QTL analysis of Cercospora leaf spot resistance in sugar beet

The inheritance of Cercospora leaf spot resistance in sugar beet was investigated by means of quantitative trait loci (QTL) analysis of a segregating population of 193 individuals, using 110 AFLP and 35 restriction fragment length polymorphism (RFLP) markers. Five QTL were found through composite interval mapping on linkage groups 1, 2, 3, and 9, respectively, two of which were linked on linkage group 3. The significance of these QTL was tested by permutation analysis The QTL had mostly additive, but also certain negative dominance effects; all the resistance alleles came from the Cercospora-resistant parent. Each quantitative trait locus accounted for 7-18% of the phenotypic variation, leaving 37% of the variation unexplained. The results are discussed in relation to the potential use of marker-assisted breeding for Cercospora leaf spot resistance in sugar beet.     

Mapping QTL involved in powdery mildew resistance of the apple clone U 211

Scab and powdery mildew, caused by Venturia inaequalis (Cke.) Wint. and Podosphaera leucotricha (Ellis et Ev.) Salm. are the most important apple diseases. The apple clone U 211 is resistant to scab and is also highly resistant to powdery mildew under field conditions. The interval mapping method was applied for the identification of genomic regions conferring U 211 resistance to powdery mildew. The genetic maps of the ‘Idared’ and U 211 genome sectors were constructed using amplified fragment lenght polymorphism and simple sequence repeat markers and 98 individuals from the progeny of the cross ‘Idared’× U 211. On the basis of the phenotypic and molecular marker data 10 powdery mildew resistance quantitative trait loci (QTL) were identified in U 211 and ‘Idared’. One of the QTL in the clone U 211 explained 48‐72% of the phenotypic variation and its effect was stable over years.     

Molecular mapping of powdery mildew resistance genes in wheat: A review

Powdery mildew, caused by Blumeria graminis f. sp. tritici (syn. Erysiphe graminis f. sp. tritici), is one of the most important diseases of common wheat (Triticum aestivum L.) worldwide. Molecular mapping and cloning of genes for resistance to powdery mildew in hexaploid wheat will facilitate the study of molecular mechanisms underlying resistance to powdery mildew diseases and help understand the structure and function of powdery mildew resistance genes, and permit marker-assisted selection in breeding programs. So far, 48 genes/alleles for resistance to powdery mildew at 32 loci have been identified and located on 16 different chromosomes, of which 21 resistance genes/alleles have been tagged by restriction fragment length polymorphisms (RFLPs), random-amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), sequence characterized amplified regions (SCARs), sequence-tagged sites (STS) or simple sequence repeats (SSRs). Several quantitative trait loci (QTLs) for adult plant resistance (APR) to powdery mildew have been associated with molecular markers. The detailed information on chromosomal location and molecular mapping of these genes has been reviewed. Isolation of powdery mildew resistance genes and development of valid molecular markers for pyramiding resistance genes in breeding programs is also discussed.     

A genetic linkage map of rhodesgrass based on an F1 pseudo-testcross population

The linkage relationships between 164 polymorphic amplified fragment length polymorphism (AFLP) and 25 restriction fragment length polymorphism (RFLP) fragments assayed in a pseudo‐testcross population generated from the mating of single genotypes from two divergent cultivars were used to construct female, ‘Katambora’ (‘Kat’) and male, ‘Tochirakukei’ (‘Toch’) parental genetic maps for rhodesgrass. The ‘Kat’ genetic map consists of 84 marker loci (72 AFLP and 12 RFLP markers) distributed on 14 linkage groups and spans a total length of 488.3 cM, with an average distance of 7.8 cM between adjacent markers. The ‘Toch’ genetic map consists of 61 marker loci (52 AFLP and nine RFLP) mapped on 12 linkage groups spanning a total length of 443.3 cM, with an average spacing of 9.0 cM between adjacent markers. About 23% of the markers remained unassigned. The level of segregation distortion observed in this cross was 11.1%. In both maps, linked duplicated RFLP loci were found. These linkage maps will serve as a starting point for linkage studies in rhodesgrass with potential application for marker‐assisted selection in breeding programmes.     

