ABSTRACT
We analyzed the sequence
alignment on 25 AA rice and 24 non-AA rice chloroplasts using two length diversity
markers (ORF 100 and ORF29-TrnCGCA) and
four sequence markers existed in introns of rps16 gene and TrnTUGU-TrnLUAA spacer to explore the chloroplast diversity of different types of rice using
PCR amplification and sequencing. Results showed that in terms of the length of
ORF100 and ORF29-TrnCGCA, chloroplast DNA (cp DNA) of Hainan
ordinary wild rice, Dongxiang ordinary wild rice, Hepu ordinary wild rice and
three-line cytoplasmic male sterile wild rice were indica-type, Chaling
ordinary wild rice, Fusui ordinary wild rice, Niwara wild rice, Brazilian
upland rice and Lemont were japonica-type among in AA genome. Besides, all
non-AA wild rice was japonica-type. There were 4 indica-japonica markers
utilizing introns of rps16 gene and TrnTUGU-TrnLUAA. We found
that all the ordinary wild rice in Chaling and Fusui of AA genome presented as
japonica specific sites, while the others owned two indica and japonica
specific sites, respectively. There were two indica-japonica sites separately
and a 6-base specific fragment in three-line cytoplasmic male sterile materials
except Yuetai A, simultaneously, 2-base difference from Hainan wild rice.
Moreover, Brazilian upland rice and Lemont were entire japonica specific sites.
Result of three markers indicated that the cp DNA of non-AA wild rice was
japonica-type and result of one marker showed indica-type. Sequencing results
also suggested that wild rice existed many polymorphic base sites, CCDD genome,
wart wild rice and malay wild rice had their own specific sites. In conclusion,
significant differentiation trend of indica-japonica exhibits in chloroplast of
ordinary wild rice, and non-AA wild rice is generally japonica-type. The
cytoplasmic polymorphism level of three-line sterile lines is low. It is worth
considering whether the cytoplasm of Honglian-type sterile line Yuetai A comes
from Hainan ordinary wild rice. Furthermore, genetic polymorphisms in wild rice
are far more than in cultivar.
Share and Cite:
Wu, H. , Pu, L. , Shu, Y. , Li, Y. , Meng, J. , Yang, H. and Zhao, H. (2020) Chloroplast DNA Polymorphism in Rice (
Oryza sativa L.).
American Journal of Plant Sciences,
11, 454-464. doi:
10.4236/ajps.2020.113033.