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Marker-assisted Selection (marker-assisted + selection)
Selected AbstractsProspects for using marker-assisted breeding to improve maize production in AfricaJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 5 2008Robyn Stevens Abstract Maize (Zea mays L.) production in sub-Saharan Africa has historically been constrained by a number of biotic and abiotic factors, including drought, insects, disease, and weeds. New agricultural research involving genomics and molecular markers may assist plant breeders in developing new varieties that will benefit producers and consumers in this region. Over the past few decades, plant breeders have used molecular markers to identify numerous genomic regions affecting maize production and nutritional value. Marker-assisted selection (MAS) presents the potential to improve the efficiency of plant breeding by allowing for the transfer of these specific genomic regions of interest and accelerating the recovery of the elite parent background. However, to this point, few examples of successful MAS in breeding programs, particularly those with benefits in Africa, have been noted. This review discusses the use of molecular markers in the identification of quantitative trait loci (QTL) affecting the production and nutritional quality of maize, as well as the potential to use the results from the vast number of QTL studies that have been performed in MAS breeding programs. Copyright © 2008 Society of Chemical Industry [source] Variation in the response of melon genotypes to Fusarium oxysporum f.sp. melonis race 1 determined by inoculation tests and molecular markersPLANT PATHOLOGY, Issue 2 2003Y. Burger Screening of genotypes of melon (Cucumis melo) for resistance to wilt caused by Fusarium oxysporum f.sp. melonis is often characterized by wide variability in their responses to inoculation, even under carefully controlled conditions. The variability at the seedling stage of 17 genotypes susceptible to race 1 was examined in growth-chamber experiments. Disease incidence varied from 0 to 100% in a genotype-dependent manner. Using four combinations of light (60 and 90 µE m,2 s,1) and temperatures of (27 and 31°C), only light intensity showed a statistically significant effect. Marker-assisted selection for fusarium resistance breeding using cleaved amplified polymorphic sequence (CAPS) and sequence-characterized amplified region (SCAR) markers were compared using a single set of genotypes that included 24 melon accessions and breeding lines whose genotype regarding the Fom-2 gene was well characterized. The practical value of the markers for discriminating a range of genotypes and clarifying the scoring of phenotypes was also tested using a segregating breeding population which showed codominant SCAR markers to be useful in marker-assisted selection. [source] Mapping of quantitative trait loci affecting eggshell quality on chromosome 9 in an F2 intercross between two chicken lines divergently selected for eggshell strengthANIMAL GENETICS, Issue 5 2009H. Takahashi Summary Broken and cracked eggshells are major causes of significant economic losses to the egg production industry. The quantitative trait loci (QTL) on chromosome 9 influencing the quality of eggshells were identified by analysing an intercross between two parent lines developed from the same founder population by a two-way selection for eggshell strength with non-destructive deformation conducted over 14 generations. Chromosome-wide highly significant (P < 0.01) QTL associated with egg weight (EW), short length of egg (SLE), long length of egg (LLE) and eggshell weight were mapped to the distal region of chromosome 9. Among the QTL affecting EW, SLE and LLE, ovocalyxin-32 was identified as a potential candidate gene influencing eggshell traits. Marker-assisted selection based on these QTL could be used to develop strategies for reducing the breakage and cracking of eggs in commercial layer houses. [source] Relationship of Carbon Isotope Discrimination to Water Use Efficiency and Productivity of Barley Under Field and Greenhouse ConditionsJOURNAL OF AGRONOMY AND CROP SCIENCE, Issue 5 2007A. O. Anyia Abstract This study was conducted to evaluate the application of carbon isotope discrimination (CID) as a selection criterion for improving water use efficiency (WUE) and productivity of barley (Hordeum vulgare L.) under field and drought-stress conditions in a greenhouse. A total of 54 genotypes were screened for variability in CID under field conditions, while 23 genotypes were evaluated under water-deficit conditions in the greenhouse. A survey of leaf CID of 54 genotypes at two field locations showed more than 2.14, difference between extreme genotypes. Significant (P , 0.05) genotypic variation was found in WUE and CID that had a negative strong correlation. There was a negative correlation between leaf CID and aerial biomass in the greenhouse and among six-row genotypes in the field. Correlations between leaf CID across field locations and across irrigation regimes in the greenhouse were significant (experiment 1, r = 0.79 and 0.94 for six- and two-row genotypes), suggesting stability of the CID trait across different environments. Overall, these results indicate the potential of leaf CID as a reliable method for selecting for high WUE and productivity in barley breeding programmes in the Canadian