Characteristics of the short rachillae of rice from archaeological sites dating to 7000 years ago

The abscission layer formed on a pedicel situated at the basal part of a short rachilla is an important characteristic for discriminating between wild, japonica, and indica rice. The short rachillae of paddy rice grains excavated from the Kuahuqiao, Luojiajiao, and Tianluoshan sites, located in the lower reaches of the Yangtze River and dating to 7000 years old, were observed. The results showed that the short rachillae could be divided into two types: a wild type and japonica type. These results indicated that the rice had been domesticated, but was a primitive cultivated rice that retained some of the characteristics of wild rice. The results also suggested that the rice was changing to resemble japonica type rice. Based on the ratios of wild and japonica types, it was inferred that rice domestication began 10000 years ago.     

Identification and mapping of quantitative trait loci controlling cold-tolerance of Chinese common wild rice (O. rufipogon Griff.) at booting to flowering stages

Cold injury is an important limitation of rice production. Therefore, screening for cold-tolerant genetic resources and the development of highly cold-tolerant cultivars is crucial for higher yield potential and stable yield of rice. There have been several reports on the genetic analysis and QTL mapping of the cold-tolerance at the booting stage. Toriyama et al.[1,2] and Futsuhara et al.[3,4] reported that 4 or more genes were involved in the cold-tolerance. Several QTLs at the booting sta…     

Geographical genetic diversity and divergence of common wild rice （O. rufipogon Griff.） in China

Using 36 SSR markers and 889 accessions of common wild rice in China, the genetic diversity and the divergence among different geographical populations are investigated. Guangdong Province has the largest number of alleles, which account for 84% of the total alleles detected in the study, followed by Guangxi Province. The Nei＇s gene diversity indices, from high to low, are in the sequence of Hainan, Guangdong, Guangxi, Fujian, Hunan, Jiangxi, and Yunnan provinces. Two genetic diversity centers of Chinese common wild rice are detected on the basis of geographic analysis, i.e., the region covering Boluo, Zijin, Lufeng, Haifeng, Huidong and Huiyang counties of Guangdong Province and the region covering Yongning, Longan, Laibin and Guigang counties of Guangxi Province. The common wild rice in Yunnan, Hunan, Jiangxi, and Fujian provinces are diverged into respectively independent populations with relatively large genetic distances, whereas, those in Hainan, Guangdong and Guangxi provinces have relatively low genetic divergence. Under the condition of geographic separation, natural selection is considered as one of the primary forces contributing to the divergence of common wild rice in China.     

Geographical genetic diversity and divergence of common wild rice (O. rufipogon Griff.) in China

Using 36 SSR markers and 889 accessions of common wild rice in China, the genetic diversity and the divergence among different geographical populations are investigated. Guangdong Province has the largest number of alleles, which account for 84% of the total alleles detected in the study, followed by Guangxi Province. The Nei's gene diversity indices, from high to low, are in the sequence of Hainan, Guangdong, Guangxi, Fujian, Hunan, Jiangxi, and Yunnan provinces. Two genetic diversity centers of Chinese common wild rice are detected on the basis of geographic analysis, i.e., the region covering Boluo, Zijin, Lufeng, Haifeng, Huidong and Huiyang counties of Guangdong Province and the region covering Yongning, Longan, Laibin and Guigang counties of Guangxi Province. The common wild rice in Yunnan, Hunan, Jiangxi, and Fujian provinces are diverged into respectively independent populations with relatively large genetic distances, whereas, those in Hainan, Guangdong and Guangxi provinces have relatively low genetic divergence. Under the condition of geographic separation, natural selection is considered as one of the primary forces contributing to the divergence of common wild rice in China.     

