Evolutionary Genomics of Weedy Rice in the USA

Red rice Is an Interfertlle, weedy form of cultivated rice （Oryza sativa L.） that competes aggressively with the crop In the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America and the weed has been proposed to have evolved through multiple mechanisms, Including ＂de-domestication＂ of US crop cultlvars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedy Oryza strains. The phenotype of US red rice ranges from ＂crop mimics＂, which share some domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have Indicated that many weed strains are closely related to Asian taxa （Including indica and aus rice varieties, which have never been cultivated In the US, and the Asian crop progenitor O. ruflpogon）, whereas others show genetic similarity to the tropical Japonica varieties cultivated In the southern US. Herein, we review what Is known about the evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to further characterize the evolutionary genomlcs of this aggressive weed.     

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.     

稻田杂草稻发生情况调查

2007年杂草稻在江苏省海安县各类稻田中的发生率达44．35％,平均每公顷穴数和穗数分别为1023穴和10796穗,最高田块分别达12万穴和180万穗,已成为水稻生产上的潜在威胁。杂草稻在不同稻田的发生程度表现以下趋势：轻-中壤〉砂-轻壤〉重壤土稻田、直播〉抛栽〉机插〉手栽稻田、非统一供种〉统一供种稻田。     

杂草稻的研究现状与展望

杂草稻属于野生稻与栽培稻中间类型.一方面,由于杂草稻与栽培稻之间的前期形态、生理生化特性相似,很难化学控制其在稻田发生,影响水稻产量与品质;另一方面,杂草稻长期自然生长繁衍,其抗病、虫、寒、旱、盐碱等特性优于栽培稻,而且与栽培稻的亲缘关系相对接近,是一种改良栽培稻抗逆性的天然基因库.     

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%。     

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.     

宁夏杂草稻的遗传多样性及其亲缘关系分析

以宁夏杂草稻、选育品种、地方品种共143份水稻种质为试验材料,进行主要农艺性状的的表型鉴定评价,并利用24对SSR引物进行不同类型水稻种质的遗传多样性比较、遗传相似性和聚类分析。表型评价表明,宁夏杂草稻表现为矮秆和早熟,表型变异范围较大;多数杂草稻种皮呈红色,颖壳呈秆黄色,均落粒。SSR标记分析结果,共检测到141个等位基因,每个位点等位基因数目变异在3~11个,平均为5.8333个;Nei's基因多样性指数变幅为0.2241~0.8065,平均为0.5219。杂草稻种质的等位基因数、有效等位基因数、Shannon指数均高于选育品种和地方品种。在不同来源杂草稻群体中,来自吴忠和永宁东河的杂草稻Nei's基因多样性指数最高,分别为0.4912和0.4814,而来自青铜峡的杂草稻Nei's基因多样性指数最低,为0.2802。相似性分析表明,杂草稻与地方品种高度相似,相似系数高达0.9585,而杂草稻与选育品种的相似性较低,其相似系数为0.4584;选育品种与地方品种的相似系数只有0.3560。聚类分析表明,参试材料分为3个类群,其中选育品种单独聚类于第Ⅰ类群,其遗传背景明显区别于杂草稻和地方品种;第Ⅱ类包括大部分杂草稻和地方品种,不同来源杂草稻及地方品种间分布比较均匀;第Ⅲ类是由小部分杂草稻和地方品种组成。宁夏杂草稻的分布没有明显的区域性,宁夏杂草稻与地方品种高度融合且遗传相似性很高。     

Genetic Diversity and Population Differentiation of Liaoning Weedy Rice Detected by RAPD and SSR Markers

Weedy rice refers to populations of usually annual Oryza species that diminish farmer income through reduction of grain yield and lowered commodity value at harvest. The genetic diversity and population genetic structure of weedy rice in Liaoning Province were studied by RAPD and SSR markers. The results indicate that the level of genetic diversity of Liaoning weedy rice is very low, with polymorphic loci being only 3.70% (RAPDs) and 47.62% (SSRs). On the other hand, high genetic differentiation was found among populations, in particular between two regions (Shenyang and Dandong), with Fst values of 0.746 (RAPDs) and 0.656 (SSRs), suggesting that more than two thirds of the genetic variation resides among regions. Combined with our investigations of cultural traditions, the low level of genetic diversity in Liaoning Province is attributed to its narrow genetic background enhanced by exchanges of cultivar seeds, whereas the high genetic differentiation between the two regions is most likely the result of different founding parents and gene flow from local rice varieties to weedy rice. The rice cultivars in the two regions are all local varieties and are different genetically. A comparison of the two marker systems demonstrates that SSR is more informative and powerful in terms of the assessment of genetic variability, although both RAPD and SSR provide useful genetic information on weedy rice.     

