Expressed sequence tag (EST) projects have generated a vast amount of publicly available sequence data from plant species; these data can be mined for simple sequence repeats (SSRs). These SSRs are useful as molecular markers because their development is inexpensive, they represent transcribed genes and a putative function can often be deduced by a homology search. Because they are derived from transcripts, they are useful for assaying the functional diversity in natural populations or germplasm collections. These markers are valuable because of their higher level of transferability to related species, and they can often be used as anchor markers for comparative mapping and evolutionary studies. They have been developed and mapped in several crop species and could prove useful for marker-assisted selection, especially when the markers reside in the genes responsible for a phenotypic trait. Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed.

Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications.

Several recent molecular developments provide new genetic tools for addressing difficult problems in weed ecology. In this review, we describe some of the techniques and the DNA markers they generate [including amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs) or microsatellites, and intron‐polymerase chain reaction (intron‐PCR)], contrast their relative advantages and disadvantages, and discuss how they might be used in weed research. As these new markers generally reveal higher levels of variation than other techniques, they promise to improve our understanding of breeding systems, assist in determining the origin(s) of invaders, help to resolve taxonomic boundaries and relationships between closely related taxa and enable the identification of phenotypic linked markers. In addition, compared with other techniques, some of these markers may be more cost‐effective, less technically demanding and more reliable. Regardless of the marker adopted, all genetic studies will benefit from careful consideration of experimental design and the formulation of testable hypotheses with practical outcomes.

The advent of complete genetic linkage maps consisting of codominant DNA markers [typically restriction fragment length polymorphisms (RFLPs)] has stimulated interest in the systematic genetic dissection of discrete Mendelian factors underlying quantitative traits in experimental organisms. We describe here a set of analytical methods that modify and extend the classical theory for mapping such quantitative trait loci (QTLs). These include: (i) a method of identifying promising crosses for QTL mapping by exploiting a classical formula of SEWALL WRIGHT; (ii) a method (interval mapping) for exploiting the full power of RFLP linkage maps by adapting the approach of LOD score analysis used in human genetics, to obtain accurate estimates of the genetic location and phenotypic effect of QTLs; and (iii) a method (selective genotyping) that allows a substantial reduction in the number of progeny that need to be scored with the DNA markers. In addition to the exposition of the methods, explicit graphs are provided that allow experimental geneticists to estimate, in any particular case, the number of progeny required to map QTLs underlying a quantitative trait.

In many plants, single nucleotide polymorphism (SNP) markers are increasingly becoming the marker system of choice. However, for many crop plants there are surprisingly low numbers of validated SNP markers available although they are needed in large numbers for studies regarding genetic variation, linkage mapping, population structure analysis, association genetics, map-based gene isolation, and plant breeding. This review summarizes the current status of SNP marker development technologies for major crop plants. It will also provide an outlook into the future regarding possible SNP identification approaches in crop plants on the basis of current development in model systems such as Arabidopsis which will become available with the full sequencing of more plant genomes, genome resequencing, and in conjunction with the next-generation sequencing technologies.

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive disease seriously threatening yield and quality of common wheat (Triticum aestivum L., 2n=6x=42, AABBDD). Characterization of resistance genes against powdery mildew is useful in parental selection and for developing disease resistant cultivars. Chinese wheat breeding line KN0816 has superior agronomic performance and resistance to powdery mildew at all growth stages. Genetic analysis using populations of KN0816 crossed with different susceptible parents indicated that a single dominant gene, tentatively designated PmKN0816, conferred seedling resistance to different Bgt isolates. Using a bulked segregant analysis (BSA), PmKN0816 was mapped to the Pm6 interval on chromosome arm 2BL using polymorphic markers linked to the catalogued genes Pm6, Pm52, and Pm64, and flanked by markers CISSR02g-6 and CIT02g-2 both with genetic distances of 0.7 cM. Analysis of closely linked molecular markers indicated that the marker alleles of PmKN0816 differed from those of other powdery mildew resistance genes on 2BL, including Pm6, Pm33, Pm51, Pm64, and PmQ. Based on the genetic and physical locations and response pattern to different Bgt isolates, PmKN0816 is most likely a new powdery mildew resistance gene and confers effective resistance to all the 14 tested Bgt isolates. In view of the elite agronomic performance of KN0816 combined with the resistance, PmKN0816 is expected to become a valuable resistance gene in wheat breeding. To transfer PmKN0816 to different genetic backgrounds using marker-assisted selection (MAS), closely linked markers of PmKN0816 were evaluated and four of them (CIT02g-2, CISSR02g-6, CIT02g-10, and CIT02g-17) were confirmed to be applicable for MAS in different genetic backgrounds.

Zhengmai 7698 is an elite winter wheat variety widely cultivated in the Southern regions of the Yellow-Huai River Valley of China. Here, we report the molecular markers used for breeding Zhengmai 7698 and the genome composition of this cultivar revealed using genome-wide SNPs. A total of 26 DNA markers derived from the genes controlling gluten protein quality, grain hardness, flour color, disease resistance, or pre-harvesting sprouting resistance were used during breeding. Consequently, Zhengmai 7698 had strong gluten, high grain hardness index, white flour color, and high levels of resistance to powdery mildew, stripe rust infections, and pre-harvesting sprouting. Using genome complexity reduction, 28,996 high-quality SNPs distributed on 21 wheat chromosomes were identified among Zhengmai 7698 and its three parental lines (4B269, Zhengmai 9405 and Zhoumai 16). Zhengmai 7698 shared 12,776, 14,411 and 16,085 SNPs with 4B269, Zhengmai 9405 and Zhoumai 16, respectively. Thus, the contributions of 4B269, Zhengmai 9405 and Zhoumai 16 to the genome of Zhengmai 7698 were comparable. Interestingly, Zhengmai 7698 had 307 unique SNPs that are absent in all three parents. We suggest that molecular markers facilitate selection of a wheat cultivar with multiple elite traits. Analysis of genome composition with SNPs may provide useful clues for further dissecting the genetic basis of improved wheat performance.