prairies. Further work is currently underway to determine heritability/genetics of leaf CID and application of molecular marker-assisted selection for the traits in barley breeding programmes. [source] Top down preselection using marker assisted estimates of breeding values in dairy cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2004Jörn Bennewitz Summary Top down preselection of young bulls before entering progeny testing has been proposed as a practicable form of marker-assisted selection (MAS), especially in dairy cattle populations with large male paternal half-sib families. Linkage phase between the superior (Q) and the inferior (q) QTL alleles of heterozygous sires (Qq at the QTL) with informative markers is established within each paternal half-sib family and may be used for selection among grand-progeny. If, additionally to sires, bulldams are also genotyped and data from consecutive generations are used, then a marker-assisted best linear unbiased prediction (MA-BLUP) model can be employed to connect the information of all generations and families of a top down design, and to select across all families. A customized ,augmented' sire model (with sires and dams of sires as random effects) is introduced for this purpose. Adapted formulae for the mixed model equations are given and their equivalence to a corresponding animal model and to a certain variant of previously proposed reduced animal models is shown. The application of the augmented sire model in MA-BLUP estimation from daughter-yield deviations and effective daughter contributions is presented. Zusammenfassung Die Top down Vorselektion von jungen Bullen vor der Nachkommenschaftsprüfung ist bekannt als eine praktikable Form der markergestützten Selektion in Milchrinderpopulationen. Die Kopplungsphasen zwischen dem günstigen (Q) und dem ungünstigen (q) Allel eines QTL heterozygoten Vaters (Qq am QTL) mit den Allelen gekoppelter genetischer Marker werden innerhalb Familien festgestellt und können zur Vorselektion von Enkeln genutzt werden. Wenn zusätzlich zu den Vätern die Mütter genotypisiert sind und Daten von mehreren Generationen vorliegen, können MA-BLUP Modelle genutzt werden, um Informationen von mehreren Familien und mehreren Generationen eines Top down Designs zusammenzuführen und um eine Vorselektion über Familien hinweg vorzunehmen. Hierfür wird ein geeignetes ,erweitertes' Vatermodell eingeführt, welches die Väter und zusätzlich die Mütter der Väter als zufällige Effekte enthält. Angepasste Formeln für die gemischten Modell Gleichungen werden beschrieben. Die Gleichheit dieses erweiterten Vatermodells mit einem entsprechenden Tiermodell und mit einer Variante des reduzierten Tiermodells wird gezeigt. Die Anwendung des erweiterten Vatermodells zur MA-BLUP Schätzung mit daughter yield deviations und effective daughter contributions ist beschrieben. [source] Identification and Mapping of Two New Genes Conferring Resistance to Powdery Mildew from Aegilops tauschii (Coss.) SchmalJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 10 2006Xiao-Li Sun Abstract Two powdery mildew resistance genes were identified from Aegilops tauschii accessions Y201 and Y212 and mapped using two different F2 populations derived from the crosses between susceptible accession Y2272 and Y201, and susceptible accession Y2263 and Y212. Genetic analysis of resistance to powdery mildew indicated that the resistance of Y201 was controlled by a single dominant gene, whereas the resistance of Y212 was controlled by a single recessive gene. We have temporarily designated these genes as PmY201 and PmY212, respectively. By bulk segregation analysis, six microsatellite markers including Xgwm174, cfd26, cfd57, cfd102, Xgwm583 and Xgwm639 were found to be linked to PmY201 with genetic distances of 5.2, 7.7, 9.6, 12.5, 20.2 and 22.1 cM, respectively. Five SSR markers, including cfd57, Xgwm182, cfd7, cfd102, and cfd12, were found to be linked to PmY212 with distances of 5.6, 7.2, 11.5, 14.7, and 18.5 cM, respectively. According to the locations of the linked markers, the two resistance genes were located in the 5DL region. Based on the chromosomal locations and the resistance patterns of the two genes, we propose that PmY201 and PmY212 are two novel powdery mildew resistance genes, and are suitable for marker-assisted selection. (Managing editor: Ya-Qin Han) [source] Phenotypic Reaction and Genetic Analysis Using AFLP-derived SCARs for Resistance to Apple ScabJOURNAL OF PHYTOPATHOLOGY, Issue 5 2004E. M. Huaracha Abstract Six sequence-characterized amplified region (SCAR) markers linked to the apple scab resistance gene Vf were evaluated for their utility in marker-assisted selection (MAS) in apple breeding. Of the six SCARs used in this study, ACS-6 was located left of the Vf gene, ACS-7 and ACS-9 co-segregated with Vf, and ACS-8, ACS-4, ACS-5 were located right of the Vf gene. Three families derived from crosses between scab-resistant and scab-susceptible cultivars, including ,Liberty' × ,Deljub', ,Liberty' × ,Delcorf', and ,Florina' ×,Delcorf', previously screened for scab resistance following greenhouse inoculation with the fungal pathogen Venturia inaequalis, were genotyped and compared with phenotypic reactions to scab infection in the field. For each family, a subset progeny of 30 seedlings (propagated onto Malling 9 rootstock and of 7 years old) was selected based on fungal sporulation