Lu Baorong

Differentiation of Indica-Japonica rice revealed by insertion/deletion (InDel) fragments obtained from the comparative genomic study of DNA sequences between 93-11 (Indica) and Nipponbare (Japonica)

DNA polymorphisms from nucleotide insertion/deletions (InDels) in genomic sequences are the basis for developing InDel molecular markers. To validate the InDel primer pairs on the basis of the comparative genomic study on DNA sequences between an Indica rice 93-11 and a Japonica rice Nipponbare for identifying Indica and Japonica rice varieties and studying wild Oryza species, we studied 49 Indica, 43 Japonica, and 24 wild rice accessions collected from ten Asian countries using 45 InDel primer pairs. Results indicated that of the 45 InDel primer pairs, 41 can accurately identify Indica and Japonica rice varieties with a reliability of over 80%. The scatter plotting data of the principal component analysis (PCA) indicated that: (i) the InDel primer pairs can easily distinguish Indica from Japonica rice varieties, in addition to revealing their genetic differentiation; (ii) the AA-genome wild rice species showed a relatively close genetic relationship with the Indica rice varieties; and (iii) the non-AA genome wild rice species did not show evident differentiation into the Indica and Japonica types. It is concluded from the study that most of the InDel primer pairs obtained from DNA sequences of 93-11 and Nipponbare can be used for identifying Indica and Japonica rice varieties, and for studying genetic relationships of wild rice species, particularly in terms of the Indica-Japonica differentiation.

Sampling strategy for wild soybean (Glycine soja) populations based on their genetic diversity and fine-scale spatial genetic structure

A total of 892 individuals sampled from a wild soybean population in a natural reserve near the Yellow River estuary located in Kenli of Shandong Province (China) were investigated. Seventeen SSR (simple sequence repeat) primer pairs from cultivated soybeans were used to estimate the genetic diversity of the population and its variation pattern versus changes of the sample size (sub-samples), in addition to investigating the fine-scale spatial genetic structure within the population. The results showed relatively high genetic diversity of the population with the mean value of allele number (A) being 2.88, expected heterozygosity (He) 0.431, Shannon diversity index (I) 0.699, and percentage of polymorphic loci (P) 100%. Sub-samples of different sizes (ten groups) were randomly drawn from the population and their genetic diversity was calculated by computer simulation. The regression model of the four diversity indexes with the change of sample sizes was computed. As a result, 27–52 individuals can reach 95% of total genetic variability of the population. Spatial autocorrelation analysis revealed that the genetic patch size of this wild soybean population is about 18 m. The study provided a scientific basis for the sampling strategy of wild soybean populations.

What is a species: Conflict between evolutionarycontinuity and taxonomic discontinuity

What is a species? This is a question seemingly simple but difficult to be addressed clearly. If only by a simple definition, a “species” can be described as the basic category or unit for taxonomic classification of organisms (including animals, plants, and microbes). On the other hand, it is extremely difficult to define a “species” or “species concept” that are generally acceptable by all biologists. Substantial debates exist over the “species concept” and have lasted for more than a contrary. During this time span, many species concepts have been proposed by various groups of biologists who work in different disciplines. However, it is extremely difficult to have a clear definition for “species” and particularly for “species concept” that are universally agreeable. Among the proposed species concepts, only some of them are influential, including those: taxonomic species concept, Darwin’s species concept, biological species concept, genetic species concept, and phylogenetic species concept. Obviously, biologists who proposed their species concepts attempt to interpret what “species” are only by emphasizing the specific features of a species appreciable from their perspectives. For example, biologists who have proposed taxonomic species concept highlight the classification feature of a species; whereas those who have Darwin’s species concept stress the evolutionary process of a species. Disagreements always exist among biologists when define the species concept. Some biologists believe that a species is a natural unit, which is strictly followed for the classification of a species. However, other biologists do not believe a species to be a natural unit, instead, they emphasize more on the evolution and reproductive aspects of a species. The extreme groups even reject “species” as a natural units. They only accept individuals as the natural unit. Obviously, the dilemma is due to the diverged understanding and opinion of species. We know that species are the outcomes of evolution—biodiversity. From the practical viewpoint, it is necessary to categorize the evolution-resulted biodiversity using a stable classification system. Therefore, taxonomists prefer to use a discontinued unit to classify species. On the other hand, evolutionists emphasize more on the variation of organisms. Thus, the characteristics of evolutionary continuity and taxonomic discontinuity have stimulated such debates over a species—a natural unit or an artificial category. Species are outcomes of continued evolutionary process and categories of discontinued taxonomy. As such, one can recognize, understand, and define a species according to the objectives and demands to suit his or her research, without being troubled too much by a universally unified concept of species. Thus, to answer what is a species, we prefer the definition that a species is an individual collection that occurs in a particularly space/time, shares similar morphological and physiological features with a common ancestor. Members of the same species are able to interbreed and reproduce normal descendants.

