水稻CMS-DA育性恢复基因定位及其互作分析

在由210个测交组合组成的青早A／（协青早B／密阳46）F6群体中,构建了由129个RFLP、SSLP组成的连锁遗传图普。应用QTL分析方法,对水矮败型质雄性不育恢复基因进行了定位。检测到一个主效基因和3个效应较小的QTL（qRf－1、qRf－1、qRf－5）,这些基因这宰存在复杂的相互作用。     

A quantitative trait locus for cold tolerance at the booting stage on rice chromosome 8

A quantitative trait locus (QTL) for cold tolerance at the booting stage of a cold-tolerant rice breeding line, Hokkai-PL9, was analyzed. A total of 487 simple sequence repeat (SSR) markers distributed throughout the genome were used to survey for polymorphism between Hokkai-PL9 and a cold-sensitive breeding line, Hokkai287, and 54 markers were polymorphic. Single marker analysis revealed that markers on chromosome 8 are associated with cold tolerance. By interval mapping using an F₂ population between Hokkai-PL9 and Hokkai287, a QTL for cold tolerance was detected on the short arm of chromosome 8. The QTL explains 26.6% of the phenotypic variance, and its additive effect is 11.4%. Substitution mapping suggested that the QTL is located in a 193-kb interval between SSR markers RM5647 and PLA61. We tentatively designated the QTL as qCTB8 (quantitative trait locus for cold tolerance at the booting stage on chromosome 8).     

Genetic analysis and molecular mapping of a new fertility restorer gene Rf8 for Triticum timopheevi cytoplasm in wheat (Triticum aestivum L.) using SSR markers

A study on mode of inheritance and mapping of fertility restorer (Rf) gene(s) using simple sequence repeat (SSR) markers was conducted in a cross of male sterile line 2041A having Triticum timopheevi cytoplasm and a restorer line PWR4099 of common wheat (Triticum aestivum L.). The F₁ hybrid was completely fertile indicating that fertility restoration is a dominant trait. Based on the pollen fertility and seed set of bagged spikes in F₂ generation, the individual plants were classified into fertile and sterile groups. Out of 120 F₂ plants, 97 were fertile and 23 sterile (based on pollen fertility) while 98 plants set ≥5 seeds/spike and 22 produced ≤4 or no seed. The observed frequency fits well into Mendelian ratio of 3 fertile: 1 sterile with χ² value of 2.84 for pollen fertility and 2.17 for seed setting indicating that the fertility restoration is governed by a single dominant gene in PWR4099. The three linked SSR markers, Xwmc503, Xgwm296 and Xwmc112 located on the chromosome 2DS were placed at a distance of 3.3, 5.8 and 6.7 cM, respectively, from the Rf gene. Since, no known Rf gene is located on the chromosome arm 2DS, the Rf gene in PWR4099 is a new gene and proposed as Rf8. The closest SSR marker, Xwmc503, linked to the Rf8 was validated in a set of Rf, maintainer and cytoplasmic male sterile lines. The closely linked SSR marker Xwmc503 may be used in marker-assisted backcross breeding facilitating the transfer of fertility restoration gene Rf8 into elite backgrounds with ease.     

Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line

Low temperature at the booting stage is a serious abiotic stress in rice, and cold tolerance is a complex trait controlled by many quantitative trait loci (QTL). A QTL for cold tolerance at the booting stage in cold-tolerant near-isogenic rice line ZL1929-4 was analyzed. A total of 647 simple sequence repeat (SSR) markers distributed across 12 chromosomes were used to survey for polymorphisms between ZL1929-4 and the cold-sensitive japonica cultivar Towada, and nine were polymorphic. Single marker analysis revealed that markers on chromosome 7 were associated with cold tolerance. By interval mapping using an F₂ population from ZL1929-4 × Towada, a QTL for cold tolerance was detected on the long arm of chromosome 7. The QTL explained 9 and 21% of the phenotypic variances in the F₂ and F₃ generations, respectively. Recombinant plants were screened for two flanking markers, RM182 and RM1132, in an F₂ population with 2,810 plants. Two-step substitution mapping suggested that the QTL was located in a 92-kb interval between markers RI02905 and RM21862. This interval was present in BAC clone AP003804. We designated the QTL as qCTB7 (quantitative trait locus for cold tolerance at the booting stage on chromosome 7), and identified 12 putative candidate genes.     

