Molecular mapping of a novel yellow rust resistance gene of wheat using microsatellite markers

Identification and genetic analysis of yellow rust resistance have suggested that wheat line R55 carries single dominant gene conferring yellow rust resistance. The bulked segregant analysis (BSA) for an F₂ population using microsatellite marker technique has indicated that the yellow rust resistance gene is located on the short arm of chromosome 1B, tightly linked to the microsatellite markers WMS11-193 bp and WMS18-184 bp, the linkage distance between the markers and the gene is 1.9 cM. This gene has been formally namedYr26. It is inferred from the pedigree, resistance and gene locus analysis that theYr26 has been transferred fromTriticum turgidum L. and is different from the other known yellow rust resistance genes.     

Mapping of a new gene for brown planthopper resistance in cultivated rice introgressed fromOryza eichingeri

Wild rice species is an important source of useful genes for cultivated rice improvement. Some accessions of Oryza eichingeri (2n = 24, CC) from Africa confer strong resistance to brown planthopper (BPH), whitebacked planthopper (WBPH) and bacterial blight (BB). In the present study, restriction fragments length polymorphism (RFLP) and simple sequence repeats (SSR) analysis were performed on disomic backcross plants between Oryza sativa (2n = 24, AA) and O. eichingeri in order to identify the presence of O. eichingeri segments and further to localize BPH-resistant gene. In the introgression lines, 1—6 O. eichingeri segments were detected on rice chromosomes 1, 2, 6, or/and 10. The dominant BPH resistant gene, tentatively named Bph13(t), was mapped to chromosome 2, being 6.1 and 5.5 cM away from two microsatellite markers RM240 and RM250, respectively. The transfer and localization of this gene from O. eichingeri will contribute to the improvement of BPH resistance in cultivated rice.     

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.     

Construction of a genetic map and location of quantitative trait loci for dwarf trait in maize by RFLP markers

Using F₂ population derived from the cross of tall inbred 7922 by dwarf inbred 5003, an RFLP linkage map of maize has been constructed, on which 85 markers are distributed among 10 linkage groups and span maize genome about 1827.8 cM with an average distance (24.4 cM) between markers. 106 F_2:3 lines of the population were grown in a 10 × 11 simple rectangular lattice design of one-raw plots with two replications and evaluated for plant height (PH). With interval mapping procedure, 5 QTLs controlling plant height have been identified and their genetic effects and gene action determined. 2 major QTLs with opposite effect have been discovered. One for increasing plant height isph1 which is located at chromosome 2 and accounts for 51.8% of the total phenotypic variation; the other for decreasing plant height isph3 which is located at chromosome 5 and accounts for 38.6% of the total phenotypic variation. The chromosomal location ofph3 might be the same as or close to the position ofbv1, a dwarf mutant of maize.     

Physical location ofHelminthosporium carbonum susceptibility gene hm1 by FISH of a RFLP marker umc119 in Maize

A fluorescencein situ hybridization (FISH) procedure was adopted to physically map a RFLP marker, umc119 near the centromere of the long arm of linkage group1 in maize. The hm1 gene (Helminthosporium carbonum susceptibility gene) was linked closely with the marker umc119. RFLP markers are very good landmarks for mapping genes. Therefore, we also determined the position of the gene hm1 on the chromosome based on the physical location of umc119. The disease induced by infection ofHelminthosporium carbonum is one of the serious maize diseases and it distributes in many countries including China. Hybridization sites were showed on 1 L (long arm of chromosome1) and 5 L. The percentage distance from centromere to the hybridization site was 22.86 on 1 L and 58.23 on 5 L the detection rate was about 12% for mitotic cells. In interphase nuclei five hybridized sites were detected. It demonstrated that umc119 was multiplicated sequences. FISH has more advantages overin situ hybridization (ISH) detected by DAB for increasing the detection ratio and contrast between chromosomes and hybridization signals. The ability to detect the hybridization signal of a small low copy DNA sequence is a very important key towards wide application of FISH for plant genome mapping. Supported by the National Natural Science Foundation and Doctorate Vesting Point Foundation of the Education Committee of China Li Lijia: born in 1967. Ph. D.     