Short Communication Comparison between QTL analysis of powdery mildew resistance in barley based on detached primary leaves and on field data

A quantitative trait loci (QTL) analysis of quantitative powdery mildew resistance was performed on 216 doubled haploid lines derived from a cross between the winter-barley varieties ‘Igri’ and ‘Danilo’ using 67 RFLP loci. Resistance to powdery mildew was determined in the field with natural infection and on detached primary leaves with a specific isolate. The major QTL found in both sets of analysis mapped to the same chromosomal region. No further QTL could be found in the analysis based on detached leaves and one additional minor QTL was found in the analysis based on field data.     

Mapping of quantitative trait loci controlling powdery mildew resistance in Mungbean (<Emphasis Type="Italic">Vigna radiata</Emphasis> (L.) Wilczek)

Powdery mildew disease in mungbean is caused by the fungus, Erysiphe polygoni D.C. We identified two quantitative trait loci (QTLs) controlling resistance to the disease in a RIL population of 190 F₇ lines. The population was developed from the cross between a susceptible cultivar, “Kamphaeng Saen 1” and a resistant line, “VC6468-11-1A”. Reaction to the disease was evaluated for resistance in field and greenhouse conditions. Results from analysis of variance revealed that 15 SSR loci on three linkage groups (LG) associated with the resistance. Composite interval mapping consistently identified two QTLs on two LGs, qPMR-1 and qPMR-2, conferring the resistance. qPMR-1 and qPMR-2 accounted for 20.10 and 57.81% of the total variation for plant response to the disease, respectively. Comparison based on common markers used in our and previous studies suggested that qPMR-2 is possibly the same as the major QTL reported earlier using another resistant source. The SSR markers flanking and closely linked to qPMR-1 (CEDG282 and CEDG191) and qPMR-2 (MB-SSR238 and CEDG166) are useful for marker-assisted selection for mungbean resistance to powdery mildew.     

Quantitative trait loci for grain yield and yield components in a cross between a six-rowed and a two-rowed barley

Summary The positions of quantitative trait loci (QTL) for yield and yield components were estimated using a 85-point linkage map and phenotype data from a F₁-derived doubled haploid (DH) population of barley. Yield and its components were recorded in two growing seasons. Highly significant QTL effects were found for all traits at several sites in the genome. A major portion of the QTL was found on chromosome 2. The effect of the alleles in locus v on thousand grain weight and kernels per ear explained 70–80% of the genetic variation in the traits. QTL × year interaction was found for grain yield. Several different QTL were found within the two-rowed DH lines compared to those found in the six-rowed DH lines. Epistasis between locus v and several loci for yield and yield components indicates that genes are expressed differently in the two ear types. This may explain the difficulties of selecting high yielding lines from crosses between two-rowed and six-rowed barley.Abbreviations DH doubled haploid - QTL quantitative trait locus/loci - RAPD random amplified polymorphic DNA - RFLP restriction fragment length polymorphism - T. Prentice Tystofte Prentice - V. Gold Vogelsanger Gold     

Construction of a genetic linkage map with SSR,AFLP and morphological markers to locate QTLs controlling pathotype-specific powdery mildew resistance in diploid roses

Disease resistance is a sought-after trait in plant breeding programmes. One strategy to make resistance more durable is to increase the number of resistance genes, thereby increasing the number of pathotypes withstood. One of the most important diseases on roses is powdery mildew (PM) (Podosphaera pannosa). Recent studies show that pathotypes of PM and different types of resistances in roses exist. The results of this study aim to contribute to PM resistance in roses by the development of pathotype-specific markers on a genetic map. A diploid rose population (90 genotypes) derived from a cross between Rosa wichurana and Rosa ‘Yesterday’ was used to construct a genetic linkage map encompassing 20 AFLP primer combinations, 43 SSR, and 2 morphological markers. By applying the F1 pseudo test cross population strategy, two parental linkage maps were constructed (parent ‘Yesterday’ 536 cM; parent R. wichurana 526 cM). Both parental maps consisted of seven linkage groups with an average length of 70 cM (Kosambi) corresponding to the seven haploid rose chromosomes. These new maps were used to identify QTLs controlling disease resistance. The offspring population was screened for resistance to two PM pathotypes, R–E and R–P. QTLs for controlling pathotype-specific disease resistance were mapped by applying Kruskal–Wallis rank-sum tests and simple interval mapping. With two pathotypes analysed, nine QTL loci were detected on linkage groups 2, 3, 5 and 6, explaining 15–73% of the phenotypic variance for pathotype-specific disease response. The genetic maps developed here will be useful for future rose breeding, pathotype-specific resistance research and development of a consensus map for roses.     

