De-Yuan Hong

Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers

Abstractu2002Genetic variation within and between five populations of Oryza granulata from two regions of China was investigated using RAPD (random amplified polymorphic DNA) and ISSR (inter-simple sequence repeat amplification) markers. Twenty RAPD primers used in this study amplified 199 reproducible bands with 61 (30.65%) polymorphic; and 12 ISSR primers amplified 113 bands with 52 (46.02%) polymorphic. Both RAPD and ISSR analyses revealed a low level of genetic diversity in wild populations of O. granulata. Furthermore, analysis of molecular variance (AMOVA) was used to apportion the variation within and between populations both within and between regions. As the RAPD markers revealed, 73.85% of the total genetic diversity resided between the two regions, whereas only 19.45% and 6.70% were present between populations within regions and within a population respectively. Similarly, it was shown by ISSR markers that a great amount of variation (49.26%) occurred between the two regions, with only 38.07% and 12.66% between populations within regions and within a population respectively. Both the results of a UPGMA cluster, based on Jaccard coefficients, and pairwise distance analysis agree with that of the AMOVA partition. This is the first report of the partitioning of genetic variability within and among populations of O. granulata at the DNA level, which is in general agreement with a recent study on the same species in China using allozyme analysis. Our results also indicated that the percentage of polymorphic bands (PPB) detected by ISSR is higher than that detected by RAPD. It seems that ISSR is superior to RAPD in terms of the polymorphism detected and the amplification reproducibility.

RAPD variation within and between natural populations of the wild rice oryza rufipogon from china and brazil

Genetic variation within and between eight natural populations of Oryza rufipogon from China and Brazil was investigated at the DNA level by analysis of RAPD fragments. Out of 60 random primers, which were initially screened against DNA from four individuals, 20 generated highly reproducible RAPD fragments which were then used for further population analysis. With these primers, 95 discernible DNA fragments were produced and 78 (82.1%) were polymorphic, which indicated that high levels of genetic variation existed in these natural populations. In addition, the Chinese populations showed greater polymorphism than those from Brazil at both the population and regional levels. This is noteworthy considering that the Chinese populations are from a relatively restricted area of China. The factors responsible for these findings include the contrasting mating systems in the Brazilian and Chinese populations, and gene flow from annual cultivated rice to perennial natural populations in China. An Analysis of Molecular Variance (AMOVA) was used to apportion the variation between individuals within populations, between populations within regions, and between regions. Results showed that 61.8% of the total genetic diversity resided between the two continents, whereas only 14.9% and 23.3% was attributable to population differences within regions and to individual differences within a population, respectively. The great genetic differentiation between the Chinese and Brazilian populations is in agreement with recent treatment of the American form of O. rufipogon as a separate species, O. glumaepatula.

Cytoplasmic composition in Pinus densata and population establishment of the diploid hybrid pine

Sequence and restriction site analyses of the paternally inherited chloroplast rbcL gene and maternally inherited mitochondrial nad1 fragments from the same set of populations and individuals were used to investigate cytoplasmic composition and population establishment of Pinus densata, a diploid pine that originated through hybridization between P. tabuliformis and P. yunnanensis. Two variable sites and three chlorotypes (TT, TC and GC) were detected on the rbcL gene of the three pines. P. densata harboured the three chlorotypes, two of which (TT, GC) were characteristic of the parental species, respectively. The third chlorotype (TC) was distributed extensively in seven of the 10 P. densata populations analysed, and might represent a mutation type or have been derived from an extinct parent. The distribution of chlorotypes, together with that of mitotypes, indicated that significant founder effect and backcross happened during the population establishment of the hybrid pine. P. tabuliformis and P. yunnanensis had acted as both mother and father donors, i.e. bi‐directional gene flow existed between the two parental species in the past. Population differentiation of P. densata is high, as detected from the cytoplasmic genomes: GST = 0.533 for cpDNA and GST = 0.905 for mtDNA. The differences in cytoplasmic composition among the hybrid populations suggest that the local populations have undergone different evolutionary histories.

Clonality in wild rice (Oryza rufipogon, Poaceae) and its implications for conservation management

Correlations were examined between habitat characters and clonal structures determined by the RAPD (random amplified polymorphic DNA) assay in five populations of Oryza rufipogon in China. Nine of 175 decameric primers were used in the study because they reproducibly amplified polymorphisms. The extent of clonality together with the clonal and sexual reproductive strategies varied greatly among the five populations and correlated with the habitats where they occur. The populations under serious disturbance or seasonal drought tended to have small clones with relatively high clonal diversity caused by sexual reproduction, whereas the populations with little disturbance and sufficient supply of water were prone to have large clones with relatively low clonal variation and low sexual reproduction. Therefore, the dynamics of sexual vs. clonal reproduction of this species depended mainly on environmental factors, such as external disturbance and water supply, rather than latitudes indicated by previous study. These results have important implications for in situ conservation of O. rufipogon. Adequate external disturbance and water supply control are essential for maintaining high clone diversity of in situ conserved populations. According to the extent of clonality of the populations examined, we recommend that an interval of >12 m should be required for collecting samples for ex situ conservation and for population genetic studies to capture possible genetic diversity for O. rufipogon in China.