Quantitative trait loci (QTL) is one of the most important steps in marker-assisted selection. Few studies have validated quantitative trait loci for marker-assisted selection of yield traits under drought stress conditions in wheat. A set of 138 highly diverse wheat genotypes were tested under normal and drought stress conditions for 2 years. Plant height, heading date, spike length, grain number per spike, grain yield per spike, and 1000-kernel weight were scored. High genetic variation was found among genotypes in all traits scored under both conditions in the 2 years. The same panel was genotyped using a diversity-array technology (DArT) marker, and a genome-wide association study was performed to find alleles associated with yield traits under all conditions. A set of 191 significant DArT markers were identified in this study. The results of the genome-wide association study revealed eight common markers in wheat that were significantly associated with the same traits under both conditions in the 2 years. Out of the eight markers, seven were located on the D genome except one marker. Four validated markers were located on the 3D chromosome and found in complete linkage disequilibrium. Moreover, these four markers were significantly associated with the heading date under both conditions and the grain yield per spike under drought stress condition in the 2 years. This high-linkage disequilibrium genomic region was located within the TraesCS3D02G002400 gene model. Furthermore, of the eight validated markers, seven were previously reported to be associated with yield traits under normal and drought conditions. The results of this study provided very promising DArT markers that can be used for marker-assisted selection to genetically improve yield traits under normal and drought conditions.

Wheat (Triticum aestivum L.) is a staple food crop for the global human population, and thus wheat breeders are consistently working to enhance its yield worldwide. In this study, we utilized a sub-set of Indian wheat mini core germplasm to underpin the genetic architecture for seed shape-associated traits. The wheat mini core subset (125 accessions) was genotyped using 35K SNP array and evaluated for grain shape traits such as grain length (GL), grain width (GW), grain length, width ratio (GLWR), and thousand grain weight (TGW) across the seven different environments (E1, E2, E3, E4, E5, E5, E6, and E7). Marker-trait associations were determined using a multi-locus random-SNP-effect Mixed Linear Model (mrMLM) program. A total of 160 non-redundant quantitative trait nucleotides (QTNs) were identified for four grain shape traits using two or more GWAS models. Among these 160 QTNs, 27, 36, 38, and 35 QTNs were associated for GL, GW, GLWR, and TGW respectively while 24 QTNs were associated with more than one trait. Of these 160 QTNs, 73 were detected in two or more environments and were considered reliable QTLs for the respective traits. A total of 135 associated QTNs were annotated and located within the genes, including ABC transporter, Cytochrome450, Thioredoxin_M-type, and hypothetical proteins. Furthermore, the expression pattern of annotated QTNs demonstrated that only 122 were differentially expressed, suggesting these could potentially be related to seed development. The genomic regions/candidate genes for grain size traits identified in the present study represent valuable genomic resources that can potentially be utilized in the markers-assisted breeding programs to develop high-yielding varieties.

Wheat is a cereal that is majorly consumed around the world. There is a dire need for the advancement of wheat cultivars that are producing high yield. The experiment was conducted to characterize the spike related traits of wheat genotypes. Twenty wheat genotypes comprising three replications were experimented using randomized complete block design. The difference was significant among the studied twenty genotypes revealed by analysis of variance. Correlation Pearson’s revealed that the number of grains per spike (GPS) has positive relationship among all the studied traits such as the number of tillers per plant (NTP), spike weight (SWT), spike length (SL), and grain yield per plant (GYP). The GYP has a strong positive association with GPS (0.81**), GYS (0.78**), and SL (0.68**). The biological yield had a non-significant association with GYS (0.28) and GPS (0.13). All studied attributes have variations in the mean values which were represented by Radar analysis. The genotype Sadiq-21 was the best performing genotype among the SWT, GYS and BY followed by genotype Nawab-21 which performed best among the NTP, GYS and GPS and genotype Ghazi-19 which performed good among BY, SWT and GPS. The genotypes that were among the worst performing were Suren-10, Galaxy-13 and Borluag-16. The result of our study showed grain yield was mainly affected by NTP, GYS and GPS. For the improvement of wheat yield, these attributes must be improved for selection so that the yield of the wheat can be increased because these have a strong association with the grain yield.

Drought is most likely the most significant abiotic stress affecting wheat yield. The discovery of drought-tolerant genotypes is a promising strategy for dealing with the world's rapidly diminishing water resources and growing population. A genome-wide association study (GWAS) was conducted on 298 Iranian bread wheat landraces and cultivars to investigate the genetic basis of yield, yield components, and drought tolerance indices in two cropping seasons (2018-2019 and 2019-2020) under rainfed and well-watered environments.A heatmap display of hierarchical clustering divided cultivars and landraces into four categories, with high-yielding and drought-tolerant genotypes clustering in the same group. The results of the principal component analysis (PCA) demonstrated that selecting genotypes based on the mean productivity (MP), geometric mean productivity (GMP), harmonic mean (HM), and stress tolerance index (STI) can help achieve high-yield genotypes in the environment. Genome B had the highest number of significant marker pairs in linkage disequilibrium (LD) for both landraces (427,017) and cultivars (370,359). Similar to cultivars, marker pairs on chromosome 4A represented the strongest LD (r = 0.32). However, the genomes D, A, and B have the highest LD, respectively. The single-locus mixed linear model (MLM) and multi-locus random-SNP-effect mixed linear model (mrMLM) identified 1711 and 1254 significant marker-trait association (MTAs) (-log10 P > 3) for all traits, respectively. A total of 874 common quantitative trait nucleotides (QTNs) were simultaneously discovered by both MLM and mrMLM methods. Gene ontology revealed that 11, 18, 6, and 11 MTAs were found in protein-coding regions (PCRs) for spike weight (SW), thousand kernel weight (TKW), grain number per spike (GN), and grain yield (GY), respectively.The results identified rich regions of quantitative trait loci (QTL) on Ch. 4A and 5A suggest that these chromosomes are important for drought tolerance and could be used in wheat breeding programs. Furthermore, the findings indicated that landraces studied in Iranian bread wheat germplasm possess valuable alleles, that are responsive to water-limited conditions. This GWAS experiment is one of the few types of research conducted on drought tolerance that can be exploited in the genome-mediated development of novel varieties of wheat.© 2023. BioMed Central Ltd., part of Springer Nature.

