紧穗野生稻（O．eichingeriA．Peter）控制红色果皮基因的定位

将绿色果皮的紧穗野生稻与白色果皮的栽培稻(Oryza sativa L.)中花九号杂交,在以中花九号为轮回亲本的回交后代中分离出具有红色果皮的种子,自交后获得BC4F3分离群体,经卡平方测验,红、白子粒单株比例符合3∶1分离比例,初步确定该红色果皮性状来自于紧穗野生稻的单片段代换系且受一对显性基因控制.利用123对SSR引物对其中1个分离群体的115个隐性单株进行基因定位,将该基因初步定位于第7染色体短臂上的RM1253和RM8262标记之间,其遗传距离分别是2.61cM和3.48cM,初步命名为Rf.     

海南黎族聚居区山栏稻的起源演化研究

以14份海南黎族聚居区的山栏稻为研究材料、以原产于中国的69份亚洲栽培稻和110份普通野生稻为对照组,分别对核中SSⅡ基因、ITS基因和Ehd1基因、叶绿体中ndhC-trnV基因以及线粒体中cox3基因等5段序列进行测序,分析基因序列多样性和单倍型,并揭示海南黎族聚居区山栏稻的起源地和驯化过程。结果表明,黎族聚居区山栏稻的基因多样性低于亚洲栽培稻,而亚洲栽培稻的基因多样性低于普通野生稻;85%左右的山栏稻为偏粳型;山栏稻与广东和湖南的普通野生稻亲缘关系较近,而与海南的普通野生稻的亲缘关系较远,推测黎族的山栏稻可能起源于广东和湖南的普通野生稻。     

有色稻米研究进展

有色稻米是一类特异水稻种质资源,主要由不同色素沉积在水稻种子的种皮内而形成,有色稻米富含蛋白质、氨基酸、植物脂肪、纤维素和人体必需的矿物质,具有特殊的生理功能,而且有色稻米种皮内的色素可作为安全的天然色素用做食品添加剂.其中最为常见的是红色稻米与紫色稻米.水稻红色种皮是由于其种皮内含有原花色素所致,该性状受Rc/rc和Rd/rd 2对基因控制,红色为显性,白色为隐性.RcRd表现红色,Rcrd表现褐色,rcRd和rcrd则呈现白色.Rc已被定位于水稻第7染色体上,而Rd则位于第1染色体上.前人研究表明,Rc基因编码一个典型的含bHLH结构的Myc类转录因子,其第6外显子内一个14bp片段的缺失致使种皮颜色由原先的红色变为白色.水稻紫色种皮是由于其种皮内沉积花色素苷所致.该性状由基因Pb与其互补基因Pa共同作用导致.当Pa基因单独存在时,种皮呈白色;当Pb基因单独存在时,种皮呈棕色;当P6基因和Pa同时存在时,种皮呈紫色.P6基因已被定位于水稻第4染色体上,而Pa基因则位于第1染色体上.     

栽培稻及其近缘野生种间杂交揭示杂草稻的起源

通过水稻种间、亚种间和品种间的杂交,在套袋隔离和自然授粉两种条件下,对其杂交亲本主要农艺性状类型及杂交后代群体中杂草稻发生频率、类型及主要特征以及杂草稻的发生趋势进行调查分析,直接验证和重演杂草稻起源的主要路径。杂草稻的主要特征为:颖壳褐色或金色,种皮红色,散穗、易落粒,中长芒或无芒。结果表明,如果以近缘野生种为亲本,在其F2群体中比较容易发生类似杂草稻的单株;杂交组合中杂草稻出现频率的大小依次为:杂草稻或野生稻/粳稻(44.16%)>杂草稻或野生稻/籼稻(27.84%)>籼稻/粳稻(3.30%)>籼稻/籼稻(1.41%)>粳稻/粳稻(0)。这一结果显示杂交亲本间遗传差异越大,在后代中出现杂草稻类型植株的频率就越高。套袋条件下,后代中杂草稻出现的频率为10.70%,而不套袋情况下为4.90%。     