Genetic Identification of Quantitative Trait Loci for Contents of Mineral Nutrients in Rice Grain

In present study, Fe, Zn, Mn, Cu, Ca, Mg, P and K contents of 85 introgression lines （ILs） derived from a cross between an elite indica cultivar Teqing and the wild rice （Oryza rufipogon） were measured by inductively coupled argon plasma （ICAP） spectrometry. Substantial variation was observed for all traits and most of the mineral elements were significantly positive correlated or independent except for Fe with Cu. A total of 31 putative quantitative trait loci （QTLs） were detected for these eight mineral elements by single point analysis. Wild rice （O. rufipogon） contributed favorable alleles for most of the QTLs （26 QTLs）, and chromosomes 1,9 and 12 exhibited 14 QTLs （45%） for these traits. One major effect of QTL for zinc content accounted for the largest proportion of phenotypic variation （11%-19%） was detected near the simple sequence repeats marker RM152 on chromosome 8. The co-locations of QTLs for some mineral elements observed in this mapping population suggested the relationship was at a molecular level among these traits and could be helpful for simultaneous improvement of these traits in rice grain by marker assisted selection.     

东北地区杂草稻与栽培稻的遗传多样性及籼粳分化

利用88对籼粳特异性分子标记对收集于我国东北三省的35份杂草稻和36份栽培稻遗传基础及籼粳分化进行研究,结果表明上述标记能够高效地鉴别稻属资源的籼粳属性,共检测到156个等位基因,平均有效等位基因(Na)为1.773。遗传多样性分析表明,东北地区杂草稻多样性水平略高于当地栽培稻,其中杂草稻的等位基因数(Na)、杂合度(He)、基因多样性(Hsk)以及多态性信息含量(PIC)分别为1.659、0.006、0.076和0.085,而东北栽培稻分别为1.557、0.004、0.060和0.067。遗传结构和聚类分析结果表明,东北地区杂草稻与栽培稻具有较近的亲缘关系,均存在一定程度的籼粳分化。进一步对籼粳血缘进行相对量化分析发现,杂草稻的籼型基因型频率(F_i=0.050)略高于当地栽培稻(F_i=0.043)。东北三省籼型基因型频率变化趋势为:辽宁杂草稻(0.062)辽宁栽培稻(0.058)吉林栽培稻(0.048)黑龙江杂草稻(0.041)吉林杂草稻(0.024)黑龙江栽培稻(0.020)。     

杂草稻红色果皮基因的遗传分析

以江苏扬中红色果皮杂草稻W16、粳型广亲和品种02428(S5n)及以它们为亲本的衍生世代F1、F2和F3为材料,研究了杂草稻红色果皮性状的遗传特征;根据已克隆的普通野生稻(O.rufipogen)红色果皮Rc与白色果皮rc等位基因第6外显子的差异,设计了InDel标记RID14,利用RID14标记对F2群体、江淮流域所收集到的24份红色果皮杂草稻、3份普通野生稻以及423份品种资源进行了标记基因型分析;选取5份江淮流域杂草稻的RID14标记PCR产物进行测序分析.结果显示:以白色果皮02428为母本的杂交种F1的颜色为白色,而以红色果皮杂草稻W16为母本,杂交种F1的果皮颜色为红色;正反交杂种F1所结F2种子都是红色,F2植株所结F3种子果皮颜色发生分离,符合3∶1分离比例;在F2群体中,RID14标记与果皮颜色共分离,在450份材料中,红色果皮均为非缺失带型,而白色果皮和紫色果皮为缺失带型;5份江淮流域杂草稻的RID14标记PCR产物序列与已登录的普通野生稻序列完全一致.研究表明,扬中杂草稻红色果皮为单基因控制的显性性状,并由母体基因型决定,是典型的延迟遗传,由Rc基因控制;在白色果皮材料资源中都存在14 bp缺失的等位基因rc,RID14标记可以作为准确鉴定红色果皮杂草稻的分子标记.     