Fine mapping of the red plant gene R1 in upland cotton(Gossypium hirsutum)

Sub 16 is a substitution line with G. hirsutum cv. TM-1 genetic background except that the 16th chromosome (Chr. 16) is replaced by the corresponding homozygous chromosome of G. barbadense cv. 3-79, and T586 is a G. hirsutum multiple gene marker line with 8 dominant mutation genes. The R ₁ gene for anthocyanin pigmentation was tagged in Chr. 16 in T586. The objective of this research was to screen SSR markers tightly linked with R ₁ by using the F₂ segregating population containing 1259 plants derived from the cross of Sub 16 and T586 and the backbone genetic linkage map from G. hirsutum×G. barbadense BC₁ newly updated by our laboratory. Genetic analysis suggested that the segregation ratio of red plants in the F₂ population fit Mendelian 1:2:1 inheritance, confirming that the red plant trait was controlled by an incomplete dominance gene. Preliminary mapping of R ₁ was conducted using 237 randomLy selected F₂ individuals and JoinMap v3.0 software. Then, a fine map of R1 was constructed using the F₂ segregating population containing 1259 plants, and R ₁ was located between NAU4956 and NAU6752, with only 0.49 cM to the nearest maker loci (NAU6752). These results provided a foundation for map-based cloning of R ₁ and further development of cotton cultivars with red fibers by transgenic technology. Supported by National Natural Science Foundation of China (Grant No. 30730067) and Programme of Introducing Talents of Discipline to Universities (Grant No. B08025)     

QTL mapping of resistance to sheath blight in maize（Zea mays L.）

Maize sheath blight (Rhizoctonia Solani) is a widely occurring fungus disease with great harm to corn-pro- ducing regions in the world. The first happening of sheath blight in China was reported in Jilin Province as early as in 1966[1]. Since the 1970s, the enlargement of corn- growing regions, the application of maize hybrids, the increasing use of fertilizers, especially the nitrogenous fertilizer, and a higher growth-density, all have caused a quick spread of sheath blight, the occurring …     

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.     

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.     

Comparative physical mapping of rice BAC clones linked to resistance genes Glh,Bph-3 and xa-5 in Oryza sativa L. and O. granulata Nees et Arn. ex Watt.

Oryza granulata Nees et Arn. ex Watt. is one of the three wild relatives of rice,which are the most valuable for study and utilization in China.In this study,the homology and physical locations of three rice resistance genes,Glh,Bph-3 and xa-5 are comparatively analyzed between O.sativa and O. granulata by Southern blotting and fluorescence in situ hybridization (FISH).The results of Southern blotting indicate that there exist homologous sequences of the tested RFLP markers in O. granulata.By using three bacterial artificial chromosome (BAC) clones scanned by the tested RFLP as probes, FISH signals are detected on both mitotic and pachytene chromosomes in O.sativa and O.granulata.Dual-color FISH demonstrates that two of the three BAC clones (14E16 and 38J9) are located on the short arm of the same chromosome pair in O. granulata. Additionally, colinearity is shown for the two clones between O.sativa and O.granulata. Another BAC clone 44B4 is located on the end of the short arm of other chromosome pair in these two species.Although the phylogenetic relationship between O.sativa and O.granulata is the most distinct in Oryza and these two species have evidently different biological features and ecological habits, the relative lengths and arm ratios of the detected chromosomes and the relative positions of the tested clone signals on chromosomes in O. granulata are quite similar to those in O. sativa.     

Comparative mapping of QTLs for Al tolerance in rice and identification of positional Al-induced genes

Aluminum (A1) toxicity is the major factor limiting crop productivity in acid soils. In this study, a recombinant inbreed line (RIL) population derived from a cross between an A1 sensitive lowland indica rice variety IR1552 and an A1 tolerant upland japonica rice variety Azucena, was used for mapping quantitative trait loci (QTLs) for A1 tolerance. Three QTLs for relative root length (RRL) were detected on chromosome 1,9, 12, respectively, and 1 QTL for root length under A1 stress is identical on chromosome 1 after one week and two weeks stress. Comparison of QTLs on chromosome 1 from different studies indicated an identical interval between C86 and RZ801 with gene(s) for A1 tolerance. This interval provides an important start point for isolating genes responsible for A1 tolerance and understanding the genetic nature of Al tolerance in rice. Four A1 induced ESTs located in this interval were screened by reverse Northern analysis and confirmed by Northern analysis. They would be candidate genes for the QTL.     

Molecular markers linked to Rsa resistant to soybean mosaic virus

Soybean mosaic virus (SMV) is a severe disease in worldwide soybean production. A cross was made between Kefeng No. 1 with broad spectrum resistance to SMV and Nannong 1138–2, a susceptible cultivar. The inheritance of resistance to SMV strain Sa prevailing in southern China was analyzed. Results of x² test from inoculation experiment on parents F1, F2 and F3 lines showed that the resistance to strain Sa was controlled by a single dominant gene Rsa. BSA method was adopted and 900 random 10-mer primers were used to amplify total DNA from resistant pool and susceptible pool in order to obtain polymorphic bands in two bulks. 16 primers could generate polymorphic bands, of which OPW-05 and OPAS-06 could generate the most stable RAPD patterns. RAPD markers OPW-05₆₆₀ and OPAS-06₁₈₀₀ were found to be linked to Rsa. Their order and genetic distance were OPAS-06₁₈₀₀22.2cM Rsa10.1 cM OPW-05₆₆₀. Southern blotting showed that both OPAS-06₁₈₀₀ and 0PW-05₆₆₀ were low copy DNA in genomic DNA. 0PW-05₆₆₀ has been converted into an RFLP marker successfully. Additionally, pK644H, an RFLP marker, has been identified to be linked to 0PW-05₆₆₀, and their genetic distance was 37.4 cM.     