水稻红米的遗传分析与组织学研究

用来源于倍加单倍体的红米水稻（rdh）与无色米水稻做正反交,结果表明：杂种F1种子颜色由其所着生的母体植株基因型决定.当rdh作母本时,所结下的F1种子全是红色,当蜀恢527,蜀恢168,蜀恢368三个具有无色颖果皮（简称无色米）水稻作母本时,所结下的F1种子全是无色的.而且不管母本有没有颜色,所产生的F2种子都是红色,F3代产生红色种子与无色种子的单株分离,而且红色种子的单株对无色种子的单株是3：1（1%水平达极显著）,根据杂种F1、F2和F3代种子颜色和植株分离比例,rdh种子红色表现型是由单显性基因控制的,并受母性影响.组织学研究发现rdh颖果皮有3个基本的结构层：果皮、种皮和糊粉层.果皮是类黄酮色素累积的部位,红色色素就在果皮层累积.在未成熟的种子中,种皮是累积叶绿素的部位,在成熟种子中叶绿素消失.在未成熟的种子中,糊粉层白色.显微镜分析灌浆期的rdh种子不显红色,而显绿色,绿色来自于种皮,果皮无色透明.风干期的rdh种子显示：红色色素在果皮层累积,同期种皮的绿色清晰可见.rdh成熟种子红色色素急剧增加,同期绿色渐渐消失,最后肉眼观测不到.组织切片显示种子外皮中,果皮是最厚的一层,糊粉层次之,种皮最薄.果皮外层由4列较小的长方形细胞构成,里层由5～8列不规则的细胞构成.种皮由3列薄壁细胞构成.糊粉层由5～8列椭圆形细胞构成.色素累积的发育时间实验显示红色的沉积是从种子风干期开始到完全成熟期为止.在蜀恢527无色种子中,绿色色素从受精后开始积累,到风干期达到最深;然后绿色开始变浅,成熟种子中没有绿色.比较而言,rdh种子在发育早期,从灌浆到风干期呈现的颜色与蜀恢527相同,均是绿色;但从风干期开始,较多的红色色素开始累积,到种子接近成熟,红色仍在加深,这时种皮的绿色还隐约可见;直到种子完全成熟,红色达到最深,同时绿色渐渐消失.     

亚洲栽培稻与AA染色体组稻种的可交配性及F1杂种育性分析

从可交配性和F1杂种育性两方面对亚洲栽培稻与AA染色体组（以下简称AA组）其他7个稻种的系统关系进行了分析。结果表明：栽培稻籼、粳亚种与AA组不同稻种杂交均具有一定的结实率,可交配性不是影响亚洲栽培稻与其他AA组稻种间基因交流的主要生殖障碍。亚洲栽培稻与普通野生稻及尼瓦拉野生稻种间F1花粉育性和小穗育性有不同程度分化,与其他稻种的F1花粉育性和小穗育性均很低,F1杂种不育是AA组内基因交流的主要障碍。综合可交配性和F1小穗育性两方面的因素,初步得出：亚洲栽培稻与AA组稻种的亲缘关系由近及远依次是：普通野生稻、尼瓦拉野生稻、南方野生稻、展颖野生稻、非洲栽培稻、长雄蕊野生稻和短舌野生稻。其中普通野生稻和尼瓦拉野生稻是AA组中可直接利用于水稻育种的野生稻资源。     

印度南瓜果皮和果肉颜色遗传分析及基因定位

以印度南瓜‘98-2-351’与‘06820-1’杂交构建F2群体,对亲本及各世代群体成熟果实果皮和果肉颜色进行调查、统计分析。结果表明:F2群体中果皮桔红色和灰色的分离比呈3∶1,说明果皮灰色是由单隐性基因控制;F2群体中果肉黄色和白色的分离比呈3∶1,说明果肉白色也是由单隐性基因控制。利用群体分离分析法结合隐性群体分析法,采用SSR分子标记,找到了2个与控制灰色果皮基因位点CmRc紧密连锁的SSR标记(PU078072和PU013839),其连锁遗传距离分别为5.9cM和14.5cM;同时找到了1个与控制白色果肉基因位点CmFc紧密连锁的SSR标记PU132712,其连锁遗传距离为6.7cM。本研究为进一步筛选与控制印度南瓜果皮和果肉颜色基因更加紧密连锁的分子标记及相关基因的精确定位奠定了基础。     

