Construction of a genetic map with SRAP markers and localization of the gene responsible for the first-flower-node trait in cucumber (Cucumis sativus L.)

Cucumber (Cucumis sativus L.) is an annualclimber originated from the tropic rain forest area inthe south of Himalayas, which belongs to the Cucur bitaceae family. Cucumber is one of the importantvegetables in the world, and its planting area is sec ond only to that of tomato[1]. However genetics re search on cucumber obviously drops behind that of thelatter. The classic genetic map of cucumber, with sixlinkage groups, is composed of more than 100 genesfor color, morphology, and dise…     

Fine mapping of an incomplete recessive gene for leaf rolling in rice （Oryza sativa L.）

Genetic analysis and fine mapping of genes controlling leaf rolling were conducted using two backcrossed generations （BC4F2, BC4F3） derived from a cross between QMX, a non-rolled leaf cultivar as a recurrent parent, and JZB, a rolled leaf NIL of ZB as a donor parent. Results indicated that leaf rolling was mainly controlled by an incompletely recessive major gene, namely rl（t）, and at the same time, affected by quantitative trait loci （QTLs） and/or the environment. A genetic linkage map was constructed using MAPMAKER/EXP3.0 with eight polymorphic markers on chromosome 2, which were screened by BAS method from 500 SSR markers and 15 newly developed insertion/deletion （InDel） markers. The position of rl（t） was estimated with composite interval mapping （CIM） method using WinQTLcart2.5. Gene rl（t） was mapped between markers InDel 112 and RM3763, and 1.0 cM away from InDel 112 using 241 plants in BC4F2 population. To fine map r（t）, one BC4F3 line with 855 plants was generated from one semi-rolled leaf plant in BC4F2. Four new polymorphic InDel markers were developed, including InDel 112.6 and InDel 113 located between markers InDe1112 and RM3763. Based on the information of recombination offered by 191 rolled leaf plants and 185 non-rolled leaf plants from the BC4F3 line ,we mapped r（t） to a 137-kb region between markers InDel 112.6 and InDel 113. Homologous gene analysis suggested that r（t）was probably related to the process of leaf development regulated by microRNA.     

Construction of a genetic linkage map for cotton based on SRAP

DNA markers have been widely used in construction of molecular genetic linkage maps in plants. The first genetic linkage map of cotton was constructed by Reinish in 1994 using RFLP (restriction fragment length polymorphism)[1], which included 705 polymorphic loci on 41 linkage groups with a total length of 4675 cM. Afterwards, several genetic linkage maps were constructed[2—7], but no map is comparable to this one in marker density. A high-density genetic linkage map could be applied effec…     

Estimation of statistical power and false discovery rate of QTL mapping methods through computer simulation

Many QTL mapping methods have been developed in the past two decades.Statistically,the best method should have a high detection power but a low false discovery rate (FDR).Power and FDR cannot be derived theoretically for most QTL mapping methods,but they can be properly evaluated using computer simulations.In this paper,we used four genetic models (two for independent loci and two for linked loci) to illustrate power and FDR estimation for interval mapping (IM) and inclusive composite interval mapping (ICIM).For each model,we simulated 1000 populations each of 200 doubled haploids.A support interval (SI) was first defined to indicate to which predefined QTL the significant QTL belonged.Power was calculated by counting the number of simulation runs with significant peaks higher than the logarithm of odds (LOD) threshold in the SI.Quantitative trait loci not identified in any SIs were viewed as false positives.The FDR is the rate at which QTLs are identified as significant when they are actually non-significant.Simulation results allowed us to estimate power and FDR of IM and ICIM for two independent and two linkage genetic models.Our estimates allowed us to readily compare the efficiencies of different statistical methods for QTL mapping,including the ability to separate linkage,under a wide range of genetic models.We used IM and ICIM as examples of how to estimate power and FDR,but the principles shown in this paper can be used for power analysis and comparison of any other QTL mapping methods,especially those based on interval tests.     

