GS6, A Member of the GRAS Gene Family,Negatively Regulates Grain Size in Rice

Grain size is an important yield-related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today’s cultivars compared with t...     

水稻粒长新基因GL12 1定位与利用分析

水稻的粒长是水稻粒型构成的因素之一,直接影响水稻的单产,而粒长又是稻米品质的重要指标之一。该研究利用选育含有稻瘟病抗性基因Pigm 1的长粒恢复系R20 4为研究材料,通过图位克隆的方法,对粒长基因进行鉴定,并对该长粒性状在育种中的应用进行了分析。结果显示：(1)该长粒为显性基因控制的性状。(2)将粒长基因GL12 1初步定位在水稻第12染色体上Indel 12 3和Indel 12 7之间,物理距离约4.5 Mb。(3)通过进一步开发标记,最终将该粒长基因GL12 1定位在标记Indel 10和Indel 16之间,物理距离约900 kb。(4)长粒恢复系R20 4与‘庆源A’、‘定源A’和‘启源A’测交组合的粒长均表现R20 4表型,而与‘靓香A’测交组合的粒长比R20 4更长。研究表明,粒长基因GL12 1为显性基因控制的性状,可能为一个新的粒长控制基因,该研究为后期GL12 1基因的克隆、功能研究以及粒型分子育种奠定了基础。     

Genetic Analysis and Molecular Mapping of a Novel Gene Conferring Resistance to Rice Stripe Virus

Rice stripe virus (RSV) is one of the most damaging diseases affecting rice in East Asia. Rice variety 502 is highly resistant to RSV, while variety 5112 is extremely susceptible. Field statistical data revealed that all “502 × 5112” F₁ individuals were resistant to RSV and the ratio of resistant to susceptible plants was 3:1 in the F₂ population and 1:1 in the BC₁F₁ population. These results indicated that a dominant gene, designated RSV1, controlled the resistance. Simple sequence repeat (SSR) analysis was subsequently carried out in an F₂ population. Sixty SSR markers evenly distributed on the 12 rice chromosomes were screened and tested. Two markers, RM229 and RM206, showed linkage with RSV1. Based on this result, six SSR markers flanking RM229 and RM206 were further selected and tested. Results indicated that SSR markers RM457 and RM473E were linked to RSV1 with a genetic distance of 4.5 and 5.0 cM, respectively. All of the four SSR markers (RM229, RM473E, RM457 and RM206) linked to RSV1 were all located on chromosome 11, therefore RSV1 should be located on chromosome 11 also. In order to find some new markers more closely linked to the RSV1 gene, sequence-related amplified polymorphism (SRAP) analysis was performed. A total of 30 SRAP primer-pairs were analyzed, and one marker SR1 showed linkage with RSV1 at a genetic distance of 2.9 cM. Finally, RSV1 gene was mapped on chromosome 11 between SSR markers RM457 and SRAP marker SR1 with a genetic distance of 4.5 cM and 2.9 cM, respectively.     

一个控制水稻籽粒长度主效基因--Lk-4(t)的BC2F2群体定位及其遗传效应分析

水稻籽粒大小和形状是影响稻米外观品质和产量的重要影响因素,对控制这些性状基因的定位和克隆有助于弄清籽粒大小基因的表达模式和相应的代谢系统,最终实现该性状的自由调控。运用SSR和CAPs标记对来源于蜀恢527//蜀恢527／小粒回交组合BC2F2群体800隐性长粒单株进行分析,定位了一个控制水稻籽粒长短的基因,Lk-4（t）。对F2和BC2F2群体籽粒大小形状和千粒重的遗传分析表明,回交能将大部分对目的基因效应具有干扰修饰作用的微效基因多态性除去,从而有利于对目的基因型的准确鉴定;在F2和BC2F2群体中只发现两类籽粒长短表现型,即短粒和长粒,并且二者分离比例符合3：1的典型一对等位基因分离比例。这说明群体中籽粒长短变异是受一对基因控制。通过对BC2F2群体中隐性（长粒）单株进行分子标记分析,将这个控制籽粒长短的主效基因定位在3个CAPs标记,P1-EcoRV,P2-SacⅠ和P3-MboⅠ附近。连锁分析表明,Lk-4（t）位于水稻第3染色体着丝粒附近,离标记P1-EcoRⅤ和P2-SacⅠ分别有0．90cM和0．50cM的距离。     