Model-based calculating tool for pollen-mediated gene flow frequencies in plants.

The potential social-economic and environmental impacts caused by transgene flow from genetically engineered (GE) crops have stimulated worldwide biosafety concerns. To determine transgene flow frequencies resulted from pollination is the first critical step for assessing such impacts, in addition to the determination of transgene expression and fitness in crop-wild hybrid descendants. Two methods are commonly used to estimate pollen-mediated gene flow (PMGF) frequencies: field experimenting and mathematical modeling. Field experiments can provide relatively accurate results but are time/resource consuming. Modeling offers an effective complement for PMGF experimental assessment. However, many published models describe PMGF by mathematical equations and are practically not easy to use. To increase the application of PMGF modeling for the estimation of transgene flow, we established a tool to calculate PMGF frequencies based on a quasi-mechanistic PMGF model for wind-pollination species. This tool includes a calculating program displayed by an easy-operating interface. PMGF frequencies of different plant species can be quickly calculated under different environmental conditions by including a number of biological and wind speed parameters that can be measured in the fields/laboratories or obtained from published data. The tool is freely available in the public domain (http://ecology.fudan.edu.cn/userfiles/cn/files/Tool_Manual.zip). Case studies including rice, wheat, and maize demonstrated similar results between the calculated frequencies based on this tool and those from published PMGF data. This PMGF calculating tool will provide useful information for assessing and monitoring social-economic and environmental impacts caused by transgene flow from GE crops. This tool can also be applied to determine the isolation distances between GE and non-GE crops in a coexistence agro-ecosystem, and to ensure the purity of certified seeds by setting proper isolation distances among field production plots.This study provide a model-based calculating tool/software that can accurately calculate pollen-mediated gene flow (PMGF) frequencies of wind-pollinated plant species by including five biological and climatic parameters. The calculating tool can easily be used by any users who are not familiar with mathematical modeling. The required parameters can be measured directly in the field without conducting PMGF experiments, which makes this tool practical to estimate PMGF frequencies. This tool will be helpful to estimate transgene flow and its potential impacts, in addition to determining isolation distances between GE and non-GE crops.

Genetic and evolutionary effects of hybridization-introgression and their implications for conservation of crop wild relative species

Genetic diversity in crop wild relatives (CWRs) includes important germplasm resources that play essential roles in crop genetic improvement. Efficient conservation and sustainable utilization of CWRs is critical to world food security. Severe habitat damage presents a major challenge to CWR survival, with many CWR populations consequently endangered or even extirpated. In addition, a neglected factor threatening the long-term CWR availability is the flow and introgression of crop alleles into CWR populations; these processes may considerably alter CWR genetic structure and integrity, leading to genetic diversity losses in in situ conserved CWR populations. Little is known, however, concerning the impacts of crop-wild gene flow and introgression on CWR conservation. The design of effective strategies, although challenging, is important to minimize the unfavorable consequences of these processes on CWR conservation.