Abstract
The origin and evolution of the waxy type of foxtail millet [Setaria italica (L.) P. Beauv] were studied by analyzing structural variation in the Waxy gene. Initially, the Waxy gene was amplified by RT-PCR, RACE and genomic PCR from a non-waxy strain to determine the structure of the wild-type gene. Secondly, we screened by PCR for polymorphisms at the Waxy locus in 79 strains with various waxy phenotypes. We then carried out genomic Southern analysis on 67 strains and identified seven RFLP classes which were designated as types I-VII. RFLP type was correlated with phenotype, such that types I and II corresponded to non-waxy, types III and VI to low-amylose, and types IV, V and VII to waxy phenotypes. The differences between RFLP types could be attributed to insertions in the Waxy gene. Types II and VI were caused by the insertion of a Tourist element into intron 1 and a SINE-like sequence into intron 12, respectively. Types III, IV, V and VII were characterized by the insertion of large sequences into the Waxy gene that may alter the expression of the gene. Thus, multiple, independent insertions in the Waxy gene appear to have caused the loss-of-function waxy phenotypes. Furthermore, the geographical distributions of the three RFLP types associated with the waxy phenotype (types IV, V and VII) were distinct, with type IV being found mainly in Taiwan and Japan, type V in Korea, and type VII in Myanmar. These results indicate a polyphyletic origin for the waxy phenotype in landraces of foxtail millet.
| Original language | English |
|---|---|
| Pages (from-to) | 214-222 |
| Number of pages | 9 |
| Journal | Molecular Genetics and Genomics |
| Volume | 268 |
| Issue number | 2 |
| DOIs | |
| Publication status | Published - 2002 |
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Keywords
- Crop evolution
- Foxtail millet
- Insertion sequence
- Setaria italica
- Waxy gene
ASJC Scopus subject areas
- Genetics
Cite this
Structural variation in the Waxy gene and differentiation in foxtail millet [Setaria italica (L.) P. Beauv.] : Implications for multiple origins of the waxy phenotype. / Fukunaga, K.; Kawase, M.; Kato, Kenji.
In: Molecular Genetics and Genomics, Vol. 268, No. 2, 2002, p. 214-222.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Structural variation in the Waxy gene and differentiation in foxtail millet [Setaria italica (L.) P. Beauv.]
T2 - Implications for multiple origins of the waxy phenotype
AU - Fukunaga, K.
AU - Kawase, M.
AU - Kato, Kenji
PY - 2002
Y1 - 2002
N2 - The origin and evolution of the waxy type of foxtail millet [Setaria italica (L.) P. Beauv] were studied by analyzing structural variation in the Waxy gene. Initially, the Waxy gene was amplified by RT-PCR, RACE and genomic PCR from a non-waxy strain to determine the structure of the wild-type gene. Secondly, we screened by PCR for polymorphisms at the Waxy locus in 79 strains with various waxy phenotypes. We then carried out genomic Southern analysis on 67 strains and identified seven RFLP classes which were designated as types I-VII. RFLP type was correlated with phenotype, such that types I and II corresponded to non-waxy, types III and VI to low-amylose, and types IV, V and VII to waxy phenotypes. The differences between RFLP types could be attributed to insertions in the Waxy gene. Types II and VI were caused by the insertion of a Tourist element into intron 1 and a SINE-like sequence into intron 12, respectively. Types III, IV, V and VII were characterized by the insertion of large sequences into the Waxy gene that may alter the expression of the gene. Thus, multiple, independent insertions in the Waxy gene appear to have caused the loss-of-function waxy phenotypes. Furthermore, the geographical distributions of the three RFLP types associated with the waxy phenotype (types IV, V and VII) were distinct, with type IV being found mainly in Taiwan and Japan, type V in Korea, and type VII in Myanmar. These results indicate a polyphyletic origin for the waxy phenotype in landraces of foxtail millet.
AB - The origin and evolution of the waxy type of foxtail millet [Setaria italica (L.) P. Beauv] were studied by analyzing structural variation in the Waxy gene. Initially, the Waxy gene was amplified by RT-PCR, RACE and genomic PCR from a non-waxy strain to determine the structure of the wild-type gene. Secondly, we screened by PCR for polymorphisms at the Waxy locus in 79 strains with various waxy phenotypes. We then carried out genomic Southern analysis on 67 strains and identified seven RFLP classes which were designated as types I-VII. RFLP type was correlated with phenotype, such that types I and II corresponded to non-waxy, types III and VI to low-amylose, and types IV, V and VII to waxy phenotypes. The differences between RFLP types could be attributed to insertions in the Waxy gene. Types II and VI were caused by the insertion of a Tourist element into intron 1 and a SINE-like sequence into intron 12, respectively. Types III, IV, V and VII were characterized by the insertion of large sequences into the Waxy gene that may alter the expression of the gene. Thus, multiple, independent insertions in the Waxy gene appear to have caused the loss-of-function waxy phenotypes. Furthermore, the geographical distributions of the three RFLP types associated with the waxy phenotype (types IV, V and VII) were distinct, with type IV being found mainly in Taiwan and Japan, type V in Korea, and type VII in Myanmar. These results indicate a polyphyletic origin for the waxy phenotype in landraces of foxtail millet.
KW - Crop evolution
KW - Foxtail millet
KW - Insertion sequence
KW - Setaria italica
KW - Waxy gene
UR - http://www.scopus.com/inward/record.url?scp=0036460392&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0036460392&partnerID=8YFLogxK
U2 - 10.1007/s00438-002-0728-8
DO - 10.1007/s00438-002-0728-8
M3 - Article
C2 - 12395195
AN - SCOPUS:0036460392
VL - 268
SP - 214
EP - 222
JO - Molecular Genetics and Genomics
JF - Molecular Genetics and Genomics
SN - 1617-4615
IS - 2
ER -