according to the following scheme. Ten seedlings with no visible scab sporulation on leaves were given phenotypic scores of 0 (deemed resistant); 10 seedlings with moderate scab sporulation were given phenotypic scores of 1.0 (deemed moderately resistant); and 10 seedlings with heavy sporulation were given phenotypic scores of 2.0 (deemed susceptible). DNA was isolated from leaf tissue collected from all 90 seedlings, parents and Malus floribunda 821, the original source of the Vf gene, and screened with all six SCARs. All six SCARs were present in the two scab-resistant parents, ,Liberty' and ,Florina', and M. floribunda 821; while, the two scab-susceptible parents, ,Deljub' and ,Delcorf', lacked all SCARs. All SCARs were either present or absent in varying numbers of seedlings in each progeny with phenotypic ratings of either 0 (resistant) or 1.0 (moderately resistant); while all seedlings with phenotypic ratings of 2.0 (susceptible) lacked all SCARs. The inconsistencies between phenotypic scab ratings and SCAR marker data are discussed. [source] Breeding upland rice for drought resistanceJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 6 2008Jérôme Bernier Abstract Upland rice, produced by smallholder farmers, is the lowest-yielding rice production system. Drought stress is the most severe abiotic constraint in upland rice. Improving productivity of rice in the upland ecosystem is essential to meet rice food security needs of impoverished upland communities. Breeding drought-resistant upland rice is therefore an increasingly important goal. Numerous secondary characters have been suggested to help plant breeders in their selections. Most of these traits are not used in selection, as they are not practical for selection purposes, exhibit low heritability, or are not highly correlated with grain yield. The use of managed drought stress, where drought stress can be imposed at specific periods, has been shown to increase the heritability of yield under stress to values similar to those obtained for yield in well-watered conditions. It has now been demonstrated that drought-tolerant upland rice can be bred by directly selecting for yield in stress environments. The use of molecular markers to perform selection may eventually provide plant breeders with more efficient selection methods. To date, many quantitative trait loci (QTL) for drought resistance have been identified in rice, but few are suitable for use in marker-assisted selection. However, large-effect drought resistance QTL have now been identified and may enable effective use of marker-assisted selection for drought resistance. Copyright © 2008 Society of Chemical Industry [source] A Microsatellite DNA Marker Developed for Identifying Disease-resistant Population of Giant Black Tiger Shrimp, Penaeus monodonJOURNAL OF THE WORLD AQUACULTURE SOCIETY, Issue 2 2009Kuntal Mukherjee White spot disease caused by white spot syndrome virus (WSSV) poses major problems that result in huge economic losses each year in shrimp aquaculture throughout the world. In the present study, microsatellite-based DNA fingerprints have been compared between naturally occurring WSSV disease-resistant and susceptible populations of giant black tiger shrimp, Penaeus monodon, to find DNA markers. For the first time, we report here a microsatellite locus, which, after amplification by polymerase chain reaction, provides a highly statistically significant DNA fingerprint of 71 bp, only in disease susceptible populations but not in disease-resistant shrimp populations, whereas a 317 bp band is common in both. The absence of the former DNA marker will be very useful to identify disease-resistant broodstock of P. monodon for marker-assisted selection in breeding programs to generate disease-free shrimps (P. monodon) in the aquaculture industry. [source] Isolation and characterization of microsatellite loci from a commercial cultivar of Musa acuminataMOLECULAR ECOLOGY RESOURCES, Issue 2 2006SILVANA CRESTE Abstract A genomic library from the commercial diploid cultivar ,Ouro' (Musa acuminata), enriched for CT- and GT-repeats, was used to isolate and characterize 23 microsatellite loci. These loci were tested in 10 Musa genotypes, representing various Musa genomic groups with distinct ploidy level. The number of alleles per locus ranged from one to seven, and 20 loci were highly informative. Four loci appeared to amplify B genome-specific alleles, while three loci seemed to be absent in the B genome. The polymorphism revealed by these loci will be extremely useful for genetic mapping, marker-assisted selection, germplasm characterization and evolutionary studies in Musa. [source] Development and characterization of novel tetra-, tri-, and dinucleotide microsatellite markers in rainbow trout (Oncorhynchus mykiss)MOLECULAR ECOLOGY RESOURCES, Issue 2 2005I. B. SPIES Abstract We discuss the development and characterization of 40 polymorphic rainbow trout (Oncorhynchus mykiss) microsatellite loci. We used enriched libraries to isolate 14 dinucleotide, seven trinucleodide, eight compound di/tetranucleotide, and 11 tetranucleotide loci. These markers will be useful for selective breeding via marker-assisted selection, population genetics studies, parentage analysis, and have already been used for genome mapping. [source] Identifying genetic components controlling fertility in the outcrossing grass species perennial