Development of PCR-based markers for a major locus conferring powdery mildew resistance in mungbean (Vigna radiata)

Powdery mildew (PM) can cause significant yield loss in mungbean and several loci conferring resistance to this disease have been identified. A restriction fragment length polymorphism (RFLP) marker (VrCS65) linked closely to one of these loci was used to screen a mungbean bacterial artificial chromosome (BAC) library and positive BAC clones identified were used to develop simple sequence repeat (SSR or microsatellite) and sequence tagged site (STS) markers. Four of the new PCR markers (including two SSRs and two STSs) co-segregated with the original RFLP marker VrCS65, and another SSR marker (VrCS SSR2) was located 0.5 cM away from it. These PCR-based and locus-specific markers could be useful in breeding cultivars with enhanced resistance to PM and in the further characterization of the locus including the isolation of gene(s) responsible for the resistance.     

A major QTL effect controlling resistance to powdery mildew in winter wheat at the adult plant stage

Powdery mildew is one of the major diseases of wheat in regions with a maritime or semi‐continental climate which can strongly affect grain yield. The objective of the study was to identify and compare quantitative resistance to powdery mildew of line RE9001 at the adult plant and vernalized seedling stages. RE9001 has no known Pm gene and shows a high level of adult plant resistance in the field. Using 104 recombinant inbred lines (RILs) of an RE9001 × ‘Courtot’ F8 population, a genetic map was developed with 363 markers distributed over 26 linkage groups and covering 3825 cM. The global map density was 1 locus/10.3 cM. RILs were assessed under field and tunnel greenhouse conditions for 2 years in two locations. Eleven quantitative trait loci (QTL) were detected at the adult stage and they explained 63% of the variation, depending on the environment. Three QTLs were found, at least, in the two environments. One QTL from RE9001, mapped on chromosome 2B, was stable in each environment. This QTL, QPm.inra.2B, explained 10.3–36.6% of the variation and could be mapped in the vicinity of the Pm6 gene. At the vernalized seedling stage, one QTL detected by the isolate 93‐27 could be an allele of the Pm3g gene present in ‘Courtot’. No residual effect of the Pm3g gene was detected at either stage. Markers flanking the QTL 2B could be useful tools to combine resistance to powdery mildew in wheat cultivars.     

Mapping of QTL for resistance to powdery mildew and resistance gene analogues in perennial ryegrass

The objective of this study was to map resistance gene analogues (RGA) and quantitative trait loci (QTL) for powdery mildew resistance in perennial ryegrass ( Lolium perenne  L.). The mapping population consisted of 184 F₂ genotypes produced from a cross between one genotype of a synthetic perennial ryegrass variety Veyo and one genotype from the perennial ryegrass ecotype Falster. The greenhouse infection was measured as number of sporulating colonies on a 10-cm leaf area with the maximum possible number of colonies to be counted set to 50. The range of infection scores in the population was 0–50 and the heritability was 71.7%. In total, two QTL for powdery mildew resistance were identified, and mapped to linkage groups (LG) LG3 and LG7. Individually, these QTL explained between 7.5% and 22.1% of the total phenotypic variation. Six RGA and three laccases were mapped to LG2, LG3, LG4, LG5 and LG7, however, no close linkage between RGA and QTL was observed.     

