药用野生稻具有丰富的遗传多样性并含有大量优异基因。对药用野生稻的利用主要存在遗传学背景不清楚、常规育种效率不高两方面的障碍。这些问题可以通过构建药用野生稻可转化大片段基因组文库和转基因技术，将大片段克隆导入栽培稻中，建立全基因组基因嵌入突变体库来解决。本文对国内外药用野生稻有利基因发掘及其利用的研究进展进行综述。

对云南省境内的3种野生稻40个原生境的植物群落进行了考察，共记录植物159种，分属于51科。按乔木层、灌木层、草本层对野生稻原生境植物种类进行分类，乔木层植物共6科1亚科11种，灌木层植物共29科60种，草本层植物共20科88种；普通野生稻原生境的植物种类95%为草本层，疣粒野生稻的植物则有明显的垂直层次结构。普通野生稻原生境植物共计20种，均为特有植物种，分属于5科，主要为禾本科和莎草科；药用野生稻原生境植物共计25种，分属于19个科，特有种15个；疣粒野生稻原生境植物共计125种，分属于45科，特有植物种数达117个。最后就3种野生稻原生境植物种类调查的意义、外来物种对野生稻的原生境威胁等问题进行了讨论。

以超高产或高产栽培稻两优培九、汕优63、威优46和93-11为对照，测定了湖南茶陵普通野生稻抽穗开花期1 d中不同时间点的净光合速率（Pn）以及Pn对不同光强、不同CO2浓度与不同温度的响应曲线。结果表明，茶陵普通野生稻的Pn在下午极显著高于对照，在高温（40℃，45℃）胁迫下也是如此；光补偿点为22.3 µmol photons m-2 s-1，与对照差异不显著(20.1~23.7 µmol photons m-2 s-1)，光饱和点为1 810 µmol photons m-2 s-1，与对照93-11无显著差异，但极显著高于其他对照材料（1 530~1 628 µmol photons m-2 s-1），表观量子效率(AQY)与对照无显著差异；CO2补偿点（52.7 μmol mol-1）稍高于对照（42.7~50.1 μmol mol-1），而饱和点(644.5 μmol mol-1)则明显高于对照(521.1~581.3 μmol mol-1)，羧化效率（0.1511 mol m-2 s-1）显著高于对照(0.1277~0.1384 mol m-2 s-1)；叶绿素含量极显著高于对照。说明茶陵普通野生稻的光合性能强于超高产或高产对照栽培稻，且在高温下表现更为突出。]]>

Plant-transformation-ready, large-insert binary bacterial artificial chromosome (BIBAC) libraries are of significance for functional and network analysis of large genomic regions, gene clusters, large-spanning genes, and complex loci in the post-genome era. Here, we report the characterization of a plant-transformation-ready BIBAC library of the sequenced Arabidopsis genome for which such a library is not available to the public, the transformation of a large-insert BIBAC of the library into tobacco by biolistic bombardment, and the expression analysis of its containing genes in transgenic plants. The BIBAC library was constructed from nuclear DNA partially digested with BamHI in the BIBAC vector pCLD04541. It contains 6144 clones and has a mean insert size of 108 kb, representing 5.2x equivalents of the Arabidopsis genome or a probability of greater than 99% of obtaining at least one positive clone from the library using a single-copy sequence as a probe. The transformation of the large-insert BIBAC and analyses of the transgenic plants showed that not only did transgenic plants have intact BIBAC DNA, but also could the BIBAC be transmitted stably into progenies and its containing genes be expressed actively. These results suggest that the large-insert BIBAC library, combined with the biolistic bombardment transformation method, could provide a useful tool for large-scale functional analysis of the Arabidopsis genome sequence and applications in plant-molecular breeding.

Jatropha curcas L. is a potentially significant bioenergy crop in the tropics and subtropics. Here we present a plant-transformation-competent binary bacterial artificial chromosome (BIBAC) library from Jatropha cultivar YN049-4. This library was constructed with BamH in the vector pCLD04541, consists of 30,720 clones and is arrayed in 80 384-well microtiter plates. Since 92.1% (28,293) of its clones were shown to contain Jatropha DNA inserts with an average size of 131.9 kb, the library is estimated to represent approximately 8.9 haploid genome equivalents of the species, thus providing a greater than 99% probability of discovering a particular single-copy sequence in the library. High-density clone filters were made from a subset of the library and hybridized with nine pairs of overgos designed from genes involved in fatty acid metabolism. Hybridization results showed that eight overgo pairs were able to identify positive clones from the subset of the library, with an average of 5.3 clones per probe, suggesting that it is suitable for Jatropha genomics and genetics research. Because this library, to our knowledge, represents the first large-insert, plant-transformation-competent BIBAC library for Jatropha, it will provide a vital resource for advanced genomics research, including isolation and characterization of genes and quantitative trait loci, integrative physical mapping and genome sequencing.