Increasing grain quality and nutritional value along with yield in bread wheat is one of the leading breeding goals. Selection of genotypes with desired traits using traditional breeding selection methods is very time-consuming and often not possible due to the interaction of environmental factors. By identifying DNA markers that can be used to identify genotypes with desired alleles, high-quality and bio-fortified bread wheat production can be achieved in a short time and cost-effectively. In the present study, 134 doubled haploid (DH) wheat lines and their four parents were phenotypically evaluated for yield components (spike characteristics), quality parameters, and grain Fe and Zn concentrations in two successive growing seasons. At the same time, ten genic simple sequence repeats (SSR) markers linked to genes related to the traits examined were validated and subsequently used for molecular characterization of trait-specific candidate genotypes. Significant genotypic variations were determined for all studied traits and many genotypes with desired phenotypic values were detected. The evaluation performed with 10 SSR markers revealed significant polymorphism between genotypes. The polymorphic information content (PIC) values of 10 markers ranged from 0.00 to 0.87. Six out of 10 SSRs could be more effective in representing the genotypic differentiation of the DH population as they demonstrated the highest genetic diversity. Both Unweighted Pair Group Method with Arithmetic Mean (UPGMA) clustering and STRUCTURE analyses divided 138 wheat genotypes into five (K = 5) main groups. These analyzes were indicative of genetic variation due to hybridization and segregation in the DH population and the differentiation of the genotypes from their parents. Single marker regression analysis showed that both Xbarc61 and Xbarc146 had significant relationships with grain Fe and Zn concentrations, while Xbarc61 related to spike characteristics and Xbarc146 related to quality traits, separately. Other than these, Xgwm282 was associated with spike harvest index, SDS sedimentation value and Fe grain concentration, while Gwm445 was associated with spikelet number, grain number per spike and grain Fe concentration. These markers were validated for the studied DH population during the present study and they could be effectively used for marker-assisted selection to improve grain yield, quality, and bio-fortification capacity of bread wheat.

Durum wheat breeding relies on grain yield improvement to meet its upcoming demand while coping with climate change. Kernel size and shape are the determinants of thousand kernel weight (TKW), which is a key component of grain yield, and the understanding of the genetic control behind these traits supports the progress in yield potential. The present study aimed to dissect the genetic network responsible for kernel size components (length, width, perimeter, and area) and kernel shape traits (width-to-length ratio and formcoefficient) as well as their relationships with kernel weight, plant height, and heading date in durum wheat. Quantitative Trait Locus (QTL) mapping was performed on a segregating population of 110 recombinant inbred lines, derived from a cross between the domesticated emmer wheat accession MG5323 and the durum wheat cv. Latino, evaluated in four different environments. A total of 24 QTLs stable across environments were found and further grouped in nine clusters on chromosomes 2A, 2B, 3A, 3B, 4B, 6B, and 7A. Among them, a QTL cluster on chromosome 4B was associated with kernel size traits and TKW, where the parental MG5323 contributed the favorable alleles, highlighting its potential to improve durum wheat germplasm. The physical positions of the clusters, defined by the projection on the T. durum reference genome, overlapped with already known genes (i.e., BIG GRAIN PROTEIN 1 on chromosome 4B). These results might provide genome-based guidance for the efficient exploitation of emmer wheat diversity in wheat breeding, possibly through yield-related molecular markers.

A set of 188 recombinant inbred lines (RILs) derived from a cross between a high-yielding Indian bread wheat cultivar HD2932 and a synthetic hexaploid wheat (SHW) Synthetic 46 derived from tetraploid Triticum turgidum (AA, BB 2n = 28) and diploid Triticum tauschii (DD, 2n = 14) was used to identify novel genomic regions associated in the expression of grain iron concentration (GFeC), grain zinc concentration (GZnC), grain protein content (GPC) and thousand kernel weight (TKW). The RIL population was genotyped using SNPs from 35K Axiom® Wheat Breeder’s Array and 34 SSRs and phenotyped in two environments. A total of nine QTLs including five for GPC (QGpc.iari_1B, QGpc.iari_4A, QGpc.iari_4B, QGpc.iari_5D, and QGpc.iari_6B), two for GFeC (QGfec.iari_5B and QGfec.iari_6B), and one each for GZnC (QGznc.iari_7A) and TKW (QTkw.iari_4B) were identified. A total of two stable and co-localized QTLs (QGpc.iari_4B and QTkw.iari_4B) were identified on the 4B chromosome between the flanking region of Xgwm149–AX-94559916. In silico analysis revealed that the key putative candidate genes such as P-loop containing nucleoside triphosphatehydrolase, Nodulin-like protein, NAC domain, Purine permease, Zinc-binding ribosomal protein, Cytochrome P450, Protein phosphatase 2A, Zinc finger CCCH-type, and Kinesin motor domain were located within the identified QTL regions and these putative genes are involved in the regulation of iron homeostasis, zinc transportation, Fe, Zn, and protein remobilization to the developing grain, regulation of grain size and shape, and increased nitrogen use efficiency. The identified novel QTLs, particularly stable and co-localized QTLs are useful for subsequent use in marker-assisted selection (MAS).

Grain protein content (GPC) is a key aspect of grain quality, a major determinant of the flour functional properties and grain nutritional value of bread wheat. Exploiting diverse germplasms to identify genes for improving crop performance and grain nutritional quality is needed to enhance food security. Here, we evaluated GPC in a panel of 255 Triticum aestivum L. accessions from 27 countries. GPC determined in seeds from three consecutive crop seasons varied from 8.6 to 16.4% (11.3% on average). Significant natural phenotypic variation in GPC among genotypes and seasons was detected. The population was evaluated for the presence of the trait-linked single nucleotide polymorphism (SNP) markers via a genome-wide association study (GWAS). GWAS analysis conducted with calculated best linear unbiased estimates (BLUEs) of phenotypic data and 90 K SNP array using the fixed and random model circulating probability unification (FarmCPU) model identified seven significant genomic regions harboring GPC-associated markers on chromosomes 1D, 3A, 3B, 3D, 4B and 5A, of which those on 3A and 3B shared associated SNPs with at least one crop season. The verified SNP–GPC associations provide new promising genomic signals on 3A (SNPs: Excalibur_c13709_2568 and wsnp_Ku_c7811_13387117) and 3B (SNP: BS00062734_51) underlying protein improvement in wheat. Based on the linkage disequilibrium for significant SNPs, the most relevant candidate genes within a 4 Mbp-window included genes encoding a subtilisin-like serine protease; amino acid transporters; transcription factors; proteins with post-translational regulatory functions; metabolic proteins involved in the starch, cellulose and fatty acid biosynthesis; protective and structural proteins, and proteins associated with metal ions transport or homeostasis. The availability of molecular markers within or adjacent to the sequences of the detected candidate genes might assist a breeding strategy based on functional markers to improve genetic gains for GPC and nutritional quality in wheat.

