Mapping of resistance to spot blotch disease caused by Bipolaris sorokiniana in spring wheat

Spot blotch caused by Bipolaris sorokiniana is a destructive disease of wheat in warm and humid wheat growing regions of the world. The development of disease resistant cultivars is considered as the most effective control strategy for spot blotch. An intervarietal mapping population in the form of recombinant inbred lines (RILs) was developed from a cross ‘Yangmai 6’ (a Chinese source of resistance) × ‘Sonalika’ (a spot blotch susceptible cultivar). The 139 single seed descent (SSD) derived F₆, F₇, F₈ lines of ‘Yangmai 6’ × ‘Sonalika’ were evaluated for resistance to spot blotch in three blocks in each of the 3 years. Joint and/or single year analysis by composite interval mapping (CIM) and likelihood of odd ratio (LOD) >2.2, identified four quantitative trait loci (QTL) on the chromosomes 2AL, 2BS, 5BL and 6DL. These QTLs were designated as QSb.bhu-2A, QSb.bhu-2B, QSb.bhu-5B and QSb.bhu-6D, respectively. A total of 63.10% of phenotypic variation was explained by these QTLs based on the mean over years. Two QTLs on chromosomes 2B and 5B with major effects were consistent over 3 years. All QTL alleles for resistance were derived from the resistant parent ‘Yangmai 6’.     

Phenotyping at hot spots and tagging of QTLs conferring spot blotch resistance in bread wheat

Spot blotch is a major foliar disease of wheat caused by Bipolaris sorokiniana in warm and humid environments of the world including South Asian countries. In India, it has a larger impact in Indo-Gangetic plains of the country. Therefore, the present study was undertaken to phenotype a mapping population at different hot spots of India and to detect quantitative trait loci (QTL) for resistance to spot blotch in wheat. For this study, 209 single seed descent (SSD) derived F₈, F₉, F₁₀ recombinant inbred lines (RILs) of the cross ‘Sonalika’ (an Indian susceptible cultivar)/‘BH 1146’ (a Brazilian resistant cultivar) were assessed for spot blotch resistance at two hot spot locations (Coochbehar and Kalyani) for three years and for two years under controlled conditions in the polyhouse (Karnal). The population showed large variation in spot blotch reaction for disease severity in all the environments indicating polygenic nature of the disease. Microsatellite markers were used to create the linkage maps. Joint and/or individual year analysis by composite interval mapping (CIM) and likelihood of odds ratio (LOD) >2.1, detected two consistent QTLs mapped on chromosome 7BL and 7DL and these explained phenotypic variation of 11.4 percent and 9.5 percent over the years and locations, respectively. The resistance at these loci was contributed by the parent ‘BH 1146’ and shown to be independent of plant height and earliness. Besides, association of some agro-morphological traits has also been observed with percent disease severity. These identified genomic regions may be used in future wheat breeding programs through marker assisted selection for developing spot blotch resistant cultivars.     

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-based PCR, expressed sequence tag 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 and 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.     

QTL for spot blotch resistance in bread wheat line Saar co-locate to the biotrophic disease resistance loci Lr34 and Lr46

Spot blotch caused by Bipolaris sorokiniana is a major disease of wheat in warm and humid wheat growing regions of the world including south Asian countries such as India, Nepal and Bangladesh. The CIMMYT bread wheat line Saar which carries the leaf tip necrosis (LTN)-associated rust resistance genes Lr34 and Lr46 has exhibited a low level of spot blotch disease in field trials conducted in Asia and South America. One hundred and fourteen recombinant inbred lines (RILs) of Avocet (Susceptible) × Saar, were evaluated along with parents in two dates of sowing in India for 3 years (2007–2008 to 2009–2010) to identify quantitative trait loci (QTL) associated with spot blotch resistance, and to determine the potential association of Lr34 and Lr46 with resistance to this disease. Lr34 was found to constitute the main locus for spot blotch resistance, and explained as much as 55 % of the phenotypic variation in the mean disease data across the six environments. Based on the large effect, the spot blotch resistance at this locus has been given the gene designation Sb1. Two further, minor QTL were detected in the sub-population of RILs not containing Lr34. The first of these was located about 40 cM distal to Lr34 on 7DS, and the other corresponded to Lr46 on 1BL. A major implication for wheat breeding is that Lr34 and Lr46, which are widely used in wheat breeding to improve resistance to rust diseases and powdery mildew, also have a beneficial effect on spot blotch.     

