Hongya Gu, Ph.D.
Professor and Deputy Dean,
College of Life Sciences, Peking University
Long Hong, Li Zhang, Junming Wei, Xihui Liang, Linchuan Li, Tong Wei, Zhiqiang Ma, Juqing Kang, Ruixi Li, Zhe Wu, Caihong Yu, Jia Wei, Kangtai Sun, Jianqiao Wang, Xinlei Wang, Qian Yang
Systematic and evolutionary botany and plant molecular biology
Genetic diversity and cold adaptation of the natural Arabidopsis thaliana populations in China
Function and evolution of certain plant gene families
Studies on the evolution of gene families such as those coding for CHS, trypsin inhibitor, Myb transcriptional factors, etc. The studies have found that CHS genes in most Angiosperm families could be classified into two groups based on their base substitution rates. One group has fast rates and the other group has relatively low rates. The copy number varies greatly in the angiosperms, while fewer copies found in the gymnosperms in their nuclear genomes. About 10 genes are found in the rice genome encoding Bowman-Birk trypsin inhibitor. The phylogenetic analysis of the coding sequences and sequence comparison of the 5' and 3' UTR showed that the genes with three-repeat structure evolved from the genes with two-repeat structure recently. Further analysis showed that some sites in the second repeat have been under the positive selection. The function of the 10 genes is under investigation now. Myb transcriptional factors represent one of the biggest gene families in plants. We cloned most of the full cDNAs of Myb genes in Arabidopsis thaliana. A few of them have been studies for their functions, such as AtMYB17 and AtMYB118. The natural variation and mechanism of adaptation of plants are also our concern. We have collected more than 30 natural populations of Arabidopsis thaliana from more than 10 provinces in China. The molecular phylogenetic studies showed that A. thaliana was distributed in China naturally, and their populations expanded along Changjiang River about 900,000 years ago. The analysis on the transcription profiles of different populations under cold treatments showed significant differences among populations and it may be correlated with environmental factors to which they have been adapted. Further focuses will be on the possible molecular mechanisms of the adaptation under low temperature.
Progress in Research
1. Myb genes involved in inflorescence and embryogenesis
AtMYB17 and AtMYB118 belong to Myb R2R3-subfamily. AtMYB17 expressed dominantly in inflorescences and siliques, while AtMYB118 only expressed in developing embryos. Microarray analysis showed that many genes encoding proteins accumulated during embryogenesis were remarkably up-regulated in AtMYB118-over-expressed transgenic plants, including late embryogenesis abundant proteins (LEA proteins), storage proteins, seed maturation proteins, and proteins related with seed dehydration, desiccation and ABA signaling pathway. These results suggest that AtMYB118 may play an important role during embryogenesis and seed maturation. The analysis on AtMYB17 showed that the LFY binding sites in the promoter region of AtMYB17 were important in fine-tuning regulation of the spatio-temporal expression of AtMYB17 in transgenic plants. Moreover, AtMYB17 was up-regulated in 35S::AGL15 plants. Taken together, our data suggest that LFY may be involved in the regulation of AtMYB17, possibly together with AGL15, and thereafter in early inflorescence development and seed germination.
2. Collection of Natural populations of A. thaliana in China, and study on their genetic diversity, populations structure, and phylogeny with other populations in the world
RAPD and ISSR markers were adopted to analyze the genetic diversity and population structure of native populations of A. thaliana in China. The AMOVA analysis indicated about 42–45% of the total genetic variation existed within populations, which is equivalent to the average level of genetic diversity in other populations in the world. The Mantel test revealed a significant correlation between the geographic distance and the genetic distance of these populations in general. Based on the observation of recolonization and extinction of naturally distributed populations of A. thaliana, and the pattern of their genetic differentiation, the distribution of this species in China might be a result of natural dispersal under the strong influence of human activity. The analysis on chloroplast intergenic regions on these Chinese populations with those in other regions and three out groups as references showed that the Chinese populations along the Changjiang River may have dispersed eastwards to their present-day locations from the Himalayas. These populations originated from a common ancestor, and a rapid demographic expansion began approximately 90,000 years ago. Two populations collected from the middle range of the Altai Mountains in China may have survived in a local refugium during late Pleistocene glaciations. The natural populations from China with specific genetic characteristics enriched the gene pools of global A. thaliana collections, and could serve as excellent materials for studies on the molecular mechanism of plant adaptation to different local environments.