A major quantitative trait locus for resistance to Turnip Yellows Virus (TuYV, syn. beet western yellows virus, BWYV) in rapeseed

Turnip yellows virus (TuYV) is responsible for a recognizable loss of yield in European winter oilseed rape cultivation. To map genes involved in TuYV resistance, a double haploid population was established by crossing a resynthesized rapeseed line (R54) as donor for TuYV resistance with an elite rapeseed line (‘Express’). Resistance was determined with 10 plants per line by double antibody sandwich‐enzyme‐linked immunosorbent assay. After screening 17 primer combinations (Pstl/Msel and EcoRI/Msel), 143 amplified fragment length polymorphism markers were mapped to 20 linkage groups representing 15 chromosomes of the rapeseed genome. Quantitative trait loci (QTL) were mapped using the composite interval mapping approach. As a result, one major quantitative trait locus was found on linkage group MS17, explaining up to 50% of the phenotypic variation. Because no other factors displaying a significant effect on the expression of resistance could be identified, a simple mode of inheritance for TuYV resistance is suggested, thus enabling marker‐assisted selection during rapeseed breeding.     

An AFLP-based linkage map of Zoysiagrass (Zoysia japonica)

To construct an amplified‐fragment length polymorphism (AFLP)‐based molecular linkage map of zoysiagrass, the selfed progenies of a clone consisting of 78 individuals were analysed using 471 AFLP markers derived from 126 PstI/MseI primer combinations. Of these markers, 364 were grouped into 26 linkage groups. The maps covered a total length of 932.5 cM, with an average spacing of 2.6 cM between markers. This information proves useful for gene targeting, quantitative trait loci mapping, and marker‐assisted selection in zoysiagrass.     

Mapping of EST-derived CAPS markers in Italian ryegrass (Lolium multiflorum Lam.)

New molecular markers derived from expressed sequence tag (EST) sequences were mapped on linkage maps of Italian ryegrass by a two-way pseudo-testcross strategy. cDNA sequences were obtained from various tissues of Italian ryegrass ( Lolium multiflorum ) and converted into cleaved amplified polymorphic sequence (CAPS) markers. Of 260 EST primer pairs that amplified a single band, 74 generated bands that showed clear polymorphisms among individuals of an F₁ mapping family. Of the 74 polymorphic marker loci, 69 were mapped on an Italian ryegrass linkage map previously constructed using amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), and simple sequence repeat (SSR) markers. The newly-developed EST-CAPS markers would be useful as an efficient tool to identify genetic markers and to identify candidate genes for quantitative trait loci (QTLs) associated with important traits in Italian ryegrass.     

Integration of AFLP markers into a linkage map of sugar beet (Beta vulgaris L.)

The AFLP (amplified fragment length polymorphism) technique has been applied in establishing an extended linkage map of sugar beet. A total of 120 AFLPs were integrated into an existing linkage map based on RFLP markers. Four primer combinations yielded between 19 and 40 polymorphic bands in an F₂ population consisting of 94 plants. The AFLP loci were evenly distributed over the nine linkage groups, with the exception of linkage group V where the number of AFLPs was significantly low. The AFLPs were found to be reproducible even against the background of different combinations of Taq DNA polymerases and buffers. However, the quantity of higher molecular weight fragments (>400 bp) was reduced when using plant DNA of poor quality as a template. The results of these experiments are discussed, together with possible applications of AFLPs in sugar beet breeding.     

Molecular characterization of <Emphasis Type="Italic">Fusarium</Emphasis> head blight resistance from wheat variety Wangshuibai

Fusarium head blight (FHB) is a destructive disease of wheat worldwide. FHB resistance genes from Sumai 3 and its derivatives such as Ning 7840 have been well characterized through molecular mapping. In this study, resistance genes in Wangshuibai, a Chinese landrace with high and stable FHB resistance, were analyzed through molecular mapping. A population of 104 F₂-derived F₇ recombinant inbred lines (RILs) was developed from the cross between resistant landrace Wangshuibai and susceptible variety Alondras. A total of 32 informative amplified fragment length polymorphism (AFLP) primer pairs (EcoRI/MseI) amplified 410 AFLP markers segregating among the RILs. Among them, 250 markers were mapped in 23 linkage groups covering a genetic distance of 2,430 cM. In addition, 90 simple sequence repeat (SSR) markers were integrated into the AFLP map. Fifteen markers associated with three quantitative trait loci (QTL) for FHB resistance (P < 0.01) were located on two chromosomes. One QTL was mapped on 1B and two others were mapped on 3B. One QTL on 3BS showed a major effect and explained up to 23.8% of the phenotypic variation for type II FHB resistance.     