Mapping quantitative trait loci associated with spot blotch and net blotch resistance in a doubled-haploid barley population

Spot blotch and net blotch are important foliar barley (Hordeum vulgare L.) diseases in Canada and elsewhere. These diseases result in significant yield reduction and, more importantly, loss of grain quality, downgrading barley from malt to feed. Combining resistance to these diseases is a breeding priority but is a significant challenge using conventional breeding methodology. In the present investigation, an evaluation of the inheritance of resistance to spot and net blotch was conducted in a doubled-haploid barley population from the cross CDC Bold (susceptible)?×?TR251 (resistant). The population was screened at the seedling stage in the Phytotron and at the adult-plant stage in the field for several years. Chi-squared analysis indicated one- to four-gene segregation depending on disease, isolate, plant development stage, location and year. A major seedling and adult-plant resistance quantitative trait locus (QTL), designated QRpt6, was re-confirmed for net-form net blotch resistance, explaining 32?C61% of phenotypic variation in different experiments. Additional QTL for seedling and adult-plant resistance to net blotch were identified. For spot blotch resistance, a major seedling resistance QTL (QRcss1) was detected on chromosome 1H for isolate WRS1909, explaining 79% of the phenotypic variation. A highly significant QTL on 3H (QRcs3) was identified for seedling resistance to isolate WRS1908 and adult-plant resistance at Brandon, MB, Canada in 2008. The identification of QTL at only one location or from 1?year suggests spot blotch resistance is complex and highly influenced by the environment. Efforts are being made to combine spot and net blotch resistance in elite barley lines using molecular marker-assisted selection.     

Effect of chitosan and vanillin-modified chitosan on wheat resistance to spot blotch

The effect of chitosan- and vanillin-based immune modulators on the development of the phytopathogen Cochliobolus sativus (S. Ito & Kurib.) Drechsler ex Dastur, which induces dark-brown blotch (helminthosporiosis) in wheat, has been studied. It was shown that treatment with these substances led to a decreased injured area in leaves and an increase in the biotrophic period of pathogen development. It was found that vanillin-modified chitosan effectively provided wheat resistance to hemibiotrophic pathogen C. sativus. Changes in leaf peroxidase activity correlated with the manifestation of disease symptoms.     

Global adaptation patterns of Australian and CIMMYT spring bread wheat

The International Adaptation Trial (IAT) is a special purpose nursery designed to investigate the genotype-by-environment interactions and worldwide adaptation for grain yield of Australian and CIMMYT spring bread wheat (Triticum aestivum L.) and durum wheat (T. turgidum L. var. durum). The IAT contains lines representing Australian and CIMMYT wheat breeding programs and was distributed to 91 countries between 2000 and 2004. Yield data of 41 reference lines from 106 trials were analysed. A multiplicative mixed model accounted for trial variance heterogeneity and inter-trial correlations characteristic of multi-environment trials. A factor analytic model explained 48% of the genetic variance for the reference lines. Pedigree information was then incorporated to partition the genetic line effects into additive and non-additive components. This model explained 67 and 56% of the additive by environment and non-additive by environment genetic variances, respectively. Australian and CIMMYT germplasm showed good adaptation to their respective target production environments. In general, Australian lines performed well in south and west Australia, South America, southern Africa, Iran and high latitude European and Canadian locations. CIMMYT lines performed well at CIMMYT’s key yield testing location in Mexico (CIANO), north-eastern Australia, the Indo-Gangetic plains, West Asia North Africa and locations in Europe and Canada. Maturity explained some of the global adaptation patterns. In general, southern Australian germplasm were later maturing than CIMMYT material. While CIANO continues to provide adapted lines to northern Australia, selecting for yield among later maturing CIMMYT material in CIANO may identify lines adapted to southern and western Australian environments. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

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Identification of resistance source in wheat germplasm against spot blotch disease caused by Bipolaris sorokiniana

Four hundred and twenty-two spring wheat germplasm (Triticum aestivum L.) lines belonging to Indian, CIMMYT and Chinese wheat programme were evaluated for their tolerance against natural epiphytotic conditions of spot blotch caused by Bipolaris sorokiniana at the hot spot location, Pusa, Bihar, India. Of the 422 entries screened, none of the genotype showed immunity to the disease, whereas 52 were resistant, 180 moderately susceptible, 171 susceptible and 19 highly susceptible. Indian germplasm lines tended to be more susceptible than lines originated from CIMMYT and China. Chirya 3, Chirya 7 and Mayoor from CIMMYT showed high degree of resistance to the disease both under field and polyhouse conditions. On the basis of the disease severity under field conditions, 20 promising resistant genotypes and 10 highly susceptible lines were isolated for further testing under artificial epiphytotic conditions in polyhouse for genetic analysis and their potential for spot blotch resistance breeding.     