3. Variation at the transcriptional level among Chinese natural populations of Arabidopsis thaliana in response to cold treatment
The Arabidopsis 25K GeneChip (ATH1, Affymetrix) was used to make a survey of the variation of the transcriptional profiles among five Chinese natural populations of Arabidopsis thaliana under cold treatment. In normal growth condition, the expression level of 2.26% (513 genes in the population from Jiujiang, Jiangxi, JXjjx) to 6.52% (1482 genes in the population from Tongliang, Chongqing, CQtlx) genes was two-fold higher than that of Col ecotype. Under cold treatment, the expression of 12.84% (2920 genes in the population from Chenggu, Shaanxi, SXcgx) to 19.46% (4426 genes in the population from Qinghe, Xinjiang, XJqhx) genes was up- or down-regulated by at least two-fold that of their controls. In general, most of up-regulated genes might be the genes essential for plant surviving at low temperature, such as genes in CBF pathway and the genes responsible for synthesizing molecules accumulated for cold tolerance. However, each natural population had some specific genes induced under cold treatment. The data indicated that some of the cold-responding genes were differentiated among the populations distributed in the natural habitats with different climate conditions. CBF3, one of the key transcription factor genes in cold responding pathway, showed significant differences in expression among populations. The sequence analysis indicated that the changes in its regulation region caused the dramatic difference in the expression pattern. Further studies on the correlation of the function of the differentially expressed genes and the cold tolerance in different populations may provide some new insight into the molecular mechanism of adaptation to local environment in Arabidopsis thaliana in China.
1. Zhang Y., Cao G., Qu L.-J., Gu H. 2009. Involvement of an R2R3-MYB transcription factor gene AtMYB118 in embryogenesis in Arabidopsis. Plant Cell Reports, 28(3):337-46.
2. Zhang Y., Cao G., Qu L.-J., Gu H. (2009). Characterization of Arabidopsis MYB transcription factor gene AtMYB17 and its possible regulation by LEAFY and AGL15. Journal of Genetics and Genomics,36(2):99-107.
3. Wang Z, Cao GG, Wang XL, Miao J, Liu XT, Chen ZL, Qu LJ, Gu HG (2008) Identification and characterization of COI1-dependent transcription factor genes involved in JA-mediated response to wounding in Arabidopsis plants. Plant Cell Reports, 27: 125-135.
4. He F, Kang JQ, Zhou X, Su Z, Qu LJ, Gu HY (2008) Variation at the transcriptional level among Chinese natural populations of Arabidopsis thaliana in response to cold stress. Chinese Science Bulletin, 53: 2989-2999.
5. Qin GJ, Ma ZQ, Zhang L, Xing SF, Hou XH, Deng J, Liu JL, Chen ZL, Qu LJ, Gu HY (2007) Arabidopsis AtBECLIN 1/AtAtg6/AtVps30 is essential for pollen germination and plant development. Cell Research, 17: 249-263.
6. He F, Kang D, Ren Y, Qu LJ, Zhen Y, Gu H (2007) Genetic diversity of the natural populations of Arabidopsis thaliana in China. Heredity, 99: 423-431.
7. Qin HL, Wang YG, Xue JM, Miao Q, Ma L, Mei T, Zhang WM, Guo W, Wang JY, Gu HY (2007) Biological effects of protons targeted to different fanges of Arabidopsis seeds. International Journal of Radiation Biology, 83:1-8.
8. Yang X, Li J, Pei M, Gu H, Chen·Z, Qu L-J, 2007, Over-expression of a flower-specific transcription factor gene AtMYB24 causes aberrant anther development. Plant Cell Rep., 26: 219–228.
9. Guo L, Wang Z, Lin H, Cui W, Chen J, Liu M, Chen Z, Qu L-J, Gu H, 2006, Expression and functional analysis of rice plasma-membrane intrinsic protein gene family. Cell Research, 16(3): 277-286.
10. Li J, Li X, Guo L, Lu F, Feng X, He K, Wei L, Chen Z, Qu L-J and Gu H, 2006, A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice. Journal of Experimental Botany, 57(6): 1263-1273.
11. Li J, Yang X, Wang Y, Li X, Gao Z, Pei M, Chen Z, Qu L-J and Gu H, 2006, Two groups of MYB transcription factors share a motif which enhances trans-activation activity. Biochemical and Biophysical Research Communications, 341(4): 1155-1163.
12. Su H, Qu L-J, He K, Zhang Z, Wang J, Chen Z and Gu H, 2003, The Great Wall of China: a physical barrier to gene flow? Heredity, 90: 212-219.
13. Zhang W, Qu L-J, Gao W, Gu H, Chen Z, 2002, Studies on the origin and evolution of tetraploid wheats-based on internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA. Theoretical and Applied Genetics, 104: 1099-1106.