大白×梅山杂交组合肉质性状的数量性状位点定位分析

为寻找影响猪肉质数量性状基因位点的染色体区域 ,以 3头英系大白公猪和 7头梅山母猪建立F2 资源家系。随机选留 14 7头F2 代个体 (1998年 81头 ,2 0 0 0年 66头 ) ,经检测均获得肉质性状表型数据。对资源家系内的所有个体位于染色体 1、2、3、4、6和 7上的 48个微卫星位点进行扩增。利用线性模型最小二乘法分别对各年度及两年综合后的肉质性状进行数量性状位点 (QTL)区间定位 ,利用置换法确定显著性阈值。研究结果表明 :在 2 0 0 0年群体中 ,猪 4号染色体 (SSC4)上定位了肌内脂肪QTL ,达到染色体极显著水平 (P <0 0 1)和基因组显著水平 (P <0 0 5) ,解释表型变异为 5 2 4% ,梅山猪具有增加肌内脂肪QTL ;两年度群体综合后 ,在上述 4号染色体同一区间 ,肌内脂肪QTL接近染色体显著水平 ;股二头肌pH值和半棘肌pH值QTL分别定位在SSC1和 3上 ;在 1998年和 2 0 0 0年群体中分别发现 1个和 3个达染色体显著水平 (P <0 0 5)的系水力QTL ;在 1998年群体中 ,肌肉含水量QTL位于SSC6;两年综合群体中 ,SSC2、6和 7上定位了肌肉含水量QTL ,达到染色体显著水平 ,含水量QTL均有印迹效应 ,梅山和大白猪各有增效基因     

Mapping Quantitative Trait Loci for Grain Appearance Traits of Rice Using a Recombinant Inbred Line Population

A linkage map consisting of 221 markers was constructed based on a recombinant inbred line (RIL) population from the cross between Zhenshan 97 and Minghui 63. Quantitative trait loci (QTL) mapping was carried out for grain appearance traits such as grain length, grain width and grain shape in rice in 1998 and 1999. Based on interval mapping method at the threshold LOD≥2.4, six, two and two QTLs were detected for grain length, grain width and grain shape, respectively, in 1998; In 1999, three, two and two QTLs were identified for the three traits, respectively. Of them, seven QTLs were simultaneously identified in both of the years. The QTL with large effects located in the interval RG393-C1087 on chromosome 3 not only controlled the grain length, but also influenced the grain shape. It explained 57.5%, 61.4% and 26.7%, 29.9% of phenotypic variation of the grain length and the grain shape in two years, respectively. The QTL with large effects located in the interval RG360-C734B on chromosome 5 affected the grain width and the grain shape. It explained 44.2%, 53.2% and 32.1%, 36.0% of phenotypic variation of the grain width and the shape in two years, respectively. Eight, five and five QTLs were identified for the grain length, width and shape, respectively, based on mixed linear-model composite interval mapping method at P =0.005. Their general contributions were 58.81%, 44.75%, and 57.47%. One QTL for the grain length was found to be significant interaction with environment.     

Mapping quantitative trait loci for bean traits and ovule number in Theobroma cacao L.

Quantitative trait loci (QTL) mapping for bean traits and the number of ovules per ovary was carried out in cocoa (Theobroma cacao L.) using three test-cross progenies derived from crosses between a lower Amazon Forastero male parent (Catongo) and three female parents: one upper Amazon Forastero (IMC78) and two Trinitario (DR1 and S52). RFLP (restriction fragment length polymorphism), microsatellite, and AFLP (amplified fragment lengthpolymorphism) markers were used for mapping. Between one and six QTL for bean traits (length, weight, and shape index) and one and four QTL for the number of ovules per ovary were detected using composite interval mapping (CIM). Individual QTL explained between 5 and 24% of the phenotypic variation. QTL clusters were identified on several chromosomes, but particularly on chromosome 4. QTL related to bean traits were detected in the same region in both Trinitario parents and in a close region in the upper Amazon Forastero parent. In reference to a previous diversity study where alleles specific to Criollo and Forastero genotypes were identified, it was possible to speculate on the putative origin (Criollo or Forastero) of favorable QTL alleles segregating in both Trinitario studied.     