Genetic analysis and fine mapping of an enclosed panicle mutant esp2 in rice （Oryza sativa L.）

The phenomenon of panicle enclosure in rice is mainly caused by the shortening of uppermost internode.Elucidating the molecular mechanism of panicle enclosure will be helpful for solving the problem of panicle enclosure in male sterile lines and creating new germplasms in rice.We acquired a monogenic recessive enclosed panicle mutant,named as esp2 (enclosed shorter panicle 2),from the tissue culture progeny of indica rice cultivar Minghui-86.In the mutant,panicles were entirely enclosed by flag leaf sheaths and the uppermost internode was almost completely degenerated,but the other internodes did not have obvious changes in length.Genetic analysis indicated that the mutant phenotype was controlled by a recessive gene,which could be steadily inherited and was not affected by genetic background.Apparently,ESP2 is a key gene for the development of uppermost internode in rice.Using an F 2 population of a cross between esp2 and a japonica rice cultivar Xiushui-13 as well as SSR and InDel markers,we fine mapped ESP2 to a 14-kb region on the end of the short arm of chromosome 1.According to the rice genome sequence annotation,only one intact gene exists in this region,namely,a putative phosphatidylserine synthase gene.Sequencing analysis on the mutant and the wild type indicated that this gene was inserted by a 5287-bp retrotransposon sequence.Hence,we took this gene as a candidate of ESP2.The results of this study will facilitate the cloning and functional analysis of ESP2 gene.     

Morphological and molecular characterization of two G. somalense monosomic alien addition lines （MAALs）

Two G. somalense monosomic alien addition lines were identified from the derived backcross progenies of allohexaploid between G. hirsutum and G. somalense through cytological and morphological observation. Furthermore, the alien addition chromosome was identified and distinguishedby RAPD analysis. A total of 160 RAPD primers were usedfor PCR amplification. Primer SBSG11 could produce a specific molecular marker (600 bp) for monosomic alien addition line Ⅰ (MAAL Ⅰ ). Primer SBSC03 could produce aspecific molecular marker (700 bp) for monosomic alien ad-dition line Ⅱ (MAAL Ⅱ). SBSE07 and SBSE08 could re-spectively produce common molecular marker for mono-somic alien addition lines Ⅰ and Ⅱ. G. somalense alienaddition lines could be important for cotton improvement.     

Reconstruction of linkage maps in the distorted segregation populations of backcross, doubled haploid and recombinant inbred lines

Non-Mendelian segregation of markers, known as distorted segregation, is a common biological phenomenon. Although segregation distortion affects the estimation of map distances and the results of quantitative trait loci (QTL) mapping, the effects of distorted markers are often ignored in the construction of linkage maps and in QTL mapping. Recently, we have developed a multipoint method via a Hidden Markov chain method to reconstruct linkage maps in an F2 population that corrects for bias of map distances between distorted markers. In this article, the method is extended to cover backcross, doubled haploid and recombinant inbred line (RIL) populations. The results from simulated experiments show that: (1) the degree that two linked segregation distortion loci (SDL) affect the estimation of map distances increases as SDL heritability and interval length between adjacent markers increase, whereas sample size has little effect on the bias; (2) two linked SDL result in the underesti- mation of linkage distances for most cases, overestimation for an additive model with opposite additive effects, and unbiased estimation for an epistatic model with negative additive-by-additive effects; (3) the proposed method can obtain the unbiased estimation of linkage distance. This new method was applied to a rice RIL population with severely distorted segregation to reconstruct the linkage maps, and a bootstrap method was used to obtain 95% confidence intervals of map distances. The results from real data analysis further demonstrate the utility of our method, which provides a foundation for the inheritance analysis of quantitative and viability traits.     

Genetic analysis and molecular mapping of a presenescing leaf gene psll in rice （Oryza sativa L.）

A rice psl1 （presenescing leaf） mutant was obtained from a japonica variety Zhonghua 11 via radiation of ^60Co-γ in M2 generation. Every leaf of the mutant began to wither after it reached the biggest length, while the leaves of the wild variety could keep green for 25--35 d. In this study, genetic analysis and gene mapping were carried out for the mutant identified. The SSR marker analysis showed that the mutant was controlled by a single recessive gene （psl1） located on chromosome 2. Fine mapping of the psl1 locus was conducted with 34 new STS markers developed around psl1 anchored region based on the sequence diversity between Nipponbare and 93-11. The psl1 was further mapped between two STS markers, STS2-19 and STS2-26, with genetic distances of 0.43 and 0.11 cM, respectively, while cosegregated with STS2-25. A BAC contig was found to span the psl1 locus, the region being delimited to 48 kb. This result was very useful for cloning of the psl1 gene.     

