Mapping spot blotch resistance genes in four barley populations

Bipolaris sorokiniana (teleomorph: Cochliobolus sativus) is the fungal pathogen responsible for spot blotch in barley (Hordeum vulgare L.) and occurs worldwide in warmer, humid growing conditions. Current Australian barley varieties are largely susceptible to this disease and attempts are being made to introduce sources of resistance from North America. In this study we have compared chromosomal locations of spot blotch resistance reactions in four North American two-rowed barley lines; the North Dakota lines ND11231-12 and ND11231-11 and the Canadian lines TR251 and WPG8412-9-2-1. Diversity Arrays Technology (DArT)-based PCR, expressed sequence tag (EST) and SSR markers have been mapped across four populations derived from crosses between susceptible parental lines and these four resistant parents to determine the location of resistance loci. Quantitative trait loci (QTL) conferring resistance to spot blotch in adult plants (APR) were detected on chromosomes 3HS and 7HS. In contrast, seedling resistance (SLR) was controlled solely by a locus on chromosome 7HS. The phenotypic variance explained by the APR QTL on 3HS was between 16 and 25% and the phenotypic variance explained by the 7HS APR QTL was between 8 and 42% across the four populations. The SLR QTL on 7HS explained between 52 to 64% of the phenotypic variance. An examination of the pedigrees of these resistance sources supports the common identity of resistance in these lines and indicates that only a limited number of major resistance loci are available in current two-rowed germplasm