ryegrass (Lolium perenne) by quantitative trait loci analysis and comparative geneticsNEW PHYTOLOGIST, Issue 3 2008I. P. Armstead Summary ,,Mutational load and resource allocation factors and their effects on limiting seed set were investigated in ryegrass by comparative mapping genomics and quantitative trait loci (QTL) analysis in two perennial ryegrass (Lolium perenne) mapping families sharing common genetic markers. ,,Quantitative trait loci for seed-set were identified on chromosome (LG) 7 in both families and on LG4 of the F2/WSC family. On LG7, seed-set and heading date QTLs colocalized in both families and cannot be unequivocally resolved. Comparative genomics suggests that the LG7 region is syntenous to a region of rice LG6 which contains both fertility (S5n) and heading date (Hd1, Hd3a) candidate genes. The LG4 region is syntenous to a region of rice LG3 which contains a fertility (S33) candidate gene. QTL maxima for seed-set and heading date on LG4 in the F2/WSC family are separated by c. 8 cm, indicating distinct genetic control. ,,Low seed set is under the control of recessive genes at both LG4 and LG7 locations. ,,The identification of QTLs associated with seed set, a major component of seed yield in perennial ryegrass, indicates that mutational load associated with these genomic regions can be mitigated through marker-assisted selection. [source] A major QTL for resistance of rice to the parasitic plant Striga hermonthica is not dependent on genetic backgroundPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 5 2009Philip J Swarbrick Abstract BACKGROUND: The use of Striga -resistant germplasm is likely to be a cost-effective control strategy for preventing loss of yield owing to Striga. Previously, the authors identified quantitative trait loci (QTL) for resistance in rice to Striga hermonthica (Del.) Benth. in backcross inbred lines (BILs) derived from a cross between two cultivars Nipponbare and Kasalath. It is essential to validate QTL in different environments and/or genetic backgrounds to develop molecular markers linked to resistance QTL for use in marker-assisted selection (MAS) programmes. This study aimed to establish whether a large-effect Kasalath-derived resistance QTL allele on chromosome 4 of rice also conferred resistance in a different mapping population derived from a cross between Koshihikari and Kasalath, and to identify any further Striga resistance QTL. RESULTS: Three Striga resistance QTL were detected in Koshihikari,Kasalath BILs, two of which were derived from the Kasalath allele and one from the Koshihkari allele. The largest QTL (Kasalath allele) explained 16% of the variation in the mapping population and was located on chromosome 4. Comparison between these data and those of the authors' previous analysis revealed that the confidence intervals of the chromosome-4 QTL in the Nipponbare,Kasalath cross and the Kasalath,Koshihikari cross overlapped between 6.5 Mbp and 8 Mbp on the physical rice genome assembly. CONCLUSION: This study has both verified and narrowed down the position of a Striga resistance QTL of major effect, and demonstrated that it may be a tractable target for MAS. Copyright © 2009 Society of Chemical Industry [source] Epigenetic chromatin modifiers in barley: I. Cloning, mapping and expression analysis of the plant specific HD2 family of histone deacetylases from barley, during seed development and after hormonal treatmentPHYSIOLOGIA PLANTARUM, Issue 3 2009Kyproula Demetriou Epigenetic phenomena have been associated with modifications of chromatin structure. These are achieved, in part, by histone post-translational modifications including acetylations and deacetylations, the later being catalyzed by histone deacetylaces (HDACs). Eukaryotic HDACs are grouped into three major families, RPD3/HDA1, SIR2 and the plant-specific HD2. HDAC genes have been analyzed from model plants such as Arabidopsis, rice and maize and have been shown to be involved in various cellular processes including seed development, vegetative and reproductive growth and responses to abiotic and biotic stress, but reports on HDACs from other crops are limited. In this work two full-length cDNAs (HvHDAC2-1 and HvHDAC2-2) encoding two members of the plant-specific HD2 family, respectively, were isolated and characterized from barley (Hordeum vulgare), an agronomically important cereal crop. HvHDAC2-1 and HvHDAC2-2 were mapped on barley chromosomes 1H and 3H, respectively, which could prove useful in developing markers for marker-assisted selection in breeding programs. Expression analysis of the barley HD2 genes demonstrated that they are expressed in all tissues and seed developmental stages examined. Significant differences were observed among tissues and seed stages, and between cultivars with varying seed size, suggesting an association of these genes with seed development. Furthermore, the HD2 genes from barley were found to respond to treatments with plant stress-related hormones such as jasmonic acid (JA), abscisic acid (ABA) and salicylic acid (SA) implying an association of these genes with plant resistance to biotic and abiotic stress. The expression pattern of HD2 genes suggests a possible role for these genes in the epigenetic regulation of seed development and stress response. [source] Quantitative trait loci and epistatic interactions in barley conferring resistance to net type net blotch (Pyrenophora teres f. teres) isolatesPLANT BREEDING, Issue 4 2010S. Gupta With 2 figures and 5 tables Abstract Net type net blotch (NTNB) is an important barley disease in Australia and elsewhere, with significant yield reduction. This trait is important in selection along with other traits of quality and agronomic value. Two-hundred doubled-haploid lines were generated through anther culture from a cross between ,Pompadour' and ,Stirling'. Quantitative trait loci (QTL) were identified against five isolates of Pyrenophora teres f. teres, which represent virulences across Australia. QTL were mapped on chromosomes 3H and 6H using simple sequence repeat (SSR) markers. The resistance locus on 6H was detected with all isolates while the 3H locus was detected with two isolates. The 6H QTL from ,Pompadour' contributed resistance to isolates 97NB1, 95NB100 and NB81, whereas 6H QTL from ,Stirling' contributed resistance to isolates NB50 and NB52B. The 3H QTL from ,Pompadour' contributed resistance to NB50 and NB52B. Significant epistatic interactions were detected between QTL on 3H and 6H. These resistance QTL are a useful resource and identifying closely linked SSR markers with allelic combinations will facilitate in marker-assisted selection to develop NTNB resistant breeding lines. [source] Association mapping of straighthead disorder induced by arsenic in Oryza sativaPLANT BREEDING, Issue 6 2009H. A. Agrama Abstract Straighthead is a physiological disorder in rice (Oryza sativa L.) resulting in sterile florets, poorly developed panicles and yield loss. Because of its sporadic nature and unidentified causes for the disorder, molecular marker assisted selection is essential for resistance improvement in breeding programmes. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association mapping to identify genetic regions associated with straighthead disorder using 547 accessions of germplasm from the USDA rice core collection. Straighthead was evaluated in arsenic treated soil and genotyping was conducted with 75 molecular markers covering the entire rice genome about every 25 cM. A mixed-linear model approach combining the principal component assignments with kinship estimates proved to be particularly promising for association mapping. The extent of linkage disequilibrium was described among the markers. Six markers were found to be significantly associated with straighthead, explaining 35% of the total phenotypic variation. However, only two SSR markers, RM413 and RM277 on chromosome 5 and 12, respectively, have a significant association with low rating indicating straighthead resistance. Confirmation of the marker-straighthead association using segregating populations is necessary before marker-assisted selection can be applied. [source] Molecular mapping of genic male-sterile genes ms15, ms5 and ms6 in tetraploid cottonPLANT BREEDING, Issue 2 2009D. Chen Abstract Two genic male sterile (GMS) lines, Lang-A conditioned by ms15 and Zhongkang-A conditioned by ms5ms6 duplicate recessive genes in Gossypium hirsutum L., were chosen to map GMS genes. These two lines were crossed with Gossypium barbadense cv. ,Hai7124' to produce segregating populations. The ms15 gene was mapped on chromosome 12, and was flanked by two simple sequence repeat (SSR) markers, NAU2176 and NAU1278, with a genetic distance of 0.8 and 1.9 cM respectively. The ms5 and ms6 genes were mapped to one pair of homoeologous chromosomes, ms5 on chromosome 12 flanked by three SSR markers, NAU3561, NAU2176 and NAU2096, with genetic distances of 1.4, 1.8 and 1.8 cM, respectively, and ms6 on chromosome 26 flanked by two SSR markers, BNL1227 and NAU460, with a genetic distance of 1.4 and 1.7 cM respectively. These tightly linked markers with the ms15, ms5 and ms6 genes can be used in the marker-assisted selection among segregating populations in a breeding programme, and provide the foundation for gene isolation by map-based cloning for these three genes. [source] Identification of a SCAR marker linked to a recessive male sterile gene (Tems) and its application in breeding of marigold (Tagetes erecta)PLANT BREEDING, Issue 1 2009Y. H. He Abstract In marigold, an F2 segregation population of 167 plants was constructed from a cross of a line (M525A) carrying the male sterility trait × an inbred line (f53f). In line M525A, the male sterility trait was controlled by the recessive gene, Tems. The intersimple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) techniques combined with bulked segregant analysis were used to develop markers linked to the trait. From a survey of the 38 ISSR primers and 170 SRAP primer combinations, only one SRAP marker that was closely linked to the target trait was identified and successfully converted into sequence characterized amplified region (SCAR) marker that was located within 2.4 cM from Tems locus. The marker was validated with five other two-type lines and in each case the male fertile plants were reliably identified. This SCAR marker therefore permits the efficient marker-assisted selection of male sterile individuals in breeding programmes of marigold and will greatly facilitate the breeding of F1 cultivars. [source] Development of molecular markers linked to the wheat powdery mildew resistance gene Pm4b and marker validation for molecular breedingPLANT BREEDING, Issue 2 2008Y. J. Yi Abstract Powdery mildew, caused by Blumeria graminis (DC.) E.O. Speer