Association mapping of spot blotch resistance in wild barley

Spot blotch, caused by Cochliobolus sativus, is an important foliar disease of barley. The disease has been controlled for over 40 years through the deployment of cultivars with durable resistance derived from the line NDB112. Pathotypes of C. sativus with virulence for the NDB112 resistance have been detected in Canada; thus, many commercial cultivars are vulnerable to spot blotch epidemics. To increase the diversity of spot blotch resistance in cultivated barley, we evaluated 318 diverse wild barley accessions comprising the Wild Barley Diversity Collection (WBDC) for reaction to C. sativus at the seedling stage and utilized an association mapping (AM) approach to identify and map resistance loci. A high frequency of resistance was found in the WBDC as 95% (302/318) of the accessions exhibited low infection responses. The WBDC was genotyped with 558 Diversity Array Technology (DArT^®) and 2,878 single nucleotide polymorphism (SNP) markers and subjected to structure analysis before running the AM procedure. Thirteen QTL for spot blotch resistance were identified with DArT and SNP markers. These QTL were found on chromosomes 1H, 2H, 3H, 5H, and 7H and explained from 2.3 to 3.9% of the phenotypic variance. Nearly half of the identified QTL mapped to chromosome bins where spot blotch resistance loci were previously reported, offering some validation for the AM approach. The other QTL mapped to unique genomic regions and may represent new spot blotch resistance loci. This study demonstrates that AM is an effective technique for identifying and mapping QTL for disease resistance in a wild crop progenitor.     

Mapping of adult plant stripe rust resistance genes in diploid A genome wheat species and their transfer to bread wheat

Stripe rust, caused by Puccinia striiformis West. f.sp. tritici, is one of the most damaging diseases of wheat worldwide. Forty genes for stripe rust resistance have been catalogued so far, but the majority of them are not effective against emerging pathotypes. Triticum monococcum and T. boeoticum have excellent levels of resistance to rusts, but so far, no stripe rust resistance gene has been identified or transferred from these species. A set of 121 RILs generated from a cross involving T. monococcum (acc. pau14087) and T. boeoticum (acc. pau5088) was screened for 3 years against a mixture of pathotypes under field conditions. The parental accessions were susceptible to all the prevalent pathotypes at the seedling stage, but resistant at the adult plant stage. Genetic analysis of the RIL population revealed the presence of two genes for stripe rust resistance, with one gene each being contributed by each of the parental lines. A linkage map with 169 SSR and RFLP loci generated from a set of 93 RILs was used for mapping these resistance genes. Based on phenotypic data for 3 years and the pooled data, two QTLs, one each in T. monococcum acc. pau14087 and T. boeoticum acc. pau5088, were detected for resistance in the RIL population. The QTL in T. monococcum mapped on chromosome 2A in a 3.6 cM interval between Xwmc407 and Xwmc170, whereas the QTL from T. boeoticum mapped on 5A in 8.9 cM interval between Xbarc151 and Xcfd12 and these were designated as QYrtm.pau-2A and QYrtb.pau-5A, respectively. Based on field data for 3 years, their R ² values were 14 and 24%, respectively. T. monococcum acc. pau14087 and three resistant RILs were crossed to hexaploid wheat cvs WL711 and PBW343, using T. durum as a bridging species with the objective of transferring these genes into hexaploid wheat. The B genome of T. durum suppressed resistance in the F₁ plants, but with subsequent backcrossing one resistance gene could be transferred from one of the RILs to the hexaploid wheat background. This gene was derived from T. boeoticum acc. pau5088 as indicated by co-introgression of T. boeoticum sequences linked to stripe rust resistance QTL, QYrtb.pau-5A. Homozygous resistant progenies with 40–42 chromosomes have been identified. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic architecture of resistance to Septoria tritici blotch in European wheat

Background

Septoria tritici blotch is an important leaf disease of European winter wheat. In our survey, we analyzed Septoria tritici blotch resistance in field trials with a large population of 1,055 elite hybrids and their 87 parental lines. Entries were fingerprinted with the 9 k SNP array. The accuracy of prediction of Septoria tritici blotch resistance achieved with different genome-wide mapping approaches was evaluated based on robust cross validation scenarios.