Genetic mapping of gray leaf spot resistance genes in maize

Thesis (PhD)--Stellenbosch University, 2000.ENGLISH ABSTRACT: Gray leaf spot (GLS) of maize, caused by the fungus Cercospora zeae-maydis, can reduce grain yields by up to 60% and it is now recognized as one of the most significant yield-limiting diseases of maize in many parts of the world. The most sustainable and long-term management strategy for GLS will rely heavily on the development of high-yielding, locally adapted GLS resistant hybrids. Molecular markers could be useful to plant breeders to indirectly select for genes affecting GLS resistance and to identify resistance genes without inoculation and at an early stage of plant development. Only two studies in the USA have examined quantitative trait loci (QTL) association with GLS resistance. The aim of this study was to map GLS resistance genes in a resistant Seed Co LTD, Zimbabwean inbred line. Molecular markers linked to the GLS resistance QTL were identified by using the amplified fragment length polymorphism (AFLP) technique together with bulked segregant analysis. Eleven polymorphic AFLP fragments were identified and converted to sequence-specific PCR (polymerase chain reaction) markers. Eight of the 11 converted AFLP markers were added to the maize marker database of the University of Stellenbosch. Five of the 8 converted AFLP markers were polymorphic between the resistant and the susceptible parent. They were amplified on the DNA of 230 plants of a segregating F2 population and linkage analysis was performed with MAPMAKER/EXP. Two linkage groups consisting of two markers each, with a linkage distance of 10.4 cM (LOD 22.83) and 8.2 cM (LOD 55.41) between the two markers, were identified. QTL mapping with MAPMAKER/QTL confirmed the presence of QTL in both linkage groups. Two publicly available recombinant inbred families (Burr et a/., 1988) were used to localize the converted AFLP markers on the genetic map of maize. The QTL, which were identified with the AFLP markers, were mapped to chromosomes 1 and 5. Another AFLP marker was mapped to chromosome 2 and a further to chromosome 3. To obtain more precise localizations of the QTL on chromosomes 1 and 5, sequence-tagged site markers and microsatellite markers were used. The markers were amplified on the DNA of the 230 plants of the F2 population and linkage analysis was performed with MAPMAKER/EXP. The order of the markers was in agreement with the UMC map of the Maize Genome Database. Interval mapping using MAPMAKERlQTL and composite interval mapping using QTL Cartographer were performed. The QTL on chromosome 1 had a LOD score of 21 and was localized in bin 1.05/06. A variance of 37% was explained by the QTL. Two peaks were visible for the QTL on chromosome 5, one was localized in bin 5.03/04 and the other in bin 5.05/06. Both peaks had a LOD score of 5 and 11% of the variance was explained by the QTL. To test the consistency of the detected QTL, the markers flanking each QTL were amplified on selected plants of two F2 populations planted in consecutive years and regression analysis was performed. Both the QTL on chromosome 1 and the QTL on chromosome 5 were detected in these populations. Furthermore, the presence of a QTL on chromosome 3 was confirmed with these populations. A variance of 8 -10% was explained by the QTL on chromosome 3. In this study, a major GLS resistance QTL was thus mapped on chromosomes 1 and two minor GLS resistance QTL were mapped on chromosomes 3 and 5 using a resistant Seed Co LTD, Zimbabwean inbred line. Markers were identified which could be used in a marker-assisted selection program to select for the GLS resistance QTL.AFRIKAANSE OPSOMMING: Grys blaarvlek (GBV) van mielies, veroorsaak deur die swam Cercospora zeaemaydis, kan graanopbrengs met tot 60% verlaag en word beskou as een van die vernaamste opbrengs-beperkende siektes wêreldwyd. Die toepaslikste langtermyn stragtegie vir GBV beheer sal wees om plaaslike mieliebasters met hoë opbrengs en GBV weerstand te ontwikkel. Molekulêre merkers kan nuttig deur plantetelers gebruik word om weerstandsgene te selekteer. Seleksie is moontlik in die afwesigheid van inokolum en op 'n vroeë stadium van plant ontwikkeling. Slegs twee vorige studies (in die VSA) het kwantitatiewe-kenmerk-Iokusse (KKL), vir GBVweerstand ondersoek. Die doel van hierdie studie was om die GBV weerstandsgene in 'n weerstandbiedende ingeteelde lyn (Seed Co BPK, Zimbabwe) te karteer. Molekulêre merkers gekoppel aan die GBV weerstands KKL is geïdentifiseer deur gebruik te maak van die geamplifiseerde-fragmentlengte-polimorfisme- (AFLP-) tegniek en gebulkte-segregaat-analise. Elf polimorfiese merkers is geïdentifiseer en omgeskakel na volgorde-spesifieke PKR (polimerase kettingreaksie) merkers. Agt van die elf omgeskakelde AFLP-merkers is by die mieliemerker databasis van die Universiteit van Stellenbosch gevoeg. Vyf van die 8 omgeskakelde AFLP-merkers was polimorfies tussen die bestande en vatbare ouers. Hulle is geamplifiseer op die DNA van 230 plante van 'n segregerende F2-populasie en is gebruik in 'n koppelingstudie met MAPMAKER/EXP. Twee koppelingsgroepe, elk bestaande uit twee merkers, met onderskeidelik koppelingsafstande van 10.4 eM (LOD 22.83) en 8.2 eM (LOD 55.41) tussen die merkers, is geïdentifiseer. KKL-kartering het getoon dat KKL in albei koppelingsgroepe aanwesig is. Twee kommersieël beskikbare, rekombinant-ingeteelde families (Burr et aI., 1988) is gebruik om die omgeskakelde AFLP-merkers op die mielie genetiese kaart te plaas. Die KKL wat met die AFLP-merkers geïdentifiseer is, is gekarteer op chromosome 1 en 5. 'n Verdere AFLP-merker is op chromosoom 2 gekarteer en 'n ander op chromosoom 3. Ten einde die KKL op chromosome 1 en 5 meer akkuraat te karteer, is volgordege- etikeerde en mikrosatelliet merkers gebruik. Die merkers is geamplifiseer op die DNA van die 230 plante van die F2-populasie en koppelings-analises is uitgevoer. Die volgorde van die merkers was dieselfde as die van die UMC-kaart in die Mielie Genoom Databasis. Interval kartering met MAPMAKER/QTL en komposiet interval kartering met QTL Cartographer is uitgevoer. Die KKL op chromosoom 1 het 'n LOD-telling van 21 gehad en is in bin 1.05/06 geplaas. Die KKL was verantwoordelik vir 37% van die variansie. Twee pieke was onderskeibaar vir die KKL op chromosoom 5, een in bin 5.03/04 geleë en die ander in bin 5.05/06. Elke piek het 'n LOD-telling van 5 gehad en die twee KKL was verantwoordelik vir 11% van die variansie. Om die herhaalbaarheid van die effek van die KKL te toets is die merkers naaste aan elke KKL geamplifiseer op geselekteerde plante van twee F2-populasies wat in opeenvolgende jare geplant is. Regressie analise is op die data gedoen. Beide die KKL op chromosoom 1 en die KKL op chromosoom 5 kon in hierdie populasies geïdentifiseer word. Verder kon die aanwesigheid van 'n verdere KKL op chromosoom 3 in hierdie populasies bevestig word. Laasgenoemde KKL was verantwoordelik vir 8-10% van die totale variansie. In hierdie studie is daar dus 'n hoof GBV-weerstands KKL gekarteer op chromosoom 1 en twee kleiner GBV-weerstands KKL gekarteer op chromosome 3 en 5. Merkers is geïdentifiseer wat moontlik in merker-gebaseerdetelingsprogramme gebruik kan word om plante te selekteer wat die GBVweerstands KKL het

Molecular markers for quantitative trait loci (QTLs) in maize gray leaf spot (GLS) resistance

Thesis (M.Sc.) -- University of Stellenbosch, 1998.Full text to be digitised and attached to bibliographic record

Chromosome composition of an F2 Triticum aestivum x T. turgidum spp. durum cross analysed by DArT markers and MCFISH

