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Cross-validated accuracy to predict Septoria tritici blotch resistance in wheat based on association mapping and two genomic selection methods BayesCπ and RR-BLUP.
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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 a...
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Citations
... [45], while analyzing data acquired over three years on STB, found a significant negative correlation between STB and PLH. In 2013 [46], reported that STB resistance is associated with increased PLH. According to Ref. [38] also, reduced PLH was usually associated with more necrosis percentage. ...
... Thus, the QTL on chromosomes 7B, 1D, 3A, 2B and 3D found in this study could be identical or in very close proximity to the previously mapped ones. In addition to these major genes, several QTL have also been identified on these chromosomes using SNPs markers: on chromosomes 6B and 7B [54], on chromosome 3A [55] and on chromosome 2B [46]. Although the markers found to be significantly associated with STB resistance in this study were located on chromosomes on which septoria tritici blotch resistant genes (Stb genes) have been mapped and/or QTL have also been identified previously, localization cannot be compared due to the use of a different type of markers for the reveal or not reveal of sequence homology. ...
Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici, anamorph Septoria tritici Rob. ex Desm., is an important wheat pathogen worldwide, reported to be major wheat production threating factor, posing considerable yield loss every year. Developing resistant cul-tivars is an efficient, economical, environmentally friendly and simple approach for managing STB. This study was carried out to evaluate spring bread wheat lines for their reaction to STB disease under field conditions; to associate phenotypic and genotypic data for identification of STB disease resistance; and to identify genomic region(s) associated with resistance to STB in spring bread wheat lines. Two hundred forty (240) spring bread wheat lines were evaluated under field conditions in non-replicated trials, using an augmented design. The trials were conducted at three locations (in 2017 main cropping season (July to December). Out of these 240 wheat lines, 123 of them were genotyped with 10263 single nucleotide poly-morphism (SNPs) markers and population structure and association mapping analysis was done. The wheat lines showed significant variations in percentage disease severity and area under the disease progress curve at all the three locations they were evaluated. The wheat lines were classified as resistant, moderately resistant, moderately susceptible and susceptible based on the percentage disease severity scored. Five wheat lines were found to be resistant to STB in all the three locations and are recommended for direct release by the national program and parentage purposes in wheat breeding programs. The 123 wheat lines were clustered into 3 subpopulations in which the first cluster contained 99 wheat lines; the second 17 and the last one 7. Among the polymorphic 8127 SNPs markers, 26 markers on chromosomes 7B, 1D, 3A, 2B, 6B and 3D were found to be significantly (P < 0.001) associated with STB resistance so that they can be utilized for marker assisted selection and gene pyramiding in resistance breeding programs.
... [45], while analyzing data acquired over three years on STB, found a significant negative correlation between STB and PLH. In 2013 [46], reported that STB resistance is associated with increased PLH. According to Ref. [38] also, reduced PLH was usually associated with more necrosis percentage. ...
... Thus, the QTL on chromosomes 7B, 1D, 3A, 2B and 3D found in this study could be identical or in very close proximity to the previously mapped ones. In addition to these major genes, several QTL have also been identified on these chromosomes using SNPs markers: on chromosomes 6B and 7B [54], on chromosome 3A [55] and on chromosome 2B [46]. Although the markers found to be significantly associated with STB resistance in this study were located on chromosomes on which septoria tritici blotch resistant genes (Stb genes) have been mapped and/or QTL have also been identified previously, localization cannot be compared due to the use of a different type of markers for the reveal or not reveal of sequence homology. ...
Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici, anamorph Septoria
tritici Rob. ex Desm., is an important wheat pathogen worldwide, reported to be major wheat
production threating factor, posing considerable yield loss every year. Developing resistant cultivars
is an efficient, economical, environmentally friendly and simple approach for managing
STB. This study was carried out to evaluate spring bread wheat lines for their reaction to STB
disease under field conditions; to associate phenotypic and genotypic data for identification of
STB disease resistance; and to identify genomic region(s) associated with resistance to STB in
spring bread wheat lines. Two hundred forty (240) spring bread wheat lines were evaluated under
field conditions in non-replicated trials, using an augmented design. The trials were conducted at
three locations (Kulumsa Agricultural Research Center, Madda Walabu University Research Site
and Sinana Agricultural Research Center) in 2017 main cropping season (July to December). Out
of these 240 wheat lines, 123 of them were genotyped with 10263 single nucleotide polymorphism
(SNPs) markers and population structure and association mapping analysis was done.
