Journal of Plant Biotechnology

  • 제43권2호
  • /
  • Pages.164-173
  • /
  • 2016
  • /
  • 1229-2818(pISSN)
  • /
  • 2384-1397(eISSN)
한국식물생명공학회 (The Korean Society of Plant Biotechnology)
권호 표지
DOI QR코드

DOI QR Code

수박계통간 염색체수준의 유전적변이 분석

Genome-wide analysis of sequence variations in eight inbred watermelon lines

  • 투고 : 2016.06.16
  • 심사 : 2016.06.20
  • 발행 : 2016.06.30
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

수박의 형태적 변이의 유전적 원인을 분석해 보기 위해 8개 계통에서 re-sequencing을 수행하였다. 유전적 변이의 수는 염색체에 따라 다르게 나왔으며 발견된 SNP의 약 12.9%만이 유전자내에서 발견되었고 나머지는 프로모터나 유전자 사이의 지역에서 발견되었다. SNP 밀도에 대한 분석 결과 염색체 6번의 말단지역에 변이가 집중되어 있는 것을 알 수 있었다. 또한 염색체 10과 11번에 잘 보존된 지역을 발견하였다. Pathway 분석을 통해 DIMBOA(일종의 항생제)-glucoside 분해 대사가 계통간 가장 차이나는 것으로 확인되었으며 이는 각 계통의 병저항성에서 차이가날 가능성을 시사하는 것이다. 당대사 관련 유전자 변이를 분석한 결과 alpha-galactosidase 유전자에 가장 변이가 많은 것으로 밝혀졌다. 이러한 연구 결과는 육종을 분자수준에서 이해하는 데 도움을 줄 것으로 생각한다.

To investigate the genetic basis of phenotypic differences, sequence variations were analyzed in 8 inbred watermelon lines by re-sequencing. The number of sequence variations differed depending on the chromosome. Only 12.9% of SNPs were found within genes, whereas the rest were detected in promoter or intergenic regions. SNP density analysis showed that there was a highly variable region at the end of chromosome 6, which is similar to previously published findings. However, this region with high SNP density did not show much variation between the lines. In contrast, highly conserved regions with a size of 6.5-10 Mb were found in chromosomes 10 and 11. Pathway analysis suggested that the DIMBOA (a natural antibiotic)-glucoside degradation pathway was significantly different between the lines, indicating that the eight lines may have different levels of pathogen resistance. Among the carbohydrate-related genes, the alpha-galactosidase gene was the most variable among the lines. Information from this study will be helpful in understanding the watermelon breeding process at the molecular level.

키워드

참고문헌

  1. Bayraktar H, Onal S (2013) Concentration and purification of alpha-galactosidase from watermelon (Citrullus vulgaris) by three phase partitioning. Seperation and Purification technology 118:835-841 https://doi.org/10.1016/j.seppur.2013.08.040
  2. Couture RM, Routley DG, Dunn GM (1971) Role of cyclic hydroxamic acids in monogenic resistance of maize to Helminthosporium turcicum. Physiol Plant Path 1:515-785 https://doi.org/10.1016/0048-4059(71)90013-0
  3. Chrost B, Schmitz K (1997) Changes in soluble sugar and activity of a-galactosidases and acid invertase during muskmelon (Cucurmis melo L.) fruit development. J Plant Physiol 151:41-45 https://doi.org/10.1016/S0176-1617(97)80034-X
  4. Crop production survey (2012) from http://kostat.go.kr
  5. FAO statistics from http://faostat.fao.org
  6. Gama RNC, Santos CAF, Dias RCS (2013) Genetic variability of watermelon accessions based on microsatellite markers. Genetics Mol Res 12(1):747-754 https://doi.org/10.4238/2013.March.13.3
  7. Gaudreault PR, Webb JA (1983) Partial purification and properties of an alkaline a-galactosidase from mature leaves of Curcurbita pepo. Plant Physiol 71:662-668 https://doi.org/10.1104/pp.71.3.662
  8. Guo et al (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature genetics 45(1):51-8 https://doi.org/10.1038/ng.2470
  9. Guo S, Sun H, Zhang H, Liu J, Ren Y, Gong G, Jiao C, Zheng Y, Yang W, Fei Z, Xu Y (2015) Comparative transcriptome analysis of cultivated and wild watermelon during fruit development. PLoS ONE 10(6):e0130267. DOI:10.1371/journal.pone.0130267
  10. Hubbard NL, Pharr DM, Huber SC (1989) Sucrose phosphate synthase and acid invertase as determinants of sucrose concentration in developing muskmelon (Cucumis melo L.) fruits. Plant Physiol 91:1527-1534 https://doi.org/10.1104/pp.91.4.1527
  11. Itoh T, Uda Y, Nakagawa H (1986) Purification and characterization of alpha-galactosidase from watermelon. J Biochem 99(1):243-50 https://doi.org/10.1093/oxfordjournals.jbchem.a135465
  12. Keller F, Pharr DM (1996) Metabolism of carbohydrates in sink and sources: galactosyl-sucrose oligosaccharides, p 157-183. In: E. Zamski, A.A. Schaffer (ed.). Photoassimilate Distribution in Plants and Crops, Marcel Dekker, New York
  13. Kwon YS, Lee WS, Cho IH (2006) Assessment of genetic relationship among watermelon varieties revealed by ISSR marker. J Life Sci 16(2):219-224 https://doi.org/10.5352/JLS.2006.16.2.219
  14. Long BJ, Dunn GM, Routley DG (1975) Relationship of hydroxamic acid content in maize and resistance to northern corn leaf blight. Crop Sci 15:333-335 https://doi.org/10.2135/cropsci1975.0011183X001500030015x
  15. Nimmakayala P, Levi A, Abburi L, Tomason YR, Saminathan T, Vajia VG, Malkaram S, Reddy R, Wehner TC, Mitchell SE, Reddy UK (2014) Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. BMC Genomics, 15:767-780 https://doi.org/10.1186/1471-2164-15-767
  16. Perkins-Veazie P, Collins JK, Davis AR, Roberts W (2006) Carotenoid content of 50 watermelon cultivars. J Agric Food Chem 54:2593-2597 https://doi.org/10.1021/jf052066p
  17. Richardson PT, Baker DA, Ho LC (1982) The chemical composition of cucurbit vascular exudates. J Exp Bot 33:1239-1247 https://doi.org/10.1093/jxb/33.6.1239
  18. Schaffer AA, Pharr DM, Madore MA (1996) Cucurbits, p. 729-757. In: E. Zamski, A.A. Schaffer (ed.). Photoassimilate Distribution in Plants and Crops. Marcel Dekker, New York
  19. Shi L, Peng G, Qianglong Z, Feishi L, Angela RD, Xiaolu W (2016) Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. And Nakai) constructed using whole-genome re-sequencing data. Breeding Sci 66:244-259 https://doi.org/10.1270/jsbbs.66.244
  20. Yoo KS, Bang H, Lee EJ, Crosby K, Patil BS (2012) Variation of carotenoid, sugar, and ascorbic acid concentrations in watermelon genotypes and genetic analysis. Hort Envir Biotech 53(6):552-560 https://doi.org/10.1007/s13580-012-0014-6