Verification and fine-mapping of QTLs conferring days to flowering in soybean using residual heterozygous lines

The results of QTL mapping based on a primary mapping population should be further verified and refined for its real utilization in marker-assisted selection or map-based cloning.The primary mapping population contains 114 BC1F1 plants of the backcross between Essex (maturity group V,MG V) as the donor parent and ZDD2315 (MG II) as the recurrent parent.In this study,a genetic linkage map with 250 SSR markers spanning a total length of 2963.5 cM on 25 linkage groups (LG) was constructed using software MAPMAK...     

应用RAPD标记构建马尾松单株树遗传连锁图谱

利用马尾松（Ｐｉｎｕｓｍａｓｓｏｎｉａｎａ）崇义群体Ｃ－１６号单株上４０粒种子的胚乳为作图群体材料，用随机扩增多态性ＤＮＡ（ＲＡＰＤ）方法构建马尾松单株遗传连锁图谱，从被步筛选的８０个引物中，得到１６个具有多态性产物的引物，对这１６种引物进行Ｍｅｎｄｅｌｉａｎ１：１分离检测（卡方检验，Ｐ＜０．０５），我们得到符合Ｍｅｎｄｅｌｉａｎ１：１分离比例的ＲＡＰＤｓ标记４９个．通过对４９个标记的连锁关系进行分析，其中２９个标记分布在１２个连锁群上，总图距为４８３．３ｃＭ，平均图距为２８．４２ｃＭ，２０个标记没有连锁到任何连锁群上，需要继续进行大量标记的连续分析，构建完善的高密度的遗传图谱，使之能够对数量性状位点ＱＴＬｓ进行定位，从而进行分子标记辅助选择育种（ＭＡＳ）．     

小麦雌性育性双向极端群体QTL定位策略初探

在极端不育群体中计算重组频率(c值)初步筛选QTL位点的基础之上,利用普通小麦中育性正常的良种藁城8901(P1)与雌性不育系XND126(P2)杂交F2群体中的189株隐性极端不育株和63株极端可育株组成的双向极端群体为定位群体,构建了连锁图,分析定位了小麦雌性育性位点taf1,获得了与F2平衡群体相同的定位位点.分析发现与taf1位点连锁较紧密的标记,其c值较小.利用极端群体的策略能快速有效的定位小麦雌性育性QTL在染色体上的位置.     

Isolation and characterization of soybean NBS analogs

Isolation of plant resistance genes is greatly helpful to crop resistance breeding and the insight of resistance mechanism. The cloned plant resistance genes are classified into four classes according to their putative structural domain, of which the majority possesses nucleotide-binding site (NBS) domain that consists of P-loop, kinase2a and kinase3a. The conservation of this domain affords the potential possibility of cloning the plant resistance genes, which is homology-based cloning technique. In the present study, the degenerate oligonucleotide primers were designed according to the tobaccoN andArabidopsis RPS2, and 358 clones were isolated from the genomic DNA of resistance soybean cultivar Kefengl, resistant to soybean mosaic virus, and 4 open-reading NBS analogs were finally characterized and designated asKNBS1, KNBS2, KNBS3 andKNBS4. Southern hybridization suggested that they were present with multicopy in the soybean genome;KNBS4 was mapped to F linkage group andKNBS2 co-located J linkage group with the SCAR marker ofRsa resistant to soybean mosaic virus by RFLP analysis. Northern analysis suggested thatKNBS2- related sequence was low and constitutively expressed in the root, stem and leaves of soybean. The detailed characterization of NBS analogs is very helpful to ultimately cloning the soybean resistance gene.     