The wheat lines showed significant variations in percentage disease severity and area under the
disease progress curve at all the three locations they were evaluated. The wheat lines were
classified as resistant, moderately resistant, moderately susceptible and susceptible based on the
percentage disease severity scored. Five wheat lines were found to be resistant to STB in all the
three locations and are recommended for direct release by the national program and parentage
purposes in wheat breeding programs. The 123 wheat lines were clustered into 3 subpopulations
in which the first cluster contained 99 wheat lines; the second 17 and the last one 7. Among the
polymorphic 8127 SNPs markers, 26 markers on chromosomes 7B, 1D, 3A, 2B, 6B and 3D were
found to be significantly (P < 0.001) associated with STB resistance so that they can be utilized
for marker assisted selection and gene pyramiding in resistance breeding programs.
... STB resistance is negatively correlated with PH and DH, which are among the most confounding factors. Several studies reported increased disease severity in earlier heading and dwarf genotypes [22,27]. [3]respectively, conferring resistance to STB. ...
Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici, poses severe challenges to wheat cultivation worldwide. Deployment of resistant cultivars renders a practical way to control this disease. Therefore, the identification of resistant sources and genes/QTLs is imperative. We attempted to elucidate the genomic architecture for adult-plant STB resistance in a Septoria Association Mapping Panel (SAMP), which has 181 cultivars and advanced breeding genotypes from bread wheat breeding programs in India and Bangladesh. Field experiments identified several accessions such as BGD52 (CHIR7/ANB//CHIR1), BGD54 (CHIR7/ANB//CHIR1), IND92 (WH 1218), IND8 (DBW 168) and IND75 (PBW 800) possessing high levels of resistance. Genetic analysis indicated 21 stable quantitative trait nucleotides (QTNs) for STB resistance on all wheat chromosomes except 2D, 3A, 3D, 4A, 4D, 5D, 6B, 6D and 7A, most of which were found on previously identified chromosome regions for STB resistance. Three QTNs exhibited bigger phenotypic effects and were identified in all three experiments, including Q.STB.5A.1, Q.STB.5B.1and Q.STB.5B.3. Additionally, QTNs on chromosomes 1A (Q.STB.1A.1), 2A (Q.STB_DH.2A.1, Q.STB.2A.3), 2B (Q.STB.2B.4), 5A (Q.STB.5A.1, Q.STB.5A.2) and 7B (Q.STB.7B.2) might represent novel resistance QTL. The resistant genotypes and molecular markers identified in the present study could be used for STB resistance breeding programmes around the globe.
Background
Septoria tritici blotch (STB) disease causes yield losses of up to 50 per cent in susceptible wheat cultivars and can pose serious threat to wheat production. In this study, genomic architecture for adult-plant STB resistance in a Septoria Association Mapping Panel (SAMP) having 181 cultivars and genomic regions governing STB resistance in a South Asian wheat panel were looked for.
Results
The study found STB resistance sources, genomic regions, QTLs, haplotypes, pleiotropic SNPs, and candidate genes in Asian bread wheat genotypes. Five of the discovered QTNs i.e. on chromosomes 1A (Q.STB.1A.1), 2A (Q.STB_DH.2A.1, Q.STB.2A.3), 2B (Q.STB.2B.4), 5A (Q.STB.5A.1, Q.STB.5A.2) and 7B (Q.STB.7B.2) were potentially unique.
Conclusion
Our findings demonstrate the importance of Asian bread wheat as a source of STB resistance alleles and novel stable QTNs for wheat breeding initiatives to generate durable and broad-spectrum Z. tritici-resistant wheat cultivars.