QTL mapping for reaction to Phaeosphaeria leaf spot in a tropical maize population

Phaeosphaeria leaf spot (PLS) is an important disease in tropical and subtropical maize (Zea mays, L.) growing areas, but there is limited information on its inheritance. Thus, this research was conducted to study the inheritance of the PLS disease in tropical maize by using QTL mapping and to assess the feasibility of using marker-assisted selection aimed to develop genotypes resistance to this disease. Highly susceptible L14-04B and highly resistant L08-05F inbred lines were crossed to develop an F₂ population. Two-hundred and fifty six F₂ plants were genotyped with 143 microsatellite markers and their F_2:3 progenies were evaluated at seven environments. Ten plants per plot were evaluated 30 days after silk emergence following a rating scale, and the plot means were used for analyses. The heritability coefficient on a progeny mean basis was high (91.37%), and six QTL were mapped, with one QTL on chromosomes 1, 3, 4, and 6, and two QTL on chromosome 8. The gene action of the QTL ranged from additive to partial dominance, and the average level of dominance was partial dominance; also a dominance × dominance epistatic effect was detected between the QTL mapped on chromosome 8. The phenotypic variance explained by each QTL ranged from 2.91 to 11.86%, and the joint QTL effects explained 41.62% of the phenotypic variance. The alleles conditioning resistance to PLS disease of all mapped QTL were in the resistant parental inbred L08-05F. Thus, these alleles could be transferred to other elite maize inbreds by marker-assisted backcross selection to develop hybrids resistant to PLS disease.     

秋稻品种Dular广亲和基因的RFLP分析

利用Ｂａｌｉｌｌａ／Ｄｕｌａｒ／ＩＲ３６和南京１１／／Ｄｕｌｕｒ／２５３３两个三交Ｆ１ 本对秋稻品种Ｄｕｌａｒ的广亲和性进行了遗传分析。为使杂种群体在相对一致的条伯下抽穗,所有三交Ｆ１植株于分化前集中进行了为期１周的短日照处理。结果表明,两个群体的小穗育性于多峰连续分布,说明三交群体的育性可能受几个主基因控制并受到微效基因的修饰,进一步采用分群分析法,以南京１１／／Ｄｕｌａｒ／２５３３为分析群体进     

Identification of <Emphasis Type="Italic">qSOR1</Emphasis>, a major rice QTL involved in soil-surface rooting in paddy fields

Specific Indonesian lowland rice (Oryza sativa L.) cultivars elongate thick primary roots on the soil surface of paddy fields. To clarify the genetic factors controlling soil-surface rooting, we performed quantitative trait locus (QTL) analyses using 124 recombinant inbred lines (RILs) derived from a cross between Gemdjah Beton, an Indonesian lowland rice cultivar with soil-surface roots, and Sasanishiki, a Japanese lowland rice cultivar without soil-surface roots. These cultivars and the RILs were tested for soil-surface rooting in a paddy field. We identified four regions of chromosomes 3, 4, 6, and 7 that were associated with soil-surface rooting in the field. Among them, one major QTL was located on the long arm of chromosome 7. This QTL explained 32.5–53.6% of the total phenotypic variance across three field evaluations. To perform fine mapping of this QTL, we measured the basal root growth angle of crown roots at the seedling stage in seven BC₂F₃ recombinant lines grown in small cups in a greenhouse. The QTL was mapped between markers RM21941 and RM21976, which delimit an 812-kb interval in the reference cultivar Nipponbare. We have designated this QTL qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1).     