粗山羊草Y189抗小麦白粉病基因SSR标记

从粗山羊草[Aegilops tauschii(Coss.)Schmal]Y189中鉴定出1个显性抗小麦白粉病基因,暂定名为PmAe Y2.应用分离群体分组法(BSA)筛选到Xgwm583-5D、Xgwm174-5D、Xgwm182-5D和Xgwm271-5D标记与该基因之间的遗传距离分别为25.7、16.7、9.1和7.0 cM.根据连锁标记所在小麦微卫星图谱的位置,PmAe Y2被定位在5DL染色体上.分析基因所在染色体的位置、抗病性特征认为PmAe Y2是一个新的抗白粉病基因,并可用于分子标记辅助选择.     

利用比较基因组学定位马铃薯抗晚疫病主效基因R10

晚疫病是马铃薯第一大病害。马铃薯抗晚疫病基因R10抗谱广、应用价值大,常用于马铃薯抗病杂交育种。R10位点位于马铃薯11号染色体的短臂末端,与已克隆的抗晚疫病基因R3a同属于抗晚疫病主效位点的单倍型。对包含195个基因型的R10基因的分离群体进行了晚疫病菌株接种和遗传分析,确定R10为抗晚疫病菌株89148-9的主效单基因。应用比较基因组学和BSA分析,开发了6个与R10连锁的分子标记,并将R10定位在1001T和C2_At5g59960两个遗传距离为2.6cM分子标记之间。R10位于已克隆的抗晚疫病基因R3a的近端粒区。本研究所获得的遗传图谱为通过图位克隆和比较基因组学克隆R10基因打下基础。     

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-assisted selection and identifying commercially important genes. Linkage maps of F. chinensis were constructed with an F2 mapping population （110 progenies） using amplified fragment length polymorphic （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 markers 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 distance 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 Chinese shrimp maps. The linkage analysis presented in this work provided some insight     

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.     

小麦中源于中间偃麦草抗白粉病基因PmCH5026的SSR定位

CH5026是衍生于八倍体小偃麦TAI7045的新品系,用高感品种(系)CH5065、晋太170分别与CH5026配置组合,于温室接种并调查F2、F3、BC1F2群体的抗感分离之比进行遗传分析,结果表明CH5026成株期对白粉菌E09小种的抗性受1对显性基因控制,暂命名为PmCH5026.使用集群分离分析法(BSA),用378对SSR引物对CH5026×CH5065 F2代群体进行分析,筛选到标记Xcfd233、Xbarc11和Xgwm539与抗性基因连锁,位置顺序为:Xcfd233-7.2cM-PmCH5026-4.9cM-Xbarc11-5.5cM-Xgwm539.根据小麦微卫星遗传连锁图及利用中国春第2同源群缺四体、双端体对SSR标记的定位结果,将PmCH5026定位在染色体2DL上.     

Genes for resistance to stripe rust on chromosome 2B and their application in wheat breeding

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most damaging diseases of wheat worldwide. Growing resistant cultivars is the most economic and environmental friendly way to control the disease. There are many resistance genes to stripe rust located on wheat chromosome 2B. Here, we propose a strategy to construct the recombinant wheat chromosome 2B with multiple resistances to stripe rust by making crosses between wheat lines or cultivars carrying Yr genes and using marker-assisted selection, based on the reported information about resistance spectrum, chromosomal location, and linked markers of the genes. Pyramiding the resistance genes on 2B would afford a valuable strategy to control the disease by cultivating varieties with durable resistance. The possibility, efficiency, and prospect of the suggested strategy are reviewed in the paper.     

菠菜转录因子MYB基因家族的鉴定及表达分析

利用生物信息学手段鉴定了76个具有典型R结构的菠菜转录因子（Spinacia oleracea） MYB,其中包括72条R2R3-MYB基因（2R-MYB）和4条R1R2R3-MYB基因（3R-MYB）。通过生物信息学对菠菜MYB转录因子家族成员的理化性质、染色体定位、结构域序列保守性和系统进化关系进行了分析,结果表明：菠菜MYB家族有32个基因位于染色体正链,另外44个基因位于染色体反链;MYB的DNA结合域中的保守域主要位于两个R重复序列的第二和第三螺旋之间,结合域中每个R重复的第一和第二色氨酸之间的氨基酸序列相对不保守;根据菠菜、拟南芥及甜菜的MYB家族系统进化关系可以推测,菠菜MYB家族中56个成员可以按功能划分为4类,在菠菜的生长发育过程中可能起着重要的调节作用,其余成员中有7个MYB基因可能参与菠菜响应氮素浓度的氮素利用及生长发育进程。