水稻SL基因调控水稻的粒形

水稻产量和稻米品质的提高是水稻研究的中心问题。水稻产量主要取决于单株穗数、每穗粒数和粒重;粒重作为一个非常重要的产量性状,由粒长、粒宽和粒厚所决定。影响粒重和粒形的基因多为数量性状基因,精细定位并克隆到的较少。本研究中,我们克隆到一个影响粒形的基因SL,超表达（SL-OE）转基因植株表现出粒长增加、粒宽减小、叶宽减小的表型;同时,SL-RNAi的转基因植株呈现出粒长缩短、叶宽增加的表型。颖壳表面细胞在超表达转基因植株中伸长,而在RNAi转基因植株中缩短。叶片横向细胞数目在转基因植株中发生变化,推测乩基因可能与细胞分裂相关。SL-OE转基因植株中G嗽因被明显上调,说明盟基因可能通过调节GW2的表达对水稻粒宽造成影响。另外,观基因影响稻米的品质。     

水稻糙米高蛋白基因的QTL定位

利用由糙米蛋白含量高达14．55％的广东省农家品种三春种配制的BC1群体进行糙米高蛋白基因的QTL定位,定位到了6个糙米蛋白基因的QTLs,其中有3个新的QTLs。有1个增效基因qCP1-2为主效基因,解释的表型变异高达44．2％,有可能是与谷蛋白基因Glu-1紧密连锁的新调控序列。本研究表明,所利用的BC1群体的糙米蛋白可能主要是由1个主效QTL所控制。     

水稻穗长基因PAL3的克隆及自然变异分析

穗型是决定水稻(Oryza sativa)产量的关键因素之一。我们从粳稻品种圣稻808 (SD808)的EMS诱变突变体库中发现4份短穗突变体,这些突变体的穗长、一级枝梗数、二级枝梗数和穗粒数发生不同程度的降低。基因定位和图位克隆表明,这些突变体的表型受同一基因控制,将该基因命名为PAL3 (PANICLE LENGT...     

Analysis of the Molecular Evolutionary History of the Ascorbate Peroxidase Gene Family: Inferences from the Rice Genome

Ascorbate peroxidase (APx) is a class I peroxidase that catalyzes the conversion of H₂O₂ to H₂O and O₂ using ascorbate as the specific electron donor. This enzyme has a key function in scavenging reactive oxygen species (ROS) and the protection against toxic effects of ROS in higher plants, algae, and Euglena. Here we report the identification of an APx multigene family in rice and propose a molecular evolutionary relationship between the diverse APx isoforms. In rice, the APx gene family has eight members, which encode two cytosolic, two putative peroxisomal, and four chloroplastic isoforms, respectively. Phylogenetic analyses were conducted using all APx protein sequences available in the NCBI databases. The results indicate that the different APx isoforms arose by a complex evolutionary process involving several gene duplications. The structural organization of APx genes also reflects this process and provides evidence for a close relationship among proteins located in the same subcellular compartment. A molecular evolutionary pathway, in which cytosolic and peroxisomal isoforms diverged early from chloroplastic ones, is proposed.Reviewing Editor: Dr. Niles Lehman     

A Germin-Like Protein Gene Family Functions as a Complex Quantitative Trait Locus Conferring Broad-Spectrum Disease Resistance in Rice

Plant disease resistance governed by quantitative trait loci (QTL) is predicted to be effective against a broad spectrum of pathogens and long lasting. Use of these QTL to improve crop species, however, is hindered because the genes contributing to the trait are not known. Five disease resistance QTL that colocalized with defense response genes were accumulated by marker-aided selection to develop blast-resistant varieties. One advanced backcross line carrying the major-effect QTL on chromosome (chr) 8, which included a cluster of 12 germin-like protein (OsGLP) gene members, exhibited resistance to rice (Oryza sativa) blast disease over 14 cropping seasons. To determine if OsGLP members contribute to resistance and if the resistance was broad spectrum, a highly conserved portion of the OsGLP coding region was used as an RNA interference trigger to silence a few to all expressed chr 8 OsGLP family members. Challenge with two different fungal pathogens (causal agents of rice blast and sheath blight diseases) revealed that as more chr 8 OsGLP genes were suppressed, disease susceptibility of the plants increased. Of the 12 chr 8 OsGLPs, one clustered subfamily (OsGER4) contributed most to resistance. The similarities of sequence, gene organization, and roles in disease resistance of GLP family members in rice and other cereals, including barley (Hordeum vulgare) and wheat (Triticum aestivum), suggest that resistance contributed by the chr 8 OsGLP is a broad-spectrum, basal mechanism conserved among the Gramineae. Natural selection may have preserved a whole gene family to provide a stepwise, flexible defense response to pathogen invasion.     