Genetic analysis and molecular mapping of a presenescing leaf gene psl1 in rice (Oryza sativa L.)

A rice psl1 (presenescing leaf) mutant was obtained from a japonica variety Zhonghua 11 via radiation of 60Co-γ in M2 generation. Every leaf of the mutant began to wither after it reached the big-gest length,while the leaves of the wild variety could keep green for 25―35 d. In this study,genetic analysis and gene mapping were carried out for the mutant identified. The SSR marker analysis showed that the mutant was controlled by a single recessive gene (psl1) located on chromosome 2. Fine mapping of the psl1 locus was conducted with 34 new STS markers developed around psl1 anchored region based on the sequence diversity between Nippon-bare and 93-11. The psl1 was further mapped be-tween two STS markers,STS2-19 and STS2-26,with genetic distances of 0.43 and 0.11 cM,respectively,while cosegregated with STS2-25. A BAC contig was found to span the psl1 locus,the region being delim-ited to 48 kb. This result was very useful for cloning of the psl1 gene.     

Characteristics of photosynthesis in rice plants transformed with an antisense Rubisco activase gene

Transgenic rice plants with an antisense gene inserted via Agrobacterium tumefaciens were used to explore the impact of the reduction of Rubisco activase (RCA) on Rubisco and photosynthesis. In this study, transformants containing 15% to 35% wild type Rubisco activase were selected, which could survive in ambient CO2 concentration but grew slowly compared with wild type controls. Gas exchange measurements indicated that the rate of photosynthesis decreased sig-nificantly, while stomatal conductance and transpiration rate did not change; and that the intercellular CO2 concentration even increased. Rubisco determination showed that these plants had approximately twice as much Rubisco as the wild types,although they showed 70% lower rate of photosynthesis, whichRubsico activase and/or the reduction in carbamylation.was likely an acclimation response to the reduction in Rubsico activase and/or the reduction in carbamylation.     

Identification and mapping of genes for improving yield from Chinese common wild rice (O. rufipogon Griff.) using advanced backcross QTL analysis

To identify useful genes from wild rice which have been lost or weakened in cultivated rice has become more and more important for modern breeding strategy. In this study, a BC4 population derived from 94W1, an acces-sion of common wild rice (Oryza rufipogon Griff.) from Dongxiang in Jiangxi Province of China, as the donor, and a high-yielding Indica cultivar (O. sativa L.), "Guichao 2", as the recipient, was used to identify quantitative trait loci (QTL) associated with yield and its components. Based on the analysis for the genotype of BC4F1 population with 87 SSR markers distributed throughout the genome and investigation of the plant height, yield and yield components of BC4F2, a total of 52 QTLs, were detected. Of 7 QTLs associated with grain yield per plant, 2 QTLs on chro-mosome 2 and chromosome 11 for grain yield, explaining 16% and 11% of the phenotypic variance respectively, were identified. The alleles from Dongxiang common wild rice in those two loci could increase the yield of "Guichao 2" by 25.9% and 23.2% respectively. The QTL on chromosome 2 increasing grain yield of cultivar is actually a major gene, which did not coincide with any previously published QTLs in rice.     

转基因水稻与野生稻(Oryza nivara Sharma et Shastry)杂交后代种子萌发率

种子休眠性是野生植物重要的适应性状,通过种子萌发实验可以分析种子休眠性强弱.通过人工杂交获得转抗虫基因栽培稻与一年生普通野生稻三种组合的杂种,对杂种的F3代和F4代种子采用直接萌发、打破休眠后萌发、埋土15 d和30 d 4种不同处理来检测种子活力和萌发率.结果显示转基因杂种后代种子表现出较强的休眠性,转基因对种子活力和休眠性没有明显的影响,种子休眠性有随种子世代的增加而逐渐减弱的趋势,提示水稻转基因逃逸后有在野生稻群体中宿存和扩散的可能性,但这种可能性可能会随世代增加而下降.这为进一步研究水稻转基因逃逸风险提供了参考.     