Rice transgene flow: its patterns,model and risk management

Progress has been made in a 12 year's systemic study on the rice transgene flow including (i) with experiments conducted at multiple locations and years using up to 21 pollen recipients, we have elucidated the patterns of transgene flow to different types of rice. The frequency to male sterile lines is 10¹ and 10³ higher than that to O. rufipogon and rice cultivars. Wind speed and direction are the key meteorological factors affecting rice transgene flow. (ii) A regional applicable rice gene flow model is established and used to predict the maximum threshold distances (MTDs) of gene flow during 30 years in 993 major rice producing counties of southern China. The MTD_0.1% for rice cultivars is basically ≤5 m in the whole region, despite climate differs significantly at diverse locations and years. This figure is particularly valuable for the commercialization and regulation of transgenic rice. (iii) The long‐term fate of transgene integrated into common wild rice was investigated. Results demonstrated that the F₁ hybrids of transgenic rice/O. rufipogon gradually disappeared within 3–5 years, and the Bt or bar gene was not detectable in the mixed population, suggesting the O. rufipogon may possess a strong mechanism of exclusiveness for self‐protection. (iv) The flowering time isolation and a 2‐m‐high cloth‐screen protection were proved to be effective in reducing transgene flow. We have proposed to use a principle of classification and threshold management for different types of rice.     

Characterization and Use of Male Sterility in Hybrid Rice Breeding

The hybrid rice （Oryza sativa L.） breeding that was Initiated In China in the 1970s led to a great improvement in rice productivity. In general, It increases the grain yield by over 20% to the inbred rice varieties, and now hybrid rice has been widely introduced into Africa, Southern Asia and America. These hybrid varieties are generated through either three-line hybrid and two-line hybrid systems; the former is derived from cytoplasmic male sterility （CMS） and the latter derived from genlc male sterility （GMS）. There are three major types of CMS （HL, BT and WA） and two types of GMS （photoperlod-sensitlve （PGMS） and temperature-sensitive （TGMS））. The BT- and HL-type CMS genes are characterized as orf79 and orfH79, which are chimeric toxic genes derived from mltochondrial rearrangement. Rf3 for CMS-WA Is located on chromosome 1, while Rf1, Rf4, Rf5 and Rf6 correspond to CMS-BT, CMSoWA and CMS- HL, located on chromosome 10. The Rfl gene for BT-CMS has been cloned recently, and encodes a mltochondriatargeted PPR protein. PGMS Is thought to be controlled by two recessive loci on chromosomes 7 and 12, whereas nine recessive alleles have been identified for TGMS and mapped on different chromosomes. Attention Is still urgently needed to resolve the molecular complexity of male sterility to assist rice breeding.     

Genetic Identification of Quantitative Trait Loci for Contents of Mineral Nutrients in Rice Grain

In present study, Fe, Zn, Mn, Cu, Ca, Mg, P and K contents of 85 Introgression linee (ILs) derived from a cross between an elite indica cultivar Teqing and the wild rice (Oryza rufipogon) were measured by inductively coupled argon plasma (ICAP) spectrometry. Substantial variation was observed for all traits and most of the mineral elements were significantly positive correlated or independent except for Fe with Cu. A total of 31 putative quantitative trait loci (QTLs) were detected for these eight mineral elements by single point analysis. Wild rice (O. rufipogon) contributed favorable alleles for most of the QTLs (26 QTLs), and chromosomes 1, 9 and 12 exhibited 14 QTLs (45%) for these traits. One major effect of QTL for zinc content accounted for the largest proportion of phenotypic variation (11%-19%) was detected near the simple sequence repeats marker RM152 on chromosome 8. The co-locations of QTLs for some mineral elements observed in this mapping population suggested the relationship was at a molecular level among these traits and could be helpful for simultaneous improvement of these traits in rice grain by marker assisted selection.     