Results

Septoria tritici blotch disease severities were normally distributed, with genotypic variation being significantly (P < 0.01) larger than zero. The cross validation study revealed an absence of large effect QTL for additive and dominance effects. Application of genomic selection approaches particularly designed to tackle complex agronomic traits allowed to double the accuracy of prediction of Septoria tritici blotch resistance compared to calculation methods suited to detect QTL with large effects.

Conclusions

Our study revealed that Septoria tritici blotch resistance in European winter wheat is controlled by multiple loci with small effect size. This suggests that the currently achieved level of resistance in this collection is likely to be durable, as involvement of a high number of genes in a resistance trait reduces the risk of the resistance to be overcome by specific pathogen isolates or races.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-858) contains supplementary material, which is available to authorized users.     

Mapping and validation of quantitative trait loci associated with wheat yellow mosaic bymovirus resistance in bread wheat

Wheat yellow mosaic (WYM) caused by wheat yellow mosaic bymovirus (WYMV) has been growing as one of the most serious diseases affecting wheat production in China. In this study, the association of quantitative trait loci (QTLs) governing WYMV resistance with molecular markers was established using 164 recombinant inbred lines (RILs) derived from 'Xifeng Wheat' (highly resistant)?×?'Zhen 9523' (highly susceptible). Phenotypic data of WYMV resistance of the RILs were collected from 4-year, two-location replicated field trials. A molecular marker-based linkage map, which was comprised of 273 non-redundant loci and represented all the 21 wheat chromosomes, was constructed with the JoinMap 4.0 software. Using the Windows QTL Cartographer V2.5 software, three QTLs associated with WYMV resistance, QYm.njau-3B.1, QYm.njau-5A.1 and QYm.njau-7B.1, were detected on chromosomes 3BS, 5AL, and 7BS, respectively. The favorable allele effects were all contributed by 'Xifeng Wheat'. Among the three QTLs, QYm.njau-3B.1 and QYm.njau-5A.1 were detected in all the four trials and the overall mean, and could explain 3.3-10.2% and 25.9-53.7% of the phenotypic variation, respectively, while QYm.njau-7B.1 was detected in one trial and the overall mean and explained 4.9 and 3.3% of the phenotypic variation, respectively. A large portion of the variability for WYMV response was explained by a major QTL, QYm.njau-5A.1. The relationship of the molecular markers linked with QYm.njau-5A.1 and the WYMV resistance was further validated using a secondary F(2) population. The results showed that three markers, i.e., Xwmc415.1, CINAU152, and CINAU153, were closely linked to QYm.njau-5A.1 with the genetic distances of 0.0, 0.0, and 0.1?cM, respectively, indicating they should be useful in marker-assisted selection (MAS) wheat breeding for WYMV resistance. A panel of germplasm collection consisting of 46 wheat varieties with known WYMV response phenotypes was further used to validate the presence and effects of QYm.njau-5A.1 and the above three markers. It was found that QYm.njau-5A.1 was present in 12 of the 34 WYMV-resistant varieties.     

Mapping and diagnostic marker development for Soil-borne cereal mosaic virus resistance in bread wheat

Monogenically-inherited resistance to Soil-borne cereal mosaic virus (SBCMV) in hexaploid bread wheat cultivars ‘Tremie’ and ‘Claire’ was mapped on chromosome 5D. The two closest flanking markers identified in the Claire-derived mapping population, Xgwm469-5D and E37M49, are linked to the resistance locus at distances of 1 and 9 cm, respectively. Xgwm469-5D co-segregated with the SBCMV resistance in the Tremie-derived population and with the recently identified Sbm1 locus in the cv. Cadenza. This suggested that Tremie and Claire carry a resistance gene allelic to Sbm1, or one closely linked to it. The diagnostic value of Xgwm469-5D was assessed using a collection of SBCMV resistant and susceptible cultivars. Importantly, all susceptible genotypes carried a null allele of Xgwm469-5D, whereas resistant genotypes presumably related to either Claire and Tremie or Cadenza revealed a 152 or 154 bp allele of Xgwm469-5D, respectively. Therefore, Xgwm469-5D is well suited for marker assisted selection for SBCMV resistance.     

