Identification of Sequence Polymorphism in the Non-Transcribed Sequence (NTS) of 5S Ribosomal DNA From Korean and Chinese Foxtail Millet (Setaria italica L.) Cultivars
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Totally, 26 collections, 17 from Korea and 9 from China, were investigated for their sequences of 5S rDNA, especially the non-transcribed spacers (NTSs). Sequences of 5S rDNA were isolated by PCR using the primers, 5s-rRNA1 and 5s-rRNA2. Genomic DNA PCR produced single amplification of 300, 330, or 350 base pair fragments. Sequence analysis revealed that all inserts contained the part of 5S rDNA gene sequence and the full length of the NTS region. Three different sizes of the fragments were confirmed due to different size of NTS and their length were 300bp, 330bp and 350bp, respectively. Among 17 Korean foxtail millets tested, 14 collections showed single 300bp amplification. Longest fragment amplification, 350bp, was obtained only from the foxtail millet from China origin, even though 2 of them include 300bp fragment. CLUSTALW multiple alignments of 26 foxtail millets clearly revealed 4 areas with certain degree of sequence heterogeneity (region I, II, III, IV). Among 4 boxed areas, foxtail millet genotypes from China have distinct insertion especially in region III. Five of them have extra insertion of sequence and their additional sequences were either 45 or 48 base pair. Three Korean foxtail millets have 32 bp insertion. Other 8 Korean collections have short insert sequences (6 to 8 bp), 3 with 8 bp and 5 with 6 bp. In addition to insert, deletion sequences were also confirmed as major deletion was observed in region II of Chinese collection. The size of deletion was 7bp long. According to phylogenic tree constructed using MEGA4 program, clear grouping was not revealed. To obtain more convincing results various collections from many countries should be obtained and analyzed to distinguish different germplasm from different origin.
Abstract
Totally, 26 collections, 17 from Korea and 9 from China, were investigated for their sequences of 5S rDNA, especially the non-transcribed spacers (NTSs). Sequences of 5S rDNA were isolated by PCR using the primers, 5s-rRNA1 and 5s-rRNA2. Genomic DNA PCR produced single amplification of 300, 330, or 350 base pair fragments. Sequence analysis revealed that all inserts contained the part of 5S rDNA gene sequence and the full length of the NTS region. Three different sizes of the fragments were confirmed due to different size of NTS and their length were 300bp, 330bp and 350bp, respectively. Among 17 Korean foxtail millets tested, 14 collections showed single 300bp amplification. Longest fragment amplification, 350bp, was obtained only from the foxtail millet from China origin, even though 2 of them include 300bp fragment. CLUSTALW multiple alignments of 26 foxtail millets clearly revealed 4 areas with certain degree of sequence heterogeneity (region I, II, III, IV). Among 4 boxed areas, foxtail millet genotypes from China have distinct insertion especially in region III. Five of them have extra insertion of sequence and their additional sequences were either 45 or 48 base pair. Three Korean foxtail millets have 32 bp insertion. Other 8 Korean collections have short insert sequences (6 to 8 bp), 3 with 8 bp and 5 with 6 bp. In addition to insert, deletion sequences were also confirmed as major deletion was observed in region II of Chinese collection. The size of deletion was 7bp long. According to phylogenic tree constructed using MEGA4 program, clear grouping was not revealed. To obtain more convincing results various collections from many countries should be obtained and analyzed to distinguish different germplasm from different origin.
참고문헌 (18)
- Baum BR, "The molecular diversity of the 5S rRNA gene in barley (Hordeum vulgare)", Genome, 37, pp.992~998 (1994)
- Buckler IV ES, "Zea systematics: ribosomal ITS evidence", Mol. Biol. Evol, 13, pp.612~622 (1996)
- Falistocco E, "Investigations of 5S rDNA of Vitis vinifera L.: sequence analysis and physical mapping", Genome, 50(10), pp.927~938 (2007)
- Fukunaga K, "Ribosomal DNA variation in foxtail millet, Setaria italica (L.) P. Beauv. and a survey of variation from Europe and Asia", Theor. Appl. Genet, 97, pp.751~756 (1997)
- "Plant Cell Rep", 2012, 323~337
- Kihara H, "Bastarde zwischen Setaria italic and S. viridis", Bot. Mag. Tokyo, 56, pp.62~67 (1942)
- 김은지, "우리나라와 중국, 파키스탄에서 수집한 조 계통들에 대한 형태적 변이", 한국육종학회지, 42(2), pp.181~187 (2010), 한국육종학회
- Küster H., "Neolithic plant remains from Eberdingenhochdorf, southern Germany, In Plants and ancient man (studies in palaeoethnobotany)", pp.307~311 (1984), AA Bakame
- Lee HS, "Characteristics of the Foxtail Millet (Setaria italica L. Beauv) Local Collections in Korea", Korean J. Breed, 19(2), pp.158~163 (1987)
- Li CH, "Interspecific crosses in Setaria II, Cytological studies of interspecific hybrids involving : 1, S. faberi and S. italica, and 2, a three way cross, F2 of S. italica x S. viridis and S. faberi", J. Hered, 33, pp.351~355 (1942)
- Li Y, "Traditional maintenance and multiplication of foxtail millet (Setaria italica (L.) P. Beauv) landraces in China", Euphytica, 87, pp.33~38 (1996)
- Lisitsina A, "Main types of ancient farming on the Caucasus on the basis of palaeo-ethnobotanical research", Ber. Deut. Bot. Ges, 91, pp.47~57 (1976)
- Lu TLD, "A green foxtail millet (Setaria viridis) cultivation experiment in the middle Yellow River valley and some related issues", Asian Perspect, 41, pp.1~14 (2002)
- Nichloas KB, "GeneDoc: analysis and visualization of genetic variation", Embnet News, 4, pp.1~4 (1997)
- Rogers SO, "Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues", Plant Mol. Biol, 5, pp.69~76 (1985)
- Sivaraman L, "Novel molecular features of millet genomes", Indian J. Biochem. Biophys, 21, pp.299~303 (1984)
- Tamura K, "MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0", Mol. Biol. Evol, 24(8), pp.1596~1599 (2007)
- Thompson JD, "The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools", Nucleic Acids Res, 25, pp.44876~44882 (1997)