somta and C. Yundaeng.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

All the experiments performed in this study comply with the current laws of Thailand.

Supplementary material

122_2013_2180_MOESM1_ESM.eps (2.4 mb)
Nucleotide substitutions in SbBADH2 gene found among fragrant sorghum IS19912, non-fragrant sorghum KU630, and the reference sequence. Position of the substitution is based on start codon of the genomic DNA sequence of SbBADH2. Asterisk indicates polymorphism site.Supplementary material 1 (EPS 2425 kb)
122_2013_2180_MOESM2_ESM.eps (1.6 mb)
Alignment of the amino acid sequences of betaine aldehyde dehydrogenase 2 (BADH2) protein encoded by SbBADH2 from fragrant sorghum IS19912, non-fragrant sorghum KU630, and the reference sequence. Asterisk indicates polymorphism site.Supplementary material 2 (EPS 1651 kb)
122_2013_2180_MOESM3_ESM.doc (36 kb)
Supplementary material 3 (DOC 35 kb)
122_2013_2180_MOESM4_ESM.doc (38 kb)
Supplementary material 4 (DOC 37 kb)
122_2013_2180_MOESM5_ESM.doc (36 kb)
Supplementary material 5 (DOC 36 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Chutintorn Yundaeng
    • 1
  • Prakit Somta
    • 2
    Email author
  • Sithichoke Tangphatsornruang
    • 3
  • Sugunya Wongpornchai
    • 4
  • Peerasak Srinives
    • 2
  1. 1.Program in Plant Breeding, Faculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
  2. 2.Department of Agronomy, Faculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
  3. 3.National Center for Genetic Engineering and BiotechnologyPathumthaniThailand
  4. 4.Center of Excellence for Innovation in Chemistry, Department of Chemistry, Faculty of ScienceChaing Mai UniversityChaing MaiThailand

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