Genetic analysis and gene mapping of leafy head （lhd）, a mutant blocking the differen-tiation of rachis branches in rice （Oryza sativa L.）

Flowers, fruits and seeds are products of plant re- productive development and provide the important sources of foods for humans. Therefore, the moleculargenetic mechanisms of floral development have been ahotspot of research of plant developmental biology[1]. Rice is one of the most important staple food crops. Theoutcome of its reproductive development would determine the yield and quality of grains. Rice is also a model plantof cereals. Hence, the study of rice reproductivedevelopment, esp…     

Fine mapping of the <Emphasis Type="Italic">Ht2 (Helminthosporium turcicum</Emphasis> resistance 2) gene in maize

Fine mapping of Helminthosporium turcicum resistance gene Ht2 is extremely valuable for map-based cloning of the Ht2 gene,gaining a better knowledge of the distribution of resistance genes in maize genome and marker-assisted selection in maize breeding.An F2 mapping population was developed from a cross between a resistant inbred line 77Ht2 and a susceptible inbred line Huobai.With the aid of RFLP marker analyses,the Ht2 gene was mapped between the RFLP markers UMC89 and BNL2.369on chromosome 8,with a genetic distance of 0.9cM to BNL2.369.There was a linkage between SSR markers UMC1202,BNLG1152,UMC1149 and the Ht2 gene by SSR assay,Among the SSR markers,the genetic distance between UMC1149 and the Ht2 gene was 7.2cM,By bulked segregant analysis 7 RAPD-amplified products which were probably linked to the Ht2 gene were selected after screening 450 RAPD primers and converted the single-copy ones into SCAR markers.Linkage analysis showed that the genetic distance between the SCAR marker SD-06633 and the Ht2 gene was 0.4cM.From these results,a part of linkage map around the Ht2 gene was constructed.     

Genetic contribution of foreign germplasm to elite Chinese soybean （Glycine max） cultivars revealed by SSR markers

Among 651 soybean (Glycine max) cultivars re- leased from 1923 to 1995, most of the parents used in the breeding program of northeast China and Huang- huai-hai valley were cultivars well adapted to local ecologic areas. Narrow parentage and lack of geneti…     

Fine mapping of the awn gene on chromosome 4 in rice by association and linkage analyses

Awnness is a key trait in rice domestication, yet no studies have been conducted on fine mapping or association mapping of the rice awn gene. In this study, we investigated the awnness and genotype of a core collection of 303 cultivated rice varieties and a BC5F2 segregating population of 200 individuals. Combining association and linkage analyses, we mapped the awnness related genes to chromosome 4. Primary association analysis using 24 SSR markers revealed five loci significantly associated with awnness on chromosome 4. The associated markers cover previously identified regions. Fine association mapping was conducted using another 29 markers within a 4-Mb region, covering the associated marker in34, which is close to the awn gene Awn4.1. Seven associated markers were revealed, distributed over an 870-kb region. Combining the fine association mapping and linkage analysis of awnness in the 200 BC5F2 segregating population, we finally identified a 330-kb region as the candidate region for Awn4.1. The results indicate that combining association mapping and linkage mapping provides an efficient and precise approach to both genome-wide mapping and fine mapping of rice genes.     

Genetic analysis and gene mapping of a narrow leaf mutant in rice ( Oryza sativa L.)

A narrow leaf mutant was obtained after T-DNA transformation conducted on a rice variety Zhonghua 11. Several abnormal morphological characteristics, including semi-dwarf, delayed flowering time, narrow and inward rolling leaves, and lower seed-setting, were observed. The rate of net photosynthesis (under saturate light) of flag leaves in the mutant was significantly lower than that of the wild type. Moreover, the leaf transpiration rate and stomatal conductance in the mutant flag leaf were lower than those of the wild type at the grain filling stage. It was found that the mutant phenotype was not caused by the T-DNA insertion. Genetic analysis showed that the mutant was controlled by a single recessive gene, designated as nal3(t). A genetic linkage map was constructed using a large F₂ mapping population derived from a cross between nal3(t) and an indica variety Longtefu B with 6 polymorphic markers on chromosome 12 identified from 366 SSR markers by the BAS method. Gene nal3(t) was mapped between the markers RM7018 and RM3331. Fine mapping of nal3(t) locus was conducted with 22 newly developed STS markers based on the sequence diversity around the region harboring nal3(t) between Nipponbare and 93–11, and nal3(t) was finally mapped to a 136-kb region between the STS markers NS10 and RH12-8. Supported by National High Technology Research and Development Program of China (863 Program) (Grant No. 2006AA10A102), National Natural Science Foundation of China (Grant No. 30600349) and Natural Science Foundation of Zhejiang Province (Grant No. Y306149)     

Molecular cloning, chromosomal mapping and expression analysis of disease resistance gene homologues in rice (Oryza sativa L.)