f. sp. tritici, is an important disease in wheat (Triticum aestivum L.). Bulk segregant analysis (BSA) was employed to identify SRAP (sequence-related amplified polymorphism), sequence tagged site (STS) and simple sequence repeat (SSR) markers linked to the Pm4b gene, which confers good resistance to powdery mildew in wheat. Out of 240 SRAP primer combinations tested, primer combinations Me8/Em7 and Me12/Em7 yielded 220-bp and 205-bp band, respectively, each of them associated with Pm4b. STS- 241 also linked to Pm4b with a genetic distance of 4.9 cM. Among the eight SSR markers located on wheat chromosome 2AL, Xgwm382 was found to be polymorphic and linked to Pm4b with a genetic distance of 11.8 cM. Further analysis was carried out using the four markers to investigate marker validation for marker-assisted selection (MAS). The results showed that a combination of the linked markers STS,241, Me8/Em7,220 and Xgwm382 could be used for marker-assisted selection of the resistance gene Pm4b in wheat breeding programmes. [source] Development of STS markers and QTL validation for common bacterial blight resistance in common beanPLANT BREEDING, Issue 1 2008S. Liu Abstract Common bacterial blight (CBB) of common bean (Phaseolus vulgaris L.), is one of the major diseases that decrease yield and quality. A major quantitative trait locus (QTL) for CBB resistance from line XAN 159 was transferred into two bean lines, HR45 and HR67. Previous studies identified that two markers are linked to this QTL but the chromosome location was not consistent. To identify more tightly linked markers and to verify the chromosome location, 65 additional markers were mapped using 81 recombinant inbred lines (RILs) derived from a cross HR67 × OAC95-4. The QTL was mapped to a 13 cM region on chromosome 1 and defined by eight molecular markers that explained 25,52% of the phenotypic variation. Six tightly linked amplified fragment length polymorphism markers (0.6,9.7 cM from the QTL peak) were converted into seven sequence tagged site markers, three of which were mapped to this QTL. Five tightly linked markers were used to screen 907 F2 plants derived from a cross HR45 × ,OAC Rex' and four of them were linked to each other within 4.2 cM. These markers may be useful in marker-assisted selection and map-based cloning of this major QTL. [source] Molecular markers for Ve1 and Ve2 Verticillium resistance genes from Italian tomato germplasmPLANT BREEDING, Issue 6 2007N. Acciarri Abstract The so-called Rosa (= pink) tomatoes, which are typically grown in the Southern Italian area, are characterized by the pink colour of the fruit, due to the gene y, colourless fruit skin. In a preliminary survey, it was found that among these Rosa tomatoes there were some ,Rosa di Sorrento' local landraces showing resistance to Verticillium wilt (race 1). In tomato, resistance to race 1 of V. dahliae and V. albo-atrum is conferred by two strictly associated genes, Ve1 and Ve2, which independently confer resistance to the same pathogen. The development of two new markers for Ve1 and Ve2, based respectively on selective allele-specific PCR amplification and on a PCR amplification followed by enzymatic restriction, is reported. These two markers allow the identification of both allelic forms at the Ve loci and they are of potential interest for use in marker-assisted selection. Furthermore, ,Rosa di Sorrento'-resistant lines have the same resistance alleles as those found in the Ve -resistant cultivars. [source] Automation of DNA marker analysis for molecular breeding in crops: practical experience of a plant breeding companyPLANT BREEDING, Issue 4 2007C. Dayteg Abstract In modern plant breeding, DNA marker analyses are of increasing importance and, as the methods become more widely adopted, the capacity for high-throughput analyses at low cost is crucial for its practical use. Automation of the analysis processes is a way to meet these requirements. In order to achieve this, while keeping adequate flexibility in the analysis processes, Svalöf Weibull AB (SW) has developed a fully automated polymerase chain reaction system. It has been evaluated on barley and canola lines and is capable of analysing up to 2200 samples per day at a cost of 0,24 , per analysis for marker-assisted selection and quality control of genetically modified organisms. A detailed description of this system is given, and improvements to the throughput and applications are discussed. [source] Development of SCAR markers for identification of stem rust resistance gene Sr31 in the homozygous or heterozygous condition in bread wheatPLANT BREEDING, Issue 6 2006B. K. Das Abstract The stem rust resistance gene Sr31, transferred from rye (Secale cereale) into wheat (Triticum aestivum L.) imparts resistance to all the virulent pathotypes of stem rust (Puccinia graminis f. sp. tritici) found in India. Wheat genotypes including carriers and non-carriers of the Sr31 gene were analysed using arbitrary primed polymerase chain reaction (AP-PCR). AP-PCR markers viz. SS30.2580(H) associated with the Sr31 gene and SS26.11100 associated with the allele for susceptibility were identified. Linkage between the markers and phenotypes was confirmed by analysing an F2 population obtained from a cross between a resistant and a susceptible genotype. The markers were tightly linked to the respective alleles. Both the AP-PCR markers were converted