This study has employed multicolour fluorescence in situ hybridisation and Diversity Array Technology markers to determine the segregation of parental A, B and D genome material into the progeny of a cross between a hexaploid bread wheat (Triticum aestivum L. var. 2-49) and a tetraploid durum wheat (T. turgidum L. spp. durum (Desf.) var. Bellaroi). In the F2 progeny from a 2-49/Bellaroi cross, 82 out of 83 F2 plants investigated with DArT analysis had some D genome material, principally as entire chromosomes, while 40 plants had at least one complete copy of all seven D genome chromosomes. Twelve plants containing partial D chromosomes were identified. MCFISH analysis of 26 additional F2 plants of the same cross showed that all 26 plants contained varying amounts of D genome material of which three carried single A-D translocations. In addition two telocentric D genome chromosomes were detected. The D genome content of each line and the breakpoint positions of the three A-D translocations were confirmed with DArT marker analysis. Overall results indicate a random recombination of A and B genome loci from the hexaploid female parent and the tetraploid male parent in this F2 population and a significant retention of the maternal D genome material. This study illustrates that the combined application of the MCFISH and DArT techniques provides a powerful approach for the analysis of crosses between cereal genotypes of different ploidy

Strategies for fine mapping QTLs for crown rot resistance in wheats

[Introduction]: Crown rot (causal organism Fusarium pseudograminearum) is of great significance to wheat yields within Australia, with losses estimated at $56M per annum. As part of the Australian Winter Cereals Molecular Marker Project (AWCMMP), our group has been responsible for identifying molecular markers for quantitative trait loci (QTLs) that contribute to crown rot resistance. Using a number of double-haploid mapping populations, we have identified genomic regions that are associated with resistance. While the markers flanking these QTLs will be of use to breeding programs for marker assisted selection, how these QTLs function in conferring resistance is not understood. This apper outlines QTLs identified in two double-haploid populations, and discusses the use of resistance gene analog (RGA) markers and rice-wheat synteny as strategies that may be helpful for understanding the underlying mechanisms for resistance

The use of high resolution melting (HRM) to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley

Using an established genetic map, a single gene conditioning covered smut resistance, Ruh.7H, was mapped to the telomere region of chromosome 7HS in an Alexis/ Sloop doubled haploid barley population. The closest marker to Ruh.7H, abg704 was 7.5 cM away. Thirteen loci on the distal end of 7HS with potential to contain single nucleotide polymorphisms (SNPs) were identiWed by applying a comparative genomics approach using rice sequence data. Of these, one locus produced polymorphic co-dominant bands of diVerent size while two further loci contained SNPs that were identiWed using the recently developed high resolution melting (HRM) technique. Two of these markers Xanked Ruh.7H with the proximal marker located 3.8 cM and the distal marker 2.7 cM away. This is the Wrst report on the application of the HRM technique to SNP detection and to rapid scoring of known cleaved ampliWed polymorphic sequence (CAPS) markers in plants. This simple, precise post-PCR technique should Wnd widespread use in the Wne-mapping of genetic regions of interest in complex cereal and other plant genomes

Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome

The original publication can be found at www.springerlink.comDespite a substantial investment in the development of panels of single nucleotide polymorphism (SNP) markers, the simple sequence repeat (SSR) technology with a limited multiplexing capability remains a standard, even for applications requiring whole-genome information. Diversity arrays technology (DArT) types hundreds to thousands of genomic loci in parallel, as previously demonstrated in a number diploid plant species. Here we show that DArT performs similarly well for the hexaploid genome of bread wheat (Triticum aestivum L.). The methodology previously used to generate DArT fingerprints of barley also generated a large number of high-quality markers in wheat (99.8% allele-calling concordance and approximately 95% call rate). The genetic relationships among bread wheat cultivars revealed by DArT coincided with knowledge generated with other methods, and even closely related cultivars could be distinguished. To verify the Mendelian behaviour of DArT markers, we typed a set of 90 Cranbrook × Halberd doubled haploid lines for which a framework (FW) map comprising a total of 339 SSR, restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP) markers was available. We added an equal number of DArT markers to this data set and also incorporated 71 sequence tagged microsatellite (STM) markers. A comparison of logarithm of the odds (LOD) scores, call rates and the degree of genome coverage indicated that the quality and information content of the DArT data set was comparable to that of the combined SSR/RFLP/AFLP data set of the FW map.Mona Akbari, Peter Wenzl, Vanessa Caig, Jason Carling, Ling Xia , Shiying Yang, Grzegorz Uszynski, Volker Mohler, Anke Lehmensiek, Haydn Kuchel, Mathew J. Hayden, Neil Howes, Peter Sharp, Peter Vaughan, Bill Rathmell, Eric Huttner and Andrzej Kilia