一个新的水稻小粒矮秆基因的分子标记定位及效应分析

从水稻(Oryza safjva L．)半矮秆品种蜀恢I62中发现一份小粒矮秆突变体“I62d”。对I62d与4个半矮秆品种杂交F1和F2代的遗传分析表明,I62d的矮生性由一对隐性基因控制。以II-32B／162d F2代作定位群体,用分子标记将I62d突变基凶定位丁水稻第3染色体短臂,该基因与微卫星标记RM218和RMI57之间的遗传距离分别为3．5cM和10．0cM。同时,利用近等基因系分析了该基因的表型效应,结果表明它可使株高降为正常高度的1／4左右,籽粒降为正常大小的1／4左右,并使叶片显著缩短、加宽,结实率显著降低。我们认为162d突变基因是一个新的水稻小粒矮秆某因,暂命名为dI62(t）。     

Evolutionary History of the Sex-Peptide (Acp70a) Gene Region in Drosophila Melanogaster

In Drosophila the products of the seminal fluid stimulate oviposition and suppress remating in the female. Of all the accessory gland peptides (Acp's) involved in these two responses, the sex-peptide (coded by the Acp70A gene) is among the best characterized at the functional level. A 1.2-kb fragment encompassing the Acp70A gene of nine lines from a natural population of D. melanogaster and one allele of D. sechellia was sequenced to study the forces shaping nucleotide variation within and between species. The coding region of D. simulans and D. mauritiana was also sequenced. A Ser to Ala replacement polymorphism at the last position of the signal peptide was detected in D. melanogaster. The Ser and Ala alleles are at intermediate frequencies. The level of nucleotide variation is lower for the derived Ala allele, which is compatible with a recent origin and an increase in frequency due to positive selection. Variation at the 5' flanking region is structured in two major highly differentiated haplotypes, whose distribution does not conform to neutral expectations. Selective and/or historical factors could contribute to the observed overall patterning of nucleotide variation at the Acp70A region.     

一个新的水稻小粒矮秆基因的分子标记定位及效应分析

一个新的水稻小粒矮秆基因的分子标记定位及效应分析 李秀兰 吴 成 邓晓建 王平荣 李仁端 杨志荣     

一份水稻矮杆小粒突变体的形态特征和基因定位

从水稻T-DNA插入突变体库中鉴定出一个矮杆小粒突变体t129,该突变体与野生型植株相比,植株明显矮化,籽粒粒长明显缩短,千粒重下降。遗传分析表明,t129的突变性状由一对隐性核基因控制,该基因(T129)经图位克隆定位于水稻第5染色体长臂上,引物InDel43和InDel57之间,物理距离为430 kb,并与标记InDel51共分离。本研究明确了该矮杆小粒突变体的表型特征及遗传规律,为进一步研究调控水稻株高和粒型基因奠定基础。     

A Revised Evolutionary History of the CYP1A Subfamily: Gene Duplication, Gene Conversion, and Positive Selection