A phylogeny of the rice tribe Oryzeae (Poaceae) based on matK sequence data

Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for 26 species representing 11 genera of the tribe Oryzeae and three outgroup species. The sequenced fragments varied from 1522 base pairs (bp) to 1534 bp in length with 15.4% variable and 7.9% phylogenetically informative sites when the outgroups were excluded. The aligned sequences were analyzed by maximum parsimony and neighbor-joining methods. Analyses of the sequence data indicated that species of Oryzeae form a strongly supported monophyletic group, concordant with previous morphological and anatomical evidence. The tribe Oryzeae can be divided into two monophyletic lineages, corresponding to the traditionally recognized subtribes Oryzinae and Zizaniinae. The first subtribe consists of Oryza and Leersia, while the subtribe Zizaniinae includes the remaining genera. The matK sequence data did not support the close affinities of the monoecious genera in Oryzeae, implying the possibility of multiple origins of the floral structures in the tribe. It is noteworthy that Porteresia coarctata is closely related to Oryza species, suggesting that it should be treated as a member in the genus Oryza rather than a separate monotypic genus.

Population genetic structure and conservation of an endangered conifer, Cathaya argyrophylla (Pinaceae)

Cathaya argyrophylla is an endangered conifer restricted to subtropical mountains of China, with total number of individuals less than 4,000. To assess levels and patterns of genetic diversity of C. argyrophylla, eight populations representing four widely separated regions were analyzed for allozyme variation, using 13 enzymes. In comparison with other coniferous species, C. argyrophylla possesses a low amount of variation, particularly at the population level (A = 1.38; P = 30.4; He = 0.102). By contrast, the level of population differentiation is much higher (FST = 0.441) compared to other conifers, and significant differentiation occurs both between regions and between populations within a region. Climate, geologic, and fossil data suggest that historical factors are mainly responsible for the unique population genetic structure in C. argyrophylla. These factors include severe bottleneck and subsequent genetic drift during Quaternary glaciations and habitat deterioration and fragmentation in postglaciation. In addition, reduced gene flow and relatively high rates of inbreeding may be factors that lead to low population variability and marked genetic differentiation among populations. Implications for the development of conservation strategies for this endangered species are discussed on the basis of these findings.

Unexpected high divergence in nrDNA ITS and extensive parallelism in floral morphology of Pedicularis (Orobanchaceae)

Abstract.Internal transcribed spacer (ITS) region sequences of nuclear ribosomal DNA (nrDNA) were used in the phylogenetic reconstruction of Pedicularis, a genus with strong adaptive radiation. Forty-two species representing 12 greges of the genus were all, except P. resupinata, sampled from the Hengduan Mountain region, China. A high level of ITS sequence variation was found among the species distributed in such a small geographical area, which had been rarely reported in other groups. The great ITS divergence in Pedicularis could be explained by a relatively ancient origin and diversification of the genus followed by migration of different floristic components into the Hengduan Mountains, or accelerated rates of molecular evolution in parasitic lineages of Orobanchaceae. In the present ITS phylogeny, almost all the main clades are not consistent with the high hierarchical taxa within Pedicularis, which implies that significant parallel evolution occurred in floral morphology of the genus, and that undue attention has been paid to corolla characters in the intragenus classifications.

Maternal lineages of Pinus densata, a diploid hybrid.

Previous morphological, allozyme and chloroplast DNA data have suggested that Pinus densata originated through hybridization between P. tabuliformis and P. yunnanensis. In the present study, sequence and restriction site analyses of maternally inherited mitochondrial nad1 intron were used to detect variation patterns in 19 populations of P. tabuliformis, P. yunnanensis and P. densata. A total of three mitotypes (A, B, C) were detected. All but one of the populations of P. yunnanensis possessed mitotype B while all populations of P. tabuliformis had mitotype A. Pinus densata populations, on the other hand, harboured both mitotypes A and B, which are characteristic of P. tabuliformis and P. yunnanensis, respectively. This result gives strong additional evidence supporting the hybrid origin of this diploid pine. The distribution of mitotypes indicated very different mating compositions and evolutionary history among P. densata populations. It seems that local founder populations and backcrosses may have played important roles in the early establishment of P. densata populations. The uplift of the Tibetan Plateau had a significant impact on the distribution of maternal lineages of P. densata populations.

LOW LEVELS OF GENETIC DIVERSITY WITHIN POPULATIONS AND HIGH DIFFERENTIATION AMONG POPULATIONS OF A WILD RICE, ORYZA GRANULATA NEES ET ARN. EX WATT., FROM CHINA

To characterize genetic diversity within and among populations of Oryza granulata Nees et Arn. ex Watt., allozyme variation was assayed for 17 loci in 15 natural populations from Hainan and Yunnan provinces, China, using starch gel electrophoresis. A low level of genetic variability within populations (the mean ndocumentclass{aastex}nusepackage{amsbsy}nusepackage{amsfonts}nusepackage{amssymb}nusepackage{bm}nusepackage{mathrsfs}nusepackage{pifont}nusepackage{stmaryrd}nusepackage{textcomp}nusepackage{portland,xspace}nusepackage{amsmath,amsxtra}nusepackage[OT2,OT1]{fontenc}nnewcommandcyr{nrenewcommandrmdefault{wncyr}nrenewcommandsfdefault{wncyss}nrenewcommandencodingdefault{OT2}nnormalfontnselectfont}nDeclareTextFontCommand{textcyr}{cyr}npagestyle{empty}nDeclareMathSizes{10}{9}{7}{6}nbegin{document}nlandscapen