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Wheat stands as the foremost cultivated crop in Pakistan, dominating in terms of acreage and production among cereals. The morphology of wheat grains has been a target of selection since the dawn of agriculture and remains a paramount focus in contemporary breeding efforts. This study sought to examine alterations in grain morphology using digital imaging across 64 bread wheat cultivars grown in Pakistan under both well-watered and water-limited conditions, while also exploring their link with the TaCWI gene. The analysis revealed a substantial range of variation in grain morphology encompassing more than 15fifteen descriptors among the cultivars. Historically significant wheat cultivars, including T9 and C-271, which predate 1930, exhibited the smallest grain area, while contemporary counterparts like, Pirsabak-2013 and Markaz-2019 showcased the largest grain area. Significantly, the wheat cell wall invertase gene, TaCwi-A1, displayed a strong association with grain size. The TaCwi-A1a allele was identified in 31 out of the 64 cultivars and was notably correlated with larger grain size. This research unveils a comprehensive understanding of variations in grain size and shape among historical wheat cultivars in Pakistan and emphasizes that modern Pakistani wheat cultivars tend to exhibit larger grain size. Furthermore, it underscores the necessity of evaluating the allelic influence of additional genes related to grain size and weight, paving the way for more targeted breeding efforts in the future. [ABSTRACT FROM AUTHOR]

Key message: Three stable QTL for grain zinc concentration were identified in wheat landrace Chinese Spring. Favorable alleles were more frequent in landraces than in modern wheat cultivars. Wheat is a major source of dietary energy for the growing world population. Developing cultivars with enriched zinc and iron can potentially alleviate human micronutrient deficiency. In this study, a recombinant inbred line (RIL) population with 245 lines derived from cross Zhou 8425B/Chinese Spring was used to detect quantitative trait loci (QTL) for grain zinc concentration (GZnC) and grain iron concentration (GFeC) across four environments. Three stable QTL for GZnC with all favorable alleles from Chinese Spring were identified on chromosomes 3BL, 5AL, and 5BL. These QTL explaining maxima of 8.7%, 5.8%, and 7.1% of phenotypic variances were validated in 125 resequenced wheat accessions encompassing both landraces and modern cultivars using six kompetitive allele specific PCR (KASP) assays. The frequencies of favorable alleles for QGZnCzc.caas-3BL, QGZnCzc.caas-5AL and QGZnCzc.caas-5BL were higher in landraces (90.4%, 68.0%, and 100.0%, respectively) compared to modern cultivars (45.9%, 35.4%, and 40.9%), suggesting they were not selected in breeding programs. Candidate gene association studies on GZnC in the cultivar panel further delimited the QTL into 8.5 Mb, 4.1 Mb, and 47.8 Mb regions containing 46, 4, and 199 candidate genes, respectively. The 5BL QTL located in a region where recombination was suppressed. Two stable and three less stable QTL for GFeC with favorable alleles also from Chinese Spring were identified on chromosomes 4BS (Rht-B1a), 4DS (Rht-D1a), 1DS, 3AS, and 6DS. This study sheds light on the genetic basis of GZnC and GFeC in Chinese Spring and provides useful molecular markers for wheat biofortification. [ABSTRACT FROM AUTHOR]

In this study, Levinson-type inequalities for the class of n-convex (n ≥ 3 ) functions are generalized using new Green functions and the Hermite interpolating polynomial involving two types of data points. Some estimations for novel functionals are derived using f-divergence. Furthermore, different inequalities involving Shannon entropies are presented. [ABSTRACT FROM AUTHOR]