The content and quality of gluten in wheat grain is a distinctive characteristic that determines the final properties of wheat flour. In this study, a genome-wide association study (GWAS) was performed on a wheat panel consisting of bread wheat varieties and the introgression lines (ILs) obtained via hybridization with tetraploid wheat relatives. A total of 17 stable quantitative trait nucleotides (QTNs) located on chromosomes 1D, 2A, 2B, 3D, 5A, 6A, 7B, and 7D that explained up to 21% of the phenotypic variation were identified. Among them, the QTLs on chromosomes 2A and 7B were found to contain three and six linked SNP markers, respectively. Comparative analysis of wheat genotypes according to the composition of haplotypes for the three closely linked SNPs of chromosome 2A indicated that haplotype TT/AA/GG was characteristic of ten ILs containing introgressions from T. timopheevii. The gluten content in the plants with TT/AA/GG haplotype was significantly higher than in the varieties with haplotype GG/GG/AA. Having compared the newly obtained data with the previously reported quantitative trait loci (QTLs) we inferred that the locus on chromosome 2A inherited from T. timopheevii is potentially novel. The introgression lines containing the new locus can be used as sources of genetic factors to improve the quality traits of bread wheat.

Wheat is grown and consumed worldwide, making it an important staple food crop for both its calorific and nutritional content. In places where wheat is used as a staple food, suboptimal micronutrient content levels, especially of grain iron (Fe) and zinc (Zn), can lead to malnutrition. Grain nutrient content is influenced by abiotic stresses, such as drought and heat stress. The best method for addressing micronutrient deficiencies is the biofortification of food crops. The prerequisites for marker-assisted varietal development are the identification of the genomic region responsible for high grain iron and zinc contents and an understanding of their genetics.

Wheat is a major staple crop and helps to reduce worldwide micronutrient deficiency. Investigating the genetics that control the concentrations of iron (Fe) and zinc (Zn) in wheat is crucial. Hence, we undertook a comprehensive study aimed at elucidating the genomic regions linked to the contents of Fe and Zn in the grain.We performed the multi-locus genome-wide association (ML-GWAS) using a panel of 161 wheat-Aegilops substitution and addition lines to dissect the genomic regions controlling grain iron (GFeC), and grain zinc (GZnC) contents. The wheat panel was genotyped using 10,825 high-quality SNPs and phenotyped in three different environments (E1-E3) during 2017-2019. A total of 111 marker-trait associations (MTAs) (at p-value < 0.001) were detected that belong to all three sub-genomes of wheat. The highest number of MTAs were identified for GFeC (58), followed by GZnC (44) and yield (9). Further, six stable MTAs were identified for these three traits and also two pleiotropic MTAs were identified for GFeC and GZnC. A total of 1291 putative candidate genes (CGs) were also identified for all three traits. These CGs encode a diverse set of proteins, including heavy metal-associated (HMA), bZIP family protein, AP2/ERF, and protein previously associated with GFeC, GZnC, and grain yield.The significant MTAs and CGs pinpointed in this current study are poised to play a pivotal role in enhancing both the nutritional quality and yield of wheat, utilizing marker-assisted selection (MAS) techniques.© 2023. The Author(s), under exclusive licence to Springer Nature B.V.

Sedimentation values and falling number in the last decades have helped maintain high baking quality despite rigorous selection for grain yield in wheat. Allelic combinations of major loci sustained the bread-making quality while improving grain yield. Glu-D1, Pinb-D1, and non-gluten proteins are associated with sedimentation values and falling number in European wheat.

Leaf rust (LR) is the most widespread disease of common wheat worldwide. In order to evaluate leaf rust resistance, 70 uncharacterized wheat cultivars and promising lines with unknown leaf rust resistance genes (Lr genes) were exposed to Kazakhstani Puccinia triticina (Pt) races at the seedling stage. Field tests were performed to characterize leaf rust responses at the adult plant growth stage in the 2020–2021 and 2021–2022 cropping seasons. The wheat collection showed phenotypic diversity when tested with two virulent races of Pt. Thirteen wheat genotypes (18.6%) showed high resistance at both seedling and adult plant stages. In most cases, breeding material originating from international nurseries showed higher resistance to LR. Nine Lr genes, viz. Lr9, Lr10, Lr19, Lr26, Lr28, Lr34, Lr37, Lr46, and Lr68, either singly or in combination, were identified in 47 genotypes. Known Lr genes were not detected in the remaining 23 genotypes. The most commonly identified resistance genes were Lr37 (17 cultivars), Lr34 (16 cultivars), and Lr46 (10 cultivars), while Lr19, Lr68, Lr26, and Lr28 were the least frequent. Four Lr genes were identified in Keremet and Hisorok, followed by three Lr genes in Aliya, Rasad, Reke, Mataj, Egana and Almaly/Obri. The molecular screening revealed twenty-nine carriers of a single Lr gene, ten carriers of two genes, six carriers of three genes, and two carriers of four genes. Most of these accessions showed a high and moderate level of APR (Adult plant resistance) and may be utilized for the incorporation of Lr genes in well-adapted wheat cultivars. The most effective combination was Lr37, Lr34, and Lr68, the carriers of which were characterized by a low disease susceptibility index. The obtained results will facilitate breeding programs for wheat resistance in Kazakhstan.

Thirteen known Yr gene-associated markers pertaining to genes (Yr5,Yr10,Yr15,Yr24/Yr26) were used to identify the genes in selected wheat germplasm which were found resistant under field conditions at two locations in Punjab, India against stripe rust. In field evaluation, 38 genotypes exhibited highly resistant response, with a final rust severity (FRS) ranging from 0 to TR. Seven genotypes expressed a resistant to moderately resistant response with FRS ranging from 5MR–10S. In race-specific phenotying against most prevalent pathotypes of Pucciniastriiformistritici (46S119,110S119 &amp;238S119) by seedling reaction test (SRT) 14 genotypes (29.2%) were found to be immune (IT = 0), 28 genotypes (58.3%) were resistant (IT = 1), and 3 genotypes (6.3%) were moderately resistant (IT = 2). Yr5 was detected in sixteen lines with the help of two markers Xwmc175 and Xgwm120 linked with Yr5. Yr10 was detected in ten lines with the marker Xpsp3000 and Yr15 was detected in fourteen lines with two linked markers; Xgwm413 and Xgwm273. Likewise, Yr24/26 was detected in 15 lines with two linked markers, namely Xbarc181 and Xbarc187. Based on the race specific phenotyping data and marker data, fourteen lines were found to carry a single gene, 16 showed the presence of two gene combinations, and seven genotypes were found to have a combination of three genes. Frequencies of Yr5, Yr15 and Yr26/Yr24 was high among test wheat germplasm in comparison to Yr10.