小粒野生稻与栽培稻杂种及回交后代的特征分析

小粒野生稻（Oryza minuta）,是栽培稻遗传改良的宝贵资源,本研究通过杂交和回交结合胚拯救技术获得了小粒野生稻与栽培稻的种间杂种及回交后代,调查了杂种与各回交后代的交配率和染色体数目,并运用175对均匀分布的SSR标记对双亲和92份二倍体的BC3F1植株进行了分析.结果表明,杂种F1,BC1,BC2和BC3的交配率分别为5.58%,0.11%,0.37%和1.62%;杂种染色体数目为36（ABC）,回交后代的染色体数目为24～48;小粒野生稻与栽培稻间SSR标记的多态性概率为93.2%;在92份二倍体的BC3F1植株中,小粒野生稻渗入片段的数目、长度、总的大小及其所占全基因组的百分数分别为24.1,17.8,438.4cM和26.2%.同时还评价了杂种和回交后代的部分农艺性状和对水稻白叶枯病的抗性表现.这些材料可以用于鉴定来自于小粒野生稻的有利基因和产量相关性状的数量性状基因座（quantitative trait loci,QTL）,为栽培稻的遗传改良提供新的操作平台.     

栽培稻与疣粒野生稻杂种F1代的基因组原位杂交鉴定

生物素标记的疣粒野生稻总DNA作探针,未标记的栽培稻总DNA封阻,对栽培稻与疣粒野生稻杂种F1体细胞染色体进行基因组原位杂交（Genomic in situ hybridization,简称GISH）分析。FITC检测表明,杂种细胞中来自瘛发粒野生稻的染色体有较多的黄色或黄绿色荧光信号,来自栽培稻的染色体只检出很少的信号。每条疣粒野生稻染色体上信号点所占的总的区域只是染色体的一小部分,表明疣粒野生稻染色体与栽培稻染色体的DNA序列大部分是同源的。     

基于叶绿体基因多样性的中国水稻起源进化研究

针对目前亚洲栽培稻起源地和进化途径学说众多、分歧巨大的现状,本研究选择原产中国的98份亚洲栽培稻和125份普通野生稻为材料,对叶绿体中atpA序列、rps16内含子序列、trnP-rpl33间隔区、trnG-trnfM序列、trnT-trnL间隔区序列的五段高突变序列进行测序,利用生物信息学方法进行比对分析,绘制Network网络图,构建系统发育树。结果表明,普通野生稻的Indel和SNP数目均比亚洲栽培稻多,序列多样性丰富;基于单倍型的Network网络图和系统发育树可将所有参试材料归为3个类群,类群I主要为粳稻与普通野生稻,类群II主要为籼稻,类群III主要为普通野生稻,而类群II和类群III亲缘关系较近,提示粳、籼两个亚种可能由偏粳、偏籼的普通野生稻分别进化而来,支持二次起源学说;所有与亚洲栽培稻亲缘关系较近的普通野生稻均来源于华南地区,支持华南地区为我国亚洲栽培稻起源中心的论点。     

Ethylene production is associated with germination but not seed dormancy in red rice

BACKGROUND AND AIMS: The relationship between ethylene production and both seed dormancy and germination was investigated using red rice (weedy rice) as a model species. METHODS: Both fully dormant and after-ripened (non-dormant) naked caryopses were incubated with or without inhibitors of ethylene synthesis [aminoethoxyvinylglycine (AVG)] and perception [silver thiosulfate (STS)], or in the presence of the natural ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). The kinetics of ethylene emissions were measured with a sensitive laser-photoacoustic system. KEY RESULTS: Dormant red rice caryopses did not produce ethylene. In non-dormant caryopses, ethylene evolution never preceded the first visible stage of germination (pericarp splitting), and ethylene inhibitors completely blocked ethylene production, but not pericarp splitting. Accordingly, endogenous ACC appeared to be lacking before pericarp splitting. However, early seedling growth (radicle or coleoptile attaining the length of 1 mm) followed ethylene evolution and was delayed by the inhibitors. Wounding the dormant caryopses induced them to germinate and produce ethylene, but their germination was slow and pericarp splitting could be speeded up by ethylene. CONCLUSIONS: The findings suggest that, in red rice, endogenous ethylene stimulates the growth of the nascent seedling, but does not affect seed dormancy or germination inception. Correspondingly, this phytohormone does not play a role in the dormancy breakage induced by wounding, but accelerates germination after such breakage has occurred.     

Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa)

Seed dormancy in rice interrelates to the weedy characteristics shattering, awn, black hull color, and red pericarp color. A cross between the weedy strain SS18-2 and the breeding line EM93-1 was developed to investigate the genetic basis and adaptive significance of these interrelationships. These characteristics or their components differed in average degree of dominance from –0.8 to 1.5, in heritability from 0.5 to 0.96, and in their contribution to phenotypic or genotypic variation in dormancy by up to 25%. Five dormancy, four shattering, and three awn-length quantitative trait loci (QTLs) were detected in the BC₁ population replicated in 2 years. Two QTLs for hull color were identified, and the SS18-2-derived and EM93-1-derived alleles increased the intensity of black, and red or yellow pigmentations, respectively. The only QTL for pericarp color co-located with the red pericarp gene Rc, with the SS18-2-derived allele increasing the intensity of black and red pigmentations. Four of the five dormancy QTLs were flanked or bracketed by one to four QTLs for the interrelated characteristics. The QTL organization pattern indicates the central role of seed dormancy in adaptive syndromes for non-domesticated plants, implies that the elimination of dormancy from cultivars could arise from the selections against multiple interrelated characteristics, and challenges the use of dormancy genes at these loci in breeding varieties for resistance to pre-harvest sprouting (PHS). However, another QTL (qSD12) provides candidate gene(s) for PHS resistance because it has a large effect in the population and it is independent of the loci for interrelated characteristics.     

Application of Cyanidin-3-Glucosides as a functional food ingredient in rice-based bakery products

BackgroundBlack pericarp rice has recently become popular among rice consumers for its diverse health benefits specially anti-cancer effect. Cyanidin-3-Glucosides (C3G), an prominant bioactive component of anthocyanins which is abundantly present in black pericarp rice.ObjectivesWe investigated, how effectively it can be used to fortify Cyanidin-3-Glucosides (C3G) content in red and white pericarp polished rice or rice based bakery products for more nutritional value.MethodIn the present study, we have characterized several black pericarp rice cultivars along with some red pericarp and white pericarp rice cultivars by physicochemical including mineral profiling, and quantified the C3G by UFLC and LCMS.ResultsC3G content was significantly reduced from raw rice to cooked rice condition. All the black pericarp rice cultivars synthesized C3G, while this content was not detected in red and white pericarp rice cultivars. However, when 25% of black pericarp rice were mixed with 75% red or white pericarp polished rice, C3G content was significantly retained in cooked rice conditions. Formulation of rice-based bakery food product using black pericarp rice powder was also remarkably retained the C3G content as compared to that of cooking. Black rice is harder in texture, difficult to digest and needs higher energy for cooking. Therefore, we tried to circumvent these challenges by fortifying 25% of black pericarp rice with white or red pericarp rice.ConclusionFortification of C3G enriched black rice (25%) with red or white pericarp rice (75%) might bring a better nutritional quality in both cooking and baking condition. This may lead a way to the effective management of the non-communicable disease such as cancer for common rice consuming population.     