Resistance-like sequences have been amplified from first strand cDNA and genomic DNA of rice by PCR using oligonucleotide primers designed from sequence motifs conserved between resistance genes of tobacco andArabidopsis thaliana. 3 PCR clones, designatedOsr1, Osr2 andOsr3 which were 98% identical in nucleotide sequence level, have been found to be significantly homologous to known plant resistance genes and all contained the conserved motifs of NBS-LRR type resistance genes, such as P-loop, kinase2a, kinase3a and transmembrane domain.Southern hybridization revealed that rice resistance gene hornologueswere organized as a cluster in the genome. RFLP mapping using a DH population derived from anindica/japonka cross (Zhaiyeqing 8/Jingxi 17) and an RFLP linkage map assigned two copies ofOsrl and one copy ofOsr3 to the distal position of chromosome 12 where a blast resistance QTL has been mapped previously. Northern blot analysis showed thatOsrl gene was constitutively transcribed in rice leaves, shoots and roots. Further study concerning isolation of full-length cDNAs would be conducive to elucidating the functions of these genes.     

Fine mapping of locus S-b for F1 pollen sterility in rice （Oryza sativa L.）

Strong heterosis existed in the hybrid of the subspe-cies in rice[1,2]. However, the partial sterility of the hy-brid hinders the utilization of the heterosis[3,4]. Ikehashi et al.[5,6] considered the female gamete as the main ste-rility form and proposed…     

Strategy for the mapping of interactive genes using bulked segregant analysis method and Mapmaker/Exp software

A qualitative trait is usually controlled by a single gene, but it may be sometimes controlled by two or even more genes. This phenomenon is called gene interaction. Rapidly searching for linked mo- lecular markers via bulked segregant analysis (BSA) and then constructing regional linkage map with Mapmaker/Exp has become a common approach to mapping single major genes. However, methods and computer programs developed for mapping single major genes cannot be simply applied to interactive genes because the genetic patterns of gene interac- tions are quite different from that of single-gene in- heritance. Up to now, experimental methods for quickly screening molecular markers linked to inter- active genes and statistical methods and corre- sponding computer softwares for simultaneously analyzing the linkage relationships of multiple mo- lecular markers to an interactive gene have not been available. To solve this problem, in this paper, we propose a strategy for mapping interactive genes using BSA and Mapmaker/Exp. We demonstrate that all interactive genes can be mapped by the 'BSA Mapmaker/Exp' strategy using F2 generation (in a few cases, F3 generation is also needed). As BSA and Mapmaker/Exp have been broadly used in gene mapping studies and are well known by many re- searchers, the strategies proposed in this paper will be useful for practical researches.     

Genetic and physical finemapping of the Sc locus conferring indica-japonica hybrid sterility in rice （Oryza sativa L.）

Hybrid sterility is a major hindrance to utilizing the heterosis in indica-japonica hybrids. To isolate a gene Sc conferring the hybrid sterility, the locus was mapped using molecular markers and an F2 population derived from a cross between near isogenic lines. A primary linkage analysis showed that Sc was linked closely with 4 markers on chromosome 3, on which the genetic distance between a marker RG227 and Sc was 0.07 cM. Chromosome walking with a rice TAC genomic library was carried out using RG227 as a starting probe, and a contig of ca. 320 kb covering the Sc locus was constructed. Two TAC clones, M45EI4 and M90J01 that might cover the Sc locus, were partially sequenced. By searching the rice sequence databases with sequences of the TACs and RG227 a japonica rice BAC sequence, OSJNBb0078P24 was identified. By comparing the TAC and BAC sequences, six new PCR-based markers were developed. With these markers the Sc locus was further mapped to a region of 46 kb. The results suggest that the BAC OSJNBb0078P24 and TAC M45EI4 contain the Sc gene. Six ORFs were predicted in the focused 46-kb region.     