The two recombinant inbred line (RIL) populations developed by crossing Almaly × Avocet S (206 RILs) and Almaly × Anza (162 RILs) were used to detect the novel genomic regions associated with adult plant resistance (APR) and seedling or all-stage resistance (ASR) to yellow rust (YR) and leaf rust (LR). The quantitative trait loci (QTLs) were detected through multi-year phenotypic evaluations (2018–2020) and using high-throughput DArTseq genotyping technology. RILs exhibited significant genetic variation with p &amp;lt; 0.001, and the coefficient of variation ranged from 9.79% to 47.99% for both LR and YR in all Environments and stages of evaluations. The heritability is quite high and ranged between 0.47 and 0.98. We identified nine stable QTLs for YR APR on chromosomes 1B, 2A, 2B, 3D, and 4D and four stable QTLs for LR APR on chromosomes 2B, 3B, 4A, and 5A. Furthermore, in silico analysis revealed that the key putative candidate genes such as cytochrome P450, protein kinase-like domain superfamily, zinc-binding ribosomal protein, SANT/Myb domain, WRKY transcription factor, nucleotide sugar transporter, and NAC domain superfamily were in the QTL regions and probably involved in the regulation of host response toward pathogen infection. The stable QTLs identified in this study are useful for developing rust-resistant varieties through marker-assisted selection (MAS).

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a severe disease in wheat worldwide, including Ethiopia, causing up to 100% wheat yield loss in the worst season. The use of resistant cultivars is considered to be the most effective and durable management technique for controlling the disease. Therefore, the present study targeted the genetic architecture of adult plant resistance to yellow rust in 178 wheat association panels. The panel was phenotyped for yellow rust adult-plant resistance at three locations. Phonological, yield, yield-related, and agro-morphological traits were recorded. The association panel was fingerprinted using the genotyping-by-sequencing (GBS) platform, and a total of 6,788 polymorphic single nucleotide polymorphisms (SNPs) were used for genome-wide association analysis to identify effective yellow rust resistance genes. The marker-trait association analysis was conducted using the Genome Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability for the considered traits ranged from 74.52% to 88.64%, implying the presence of promising yellow rust resistance alleles in the association panel that could be deployed to improve wheat resistance to the disease. The overall linkage disequilibrium (LD) declined within an average physical distance of 31.44 Mbp at r2 = 0.2. Marker-trait association (MTA) analysis identified 148 loci significantly (p = 0.001) associated with yellow rust adult-plant resistance. Most of the detected resistance quantitative trait loci (QTLs) were located on the same chromosomes as previously reported QTLs for yellow rust resistance and mapped on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7D. However, 12 of the discovered MTAs were not previously documented in the wheat literature, suggesting that they could represent novel loci for stripe rust resistance. Zooming into the QTL regions in IWGSC RefSeq Annotation v1 identified crucial disease resistance-associated genes that are key in plants’ defense mechanisms against pathogen infections. The detected QTLs will be helpful for marker-assisted breeding of wheat to increase resistance to stripe rust. Generally, the present study identified putative QTLs for field resistance to yellow rust and some important agronomic traits. Most of the discovered QTLs have been reported previously, indicating the potential to improve wheat resistance to yellow rust by deploying the QTLs discovered by marker-assisted selection.

Fusarium head blight (FHB), caused by Fusarium graminearum, is one of the most destructive wheat diseases worldwide. FHB infection can dramatically reduce grain yield and quality due to mycotoxins contamination. Wheat resistance to FHB is quantitatively inherited and many low-effect quantitative trait loci (QTL) have been mapped in the wheat genome. Synthetic hexaploid wheat (SHW) represents a novel source of FHB resistance derived from Aegilops tauschii and Triticum turgidum that can be transferred into common wheat (T. aestivum). In this study, a panel of 194 spring Synthetic Hexaploid Derived Wheat (SHDW) lines from the International Maize and Wheat Improvement Center (CIMMYT) was evaluated for FHB response under field conditions over three years (2017-2019). A significant phenotypic variation was found for disease incidence, severity, index, number of Fusarium Damaged Kernels (FDKs), and deoxynivalenol (DON) content. Further, 11 accessions displayed < 10 ppm DON in 2017 and 2019. Genotyping of the SHDW panel using a 90 K Single Nucleotide Polymorphism (SNP) chip array revealed 31 K polymorphic SNPs with a minor allele frequency (MAF) > 5%, which were used for a Genome-Wide Association Study (GWAS) of FHB resistance. A total of 52 significant marker-trait associations for FHB resistance were identified. These included 5 for DON content, 13 for the percentage of FDKs, 11 for the FHB index, 3 for disease incidence, and 20 for disease severity. A survey of genes associated with the markers identified 395 candidate genes that may be involved in FHB resistance. Collectively, our results strongly support the view that utilization of synthetic hexaploid wheat in wheat breeding would enhance diversity and introduce new sources of resistance against FHB into the common wheat gene pool. Further, validated SNP markers associated with FHB resistance may facilitate the screening of wheat populations for FHB resistance.© 2023. The Author(s).

Durum wheat is more susceptible to Fusarium head blight (FHB) than other types or classes of wheat. The disease is one of the most devastating in wheat; it reduces yield and end-use quality and contaminates the grain with fungal mycotoxins such as deoxynivalenol (DON). A panel of 265 Canadian and European durum wheat cultivars, as well as breeding and experimental lines, were tested in artificially inoculated field environments (2019–2022, inclusive) and two greenhouse trials (2019 and 2020). The trials were assessed for FHB severity and incidence, visual rating index, Fusarium-damaged kernels, DON accumulation, anthesis or heading date, maturity date, and plant height. In addition, yellow pigment and protein content were analyzed for the 2020 field season. To capture loci underlying FHB resistance and related traits, GWAS was performed using single-locus and several multi-locus models, employing 13,504 SNPs. Thirty-one QTL significantly associated with one or more FHB-related traits were identified, of which nine were consistent across environments and associated with multiple FHB-related traits. Although many of the QTL were identified in regions previously reported to affect FHB, the QTL QFhb-3B.2, associated with FHB severity, incidence, and DON accumulation, appears to be novel. We developed KASP markers for six FHB-associated QTL that were consistently detected across multiple environments and validated them on the Global Durum Panel (GDP). Analysis of allelic diversity and the frequencies of these revealed that the lines in the GDP harbor between zero and six resistance alleles. This study provides a comprehensive assessment of the genetic basis of FHB resistance and DON accumulation in durum wheat. Accessions with multiple favorable alleles were identified and will be useful genetic resources to improve FHB resistance in durum breeding programs through marker-assisted recurrent selection and gene stacking.