into sequence characterized amplified region (SCAR) markers, viz. SCSS30.2576 and SCSS26.11100 respectively. The markers were validated in two more segregating populations and 49 wheat genotypes. Using both markers it was possible to distinguish the homozygous from the heterozygous carriers of the Sr31 gene in the F2 generation. The markers developed in this study can be used for pyramiding of the Sr31 gene with other rust resistance genes and in marker-assisted selection. [source] Pyramiding of Xa7 and Xa21 for the improvement of disease resistance to bacterial blight in hybrid ricePLANT BREEDING, Issue 6 2006J. Zhang Abstract ,Minghui 63' is a restorer line widely used in hybrid rice production in China for the last two decades. This line and its derived hybrids, including ,Shanyou 63', are susceptible to bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo). To improve the bacterial blight resistance of hybrid rice, two resistance genes Xa21 and Xa7, have been introgressed into ,Minghui 63' by marker-assisted selection and conventional backcrossing, respectively. The single resistance gene-introgressed lines, Minghui 63 (Xa21) and Minghui 63 (Xa7) had higher levels of resistance to bacterial blight than their derived hybrids, Shanyou 63 (Xa21) or Shanyou 63 (Xa7). Both Xa21 and Xa7 showed incomplete dominance in the heterozygous background of rice hybrids by infection with GX325 and KS-1-21. The improved restorer lines, with the homozygous genotypes, Xa21Xa21 or Xa7Xa7, were more resistant than their hybrids with the heterozygous genotypes Xa21xa21 or Xa7xa7. To further enhance the bacterial blight resistance of ,Minghui 63' and its hybrids, Xa21 and Xa7 were pyramided into the same background using molecular marker-aided selection. The restorer lines developed with the resistance genes Xa21 and Xa7, and their derived hybrids were evaluated for resistance after inoculation with 10 isolates of pathogens from China, Japan and the Philippines, and showed a higher level of resistance to BB than the restorer lines and derived hybrids having only one of the resistance genes. The pyramided double resistance lines and their derived hybrids have the same high level of resistance to BB. These results clearly indicate that pyramiding of dominant genes is a useful approach for improving BB resistance in hybrid rice. [source] Potential for effective marker-assisted selection of three quantitative trait loci conferring adult plant resistance to powdery mildew in elite wheat breeding populationsPLANT BREEDING, Issue 5 2006D. M. Tucker Abstract Three quantitative trait loci (QTL) associated with adult plant resistance (APR) to powdery mildew (Blumeria graminis) in wheat (Triticum aestivum) cultivar ,Massey' were mapped in a previous study. The three QTL were located on chromosomes 2A, 2B and 1B, and explained 50% of the total phenotypic variation. A 293 recombinant inbred line (RIL) breeding population (UJ) derived from the cross of ,USG 3209', a derivative of ,Massey', and ,Jaypee' was used to evaluate the potential effectiveness of marker-assisted selection (MAS) for APR. Powdery mildew severities of the 293 UJ RILs were evaluated in 2002 (F5 : 6) and 2003 (F6 : 7) under natural disease pressure in the field. The 293 RILs were also evaluated for disease severity in a 2004 (F7 : 8) greenhouse experiment using a composite of five different isolates of B. graminis. Selection of RILs possessing the QTL on chromosome 2A, and to a lesser extent, the one on chromosome 1B was effective in identifying powdery mildew resistance in both greenhouse and field experiments. Overall, selecting RILs with QTL on chromosomes 2A and 2B was most successful in identifying highly resistant RILs, which had mean mildew severities of 4.4% and 3.2% in 2002 and 2003 field experiments, respectively. Breeders implementing MAS programs for APR to powdery mildew via selection of RILs containing the two QTL on chromosomes 2A and 2B likely will obtain RILs having high levels of resistance in the field, however combining all three QTL may ensure greater durability. [source] QTL analysis of resistance to Fusarium head blight in wheat using a ,Wangshuibai'-derived populationPLANT BREEDING, Issue 4 2005M. Mardi Abstract Fusarium head blight (FHB) is a devastating disease that reduces the yield, quality and economic value of wheat. For quantitative trait loci (QTL) analysis of resistance to FHB, F3 plants and F3:5 lines, derived from a ,Wangshuibai' (resistant)/,Seri82'(susceptible) cross, were spray inoculated during 2001 and 2002, respectively. Artificial inoculation was carried out under field conditions. Of 420 markers, 258 amplified fragment length polymorphism and 39 simple sequence repeat (SSR) markers were mapped and yielded 44 linkage groups covering a total genetic distance of 2554 cM. QTL analysis was based on the constructed linkage map and area under the disease progress curve. The analyses revealed a QTL in the map interval Xgwm533-Xs18/m12 on chromosome 3BS accounting for up to 17% of the phenotypic variation. In addition, a QTL was detected in the map interval Xgwm539-Xs15/m24 on chromosome 2DL explaining up to 11% of the phenotypic variation. The QTL alleles originated from ,Wangshuibai' and were tagged with SSR markers. Using these SSR markers would facilitate marker-assisted selection to improve FHB resistance in wheat. [source] Linkage map construction and