... A large genetic variation for YR resistance was uncovered by molecular means in the closely-related durum wheats of European (Liu et al. 2017b;Miedaner et al. 2019), Canadian (Singh et al. 2013), and Ethiopian (Alemu et al. 2021;Liu et al. 2017c) origin. Because monogenic resistances for all three diseases are notoriously instable due to the highly flexible adaptation of the pathogen populations, the use of quantitative resistance in breeding is recommended (Miedaner et al. 2013). This strategy involves many genes (QTLs) and is best followed by genomic selection. ...
... Heading date had moderate correlations to YR and PM resistances, while plant height correlated with YR and STB resistances. The latter is known from literature (Miedaner et al. 2013) and might be related to plant architecture. Tallness of the emmer wheat might be a passive resistance mechanism to STB. ...
Emmer is a progenitor of bread wheat and evolved in the Levant together with the yellow rust (YR), powdery mildew (PM) fungi, and a precursor of Zymoseptoria tritici causing Septoria tritici blotch (STB). We performed a genome-wide association mapping for the three disease resistances with 143 cultivated emmer accessions in multi-environmental trials. Significant (P < 0.001) genotypic variation was found with high heritabilities for the resistances to the two biotrophs and a moderate heritability for STB resistance. For YR, PM, and STB severity nine, three, and seven marker-trait associations, respectively, were detected that were significant across all environments. Most of them were of low to moderate effect, but for PM resistance a potentially new major gene was found on chromosome 7AS. Genomic prediction abilities were high throughout for all three resistances (≥ 0.8) and decreased only slightly for YR and PM resistances when the prediction was done for the second year with the first year as training set (≥ 0.7). For STB resistance prediction ability was much lower in this scenario (0.4). Despite this, genomic selection should be advantageous given the large number of small QTLs responsible for quantitative disease resistances. A challenge for the future is to combine these multiple disease resistances with better lodging tolerance and higher grain yield.
... In addition to the major resistance loci, nearly 100 regions of the genome carrying quantitative trait loci (QTLs) and meta-QTLs with small effects have been identified (Brown et al. 2015;Piaskowska et al. 2021;Langlands-Perry et al. 2022). Significant loci associated with STB resistance have also been identified by genome-wide association studies (GWAS) (Kollers et al. 2013;Miedaner et al. 2013;Gurung et al. 2014;Odilbekov et al. 2019;Louriki et al. 2021;Yang et al. 2022). This method uses a diverse panel of genotypes consisting of varieties with a broad spectrum of resistance responses and diverse genetic backgrounds, thus bypassing the time-consuming process of crossing and crossing and breeding mapping progeny. ...
Knowledge of the magnitude of gene effects and their interactions, their nature, and contribution to determining quantitative traits is very important in conducting an effective breeding program. In traditional breeding, information on the parameter related to additive gene effect and additive-additive interaction (epistasis) and higher-order additive interactions would be useful. Although commonly overlooked in studies, higher-order interactions have a significant impact on phenotypic traits. Failure to account for the effect of triplet interactions in quantitative genetics can significantly underestimate additive QTL effects. Understanding the genetic architecture of quantitative traits is a major challenge in the post-genomic era, especially for quantitative trait locus (QTL) effects, QTL–QTL interactions, and QTL–QTL–QTL interactions. This paper proposes using weighted multiple linear regression to estimate the effects of triple interaction (additive–additive–additive) quantitative trait loci (QTL–QTL–QTL). The material for the study consisted of 126 doubled haploid lines of winter wheat (Mandub × Begra cross). The lines were analyzed for 18 traits, including percentage of necrosis leaf area, percentage of leaf area covered by pycnidia, heading data, and height. The number of genes (the number of effective factors) was lower than the number of QTLs for nine traits, higher for four traits and equal for five traits. The number of triples for unweighted regression ranged from 0 to 9, while for weighted regression, it ranged from 0 to 13. The total aaa gu effect ranged from − 14.74 to 15.61, while aaa gw ranged from − 23.39 to 21.65. The number of detected threes using weighted regression was higher for two traits and lower for four traits. Forty-nine statistically significant threes of the additive-by-additive-by-additive interaction effects were observed. The QTL most frequently occurring in threes was 4407404 (9 times). The use of weighted regression improved (in absolute value) the assessment of QTL–QTL–QTL interaction effects compared to the assessment based on unweighted regression. The coefficients of determination for the weighted regression model were higher, ranging from 0.8 to 15.5%, than for the unweighted regression. Based on the results, it can be concluded that the QTL–QTL–QTL triple interaction had a significant effect on the expression of quantitative traits. The use of weighted multiple linear regression proved to be a useful statistical tool for estimating additive-additive-additive ( aaa ) interaction effects. The weighted regression also provided results closer to phenotypic evaluations than estimator values obtained using unweighted regression, which is closer to the true values.
