S-Space College of Agriculture and Life Sciences (농업생명과학대학) Dept. of Plant Science (식물생산과학부) Theses (Master's Degree_식물생산과학부)
Search fo Allopolyploid Genome Donor of Vigna reflexo-pilosa
- 농업생명과학대학 식물생산과학부(작물생명과학전공)
- Issue Date
- 서울대학교 대학원
- 학위논문 (석사)-- 서울대학교 대학원 : 식물생산과학부(작물생명과학전공), 2014. 2. 이석하.
- Vigna is a genus of flowering plants in the legume family, consists of three subgenus, Vigna, Plectotropis and Ceratotropis. About 100 species belongs to this genus, including azuki bean, blackgram and mungbean which are well-known in Asia.
Among the species in Vigna genus, Vigna reflexo-pilosa has its own unique characteristics form as allotetraploid (2n=4x=44), whereas other Vigna species exist as diploid form (2n=2x=22).
In this study, we de novo assembled V. reflexo-pilosa genome and 22 accessions of 18 Vigna species transcriptome using NGS platform. We calculated the Ks values of synteny blocks within V. reflexo-pilosa to determine the whole-genome duplication event existence, and compare the result of V. radiata and the result of G. max. As a result, we found the fact that there were two WGD events had occurred on Vigna reflexo-pilosa unlike Vigna radiata which only occurred once.
After that, we tried to find out the genome donor which species did contribute to V. reflexo-pilosa formation using transcriptome assemble results of 22 Vigna accessions. Ks value calculation between the transcriptome assemble results and predicted gene sets of V. reflexo-pilosa has been excuted.
Through the calculation, V. trinervia showed 2 peaks (0.0075, 0.0495) on its Ks value bin distribution and confirmed as A-type genome donor. Based on the peak value, we considered the predicted genes of V. reflexo-pilosa in Ks value range from 0.000 to 0.030 as A-type genes, inherited from V. trinervia and Ks value range from 0.033 to 0.072 as B-type genes, inherited from other genome donor.
Re-calculating the Ks values of 4,796 predicted genes in B-type with the transcriptome assemble results of 22 Vigna accessions, we were able to find 6 Vigna species, V. umbelleta(CIAT34386), V. umbelleta(2004T2), V. nakashimae, V. nepalensis, V. riukiuensis, V. minima as candidate B-type genome donor.