Powdery mildew (PM) of wheat caused by Blumeria graminis f. sp. tritici is among the most important wheat diseases, causing significant yield and quality losses in many countries worldwide. Considerable progress has been made in resistance breeding to mitigate powdery mildew. Genetic host resistance employs either race-specific (qualitative) resistance, race-non-specific (quantitative), or a combination of both. Over recent decades, efforts to identify host resistance traits to powdery mildew have led to the discovery of over 240 genes and quantitative trait loci (QTLs) across all 21 wheat chromosomes. Sources of PM resistance in wheat include landraces, synthetic, cultivated, and wild species. The resistance identified in various genetic resources is transferred to the elite genetic background of a well-adapted cultivar with minimum linkage drag using advanced breeding and selection approaches. In this effort, wheat landraces have emerged as an important source of allelic and genetic diversity, which is highly valuable for developing new PM-resistant cultivars. However, most landraces have not been characterized for PM resistance, limiting their use in breeding programs. PM resistance is a polygenic trait; therefore, the degree of such resistance is mostly influenced by environmental conditions. Another challenge in breeding for PM resistance has been the lack of consistent disease pressure in multi-environment trials, which compromises phenotypic selection efficiency. It is therefore imperative to complement conventional breeding technologies with molecular breeding to improve selection efficiency. High-throughput genotyping techniques, based on chip array or sequencing, have increased the capacity to identify the genetic basis of PM resistance. However, developing PM-resistant cultivars is still challenging, and there is a need to harness the potential of new approaches to accelerate breeding progress. The main objective of this review is to describe the status of breeding for powdery mildew resistance, as well as the latest discoveries that offer novel ways to achieve durable PM resistance. Major topics discussed in the review include the genetic basis of PM resistance in wheat, available genetic resources for race-specific and adult-plant resistance to PM, important gene banks, and conventional and complimentary molecular breeding approaches, with an emphasis on marker-assisted selection (MAS).

Wheat powdery mildew (PM) causes significant yield losses worldwide. None of the Egyptian wheat cultivars was detected to be highly resistant to such a severe disease. Therefore, a diverse spring wheat panel was evaluated for PM seedling resistance using different Bgt conidiospores collected from Egyptian fields in two growing seasons. The evaluation was done in two separate experiments. Highly significant differences were found between the two experiments suggesting the presence of different isolates populations. Highly significant differences were found among the tested genotypes confirming the ability to improve PM resistance using the recent panel. Genome-wide association study (GWAS) was done for each experiment separately and a total of 71 significant markers located within 36 gene models were identified. The majority of these markers are located on chromosome 5B. Haplotype block analysis identified seven blocks containing the significant markers on chromosome 5B. Five gene models were identified on the short arm of the chromosome. Gene enrichment analysis identified five and seven pathways based on the biological process and molecular functions respectively for the detected gene models. All these pathways are associated with disease resistance in wheat. The genomic regions on 5B seem to be novel regions that are associated with PM resistance under Egyptian conditions. Selection of superior genotypes was done and Grecian genotypes seem to be a good source for improving PM resistance under Egyptian conditions.

Powdery mildew (PM), caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), significantly threatens global bread wheat production. Although the use of resistant cultivars is an effective strategy for managing PM, currently available wheat cultivars lack sufficient levels of resistance. To tackle this challenge, we conducted a comprehensive genome-wide association study (GWAS) using a diverse panel of 286 bread wheat genotypes. Over three consecutive years (2020–2021, 2021–2022, and 2022–2023), these genotypes were extensively evaluated for PM severity under field conditions following inoculation with virulent Bgt isolates. The panel was previously genotyped using the Illumina 90K Infinium iSelect assay to obtain genome-wide single-nucleotide polymorphism (SNP) marker coverage. By applying FarmCPU, a multilocus mixed model, we identified a total of 113 marker–trait associations (MTAs) located on chromosomes 1A, 1B, 2B, 3A, 3B, 4A, 4B, 5A, 5B, 6B, 7A, and 7B at a significance level of p ≤ 0.001. Notably, four novel MTAs on chromosome 6B were consistently detected in 2020–2021 and 2021–2022. Furthermore, within the confidence intervals of the identified SNPs, we identified 96 candidate genes belonging to different proteins including 12 disease resistance/host–pathogen interaction-related protein families. Among these, protein kinases, leucine-rich repeats, and zinc finger proteins were of particular interest due to their potential roles in PM resistance. These identified loci can serve as targets for breeding programs aimed at developing disease-resistant wheat cultivars.

Septoria tritici blotch (STB) is a destructive foliar diseases threatening wheat grain yield. Wheat breeding for STB disease resistance has been identified as the most sustainable and environment-friendly approach. In this work, a panel of 316 winter wheat breeding lines from a commercial breeding program were evaluated for STB resistance at the seedling stage under controlled conditions followed by genome-wide association study (GWAS) and genomic prediction (GP). The study revealed a significant genotypic variation for STB seedling resistance, while disease severity scores exhibited a normal frequency distribution. Moreover, we calculated a broad-sense heritability of 0.62 for the trait. Nine single- and multi-locus GWAS models identified 24 marker-trait associations grouped into 20 quantitative trait loci (QTLs) for STB seedling-stage resistance. The seven QTLs located on chromosomes 1B, 2A, 2B, 5B (two), 7A, and 7D are reported for the first time and could potentially be novel. The GP cross-validation analysis in the RR-BLUP model estimated the genomic-estimated breeding values (GEBVs) of STB resistance with a prediction accuracy of 0.49. Meanwhile, the GWAS assisted wRR-BLUP model improved the accuracy to 0.58. The identified QTLs can be used for marker-assisted backcrossing against STB in winter wheat. Moreover, the higher prediction accuracy recorded from the GWAS-assisted GP analysis implies its power to successfully select superior candidate lines based on their GEBVs for STB resistance.