Construction of AFLP-based genetic linkage maps for the Chinese shrimp Fenneropaeneus chinensis

Fenneropaeneus chinensis is an important species in marine fishery resources and aquaculture in China. A genetic linkage map is essential for improving the efficiency of its breeding by marker-as- sisted selection and identifying commercially important genes. Linkage maps of F. chinensis were constructed with an F2 mapping population (110 progenies) using amplified fragment length polymor- phic (AFLP) marker in this study. Fifty-five AFLP primer combinations produced 532 AFLP markers fitting for map strategy in mapping family. The markers with 3:1 segregating ratios were analyzed using F2 intercross model for the common linkage map, while the markers with 1:1 ratio were analyzed using the pseudo-testcross strategy. The maps of male, female and common were constructed. The female map included 103 markers that formed 28 linkage groups, covering a total length of 1090 cM. All mark- ers were linked with the linkage groups. Segregation distortion was observed for 6 of 103 markers in the female map. The average distance between markers was 14.53 cM and ranged from 4.4 to 24.8 cM. The male map included 144 markers that formed 35 linkage groups. Ten markers remained unlinked in male map. Segregation distortion was observed for 7 of 144 markers in the male map. The total dis- tance of male map covered 1617 cM. The average distance between markers was 16.36 cM. The male map was 32.6% longer than the female map, which may reflect sex-specific recombination rates in Chinese shrimp. The common map was composed of 216 markers, including in 44 linkage groups covering a total distance of 1772.1 cM. Two markers remained unlinked. No distorted markers of 216 markers were shown in the common map. The distance between markers was 10.42 cM. An average estimated genome size for the Chinese shrimp was 2420 cM, which was consistent with the relative size of the Penaeid genome. The distribution of AFLP markers was relatively even in chromosomes of Chi- nese shrimp maps. The linkage analysis presented in this work provided some insight into the level of polymorphism and genetic variation of Chinese shrimp.     

一种新的TDCS基函数随机相位产生方法及性能分析

针对一维M序列生成变换域通信系统伪随机相位的不足,提出了一种采用双混沌序列生成基函数伪随机相位的方法,利用混沌序列映射替代M序列映射,并增加由混沌序列决定的映射控制抽头将伪随机相位产生法由一维扩展到二维,分析了采用双混沌序列生成基函数的各项性能指标变化。通过仿真验证,结果表明,采用双混沌序列的基函数伪随机相位生成法,无论是在单用户或是多用户情况下,都能有效地降低系统的误比特率,提高系统的抗截获性能以及多址信道容量。     

Morphology and mapping analysis of rice (Oryza sativa L.) clustered spikelets( Cl) mutant

The rice clustered spikelets (Cl) mutant exhibits a phenotype that most of branch apical have 2-3 spikelets clustered together,SEM (scanning electron microscope )observation suggested that the Cl gene controlled branch apical development,and influenced the terminal spikelets elongation,The spikelet number was reduced in mutant,indicating that Cl may also have an effect on spikelet number,To map Cl locus,two F2 mapping populations derived from the crosses between the Cl and ZhongHua11,and Cl and ZheFu802 were constructed ,respectively,The Cl locus was roughly mapped between two CAPS markers CK0214 and SS0324,A further fine mapping analysis showed that the Cl locus was mapped between makers R0674E and Cl12560,with genetic distances of 0.2 and 2.1 cM,respectively ,Then we found a PAC conting spanning Cl locus,the region was delimited to 196 kb.This results was useful for cloning of the Cl gene,Allelism test demonstrated that Cl was allelic to Cl2 another rice clustered spikelets mutant.