对水稻4号染色体一个编码S位点相关的受体样蛋白激酶基因簇的分析

通过对水稻(Oryza sativa L.) 4号染色体一段323 kb 的序列测定和分析,在其中108 kb的区域内发现了一个由14个编码S位点相关的受体样蛋白激酶(SRK)基因组成的基因簇.RT-PCR实验证明了这14个基因中有9个基因表达,并且这9个基因有不同的表达模式: 其中2个基因主要在生殖器官中表达, 而另外7个基因在水稻的营养和生殖器官中均有表达.对这些基因的预测的氨基酸序列进行分析表明他们的细胞外受体部分均和甘蓝的SLG蛋白高度同源,而细胞内的激酶区都包含有丝氨酸/苏氨酸激酶中特异的氨基酸.     

Proteomic Analysis of the Response of Liangyoupeijiu （Super High-Yield Hybrid Rice） Seedlings to Cold Stress

Liangyoupeijiu is a super high-yield hybrid rice. Despite its advantages with respect to yield and grain quality, it is sensitive to cold, which keeps it from being widely cultivated. We subjected Liangyoupeijiu seedlings to 4 ℃ cold treatment, then extracted the leaf proteins. After 2-D gel electrophoresis separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis, a series of differentially displayed proteins were identified. Some metabolism-associated proteins were found among the downregulated proteins, such as carbamoyl phosphate synthetase, transketolase 1, dihydrolipoamide dehydrogenase and glyceraldehyde 3-phosphate dehydrogenase. The upregulated proteins included both stress-resistance proteins such as nucleoside diphosphate kinase I and proteins that are negative for rice growth, such as FtsH-like protein, plastid fusion and/or translocation factor （Pftf） and actin. Our results indicate that cold may inhibit Liangyoupeijiu growth through decreasing metabolic activity and damaging cell structure.     

Enhanced genetic diversity of weedy rice populations associated with latitude decreases revealed by simple sequence repeat fingerprints

Weedy rice (WR, Oryza sativa L. f. spontanea) is a noxious agricultural weed, infesting rice fields worldwide and causing tremendous yield losses of cultivated rice. However, little is known about the relationship between genetic diversity and distribution of WR populations across a wide latitudinal gradient, in addition to its reasons for genetic differentiation. To determine the distribution of genetic diversity and differentiation, we analyzed 20 WR populations collected from wide geographic ranges of rice-planting regions across Northeast, Jiangsu and Guangdong provinces of China, and Sri Lanka, based on 20 simple sequence repeat loci. Our results indicated a significant negative correlation (R = 0.84, P < 0.01) between genetic diversity and latitudinal locations of WR populations. The Mantel test (R² = 0.49, P < 0.01) showed distinct groupings of WR populations from different rice-planting regions, fitting an isolation-by-distance pattern. In addition, the STRUCTURE analysis and principal coordinates (PCoA) analysis indicated considerable genetic differentiation of WR from different rice-planting regions, which was associated with the types of co-occurring rice cultivars. We conclude based on the above results that WR genetic diversity is affected by the latitudes where WR populations are located. The genetic differentiation of WR populations is determined by their spatial distances and co-occurring rice cultivars. Such a pattern of genetic diversity and differentiation across different regions may facilitate the design of effective WR control, in addition to understanding adaptive evolution of this weed.     

对水稻4号染色体一个编码S位点相关的受体样蛋白激酶基因簇的分析

通过对水稻 (OryzasativaL .) 4号染色体一段 32 3kb的序列测定和分析 ,在其中 10 8kb的区域内发现了一个由 14个编码S位点相关的受体样蛋白激酶 (SRK)基因组成的基因簇。RT_PCR实验证明了这 14个基因中有 9个基因表达 ,并且这 9个基因有不同的表达模式 :其中 2个基因主要在生殖器官中表达 ,而另外 7个基因在水稻的营养和生殖器官中均有表达。对这些基因的预测的氨基酸序列进行分析表明他们的细胞外受体部分均和甘蓝的SLG蛋白高度同源 ,而细胞内的激酶区都包含有丝氨酸 /苏氨酸激酶中特异的氨基酸。