Identification of a major QTL in cocoa (Theobroma cacao L.) associated with resistance to witches' broom disease

The witches’ broom disease caused by the fungus Crinipellis perniciosa is the main limiting factor for cocoa production in South America and the Caribbean. In Brazil, this disease affects almost all cocoa‐growing regions, causing serious economic, social and ecological damage. The aim of this study was to map genomic regions associated with resistance to C. perniciosa using an F₂ population derived from a cross between ‘Scavina‐6’(resistant) and ‘ICS‐1’(susceptible). The phenotypic index was determined as the average number of vegetative witches’ brooms per canopy area of each plant, the witches’ brooms were counted and eliminated during six field evaluations between May 1998 and August 1999. A total of 124 random amplified polymorphic DNA (RAPD) and 69 amplified fragment length polymorphism (AFLP) markers were mapped along 25 linkage groups covering 1713 cM of cocoa genome. After employing single factor and composite interval mapping analyses, a major quantitative trait loci (QTL) flanked by the marker AV14.940 was identified in the linkage group 11, explaining almost 35% of the resistance to witches’ broom. The present result suggests that this QTL acts as a major dominant component of resistance to this pathogen, with great potential for use in marker‐assisted selection procedures in cocoa breeding programmes.     

Comparison of QTLs mapped in RILs and their test-cross progenies of tropical maize for insect resistance and agronomic traits

Quantitative trait loci (QTL) affecting resistance to south-western corn borer Diatraea grandiosella (SWCB) and sugarcane borer Diatraea saccharalis (SCB) have been identified previously in F_2:3 lines and recombinant inbred lines (RILs) of tropical maize using restriction fragment length polymorphism (RFLP) analyses. Our objective was to determine whether QTLs identified in these generations are also expressed in test crosses (TC) of RILs. A population of 166 TC progenies was developed by crossing RILs from the cross CML131 (susceptible) × CML67 (resistant) with the unrelated, susceptible tester line CML216. Resistance to first-generation SWCB, measured as leaf-feeding damage (LFD) under artificial infestation, and other agronomic traits were evaluated in two environments for the TC progenies and three environments for 183 RILs. The correlation between line per se and TC performance was low for LFD and intermediate for most agronomic traits. Estimates of the genotypic variance and heritabilities were smaller in the TC progenies than in the RILs for all traits. Quantitative trait loci were identified using an RFLP linkage map with 136 loci. For LFD, four QTLs were detected in the TC progenies, of which two were in common with nine QTLs previously mapped in the RILs. Few QTLs for agronomic traits were common to the two types of progeny, because of the low consistency of QTL positions for all traits in RIL and TC progenies, the use of TC progenies should be considered in QTL mapping studies as the first step for marker-assisted selection in hybrid breeding.     

QTL analysis of resistance to Fusarium head blight in wheat using a 'Wangshuibai'-derived population

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 F_3:5 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.     

Integration of AFLP markers into an RFLP-based map of durum wheat

Amplified fragment length polymorphism (AFLP) is a powerful technique which can readily be applied to a wide range of species for mapping purposes. AFLPs were added to a linkage map of durum wheat constructed using restriction fragment length polymorphisms (RFLPs). The mapping population included 65 recombinant inbred lines derived from a cross between the durum wheat cultivar ‘Messapia’ and accession ‘MG4343’ of the wild Triticum turgidum ssp. dicoccoides (Körn.). Genomic DNA was digested with MseI (4‐cutter) and Sse83871 (8‐cutter). Using a silver‐staining protocol, 14 primer combinations revealed 421 clearly scorable amplicons including 100 polymorphisms. The presence of nine pairs of bands linked in repulsion phase with each pair generated by one primer combination suggested the presence of codominant alleles; sequence analysis of four band pairs confirmed their codominant nature. The integration of 80 AFLP loci extended the map in several telomeric regions, reduced the size of four large gaps present in the previous map, and eliminated one gap. The new map obtained after the inclusion of the 80 AFLP loci and eight additional RFLP loci spans 2063cM which represent a 52.6% increment compared with the previous map. Compared with the distribution of RFLPs, no significant clustering of AFLP markers was observed.