不同发育时期小麦粒重性状QTL的动态分析

利用6044×01-35构建的重组自交系(RIL)群体为试验材料,对小麦粒重性状进行发育动态QTL分析。结果表明,在小麦花后子粒灌浆的7个不同时期,两个试验点共检测到16个与粒重性状相关的QTL。其中开花后20d检测到的单穗粒重QTL位于2A染色体上,解释率达12%,遗传效应超过10;两环境下控制千粒重QTL在7个时期均被检测到。花后的各个时期均能在Xgwm448-Xgpw7399标记区间定位到千粒重QTL。其中花后10d检测到1个千粒重QTL,位于2A染色体的Xgwm448-Xgpw7399标记区间,解释较大的表型变异,达到18%。Qtl8、Qtl13和Qtl14均定位在Xgwm448-Xgpw7399标记区间的同一位置,共同解释11%的表型变异。花后20d和花后25d均检测到1个QTL,位于2A染色体的Xgwm372-Xgwm95标记区间的不同位点,均能解释4%的表型变异。花后40d检测到1个QTL,位于1D染色体的Xwmc93-Xgpw2224标记区间,解释1%的表型变异。从连锁群的位置上看,控制千粒重的QTL主要集中在2A染色体的Xgwm448-Xgpw7399标记区间,这是一个控制千粒重QTL的富集区域,以期进行精细定位和图位克隆。     

Genetic architecture of male fertility restoration of <Emphasis Type="Italic">Triticum timopheevii</Emphasis> cytoplasm and fine-mapping of the major restorer locus <Emphasis Type="Italic">Rf3</Emphasis> on chromosome 1B

Key message

Restoration of fertility in the cytoplasmic male sterility-inducing Triticum timopheevii cytoplasm can be achieved with the major restorer locus Rf3 located on chromosome 1B, but is also dependent on modifier loci.

Abstract

Hybrid breeding relies on a hybrid mechanism enabling a cost-efficient hybrid seed production. In wheat and triticale, cytoplasmic male sterility based on the T. timopheevii cytoplasm is commonly used, and the aim of this study was to dissect the genetic architecture underlying fertility restoration. Our study was based on two segregating F₂ triticale populations with 313 and 188 individuals that share a common female parent and have two different lines with high fertility restoration ability as male parents. The plants were cloned to enable replicated assessments of their phenotype and fertility restoration was evaluated based on seed set or staining for pollen fertility. The traits showed high heritabilities but their distributions differed between the two populations. In one population, a quarter of the lines were sterile, conforming to a 3:1 segregation ratio. QTL mapping identified two and three QTL in these populations, with the major QTL being detected on chromosome 1B. This QTL was collinear in both populations and likely corresponds to Rf3. We found that Rf3 explained approximately 30 and 50% of the genotypic variance, has a dominant mode of inheritance, and that the female parent lacks this locus, probably due to a 1B.1R translocation. Taken together, Rf3 is a major restorer locus that enables fertility restoration of the T. timopheevii cytoplasm, but additional modifier loci are needed for full restoration of male fertility. Consequently, Rf3 holds great potential for hybrid wheat and triticale breeding, but other loci must also be considered, either through marker-assisted or phenotypic selection.

     

QTL Conferring Fusarium Crown Rot Resistance in the Elite Bread Wheat Variety EGA Wylie

Fusarium crown rot (FCR) is one of the most damaging cereal diseases in semi-arid regions worldwide. The genetics of FCR resistance in the bread wheat (Triticum eastivum L.) variety EGA Wylie, the most resistant commercial variety available, was studied by QTL mapping. Three populations of recombinant inbred lines were developed with this elite variety as the resistant parent. Four QTL conferring FCR resistance were detected and resistance alleles of all of them were derived from the resistant parent EGA Wylie. One of these loci was located on the short arm of chromosome 5D (designated as Qcrs.cpi-5D). This QTL explains up to 31.1% of the phenotypic variance with an LOD value of 9.6. The second locus was located on the long arm of chromosome 2D (designated as Qcrs.cpi-2D) and explained up to 20.2% of the phenotypic variance with an LOD value of 4.5. Significant effects of both Qcrs.cpi-5D and Qcrs.cpi-2D were detected in each of the three populations assessed. Another two QTL (designated as Qcrs.cpi-4B.1 and Qcrs.cpi-4B.2, respectively) were located on the short arm of chromosome 4B. These two QTL explained up to 16.9% and 18.8% of phenotypic variance, respectively. However, significant effects of Qcrs.cpi-4B.1 and Qcrs.cpi-4B.2 were not detected when the effects of plant height was accounted for by covariance analysis. The elite characteristics of this commercial variety should facilitate the incorporation of the resistance loci it contains into breeding programs.     