... Genome-wide association study (GWAS) has been successfully used to mine multiple putative QTLs/genes related to agronomically important features in a variety of plants, including disease resistance (Bartoli and Roux 2017;Kidane et al. 2017;Juliana et al. 2018;Odilbekov et al. 2019;Alemu et al. 2021;Mekonnen et al. 2021). For leaf blotch disease, several valuable QTLs/ genes have been discovered by GWAS and linkage mapping (Schilly et al. 2011;Tabib Ghaffary et al. 2012;Miedaner et al. 2013;Dreisigacker et al. 2015;Mirdita et al. 2015;Muqaddasi et al. 2019;Odilbekov et al. 2019). ...
Septoria tritici blotch or Septoria leaf blotch has been used for long time, but leaf blotch is a correct disease name. Moreover, Lb resistant gene is the correct name, but, not Stb gene. It has sexual and asexual parts on the mycelia, known as heterothallic fungi. Its pathogenic diversity ranged from 40% to 93% and has produced a wide variety of AvrLb6 haplotypes. M. graminicola has a plasmogamy and karyogamy sexual process. The pathogen can use macropycnidiospores, micropycnidiospores, and pycnidia vegetative growths for infection and overwintering. Synthetic M3, Kavkaz-K4500, Synthetic 6×, and TE9111 wheat genotypes have horizontal resistance. Avirulence (Avr) genes in Z. tritici and their matching wheat (R) genes indicate gene for gene mechanisms of resistance. Twenty-two R genes (vertical resistance) have been identified. In both horizontal and vertical resistance, different Lb genes have been broken down due to new Z.tritici virulent gene and currently Lb19 resistant gene is being recommended. Mixing of resistant and susceptible cultivars is also the most effective management strategy. Moreover, different cultural practices and biological control have been proposed. Lastly, different fungicides are also available. However, in developing countries cultivar mixture, isolates diversity, biological control, and epidemic studies have been greatly missed.
... Planting cultivars with durable genetic resistance is the most costeffective, long-lasting, and environmentally friendly way to control Septoria tritici blotch. Finding and using sources of resistance are top priorities in most breeding programs [55]. ...
Septoria tritici blotch (STB) caused by the fungus Mycosphaerella graminicola, is one of the most important foliar diseases of wheat (T. aestivum spp., aestivum L.) worldwide. The disease is pervasive and economically significant throughout Ethiopia's wheat-growing regions. Naturally susceptible wheat cultivars of STB disease were found in the Central Highlands of Ethiopia, where incidence (98%) and severity (97%) of the disease, as well as yield loss (41%), were documented. This disease has been managed using a variety of techniques, including cultural control, chemical control, and genetic controls have been utilized to control this disease and subsequently reduce yield losses. The lack of information on the diversity of diseases worldwide and in Ethiopia now hampers the screening and selection of wheat genotypes for disease resistance. In this review, wheat septoria disease management and molecular breeding approaches in Ethiopia were assessed.
... [45], while analyzing data acquired over three years on STB, found a significant negative correlation between STB and PLH. In 2013 [46], reported that STB resistance is associated with increased PLH. According to Ref. [38] also, reduced PLH was usually associated with more necrosis percentage. ...
... Thus, the QTL on chromosomes 7B, 1D, 3A, 2B and 3D found in this study could be identical or in very close proximity to the previously mapped ones. In addition to these major genes, several QTL have also been identified on these chromosomes using SNPs markers: on chromosomes 6B and 7B [54], on chromosome 3A [55] and on chromosome 2B [46]. Although the markers found to be significantly associated with STB resistance in this study were located on chromosomes on which septoria tritici blotch resistant genes (Stb genes) have been mapped and/or QTL have also been identified previously, localization cannot be compared due to the use of a different type of markers for the reveal or not reveal of sequence homology. ...
