Domestication and geographic origin of Oryza sativa in China: insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon

Previous studies have indicated that China is one of the domestication centres of Asian cultivated rice (Oryza sativa), and common wild rice (O. rufipogon) is the progenitor of O. sativa. However, the number of domestication times and the geographic origin of Asian cultivated rice in China are still under debate. In this study, 100 accessions of Asian cultivated rice and 111 accessions of common wild rice in China were selected to examine the relationship between O. sativa and O. rufipogon and thereby infer the domestication and evolution of O. sativa in China through sequence analyses of six gene regions, trnC‐ycf6 in chloroplast genomes, cox3 in mitochondrial genomes and ITS, Ehd1, Waxy, Hd1 in nuclear genomes. The results indicated that the two subspecies of O. sativa (indica and japonica) were domesticated independently from different populations of O. rufipogon with gene flow occurring later from japonica to indica; Southern China was the genetic diversity centre of O. rufipogon, and the Pearl River basin near the Tropic of Cancer was the domestication centre of O. sativa in China.     

A large-scale field study of transgene flow from cultivated rice (Oryza sativa) to common wild rice (O. rufipogon) and barnyard grass (Echinochloa crusgalli)

The introgression of transgenes into wild relatives or weeds through pollen-mediated gene flow is a major concern in environmental risk assessment of transgenic crops. A large-scale (1.3–1.8 ha) rice gene flow study was conducted using transgenic rice containing the bar gene as a pollen donor and Oryza rufipogon as a recipient. There was a high frequency of transgene flow (11%−18%) at 0–1 m, with a steep decline with increasing distance to a detection limit of 0.01% by 250 m. To our knowledge, this is the highest frequency and longest distance of gene flow from transgenic rice to O. rufipogon reported so far. On the basis of these data, an adequate isolation distance from both conventional and transgenic rice should be taken for in situ conservation of common wild rice. Meanwhile, there is no evidence of transgene introgression into barnyard grass, even when it has coexisted with transgenic rice containing the bar gene for five successive years. Thus, the environmental risk of gene flow to this weedy species is of little concern.     

Ecological divergence in the presence of gene flow in two closely related Oryza species (Oryza rufipogon and O. nivara)

Ecological divergence plays a prominent role in the process of speciation, but how divergence occurs in the face of gene flow is still less clear, and remains controversial among evolutionists. Here we investigated the nucleotide diversity, divergence and gene flow between Oryza nivara and O. rufipogon using sequences of seven chloroplast and nuclear loci. By analysing samples from 26 wild populations across the geographic ranges of the two species, we showed that both species were highly structured and O. rufipogon maintained a higher level of species‐wide diversity than O. nivara. Notably, phylogenetic, amova and F_ST analyses were unable to detect significant nucleotide differentiation between the two species. We estimated that the two species began to diverge at c. 0.16 million years ago. Our coalescent‐based simulations strongly rejected the simple isolation model of zero migration between species, but rather provided unambiguous evidence of bidirectional gene flow between species, particularly from O. rufipogon to O. nivara. Our simulations also indicated that gene flow was recurrent during the divergence process rather than arising from secondary contact after allopatric divergence. In conjunction with different morphological and life‐history traits and habitat preference in the two species, this study supports the hypothesis that these Oryza species are better treated as ecotypes that diverged quite recently and are still under the process of divergence. Importantly, we demonstrate the ecological divergence between O. rufipogon and O. nivara in the presence of significant gene flow, implying that natural selection plays a primary role in driving the divergence of the two Oryza species.     

东乡野生稻与栽培稻正反交种间杂种F_1的雄配子发生与发育

该文以东乡野生稻与栽培稻（美国光壳稻P1003）的正反交种间杂种F1（正交为光壳稻P1003×东乡野生稻;反交为东乡野生稻×光壳稻P1003）为试材,研究其各个减数分裂时期的染色体行为特征、染色体交换重组及雄配子发育特点。结果表明：正反交杂种F1花粉母细胞细胞核减数分裂的同步性较高,细胞质为连续型胞质分裂类型。在细胞核分裂的过程中,核仁在前期I到中期I逐渐消失。染色体在前期I到中期I逐渐收缩,变得更加清晰可见。在终变期和中期I,90.54%以上的花粉母细胞能形成12个二价体（含少数棒状二价体和8字型二价体）,部分花粉母细胞（正交9.46%,反交7.65%）出现少量的单价体、三价体和四价体。后期I观察到1.27%–1.35%的花粉母细胞含有1至数条落后染色体。最终有92.6%–94.8%的小孢子能发育成形态正常、染色能力强的成熟花粉粒。另外,在正交杂种F1的粗线期中存在2个核仁,而反交杂种F1及其双亲的粗线期只有1个核仁。这些研究结果可为作物品种改良、种质资源创新以及种间亲缘关系研究提供细胞学证据。     