mapping QTL for cotton fibre quality using SRAP, SSR and RAPDPLANT BREEDING, Issue 2 2005Z. Lin Abstract Tetraploid cotton is one of the most extensively cultivated species. Two tetraploid species, Gossypium hirsutum L. and G. barbadense L., dominate the world's cotton production. To better understand the genetic basis of cotton fibre traits for the improvement of fibre quality, a genetic linkage map of tetraploid cotton was constructed using sequence-related amplified polymorphisms (SRAPs), simple sequence repeats (SSRs) and random amplified polymorphic DNAs (RAPDs). A total of 238 SRAP primer combinations, 368 SSR primer pairs and 600 RAPD primers were used to screen polymorphisms between G. hirsutum cv. Handan208 and G. barbadense cv. Pima90 which revealed 749 polymorphic loci in total (205 SSRs, 107 RAPDs and 437 SRAPs). Sixty-nine F2 progeny from the interspecific cross of ,Handan208'×,Pima90' were genotyped with the 749 polymorphic markers. A total of 566 loci were assembled into 41 linkage groups with at least three loci in each group. Twenty-eight linkage groups were assigned to corresponding chromosomes by SSR markers with known chromosome locations. The map covered 5141.8 cM with a mean interlocus space of 9.08 cM. A × test for significance of deviations from the expected ratio (1: 2: 1 or 3: 1) identified 135 loci (18.0%) with skewed segregation, most of which had an excess of maternal parental alleles. In total, 13 QTL associated with fibre traits were detected, among which two QTL were for fibre strength, four for fibre length and seven for micronaire value. These QTL were on nine linkage groups explaining 16.18-28.92% of the trait variation. Six QTL were located in the A subgenome, six QTL in the D subgenome and one QTL in an unassigned linkage group. There were three QTL for micronaire value clustered on LG1, which would be very useful for improving this trait by molecular marker-assisted selection. [source] Single nucleotide polymorphism genotyping of the barley waxy gene by polymerase chain reaction with confronting two-pair primersPLANT BREEDING, Issue 3 2004E. Domon Abstract A high-throughput single nucleotide polymorphism (SNP) genotyping procedure was developed to select amylose-free barley mutants whose waxy genes had a C- to T-base substitution in exon 5, which converted Gln-89 of the wild-type gene into a termination codon. An F2 population carrying an amylose-free waxy gene was checked for segregation. Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) produced allele-specific PCR products that have different sizes and are inherited in a co-dominant manner. Two alleles of the barley waxy gene with SNP were correctly identified in parental strains using the PCR-CTPP procedure. Segregation of the SNP as detected by PCR-CTPP in an F2 population fitted the expected 1:2:1 ratio. The PCR-CTPP procedure can provide a time saving and cost-effective alternative to derived cleaved amplified polymorphic sequence in marker-assisted selection. [source] Molecular marker analysis of kernel size and shape in bread wheatPLANT BREEDING, Issue 5 2003B. B. Dholakia Abstract The economic value of wheat grain is determined by the kernel morphology which is an important parameter for manufacturing different food products requiring specific grain characteristics. Although kernel size and shape have emerged as important breeding objectives, not much information is available about the number or location of associated gene(s)/quantitative trait loci. In the present study, a recombinant inbred line population of 106 plants (F7) was phenotyped for four traits, namely kernel length, width, weight and factor form density (FFD) and genotyped with different polymerase chain reaction-based markers. Transgressive segregants were observed for all the traits and genetic correlation studies showed positive correlations between the majority of the traits. The number of markers associated with each trait ranged from two to nine and the phenotypic contribution by an individual marker ranged from 3.3 to 16.6%. Many of the markers showed linkage to more than one trait. Strategies for improving the wheat grain quality traits and the utility of such markers in marker-assisted selection (MAS) efforts are discussed. [source] Microsatellite marker for yellow rust resistance gene Yr5 in wheat introgressed from spelt wheatPLANT BREEDING, Issue 6 2002Q. Sun Abstract Yellow rust of wheat caused by Puccinia striiformis f sp. tritici has been periodically epidemic and severely damaged wheat production in China and throughout the world. Breeding for resistant cultivars has been proved to be an effective way to resolve the problem. A yellow rust resistance gene, Yr5, derived from Triticum spelta shows immunity or high resistance to the most popular isolates Tiaozhong 30 and 31 in China. Establishment of DNA markers for the Yr5 gene will facilitate marker-assisted selection and gene pyramiding in the breeding programme. Since the Yr5 gene was cytologically located on the long arm of chromosome 2B, By33, the donor of Yr5, was crossed and backcrossed with the susceptible line 441, and BC3F2 and BC3F3 segregating populations were screened for polymorphism by using 11 microsatellite primers mapped on chromosome 2B. A marker, Xgwm501-195 bp/160 bp, was found to be linked to Yr5, with a genetic distance of 10.5-13.3 cM. 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