Background: Hexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity and resulted in duplication and neofunctionalization of major agronomic genes. The genetic architecture of polyploid wheat not only confers adaptive plasticity but also offers huge genetic diversity. However, the contribution of different gene copies (homeologs) encoded from different subgenomes (A, B, D) at different growth stages remained unexplored. Methods: In this study, hybrid of elite cultivars of wheat were developed via reciprocal crosses (cytoplasm swapping) and phenotypically evaluated. We assessed differential expression profiles of yield-related negative regulators in these cultivars and their F1 hybrids and identified various cis-regulatory signatures by employing bioinformatics tools. Furthermore, the preferential expression patterns of the syntenic triads encoded from A, B, and D subgenomes were assessed to decipher their functional redundancy at six different growth stages. Results: Hybrid progenies showed better heterosis such as up to 17% increase in the average number of grains and up to 50% increase in average thousand grains weight as compared to mid-parents. Based on the expression profiling, our results indicated significant dynamic transcriptional expression patterns, portraying the different homeolog-dominance at the same stage in the different cultivars and their hybrids. Albeit belonging to same syntenic triads, a dynamic trend was observed in the regulatory signatures of these genes that might be influencing their expression profiles. Conclusion: These findings can substantially contribute and provide insights for the selective introduction of better cultivars into traditional and hybrid breeding programs which can be harnessed for the improvement of future wheat. [ABSTRACT FROM AUTHOR]

Background: SnRK2 plays vital role in responding to adverse abiotic stimuli. The applicability of TaSnRK2.4 and TaSnRK2.9 was investigated to leverage the potential of these genes in indigenous wheat breeding programs. Methods: Genetic diversity was assessed using pre-existing markers for TaSnRK2.4 and TaSnRK2.9. Furthermore, new markers were also developed to enhance their broader applicability. KASP markers were designed for TaSnRK2.4, while CAPS-based markers were tailored for TaSnRK2.9. Results: Analysis revealed lack of polymorphism in TaSnRK2.4 among Pakistani wheat germplasm under study. To validate this finding, available gel-based markers for TaSnRK2.4 were employed, producing consistent results and offering limited potential for application in marker-assisted wheat breeding with Pakistani wheat material. For TaSnRK2.9-5A, CAPS2.9-5A-1 and CAPS2.9-5A-2 markers were designed to target SNP positions at 308 nt and 1700 nt revealing four distinct haplotypes. Association analysis highlighted the significance of Hap-5A-1 of TaSnRK2.9-5A, which exhibited association with an increased number of productive tillers (NPT), grains per spike (GPS), and reduced plant height (PH) under well-watered (WW) conditions. Moreover, it showed positive influence on NPT under WW conditions, GPS under water-limited (WL) conditions, and PH under both WW and WL conditions. High selection intensity observed for Hap-5A-1 underscores the valuable role it has played in Pakistani wheat breeding programs. Gene expression studies of TaSnRK2.9-5A revealed the involvement of this gene in response to PEG, NaCl, low temperature and ABA treatments. Conclusion: These findings propose that TaSnRK2.9 can be effectively employed for improving wheat through marker-assisted selection in wheat breeding efforts. [ABSTRACT FROM AUTHOR]

Digital signal processing (DSP) is one of the most effective tools that have influenced science, engineering, and technology in the twenty-first century. Since 1970, advancements in the expansive field of DSP have made it a crucial tool in many applications. Many in-depth investigations on the filters and the extraction of helpful information have been conducted by researchers in a variety of scientific domains. In this paper, digital filters have been applied on radon (thereafter called to be as 222Rn) and thoron (thereafter to be called as 220Rn) time series signals to extract meaningful information from the original signals. By employing finite impulse response (FIR) equiripple and infinite impulse response (IIR) Butterworth filters to the soil 222Rn and 220Rn signals, the extracted features have been examined to obtain the improved output of the signal. The Persistence spectrums and spectrograms of FIR and IIR filtered 222Rn and 220Rn are constructed to check the anomalous shift in frequency, power and amplitude of the signals, due to the seismic events, if any, that took place during the research period. Finding of study shows that FIR and IIR filtered 220Rn indicates the anomalous behavior, nine and eleven days, before the seismic event of M 4.3 and M 2.5 occurred during the study period on 21st and 23rd of March 2017. Radon and thoron also shows anomalous nature twelve and nine days, before the earthquake of magnitude M 4.8 occurred during the study. Some anomalies appearing in the original 222Rn and 220Rn time series are found to have no connection with seismic events rather meteorological factors are believed to be responsible for them. [ABSTRACT FROM AUTHOR]

In this paper, four new Green functions are used to generalize Levinson-type inequalities for the class of 3-convex functions. The f-divergence, Renyi entropy, Renyi divergence, Shannon entropy, and the Zipf–Mandelbrot law are also used to apply the main results to information theory. [ABSTRACT FROM AUTHOR]