Characterization of interspecific hybrids and backcross progenies from a cross between Oryza minuta and Oryza sativa

Oryza minuta, a tetraploid wild relative of cultivated rice, is an important source for the genetic improvement. Interspecific hybrids were obtained from the cross of O. sativa L. (IR24) and O. minuta (Acc. No. 101133) with 5.58% crossability, which ranged from 0.11% to 1.62% in the backcross generations. The chromosome numbers of the backcross progenies were 24 to 48. Seven yield-related traits of the parents, hybrid F₁, and backcross progenies were evaluated. Simple sequence repeat markers analysis showed that the polymorphism ratio of SSR bands between IR24 and Acc. No. 101133 was 93.2%. The average donor segment number, length, donor genome size, and percentage of donor genome of 92 BC₃F₁ plants (2n=24) were 24.1, 17.8 cM, 438.4 cM and 26.2%, respectively. They were complex variation and uneven among the chromosomes. These introgression lines could be used to identify the favorable genes of O. minuta and provide a new platform for the genetic improvement of cultivated rice.     

Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers.

We searched for SNPs in 417 regions distributed throughout the genome of three Oryza sativa ssp. japonica cultivars, two indica cultivars, and a wild rice (O. rufipogon). We found 2800 SNPs in approximately 250,000 aligned bases for an average of one SNP every 89 bp, or one SNP every 232 bp between two randomly selected strains. Graphic representation of the frequency of SNPs along each chromosome showed uneven distribution of polymorphism-rich and -poor regions, but little obvious association with the centromere or telomere. The 94 SNPs that we found between the closely related cultivars 'Nipponbare' and 'Koshihikari' can be converted into molecular markers. Our establishment of 213 co-dominant SNP markers distributed throughout the genome illustrates the immense potential of SNPs as molecular markers not only for genome research, but also for molecular breeding of rice.     

Crossability Barriers in the Interspecific Hybridization between Oryza sativa and O. meyeriana

Oryza meyeriana Baill （GG genome） is a precious germplasm in the tertiary gene pool of cultivated rice （AA genome）, and possesses important traits such as resistance and tolerance to biotic and abiotic stress. However, interspeciflc crossability barrier, a critical bottleneck restricting genes transfer from O. meyeriana to cultivars has led to no hybrids through conventional reproduction. Therefore, the reasons underlying incrossability were investigated in the present report. The results showed that： （i） at 3-7 d after pollination （DAP）, many hybrid embryos degenerated at the earlier globular-shaped stage, and could not develop into the later pear-shaped stage. Meanwhile, free endosperm nuclei started to degenerate at 1 DAP, and cellular endosperm could not form at 3 DAP, leading to nutrition starvation for young embryo development; （ii） at 11-13 DAP, almost all hybrid ovaries aborted. Even though 72.22% of hybrid young embryos were produced in the interspecific hybridization between O. sativa and O. meyeriana, young embryos were not able to further develop into hybrid plantlets via culturing in vitro. The main reason for the incrossability was hybrid embryo inviability, presenting as embryo development stagnation and degeneration since 3 DAP. Some possible approaches to overcome the crossability barriers in the interspecific hybridization between O. sativa and O. meyeriana are discussed.     

Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice （Oryza rufipogon L.） in relation to the domestication of cultivated rice （O. sativa L.）

It is generally accepted that Oryza rufipogon is the progenitor of Asian cultivated rice （O. sativa）. However, how the two subspecies of O. sativa （indica and japonica） were domesticated has long been debated. To investigate the genetic differentiation in O. rufipogon in relation to the domestication of O. sativa, we developed 57 subspecies-specific intron length polymorphism （SSILP） markers by comparison between 10 indica cultivars and 10 japonica cultivars and defined a standard indica rice and a standard japonica rice based on these SSILP markers. Using these SSILP markers to genotype 73 O. rufipogon accessions, we found that the indica alleles and japonica alleles of the SSILP markers were predominant in the O. rufipogon accessions, suggesting that SSILPs were highly conserved during the evolution of O. sativa. Cluster analysis based on these markers yielded a dendrogram consisting of two distinct groups： one group （Group I） comprises all the O. rufipogon accesions from tropical （South and Southeast） Asia as well as the standard indica rice; the other group （Group II） comprises all the O. rufipogon accessions from Southern China as well as the standard japonica rice. Further analysis showed that the two groups have significantly higher frequencies of indica alleles and japonica alleles, respectively. These results support the hypothesis that indica rice and japonica rice were domesticated from the O. rufipogon of tropical Asia and from that of Southern China, respectively, and suggest that the indica-japonica differentiation should have formed in O. rufipogon long before the beginning of domestication. Furthermore, with an O. glaberrima accession as an outgroup, it is suggested that the indica-japonica differentiation in O. ruffpogon might occur after its speciation from other AA-genome species.     

Development of Oryza rufipogon and O. sativa Introgression Lines and Assessment for Yield-related Quantitative Trait Loci

Introgression lines population was effectively used in mapping quantitative trait loci （QTLs）, identifying favorable genes, discovering hidden genetic variation, evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research. In this study, an advanced backcross and consecutive selfing strategy was used to develop introgression lines （ILs）, which derived from an accession of Oryza rufipogon Griff. collected from Yuanjiang County, Yunnan Province of China, as the donor, and an elite indica cultivar Teqing （O. sativa L.）, as the recipient. Introgression segments from O. rufipogon were screened using 179 polymorphic simple sequence repeats （SSR） markers in the genome of each IL. Introgressed segments carried by the introgression lines population contained 120 ILs covering the whole O. rufipogon genome. The mean number of homozygous O. rufipogon segments per introgression line was about 3.88. The average length of introgressed segments was approximate 25.5 cM, and about 20.8% of these segments had sizes less than 10 cM. The genome of each IL harbored the chromosomal fragments of O. rufipogon ranging from 0.54% to 23.7%, with an overall average of 5.79%. At each locus, the ratio of substitution of O. rufipogon alleles had a range of 1.67-9.33, with an average of 5.50. A wide range of alterations in morphological and yield-related traits were also found in the introgression lines population. Using single-point analysis, a total of 37 putative QTLs for yield and yield components were detected at two sites with 7%-20% explaining the phenotypic variance. Nineteen QTLs （51.4%） were detected at both sites, and the alleles from O. rufipogon at fifteen loci （40.5%） improved the yield and yield components in the Teqing background. These O. rufipogon-O, sativa introgression lines will serve as genetic materials for identifying and using favorable genes from common wild rice.     

海南普通野生稻稻瘟病的抗性鉴定与评价

在苗期应用自然诱发鉴定法对海南普通野生稻(Oryza rufipogonGriff.)41个居群的410份材料进行了2年的稻瘟病(rice blast)抗性鉴定,结果表明:经过初鉴和复鉴,410份海南普通野生稻中有21份表现高抗,占5.1%,117份表现抗,占28.5%,说明海南普通野生稻具有较好的稻瘟病抗性。     

Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers

BACKGROUND AND AIMS: Weedy rice (Oryza sativa f. spontanea) is one of the most notorious weeds occurring in rice-planting areas worldwide. The objectives of this study are to determine the genetic diversity and differentiation of weedy rice populations from Liaoning Province in North-eastern China and to explore the possible origin of these weedy populations by comparing their genetic relationships with rice varieties (O. sativa) and wild rice (O. rufipogon) from different sources. METHODS: Simple sequence repeat (SSR) markers were used to estimate the genetic diversity of 30 weedy rice populations from Liaoning, each containing about 30 individuals, selected rice varieties and wild O. rufipogon. Genetic differentiation and the relationships of weedy rice populations were analysed using cluster analysis (UPGMA) and principle component analysis (PCA). KEY RESULTS: The overall genetic diversity of weedy rice populations from Liaoning was relatively high (H(e) = 0.313, I = 0.572), with about 35 % of the genetic variation found among regions. The Liaoning weedy rice populations were closely related to rice varieties from Liaoning and japonica varieties from other regions but distantly related to indica rice varieties and wild O. rufipogon. CONCLUSIONS: Weedy rice populations from Liaoning are considerably variable genetically and most probably originated from Liaoning rice varieties by mutation and intervarietal hybrids. Recent changes in farming practices and cultivation methods along with less weed management may have promoted the re-emergence and divergence of weedy rice in North-eastern China.     