Sources of resistance and susceptibility to Septoria tritici blotch of wheat

An association genetics analysis was conducted to investigate the genetics of resistance to Septoria tritici blotch, caused by the fungus Zymoseptoria tritici (alternatively Mycosphaerella graminicola), in cultivars and breeding lines of wheat (Triticum aestivum) used in the UK between 1860 and 2000. The population was tested with Diversity Array Technology (DArT) and simple‐sequence repeat (SSR or microsatellite) markers. The lines formed a single population with no evidence for subdivision, because there were several common ancestors of large parts of the pedigree. Quantitative trait loci (QTLs) controlling Septoria resistance were postulated on 11 chromosomes, but 38% of variation was not explained by the identified QTLs. Calculation of best linear unbiased predictions (BLUPs) identified lineages of spring and winter wheat carrying different alleles for resistance and susceptibility. Abundant variation in Septoria resistance may be exploited by crossing well‐adapted cultivars in different lineages to achieve transgressive segregation and thus breed for potentially durable quantitative resistance, whereas phenotypic selection for polygenic quantitative resistance should be effective in breeding cultivars with increased resistance. The most potent allele reducing susceptibility to Septoria, on chromosome arm 6AL, was associated with reduced leaf size. Genes which increase susceptibility to Septoria may have been introduced inadvertently into UK wheat breeding programmes from cultivars used to increase yield, rust resistance and eyespot resistance between the 1950s and 1980s. This indicates the need to consider trade‐offs in plant breeding when numerous traits are important and to be cautious about the use of non‐adapted germplasm.     

Mapping QTL for water regime in spring bread wheat

For the first time, the authors assessed and mapped the chromosome QTLs (Quantitative Trait Loci) for the manifestation of morpho-physiological and agronomic indices of plant water status and related quantitative traits, such as plant height, weight, and dry matter content in spring bread wheat (Triticum aestivum L.). Following the study of ten agronomic traits, 13 QTLs were mapped on linkage groups 1A, 1B, 2B, 2D, 4A, 5A, 5B, 5D, 6A, and 6D. Some of the identified QTLs concurrently determined several traits. The physiological components of water status were shown to correlate with quantitative traits in wheat plants, such as plant height, weight, and dry matter content, and the correlation coefficients were calculated for all traits under study. Water retention capacity after 3 h correlated with water retention capacity after 24 h (r _xy = 0.47). The correlations were also established between water retention capacity after 3 h and plant height at booting stage (r _xy = 0.29) and between water retention capacity after 3 h and plant dry weight (r _xy = 0.33). Statistical calculations supported generally observed negative correlation (up to ?1) between leaf water and dry matter contents, as well as between the root indices of variance in the mapping population of wheat lines. The results obtained in the present study will promote future efforts to fine-map the genes residing within the identified QTLs, to eventually clone these genes in order to establish the physiological mechanisms for maintaining water homeostasis in higher plant cells and to accomplish the practical implementation of marker-assisted assessment of water status in wheat plants studied on the basis of morpho-physiological and economical indices.     

QTL mapping of partial resistance in winter wheat to Stagonospora nodorum blotch.

Stagonospora nodorum blotch is an important foliar and glume disease in cereals. Inheritance of resistance in wheat appears to be quantitative. To date, breeding of partially resistant cultivars has been the only effective way to combat this pathogen. The partial resistance components, namely length of incubation period, disease severity, and length of latent period, were evaluated on a population of doubled haploids derived from a cross between the partially resistant Triticum aestivum 'Liwilla' and susceptible Triticum aestivum 'Begra'. Experiments were conducted in a controlled environment and the fifth leaf was examined. Molecular analyses were based on bulked segregant analyses using 240 microsatellite markers. Four QTLs were significantly associated with partial resistance components and were located on chromosomes 2B, 3B, 5B, and 5D. The percentage of phenotypic variance explained by a single QTL ranged from 14 to 21% for incubation period, from 16 to 37% for disease severity, and from 13 to 28% for latent period,