Key message: Major QTL for grain zinc and iron concentrations were identified on the long arm of chromosomes 2D and 6D. Gene-based KASP markers were developed for putative candidate genes TaIPK1-2D and TaNAS10-6D. Micronutrient malnutrition is one of the most common public health problems in the world. Biofortification, the most attractive and sustainable solution to surmount malnutrition requires the development of micronutrient enriched new crop cultivars. In this study, two recombinant inbred line (RIL) populations, ZM175/XY60 and ZM175/LX987, were used to identify QTL for grain zinc concentration (GZnC), grain iron concentration (GFeC) and thousand grain weight (TGW). Eight QTL for GZnC, six QTL for GFeC and five QTL for TGW were detected. Three QTL on chromosomes 2DL and 4BS and chromosome 6A showed pleiotropic effects on all three traits. The 4BS and 6A QTL also increased plant height and might be Rht-B1a and Rht25a, respectively. The 2DL locus within a suppressed recombination region was identified in both RIL populations and the favorable allele simultaneously increasing GZnC, GFeC and TGW was contributed by XY60 and LX987. A QTL on chromosome 6DL associated only with GZnC was detected in ZM175/XY60 and was validated in JD8/AK58 RILs using kompetitive allele-specific PCR (KASP) marker K_AX-110119937. Both the 2DL and 6DL QTL were new loci for GZnC. Based on gene annotations, sequence variations and expression profiles, the phytic acid biosynthesis gene TaIPK1-2D and nicotianamine synthase gene TaNAS10-6D were predicted as candidate genes. Their gene-based KASP markers were developed and validated in a cultivar panel of 343 wheat accessions. This study investigated the genetic basis of GZnC and GFeC and provided valuable candidate genes and markers for breeding Zn- and Fe-enriched wheat. [ABSTRACT FROM AUTHOR]

Main conclusion: The study provided an insight toward better understanding of stay-green mechanisms for drought tolerance improvement and identified that synthetic-derived wheats proved as a promising germplasm for improved tolerance against water stress. Stay-green (SG) trait is considered to be related with the ability of wheat plants to maintain photosynthesis and CO2 assimilation. The present study explored the interaction of water stress with SG expression through physio-biochemical, agronomic and phenotypic responses among diverse wheat germplasm comprising of 200 synthetic hexaploids, 12 synthetic derivatives, 97 landraces and 16 conventional bread wheat varieties, for 2 years. The study established that variation of SG trait existed in the studied wheat germplasm and there was positive association between SG trait and tolerance to water stress. The relationship of SG trait with chlorophyll content (r = 0.97), ETR (r = 0.28), GNS (r = 0.44), BMP (r = 0.34) and GYP (r = 0.44) was particularly promising under water stress environment. Regarding chlorophyll fluorescence, the positive correlation of фPSII (r = 0.21), qP (r = 0.27) and ETR (r = 0.44) with grain yield per plant was noted. The improved ΦPSII and Fv/Fm of PSII photochemistry resulted in the high photosynthesis activity in SG wheat genotypes. Regarding relative water content and photochemical quenching coefficient, synthetic-derived wheats were better by maintaining 20.9, 9.8 and 16.1% more RWC and exhibiting 30.2, 13.5 and 17.9% more qP when compared with landraces, varieties and synthetic hexaploids, respectively, under water stress environment. Synthetic derived wheats also exhibited relatively more SG character with good yield and were more tolerant to water stress in terms of grain yield, grain weight per plant, better photosynthetic performance through chlorophyll fluorescence measurement, high leaf chlorophyll and proline content, and hence, may be used as novel sources for breeding drought tolerant materials. The study will further facilitate research on wheat leaf senescence and will add to better understanding of SG mechanisms for drought tolerance improvement. [ABSTRACT FROM AUTHOR]