Crossability Barriers in the Interspecific Hybridization between Oryza sativa and O. meyeriana

Oryza meyerlana Baill (GG genome) Is a precious germplaem in the tertiary gene pool of cultivated rice (AA genome), and possesses important traits such as resistance and tolerance to biotic and abiotic stress. However, interspecific crossability barrier, a critical bottleneck restricting genes transfer from O. meyeriana to cultivars has led to no hybrids through conventional reproduction. Therefore, the reasons undedying incrossability were investigated in the present report. The results showed that: (ⅰ) at 3-7 d after pollination (DAP), many hybdd embryos degenerated at the earlier globular-shaped stage, and could not develop into the later pear-shaped stage. Meanwhile, free endosperm nuclei started to degenerate at 1 DAP, and cellular endosperm could not form st 3 DAP, leading to nutrition starvation for young embryo development; (ⅱ) st 11-13 DAP, almost all hybrid ovaries aborted. Even though 72.22% of hybrid young embryos were produced in the interspecific hybridization between O. sativa and O. meyeriana, young embryos were not able to further develop into hybrid plantlets via culturing in vitro. The main reason for the incrossability was hybrid embryo inviability, presenting as embryo development stagnation and degeneration since 3 DAP. Some possible approaches to overcome the crossability banders in the interspecific hybridization between O. sativa and O. meyeriana are discussed.     

Regulation of Submergence-induced Enhanced Shoot Elongation in Oryza sativa L.

Rice (Oryza sativa L.) is the only cereal that can be cultivatedin the frequently flooded river deltas of South-East and SouthAsia. The survival strategies used by rice have been studiedquite extensively and the role of several phytohormones in theelongation response has been established. Deep-water rice cultivarscan diminish flooding stress by rapid elongation of their submergedtissues to keep up with the rising waters. Other rice cultivarsmay react by mechanisms of submergence tolerance. Aerenchymaand aerenchymatous adventitious roots are formed that facilitateoxygen diffusion to prevent anaerobic conditions in the submergedtissues. This paper discusses the molecular aspects of the mechanismthat leads to shoot elongation (leaves of seedlings and internodes),the regulation of which involves metabolism of, and interactionsbetween, ethylene, gibberellins and abscisic acid. Finally,the importance of new techniques in future research is assessed.Current molecular technology can reveal subtle differences ingene activity between tolerant and non-tolerant cultivars, andidentify genes that are involved in the regulation of submergenceavoidance and tolerance.     

Proteome analysis of cultivar-specific deregulations of Oryza sativa indica and O. sativa japonica cellular suspensions undergoing rice yellow mottle virus infection

We have used two-dimensional gel electrophoresis with mass spectrometry analysis to study the temporal patterns of protein expression during RYMV (Rice yellow mottle virus) infection in rice cells of two cultivars: IR64, Oryza sativa indica, susceptible, and Azucena, O. sativa japonica, partially resistant to RYMV. Proteomic analysis of nonstressed and RYMV inoculated cells showed statistically significant changes in the relative levels of 40 IR64 proteins and 24 Azucena proteins. Protein identification using mass spectrometry was attempted for all the differentially regulated proteins. This global analysis detected 32 hypothetical "new" proteins. Nineteen differentially regulated proteins were identified for IR64 cultivar, while 13 were identified for Azucena cultivar, including proteins in three functional categories: metabolism, stress-related proteins, and translation. These data revealed that a number of proteins regulated by abiotic stress response pathway were activated by RYMV in both cultivars (such as salt-induced protein, heat shock proteins (HSPs), superoxide dismutase (SOD), and others have functions consistent with the susceptibility or partially resistance trait (such as dehydrin, proteins involved in glycolysis pathway).     