BAC-derived markers converted from RFLP linked to Phytophthora capsici resistance in pepper (Capsicum annuum L.)

Phytophthora capsici Leonian, an oomycete pathogen, is a serious problem in pepper worldwide. Its resistance in pepper is controlled by quantitative trait loci (QTL). To detect QTL associated with P. capsici resistance, a molecular linkage map was constructed using 100 F(2) individuals from a cross between Capsicum annuum 'CM334' and C. annuum 'Chilsungcho'. This linkage map consisted of 202 restriction fragment length polymorphisms (RFLPs), 6 WRKYs and 1 simple sequence repeat (SSR) covering 1482.3 cM, with an average interval marker distance of 7.09 cM. QTL mapping of Phytophthora root rot and damping-off resistance was performed in F(2:3) originated from a cross between resistant Mexican landrace C. annuum 'CM334' and susceptible Korean landrace C. annuum 'Chilsungcho' using composite interval mapping (CIM) analysis. Four QTL explained 66.3% of the total phenotypic variations for root rot resistance and three 44.9% for damping-off resistance. Of these QTL loci, two were located close to RFLP markers CDI25 on chromosome 5 (P5) and CT211A on P9. A bacterial artificial chromosome (BAC) library from C. annuum 'CM334' was screened with these two RFLP probes to obtain sequence information around the RFLP marker loci for development of PCR-based markers. CDI25 and CT211 probes identified seven and eight BAC clones, respectively. Nine positive BAC clones containing probe regions were sequenced and used for cytogenetic analysis. One single-nucleotide amplified polymorphism (SNAP) for the CDI25 locus, and two SSRs and cleaved amplified polymorphic sequence (CAPS) for CT211 were developed using sequences of the positive BAC clones. These markers will be valuable for rapid selection of genotypes and map-based cloning for resistance genes against P. capsici.     

Saturation and mapping of a majorFusarium head blight resistance QTL on chromosome 3BS of Sumai 3 wheat

Fusarium head blight (FHB) is a destructive disease in wheat. The major quantitative trait locus (QTL) on 3BS from Sumai 3 and its derivatives has been used as a major source of the resistance to FHB worldwide, but the discrepancy in reported location of the major QTL could block its using in map based cloning and marker assisted selection. In this study, Chinese Spring-Sumai 3 chromosome 3B substitution line was used as resistant parent of the mapping population to reduce the confounded effect of genetic background in Sumai 3. The major QTL region was saturated with the Sequence Tagged Microsatellite (STM) and Sequence Tagged Site (STS) markers. A linkage map of chromosome 3B with 36 markers covering a genetic distance of 112.4 cM was constructed. Twelve new markers were inserted into the chromosome region where the major QTL was located. The average interval distance between markers was 1.5 cM. Multiple QTL Models (MQM) mapping indicated that the major QTL was located in the interval ofXgwm533 — Xsts9-1, and explained 45.6% of phenotypic variation of the resistance to FHB. The SSR (simple sequence repeat) markerXgwm533 and STM markerXstm748tcac are closely linked to the major QTL.     

Substitution mapping of Pup1: a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil

A major QTL for P uptake had previously been mapped to a 13-cM marker interval on the long arm of chromosome 12. To map that major QTL with higher precision and certainty, a secondary mapping population was developed by backcrossing a near-isogenic line containing the QTL from the donor parent to the recurrent parent of low P uptake. Two different mapping strategies have been followed in this study. A conventional QTL mapping approach was based on individual F(2) RFLP data and the phenotypic evaluation of family means in the F(3). The second strategy employed a substitution-mapping approach. Phenotypic and marker data were obtained for 160 F(3) individuals of six highly informative families that differed in the size of donor chromosomal segments in the region of the putative QTL. QTL mapping showed that close to 80% of the variation between families was due to a single QTL, hereafter referred to as Pup1 (Phosphorus uptake 1). Pup1 was placed in a 3-cM interval flanked by markers S14025 and S13126, which is within 1 cM of the position identified in the original QTL mapping experiment. Other chromosomal regions and epistatic effects were not significant. Substitution mapping revealed that Pup1 co-segregated with marker S13126 and that the flanking markers, S14025 and S13752, were outside the interval containing Pup1. The two mapping strategies therefore yielded almost identical results and, in combining the advantages of both, Pup1 could be mapped with high certainty. The QTL mapping appoach showed that the phenotypic variation between families was due to only one QTL without any additional epistacic interactions, whereas the advantage of substitution mapping was to place clearly defined borders around the QTL.     