... The model has an acceptable but considerable RMSE. These results agree with a similar prediction model for STB severity (Miedaner et al. 2013). ...
Septoria tritici blotch (STB) is a foliar disease of wheat ( Triticum aestivum L.) caused by the ascomycete fungus Zymoseptoria tritici . STB is a polycyclic disease and represents a significant threat to wheat production, reducing yield and grain quality. The control of STB is mainly based on fungicides. Unfortunately, Z. tritici populations have evolved high resistance levels to some of these fungicides, causing them to lose their efficacy. Therefore, increasing STB resistance through plant breeding is the most cost-effective and environmentally friendly method for control. A recombinant inbred line (RIL) population was developed from a cross between a cultivar moderately susceptible to STB, ‘Madsen’ (PI 511673), and ‘Foote’ (PI 599663), which has provided moderate resistance to STB in the Pacific Northwest (PNW) region of the U.S. The RIL population, consisting of 217 lines, was phenotyped across multiple environments for STB response and genotyped using Illumina HiSeq 3000 Sequencing. The STACKS program was used to select SNPs. The best linear unbiased prediction (BLUP) value for each accession across different environments for STB severity was used for QTL mapping. Results of quantitative trait loci (QTL) analysis indicated minor genes associated with resistance in chromosomes 4B, 5A, 6B, 6D, and 7DS. Presence of all seven QTL in RILs reduced STB severity by over 70% compared to RILs lacking any of the QTL. These QTL could be used develop breeder-friendly molecular markers for genotypic selection of improved STB resistance in wheat in the PNW.
... A total of 1300 plants per year were evaluated for the disease in unreplicated field trials, across the three years (2015-2017) for each of the different populations and generations. The experiment used an alpha design [41]. Parents were used as controls, and each accession was sown as a single row of 1.5 m length spaced 25 cm apart at a rate of 40 seeds per meter [7]. ...
... The second digit (D2) represents the severity measured as coverage of leaf area with lesions bearing Figure 1: Crossing diagram adopted for the field trials in order to assess the cytoplasmic resistance through generations evaluated in 2015, 2016, and 2017. 5 BioMed Research International pycnidia on a scale from 0 (fully resistant) to 9 (fully susceptible) [41,46,48]. For global scoring of the disease severity, the percentage was calculated using the following formula (Sharma and Duveiller 2007; [31]): ...
Septoria tritici blotch (STB) is a major disease problem of wheat worldwide. To optimize the introgression of resistance genes in elite genotypes throughout traditional or molecular breeding programs, a full understanding of the quantitative inheritance of resistance to Zymoseptoria tritici, plant height (PH), and thousand kernel weight (TKW) is needed. In this study, maternal and cytoplasmic effects of resistance to STB were investigated using P1 (susceptible, high-yielding line) and P2 (resistant, low-yielding line) durum wheat lines and their F1, RF1, F2, RF2, BC1, RBC1, BC2, and RBC2 progeny, assessed for resistance to STB during three growing seasons. Duncan mean’s analysis revealed significant differences between generation means for STB, PH, and TKW. The two parents had an extreme pattern. The F1 and RF1 segregated close to their respective parents, suggesting the presence of cytoplasmic and maternal genetic effects for Z. tritici resistance, PH, and TKW. Separate generation mean’s analysis confirmed the results of the Duncan test. A three-parameter model was found to be not adequate for all traits in all three growing years; while a digenic epistatic model with cytoplasmic or/and maternal effect was adequate for all cases. Narrow-sense heritability was in the range of 50–60%, 30–69%, and 28–31% for STB, PH, and TKW, respectively. For STB, high heritability and the presence of fixable epistatic effect is encouraging and could lead to creating varieties with the right female parent to exploit cytoplasmic and maternal effects in order to improve resistance to Z. tritici in durum wheat.