控制水稻剑叶形态相关性状的数量基因位点(QTL)的定位

水稻籽粒中一半以上的碳水化合物来自剑叶的光合作用,剑叶形态改良一直是水稻株型育种的一个重要目标．利用一个日本主要种植的粳稻品种越光（轮回亲本）和一个印度的籼稻品种Kasalath杂交产生的回交重组自交系群体（backcross recombinant inbred lines,BILs）对剑叶形态中的3个主要性状（剑叶长、叶宽以及其叶面积）进行了相关分析及其数量基因位点（quantitative trait loci,QTL）的定位．研究表明,控制剑叶形态的3个主要性状间存在极显著的正相关,并检测到影响3个性状的8个QTL,分布在第1,3,4,6条染色体上,贡献率介于4．94％～22．07％,其中第4染色体上C1016标记和第6染色体上C556标记附近的共有6个QTL,其两侧的紧密分子标记在水稻株型分子育种上具有一定应用价值．     

Fine mapping of <Emphasis Type="Italic">qHUS6.1</Emphasis>, a quantitative trait locus for silicon content in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Silicon is essential for optimal growth of rice (Oryza sativa L.). This study was conducted to fine map qHUS6.1, a quantitative trait locus (QTL) for rice hull silicon content previously located in the interval RM510–RM19417 on the short arm of chromosome 6, and to analyze the effect of this QTL on the silicon content in different organs of rice. Selfed progenies of a residual heterozygous line of rice were detected using 13 microsatellite markers in the vicinity of qHUS6.1. Three plants with overlapping heterozygous segments were selected. Three sets of near isogenic lines (NILs) were developed from the selfed progenies of the 3 plants. They were grown in a paddy field and the silicon contents of the hull, flag leaf, and stem were measured at maturity. Based on analyses of the phenotypic distribution and variance among different genotypic groups in the same NIL set, a significant genotypic effect was shown in the NIL set that was heterogenous in the interval RM19410–RM5815, whereas a significant effect was not found in the remaining 2 NIL sets that were heterogenous in either of the intervals RM4923–RM19410 or RM19417–RM204. On comparison among the physical positions of the 3 heterogenous segments, qHUS6.1 was delimited to a 64.2-kb region flanked by RM19410 and RM19417 that contains nine annotated genes according to the genome sequence of Nipponbare. This QTL showed strong effects on all of the three traits tested, and the enhancing alleles were always derived from the paternal line Milyang 46. The present study will facilitate the cloning of qHUS6.1 and the exploration of new genetic resources for QTL fine mapping.     

野栽杂交花培育种探讨

采用花药培养技术对普通野生稻白叶枯病广谱抗源RBB16与水稻品种垦系3号等一批杂交后代进行花培育种。接种花药79080个,平均愈伤组织诱导率7.94％,绿苗分化率15.08％,从获得一批野栽杂交后代的花培绿苗中选育出T209-1、14-5两个高产、或高抗白叶枯病的稳定新品系。研究表明野栽杂交花培育种技术是克服野栽杂交后代稳定难,育种周期长与加速野生稻资源利用的有效途径。     

水稻与菰属间性状转移研究

通过花粉管通道法实现了水稻与菰属间的性状转移,获得了可遗传的转基因水稻种子,所获得的转菰基因后代性状变异深刻、类型丰富,多种数量性状改良明显,得到部分形态、生育及经济性状方面有价值的材料,这些材料可望填补水稻种质资源的一些空白,而且部分材料已在多抗、高产、优质种上初见成效。     

利用CRISPR /Cas9技术快速创制香型“秀水134”水稻

以目前上海市主栽的高产常规水稻"秀水134"为材料,利用CRISPR/Cas9技术成功敲除甜菜碱醛脱氢酶2基因,获得了两种类型纯合突变体植株.采用表达载体特异性结合的引物检测T_1代转基因植株,成功获得6株不携带载体骨架的转基因植株.定量PCR分析显示,突变体植株甜菜碱醛脱氢酶2基因表达量极显著低于野生型对照(p0.01),但突变体植株成熟种子香味物质2-乙酰-1-吡咯啉(2AP)含量极显著高于野生型对照(p0.01).比较野生型对照与突变体植株的主要农艺性状和产量性状,两者间都没有显著差异(p0.05).本研究可为加快高产香型水稻在上海及周边地区的推广应用,以及为今后利用CRISPR/Cas9技术快速培育其他高产香型水稻新品种研究奠定基础.