长穗颈水稻的内源GA1、IAA和ABA含量变化

分别以携有长穗颈基因eui1、eui2和野生型基因Eui的协青早不育系和保持系6个水稻品种为材料,测定它们在抽穗始期植株中内源GA1、IAA和ABA含量的变化。结果表明,携有eui1和eui2基因的水稻可以在植株体内产生大量内源GA1,携有eui1基因的GA1含量比携有eui2基因的高。携有eui1基因的ABA含量最高,携有eui2基因的其次,而携有Eui基因的最低。IAA含量也表现出同样的趋势。表明长穗颈基因主要是通过调节内源GA1含量促进水稻最上节间的剧烈伸长。     

粳稻和籼稻D1蛋白光抑制敏感性的差异与其编码基因序列结构特征的相关性分析(英文)

粳稻 (OryzasativaL .ssp .japonica)和籼稻 (O .sativassp .indica)对光抑制的敏感程度存在差异 ,它们的叶绿体光反应中心Ⅱ核心蛋白D1的稳定性不同。以菌落原位杂交法克隆了粳稻“95 16”和籼稻“籼优 6 3”叶绿体D1蛋白的编码基因psbA。核苷酸序列同源比较显示 :两者在启动子区和 5′_UTR完全相同 ;编码区存在着个别碱基的差异 ,但均位于三联体密码的第三位 ,不影响氨基酸编码特性 ,在蛋白质氨基酸序列上没有差异 ;在 3′_UTR内存在寡聚U长度的差异。因此 ,粳稻和籼稻D1蛋白对光抑制作用敏感性的差异与其蛋白质的氨基酸序列结构无关 ,可能与调控psbA基因表达的上游因子或光保护机制的差异有关。     

低磷营养胁迫下水稻化感抑草潜力的变化特性及其作用机理

在低磷(0.5 mg·L^-1) 营养胁迫下,运用生理生化方法分析了化感水稻PI312777（PI）与非化感水稻Lemont (Le) 对稗草抑制作用潜力的变化特性及其内在机理.结果表明,在低磷营养胁迫下,化感水稻品种PI对受体稗草根干重的抑制能力明显提高,在处理后的5 、10和15 d,其对稗草地下部干重的抑制率分别增加了5.64%、3.89%和12.13%,增加幅度比非化感水稻品种Le显著.生理生化分析结果表明,与正常营养条件相比,用低磷营养下生长的化感水稻PI的根系分泌物处理稗草5、10和15 d,受体稗草叶片中POD活性的促进率分别提高了20.19%、15.47%和6.68%,吲哚乙酸氧化酶活性的促进率分别提高了18.08%、17.71%和12.50%,硝酸还原酶活性的抑制率分别增加了13.89%、18.60%和2.10%. 在低磷营养胁迫下,化感水稻通过抑制受体植物的硝酸还原酶活性,影响其对氮营养的吸收,同时显著提高了吲哚乙酸氧化酶活性,减缓了受体稗草的生长速度,提高了其抑草作用潜力.     

亚洲栽培稻与普通野生稻种间杂种花粉和胚囊败育研究

以亚洲栽培稻籼稻品种广陆矮4号（简称GLA）、粳稻品种辽粳944（简称944）、粳型亲籼系G2416．3（简称M12）与产于广东高州的普通野生稻（简称GP）配制6个正反交种间杂交组合,F1育性研究的结果表明：GLA／GP F1与GP／GLA F1之间的花粉育性（56．71％、56．15％）、胚囊育性（42．10％、33．33％）和小穗育性（33．66％、32．60％）差异较小;944／GP F1与GP/944 F1之间的花粉育性（79．01％、7．45％）、胚囊育性（50．00％、27．28％）和小穗育性（47．31％、17．59％）差异较大;M12／GP F1与GP／M12 F1的花粉育性（65．26％和49．55％）和小穗育性（73．16％和54．10％）差异介于前两者间,而胚囊育性（75．00％和40．00％）相差较大。各杂种F1败育花粉以典败类型为主;杂种F1败育胚囊主要有雌性生殖单位退化,卵器退化,极核异常排列,胚囊内组织混乱,助细胞退化且珠心组织吞噬胚囊,以及胚囊退化等。杂种胚囊育性和花粉育性直接影响小穗育性。以野生稻为母本的杂种育性较相应反交组合杂种的为低,表现出野生稻细胞质对栽野杂种育性的影响效应。可尝试利用人为创建的粳型亲籼系来开展克服栽培稻与普通野生稻种间杂种不育性的研究。