Members of cytochrome P450 subfamily 1A (CYP1As) are involved in detoxification and bioactivation of common environmental pollutants. Understanding the functional evolution of these genes is essential to predicting and interpreting species differences in sensitivity to toxicity caused by such chemicals. The CYP1A gene subfamily comprises a single ancestral representative in most fish species and two paralogs in higher vertebrates, including birds and mammals. Phylogenetic analysis of complete coding sequences suggests that mammalian and bird paralog pairs (CYP1A1/2 and CYP1A4/5, respectively) are the result of independent gene duplication events. However, comparison of vertebrate genome sequences revealed that CYP1A genes lie within an extended region of conserved fine-scale synteny, suggesting that avian and mammalian CYP1A paralogs share a common genomic history. Algorithms designed to detect recombination between nucleotide sequences indicate that gene conversion has homogenized most of the length of the chicken CYP1A genes, as well as the 5′ end of mammalian CYP1As. Together, these data indicate that avian and mammalian CYP1A paralog pairs resulted from a single gene duplication event and that extensive gene conversion is responsible for the exceptionally high degree of sequence similarity between CYP1A4 and CYP1A5. Elevated nonsynonymous/synonymous substitution ratios within a putatively unconverted stretch of ∼250 bp suggests that positive selection may have reduced the effective rate of gene conversion in this region, which contains two substrate recognition sites. This work significantly alters our understanding of functional evolution in the CYP1A subfamily, suggesting that gene conversion and positive selection have been the dominant processes of sequence evolution. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Yves Van de Peer]     

Combination of Eight Alleles at Four Quantitative Trait Loci Determines Grain Length in Rice

Grain length is an important quantitative trait in rice (Oryza sativa L.) that influences both grain yield and exterior quality. Although many quantitative trait loci (QTLs) for grain length have been identified, it is still unclear how different alleles from different QTLs regulate grain length coordinately. To explore the mechanisms of QTL combination in the determination of grain length, five mapping populations, including two F₂ populations, an F₃ population, an F₇ recombinant inbred line (RIL) population, and an F₈ RIL population, were developed from the cross between the U.S. tropical japonica variety ‘Lemont’ and the Chinese indica variety ‘Yangdao 4’ and grown under different environmental conditions. Four QTLs (qGL-3-1, qGL-3-2, qGL-4, and qGL-7) for grain length were detected using both composite interval mapping and multiple interval mapping methods in the mapping populations. In each locus, there was an allele from one parent that increased grain length and another allele from another parent that decreased it. The eight alleles in the four QTLs were analyzed to determine whether these alleles act additively across loci, and lead to a linear relationship between the predicted breeding value of QTLs and phenotype. Linear regression analysis suggested that the combination of eight alleles determined grain length. Plants carrying more grain length-increasing alleles had longer grain length than those carrying more grain length-decreasing alleles. This trend was consistent in all five mapping populations and demonstrated the regulation of grain length by the four QTLs. Thus, these QTLs are ideal resources for modifying grain length in rice.     

Evolutionary History of the 11p15 Human Mucin Gene Family

The four human mucin genes MUC6, MUC2, MUC5AC, and MUC5B are located at chromosome 11p15.5. It has been demonstrated that the three mucins MUC2, MUC5AC, and MUC5B contain several Cys-subdomains of 108 amino acid residues. In contrast, little information is available concerning MUC6. These Cys-subdomains contain 10 cysteine residues that have a highly conserved position. We present here a coherent probable evolutionary history of this human gene family after comparison of the nucleotide sequences of these Cys-subdomains. The three MUC loci MUC2, MUC5AC, and MUC5B may have evolved from a common ancestral gene by two successive duplications. Moreover, we can postulate that MUC5AC and MUC5B have evolved in a concerted manner, while MUC2 has evolved separately. Received: 30 January 1997 / Accepted: 17 April 1997     

竹亚科lea3基因的进化分析

选取竹亚科中两个超族、六个族和三个亚族的10个竹种为材料,分别是泰竹、凤尾竹、青皮竹、大叶慈、慈竹、野龙竹、毛竹、香竹、苦竹、菲白竹,分离克隆了它们的lea3基因,并将它们与外类群物种水稻进行序列比对和进化分析。结果发现在分支模型与分支位点模型的检测中,不同竹种所含lea3基因承受了不同的正选择压力,清除选择作用在lea3基因编码区中占主导地位（ω<1）。在位点模型的检测中,共检测出了18个显著性正选择位点,占总氨基酸数目的111%。对这18个显著性正选择位点进行定位后,发现其中的15个位于11个氨基酸串联重复序列附近。这说明lea3基因中的11个氨基酸串联重复序列区比基因其它区域更容易受自然选择作用影响。同时,在位点模型检测结果的基础上,通过对强烈清除选择位点的定位,发现在11个氨基酸串联重复序列区内存在一长段无强烈清除位点的序列区。