Origins and population genetics of weedy red rice in the USA

Weedy red rice (Oryza sativa spontonea) is a persistent and problematic weed of rice culture worldwide. A major hypothesis for the mechanism of production of this weed in South and Southeast Asia is hybridization between cultivated rice (Oryza sativa) and wild rice (Oryza rufipogon). However, weedy red rice can often be found outside the range of O. rufipogon leaving questions on the origin and process behind weedy rice infestations. In the USA, weedy red rice was first documented as early as 1846 and has continued to affect rice production areas. In this study, we attempt to identify the origin and population structure of weedy red rice sampled from the USA using both DNA sequence data from a neutral nuclear locus as well as microsatellite genotype data. Results suggest that two major accessions of weedy rice exist, strawhull and blackhull, and these forms may both hybridize with the cultivated rice of the USA, O. sativa japonica. Using population assignment of multilocus genotype signatures with principal component analysis and structure, an Asian origin is supported for US weedy rice. Additionally, hybridization between strawhull and blackhull varieties was inferred and may present the opportunity for the production of new weedy forms in the future.     

Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

Background  

Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution.     

Prebreeding selection of rice with colored pericarp based on genotyping <Emphasis Type="Italic">Rc</Emphasis> and <Emphasis Type="Italic">Pb</Emphasis> genes

The research was aimed at developing prebreeding resources of Kazakhstan rice varieties with colored pericarp for breeding. During the study, hybrid analysis of inheritance of the trait “colored pericarp” in breeding material used for the work was performed. Rice genotypes with colored pericarp, as well as white rice varieties possessing important breeding traits and maturing under conditions of the republic, were selected from the collection of the Institute of Plant Biology and Biotechnology, Republic of Kazakhstan. Identification of allelic status of Rc (red pericarp) and Pb (anthocyanin pericarp) genes was performed for selected samples using the PCR method. When selecting parental forms for crossing, foreign rice varieties with colored pericarp (Rubin, Mavr, Black rice, etc.) were used as recipient forms. As donors, we used local white rice varieties of Kazakhstan breeding adapted to the soil and climate conditions of rice growing regions (Madina, Marzhan, Bakanasskiy, PakLi) as well as foreign varieties. The ability to set hybrid caryopses and the percentage of sterility were determined in obtained F1 rice hybrids. As a result, the most promising prebreeding material was selected, which will be used for breeding Kazakhstan rice varieties with colored pericarp.     

The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice

Growth-related traits, such as greater height, greater biomass, faster growth rate and early flowering, are thought to enhance competitiveness of agricultural weeds. However, weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.), displays variation for growth traits. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Through a common garden experiment, we investigated whether growth trait divergence has occurred among U.S. weeds and their putative cultivated progenitors. We also determined polymorphism patterns in the growth candidate gene, SD1, to assess its possible role in the evolution of divergent phenotypes. We found considerable growth trait variation among weed groups, suggesting that growth trait convergence is not evident among weedy populations. Phenotypic divergence of weedy rice from cultivated ancestors is most apparent for flowering time. Introgression of a chromosomal block containing the SD1 allele from tropical japonica, the predominant U.S. rice cultivar, was detected in one weedy rice population and is associated with a change in growth patterns in this group. This study demonstrates the role of introgressive hybridization in evolutionary divergence of an important weed.     

Performance of Hybrids between Weedy Rice and Insect-resistant Transgenic Rice under Field Experiments： Implication for Environmental Biosafety Assessment

Transgene escape from genetically modified (GM) rice Into weedy rice via gene flow may cause undesired environmental consequences. Estimating the field performance of crop-weed hybrids will facilitate our understanding of potential introgression of crop genes (including transgenes) into weedy rice populations, allowing for effective biosafety assessment. Comparative studies of three weedy rice strains and their hybrids with two GM rice lines containing different insect-resistance transgenes (CpTl or BtlCpTI) indicated an enhanced relative performance of the crop-weed hybrids, with taller plants, more tillers, panicles, and spikelets per plant, as well as higher 1000-seed weight, compared with the weedy rice parents, although the hybrids produced less filled seeds per plant than their weedy parents. Seeds from the F1 hybrids had higher germination rates and produced more seedlings than the weedy parents, which correlated positively with 1000-seed weight. The crop-weed hybrids demonstrated a generally enhanced relative performance than their weedy rice parents in our field experiments. These findings indicate that transgenes from GM rice can persist to and introgress into weedy rice populations through recurrent crop-to-weed gene flow with the aid of slightly increased relative fitness in F1 hybrids.