Septoria tritici blotch (STB) is one of the most damaging fungal diseases of wheat in Europe, largely due to the paucity of effective resistance genes against it in breeding materials. Currently dominant protection methods against this disease, e.g. fungicides and the disease resistance genes already deployed, are losing their effectiveness. Therefore, it is vital that other available disease resistance sources are identified, understood and deployed in a manner that maximises their effectiveness and durability.

Stem rust is one of the major diseases threatening wheat production globally. To identify novel resistance quantitative trait loci (QTLs), we performed 35K Axiom Array SNP genotyping assays on an association mapping panel of 400 germplasm accessions, including Indian landraces, in conjunction with phenotyping for stem rust at seedling and adult plant stages. Association analyses using three genome wide association study (GWAS) models (CMLM, MLMM, and FarmCPU) revealed 20 reliable QTLs for seedling and adult plant resistance. Among these 20 QTLs, five QTLs were found consistent with three models, i.e., four QTLs on chromosome 2AL, 2BL, 2DL, and 3BL for seedling resistance and one QTL on chromosome 7DS for adult plant resistance. Further, we identified a total of 21 potential candidate genes underlying QTLs using gene ontology analysis, including a leucine rich repeat receptor (LRR) and P-loop nucleoside triphosphate hydrolase, which have a role in pathogen recognition and disease resistance. Furthermore, four QTLs (Qsr.nbpgr-3B_11, QSr.nbpgr-6AS_11, QSr.nbpgr-2AL_117-6, and QSr.nbpgr-7BS_APR) were validated through KASP located on chromosomes 3B, 6A, 2A, and 7B. Out of these QTLs, QSr.nbpgr-7BS_APR was identified as a novel QTL for stem rust resistance which has been found effective in both seedling as well as the adult plant stages. Identified novel genomic regions and validated QTLs have the potential to be deployed in wheat improvement programs to develop disease resistant varieties for stem rust and can diversify the genetic basis of resistance.

Wheat rust diseases are widespread and affect all wheat growing areas around the globe. Breeding strategies focus on incorporating genetic disease resistance. However, pathogens can quickly evolve and overcome the resistance genes deployed in commercial cultivars, creating a constant need for identifying new sources of resistance.

The Volga region is one of the main grain-producing regions of Russia. Wheat stem rust caused by Puccinia graminis f. sp. tritici is among the most destructive fungal diseases of wheat. Recently, its harmfulness has increased in the Volga region. In this regard, an analysis of the resistance and diversity of the Sr genes in the Russian wheat cultivars is necessary. In this work, 126 wheat cultivars (including 23 durum wheat cultivars and 103 bread wheat cultivars) approved for use in the Volga region were evaluated for their resistance to two samples of P. graminis f. sp. tritici populations from different Volga region areas at the seedling stage. Specific DNA primers were used to identify resistance genes (Sr2, Sr24, Sr25, Sr26, Sr28, Sr31, Sr32, Sr36, Sr38, Sr39, and Sr57). Highly resistant cultivars (30 from 126) were identified. In bread wheat cultivars, the genes Sr31 (in 19 cultivars), Sr24 (in one cultivar), Sr25 (in 15 spring wheat cultivars), Sr28 (in six cultivars), Sr38 (in two cultivars), and Sr57 (in 15 cultivars) and their combinations—Sr31 + Sr25, Sr31 + Sr38, Sr31 + Sr28, Sr31 + Sr57, Sr31 + Sr28 + Sr57, and Sr31 + Sr24—were identified. The obtained results may be used to develop strategies for breeding rust-resistant cultivars.

Wheat dwarf disease (WDD) is an important disease of monocotyledonous species, including economically important cereals. The causative pathogen, wheat dwarf virus (WDV), is persistently transmitted mainly by the leafhopper Psammotettix alienus and can lead to high yield losses. Due to climate change, the periods of vector activity increased, and the vectors have spread to new habitats, leading to an increased importance of WDV in large parts of Europe. In the light of integrated pest management, cultivation practices and the use of resistant/tolerant host plants are currently the only effective methods to control WDV. However, knowledge of the pathosystem and epidemiology of WDD is limited, and the few known sources of genetic tolerance indicate that further research is needed. Considering the economic importance of WDD and its likely increasing relevance in the coming decades, this study provides a comprehensive compilation of knowledge on the most important aspects with information on the causal virus, its vector, symptoms, host range, and control strategies. In addition, the current status of genetic and breeding efforts to control and manage this disease in wheat will be discussed, as this is crucial to effectively manage the disease under changing environmental conditions and minimize impending yield losses.

\n Qwdv.ifa-6A\n on chromosomes 6AL and\n Qwdv.ifa-1B\n on chromosome 1B are highly effective against wheat dwarf virus and act additively when combined.\n

Wheat blast, caused by the Pyricularia oryzae Triticum lineage (PoT), first emerged in Brazil and quickly spread to neighboring countries. Its recent appearance in Bangladesh and Zambia highlights a need to understand the disease's population biology and epidemiology so as to mitigate pandemic outbreaks. Current knowledge is mostly based on characterizations of Brazilian wheat blast isolates and comparison with isolates from non-wheat, endemic grasses. These foregoing studies concluded that the wheat blast population lacks host specificity and, as a result, undergoes extensive gene flow with populations infecting non-wheat hosts. Additionally, based on genetic similarity between wheat blast and isolates infecting Urochloa species, it was proposed that the disease originally emerged via a host jump from this grass and that Urochloa likely plays a central role in wheat blast epidemiology owing to its widespread use as a pasture grass. However, due to inconsistencies with broader phylogenetic studies, we suspected that these seminal studies had not actually sampled the populations normally found on endemic grasses and, instead, had repeatedly isolated members of PoT and the related Lolium pathogen lineage (PoL1). Re-analysis of the Brazilian data as part of a comprehensive, global, phylogenomic dataset that included a small number of South American isolates sampled away from wheat confirmed our suspicion and identified four new P. oryzae lineages on grass hosts. As a result, the conclusions underpinning current understanding in wheat blast's evolution, population biology, and epidemiology are unsubstantiated and could be equivocal.