BACKGROUND: Cotton, one of the world's leading crops, is important to the world's textile and energy industries, and is a model species for studies of plant polyploidization, cellulose biosynthesis and cell wall biogenesis. Here, we report the construction of a plant-transformation-competent binary bacterial artificial chromosome (BIBAC) library and comparative genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.) with one of its diploid putative progenitor species, G. raimondii Ulbr. RESULTS: We constructed the cotton BIBAC library in a vector competent for high-molecular-weight DNA transformation in different plant species through either Agrobacterium or particle bombardment. The library contains 76,800 clones with an average insert size of 135 kb, providing an approximate 99% probability of obtaining at least one positive clone from the library using a single-copy probe. The quality and utility of the library were verified by identifying BIBACs containing genes important for fiber development, fiber cellulose biosynthesis, seed fatty acid metabolism, cotton-nematode interaction, and bacterial blight resistance. In order to gain an insight into the Upland cotton genome and its relationship with G. raimondii, we sequenced nearly 10,000 BIBAC ends (BESs) randomly selected from the library, generating approximately one BES for every 250 kb along the Upland cotton genome. The retroelement Gypsy/DIRS1 family predominates in the Upland cotton genome, accounting for over 77% of all transposable elements. From the BESs, we identified 1,269 simple sequence repeats (SSRs), of which 1,006 were new, thus providing additional markers for cotton genome research. Surprisingly, comparative sequence analysis showed that Upland cotton is much more diverged from G. raimondii at the genomic sequence level than expected. There seems to be no significant difference between the relationships of the Upland cotton D- and A-subgenomes with the G. raimondii genome, even though G. raimondii contains a D genome (D5). CONCLUSIONS: The library represents the first BIBAC library in cotton and related species, thus providing tools useful for integrative physical mapping, large-scale genome sequencing and large-scale functional analysis of the Upland cotton genome. Comparative sequence analysis provides insights into the Upland cotton genome, and a possible mechanism underlying the divergence and evolution of polyploid Upland cotton from its diploid putative progenitor species, G. raimondii.

Oryza malampuzhaensis, one of the tetraploid taxa of the genusOryza, is geographically restricted to Western Ghats of South India. Its taxonomic status is not well established and is generally treated as a tetraploid race of O. officinalis. Sixty-three morphological traits and 262 random amplified polymorphic DNA (RAPD) markers generated by 23 random decamer primers were used to assess the genetic relationship between O. malampuzhaensis and O. officinalis. Pair wise comparisons based on both RAPDs and morphological traits revealed 60% genetic distance between the two taxa and was significantly higher (p <0.01) than the corresponding intra-specific distances. Cluster and principal component analysis (PCA) of genetic distance estimations based on RAPDs and morphological traits clearly differentiated the two taxa. High frequency of discrete O. malampuzhaensis specific RAPDs (21%) and the significantly higher (p < 0.05) mean number of amplification products per individual in O. malampuzhaensis observed in the study reflect its allopolyploid nature. Low genetic diversity within O. malampuzhaensis revealed by RAPD analysis indicates the recent origin of this taxa. The RAPD analysis further revealed the possibility that the putative ‘C’ genomeprogenitor of O. malampuzhaensis is a close relative of O. officinalis. In addition, amplification products diagnostic to O. malampuzhaensis were identified. The results of the present study clearly demonstrated that the O. malampuzhaensis is a distinct entity, and support the recent conclusion that O. malampuzhaensis has diverged enough to deserve species status.]]>

New gene origination is a major source of genomic innovations that confer phenotypic changes and biological diversity. Generation of new mitochondrial genes in plants may cause cytoplasmic male sterility (CMS), which can promote outcrossing and increase fitness. However, how mitochondrial genes originate and evolve in structure and function remains unclear. The rice Wild Abortive type of CMS is conferred by the mitochondrial gene WA352c (previously named WA352) and has been widely exploited in hybrid rice breeding. Here, we reconstruct the evolutionary trajectory of WA352c by the identification and analyses of 11 mitochondrial genomic recombinant structures related to WA352c in wild and cultivated rice. We deduce that these structures arose through multiple rearrangements among conserved mitochondrial sequences in the mitochondrial genome of the wild rice Oryza rufipogon, coupled with substoichiometric shifting and sequence variation. We identify two expressed but nonfunctional protogenes among these structures, and show that they could evolve into functional CMS genes via sequence variations that could relieve the self-inhibitory potential of the proteins. These sequence changes would endow the proteins the ability to interact with the nucleus-encoded mitochondrial protein COX11, resulting in premature programmed cell death in the anther tapetum and male sterility. Furthermore, we show that the sequences that encode the COX11-interaction domains in these WA352c-related genes have experienced purifying selection during evolution. We propose a model for the formation and evolution of new CMS genes via a

Crop yield reduction as a consequence of increasingly severe climatic events threatens global food security. Genetic loci that ensure productivity in challenging environments exist within the germplasm of crops, their wild relatives and species that are adapted to extreme environments. Selective breeding for the combination of beneficial loci in germplasm has improved yields in diverse environments throughout the history of agriculture. An effective new paradigm is the targeted identification of specific genetic determinants of stress adaptation that have evolved in nature and their precise introgression into elite varieties. These loci are often associated with distinct regulation or function, duplication and/or neofunctionalization of genes that maintain plant homeostasis.