Genetic analysis of traits distinguishing outcrossing and self-pollinating forms of currant tomato,Lycopersicon pimpinellifolium (Jusl.) Mill

The evolution of inbreeding is common throughout the angiosperms, although little is known about the developmental and genetic processes involved. Lycopersicon pimpinellifolium (currant tomato) is a self-compatible species with variation in outcrossing rate correlated with floral morphology. Mature flowers from inbreeding and outcrossing populations differ greatly in characters affecting mating behavior (petal, anther, and style lengths); other flower parts (sepals, ovaries) show minimal differences. Analysis of genetic behavior, including quantitative trait locus (QTL) mapping, was performed on representative selfing and outcrossing plants derived from two contrasting natural populations. Six morphological traits were analyzed: flowers per inflorescence; petal, anther, and style lengths; and lengths of the fertile and sterile portions of anthers. All traits were smaller in the selfing parent and had continuous patterns of segregation in the F(2). Phenotypic correlations among traits were all positive, but varied in strength. Quantitative trait locus mapping was done using 48 RFLP markers. Five QTL total were found involving four of the six traits: total anther length, anther sterile length, style length, and flowers per inflorescence. Each of these four traits had a QTL of major (>25%) effect on phenotypic variance.     

Molecular Mapping of a Gene for Fertility Restoration of Wild Abortive (WA) Cytoplasmic Male Sterility using a Basmati Rice Restorer Line

The inheritance and molecular mapping of a fertility restorer gene in basmati quality restorer line PRR-78 was carried out using an F₂ mapping population from the cross IR58025A X PRR-78 employing microsatellite markers. Dominant monogenic control of fertility restoration was observed in the F₂, and further confirmed by test cross data. Out of 44 sequence tagged microsatellite (STMS) markers used in the bulked segregant analysis (BSA), four differentiated the fertile bulk from the sterile bulk as well as the two parental lines from each other. One of these markers, RM258 located on chromosome 10, was found linked to the restorer gene at a distance of9.5 cM. Considering the RM258 location, additional STMS (RM171 and RM294A) and sequence tagged site (STS) primers derived from restriction fragment length polymorphic (RFLP) clones (G2155 and C1361) linked to fertility restorer gene(s) in other populations, were also used to find out a marker more tightly linked to the restorer gene. However, of these, RM171, RM294A and G2155 based primers amplified monomorphic fragments between parental lines and no amplification was observed with C1361. Cleaved amplified polymorphic sequence (CAPS) analysis of non-polymorphic STMS and STS markers and random amplified polymorphic DNA (RAPD) analysis using five random primers reportedly linked to restorer gene in other populations, also failed to differentiate the two parents. While, the marker RM258 is being used in the restorer breeding to identify putative restorer lines, search for additional tightly linked markers is underway.     

Quantitative trait loci affecting survival and fertility-related traits in Caenorhabditis elegans show genotype-environment interactions, pleiotropy and epistasis.

We have identified, using composite interval mapping, quantitative trait loci (QTL) affecting a variety of life history traits (LHTs) in the nematode Caenorhabditis elegans. Using recombinant inbred strains assayed on the surface of agar plates, we found QTL for survival, early fertility, age of onset of sexual maturity, and population growth rate. There was no overall correlation between survival on solid media and previous measures of survival in liquid media. Of the four survival QTL found in these two environments, two have genotype-environment interactions (GEIs). Epistatic interactions between markers were detected for four traits. A multiple regression approach was used to determine which single markers and epistatic interactions best explained the phenotypic variance for each trait. The amount of phenotypic variance accounted for by genetic effects ranged from 13% (for internal hatching) to 46% (for population growth). Epistatic effects accounted for 9-11% of the phenotypic variance for three traits. Two regions containing QTL that affected more than one fertility-related trait were found. This study serves as an example of the power of QTL mapping for dissecting the genetic architecture of a suite of LHTs and indicates the potential importance of environment and GEIs in the evolution of this architecture.