Wheat blast, caused by the fungus Magnaporthe oryzae Triticum pathotype (MoT), is a devastating disease affecting South America, Bangladesh, and Zambia. Resistance to wheat blast has strongly relied on the 2NvS translocation; however, newer MoT isolates have increased aggressiveness, threatening the 2NvS translocation’s effectiveness and durability. To identify genomic regions associated with wheat blast resistance, we performed a quantitative trait loci (QTL) mapping study using 187 double-haploid (DH) lines from a cross between the Brazilian wheat cultivars ‘TBIO Alvorada’ and ‘TBIO Sossego’, which are moderately resistant and susceptible to blast, respectively. The DH population was evaluated in a greenhouse in Brazil and Bolivia, and field conditions in Bolivia. Contrasting models best explained the relationship between traits evaluated according to differences in disease levels and the presence of the 2NvS. A large effect-locus, derived from ‘TBIO Sossego’, was identified on chromosome 2AS, which was confirmed to be 2NvS translocation and explained 33.5 to 82.4% of the phenotypic variance. Additional significant loci were identified on 5AL, 1DS, 4DS, 5DL, and 6DL chromosome arms with phenotypic variance &lt;6%, but they were not consistent across trait–environment combinations. QTL pyramiding analyses showed that some specific loci had an additive effect when combined with the 2NvS, suggesting that stacking multiple loci may be an effective strategy to help manage wheat blast. The markers associated with the 2NvS can be used as dominant diagnostic markers for this alien translocation. Additional characterization of these loci using a broader set of MoT isolates is critical to validate their effectiveness against current MoT populations.

Wheat, one of the most important food crops, is threatened by a blast disease pandemic. Here, we show that a clonal lineage of the wheat blast fungus recently spread to Asia and Africa following two independent introductions from South America. Through a combination of genome analyses and laboratory experiments, we show that the decade-old blast pandemic lineage can be controlled by the Rmg8 disease resistance gene and is sensitive to strobilurin fungicides. However, we also highlight the potential of the pandemic clone to evolve fungicide-insensitive variants and sexually recombine with African lineages. This underscores the urgent need for genomic surveillance to track and mitigate the spread of wheat blast outside of South America and to guide preemptive wheat breeding for blast resistance.

The leaf blight diseases, Septoria nodorum blotch (SNB), and tan spot (TS) are emerging due to changing climatic conditions in the northern parts of India. We screened 296 bread wheat cultivars released in India over the past 20 years for seedling resistance against SNB (three experiments) and TS (two experiments). According to a genome-wide association study, six QTLs on chromosome arms 1BL, 2AS, 5BL, and 6BL were particularly significant for SNB across all three years, of which Q.CIM.snb.1BL, Q.CIM.snb.2AS1, Q.CIM.snb.2AS.2, and Q.CIM.snb.6BL appeared novel. In contrast, those on 5BS and 5BL may correspond to Snn3 and Tsn1, respectively. The allelic combination of tsn1/snn3 conferred resistance to SNB, whereas that of Tsn1/Snn3 conferred high susceptibility. As for TS, Tsn1 was the only stably significant locus identified in this panel. Several varieties like PBW 771, DBW 277, and HD 3319, were identified as highly resistant to both diseases that can be used in future wheat improvement programs as resistant donors.

Cereal cyst nematode (CCN) is a major threat to cereal crop production globally including wheat (Triticum aestivum L.). In the present study, single-locus and multi-locus models of Genome-Wide Association Study (GWAS) were used to find marker trait associations (MTAs) against CCN (Heterodera avenae) in wheat. In total, 180 wheat accessions (100 spring and 80 winter types) were screened against H. avenae in two independent years (2018/2019 "Environment 1" and 2019/2020 "Environment 2") under controlled conditions. A set of 12,908 SNP markers were used to perform the GWAS. Altogether, 11 significant MTAs, with threshold value of -log10 (p-values) ≥ 3.0, were detected using 180 wheat accessions under combined environment (CE). A novel MTA (wsnp_Ex_c53387_56641291) was detected under all environments (E1, E2 and CE) and considered to be stable MTA. Among the identified 11 MTAs, eight were novel and three were co-localized with previously known genes/QTLs/MTAs. In total, 13 putative candidate genes showing differential expression in roots, and known to be involved in plant defense mechanisms were reported. These MTAs could help us to identify resistance alleles from new sources, which could be used to identify wheat varieties with enhanced CCN resistance.© 2023. The Author(s).

Background: Tunisia harbors a rich collection of unexploited durum wheat landraces (Triticum durum ssp. durum) that have been gradually replaced by elite cultivars since the 1970s. These landraces represent an important potential source for broadening the genetic background of elite durum wheat cultivars and for the introgression of novel genes for key traits, including disease resistance, into these cultivars.

Novel sources of genetic resistance to tan spot in Australia have been discovered using one-step GWAS and genomic prediction models that accounts for additive and non-additive genetic variation.

Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation.

\n Spot blotch (SB) caused by\n Bipolaris sorokiniana\n (teleomorph\n Cochliobolus sativus\n ) is one of the devastating diseases of wheat in the warm and humid growing areas around the world.\n B. sorokiniana\n can infect leaves, stem, roots, rachis and seeds, and is able to produce toxins like helminthosporol and sorokinianin. No wheat variety is immune to SB; hence, an integrated disease management strategy is indispensable in disease prone areas. A range of fungicides, especially the triazole group, have shown good effects in reducing the disease, and crop-rotation, tillage and early sowing are among the favorable cultural management methods. Resistance is mostly quantitative, being governed by QTLs with minor effects, mapped on all the wheat chromosomes. Only four QTLs with major effects have been designated as\n Sb1\n through\n Sb4\n. Despite, marker assisted breeding for SB resistance in wheat is scarce. Better understanding of wheat genome assemblies, functional genomics and cloning of resistance genes will further accelerate breeding for SB resistance in wheat.\n

Quantification of genotype-to-phenotype associations is central to many scientific investigations, yet the ability to obtain consistent results may be thwarted without appropriate statistical analyses. Models for association can consider confounding effects in the materials and complex genetic interactions. Selecting optimal models enables accurate evaluation of associations between marker loci and numerous phenotypes including gene expression. Significant improvements in QTL discovery via association mapping and acceleration of breeding cycles through genomic selection are two successful applications of models using genome-wide markers. Given recent advances in genotyping and phenotyping technologies, further refinement of these approaches is needed to model genetic architecture more accurately and run analyses in a computationally efficient manner, all while accounting for false positives and maximizing statistical power. Copyright © 2015 Elsevier Ltd. All rights reserved.