Key Message: A genetic framework underpinning salinity tolerance at reproductive stage was revealed by genome-wide SNP markers and major adaptability genes in synthetic-derived wheats, and trait-associated loci were used to predict phenotypes. Using wild relatives of crops to identify genes related to improved productivity and resilience to climate extremes is a prioritized area of crop genetic improvement. High salinity is a widespread crop production constraint, and development of salt-tolerant cultivars is a sustainable solution. We evaluated a panel of 294 wheat accessions comprising synthetic-derived wheat lines (SYN-DERs) and modern bread wheat advanced lines under control and high salinity conditions at two locations. The GWAS analysis revealed a quantitative genetic framework of more than 200 loci with minor effect underlying salinity tolerance at reproductive stage. The significant trait-associated SNPs were used to predict phenotypes using a GBLUP model, and the prediction accuracy (r2) ranged between 0.57 and 0.74. The r2 values for flag leaf weight, days to flowering, biomass, and number of spikes per plant were all above 0.70, validating the phenotypic effects of the loci discovered in this study. Furthermore, the germplasm sets were compared to identify selection sweeps associated with salt tolerance loci in SYN-DERs. Six loci associated with salinity tolerance were found to be differentially selected in the SYN-DERs (12.4 Mb on chromosome (chr)1B, 7.1 Mb on chr2A, 11.2 Mb on chr2D, 200 Mb on chr3D, 600 Mb on chr6B, and 700.9 Mb on chr7B). A total of 228 reported markers and genes, including 17 well-characterized genes, were uncovered using GWAS and EigenGWAS. A linkage disequilibrium (LD) block on chr5A, including the Vrn-A1 gene at 575 Mb and its homeologs on chr5D, were strongly associated with multiple yield-related traits and flowering time under salinity stress conditions. The diversity panel was screened with more than 68 kompetitive allele-specific PCR (KASP) markers of functional genes in wheat, and the pleiotropic effects of superior alleles of Rht-1, TaGASR-A1, and TaCwi-A1 were revealed under salinity stress. To effectively utilize the extensive genetic information obtained from the GWAS analysis, a genetic interaction network was constructed to reveal correlations among the investigated traits. The genetic network data combined with GWAS, selective sweeps, and the functional gene survey provided a quantitative genetic framework for identifying differentially retained loci associated with salinity tolerance in wheat. [ABSTRACT FROM AUTHOR]

Background: The COBL genes encode a plant-specific glycosylphosphatidylinositol (GPI)-anchored protein. Recently identified COBRA genes are supposed as a key regulator of the orientation of cell expansion in the root indicating that COBRA gene family members are likely to be important players at the plasma membrane-cell wall interface. Methods and results: Five COBL gene namely, TaCOBL 1, TaCOBL 2, TaCOBL 3, TaCOBL 4 and TaCOBL 5 were identified using database search and domain predictions. Chromosomal location of each gene was mapped on karyotype. Structure of genes, promoter analysis and phylogenetic analysis were performed using different bioinformatics tools. Set of novel SNPs were also predicted. Gene ontologies were analyzed, and the processes and pathways were identified in which COBRA genes were involved. The molecular weight all the cobra proteins was in range of 50–75 KDa with 429–461 amino acid residues. The COBL genes were mapped on homeologous groups 2, 4, 5, 6 and 7. Gene ontology analysis revealed that TaCOBL genes were involved in cellulose microfibril organization, mucilage biosynthetic process involved in seed coat development, plant-type cell wall biogenesis plant-type cell wall cellulose biosynthetic process, seed coat development and seed development. Three drought responsive cis-elements (WRKY, ABRE and DRE) were found nearby COBL genes The qRT-PCR revealed TaCOBL genes are drought responsive and can be further explored to understand their role in drought tolerance in wheat. Conclusion: The comprehensive annotation and expression profiling of COBL genes revealed that all five COBL genes are drought response. The promoter cis-regulatory element analysis revealed that COBL genes had stress related WRKY, ABRE and DRE cis-regulatory elements. This evidence suggest that TaCOBL genes are involved in drought stress tolerance. [ABSTRACT FROM AUTHOR]

Kazakhstan-Siberia Network for Spring Wheat Improvement (KASIB) was established in 2000 to conduct multi-location cooperative yield trials for the exchange of breeding material and to evaluate agronomic traits such as grain yield and disease resistance. In 2016, aggregated KASIB data were analyzed and 120 cultivars and breeding lines demonstrating different degrees of resistance to leaf rust selected. They were tested for leaf rust and agronomic traits in Omsk, Russia; Almaty, Kazakhstan and Sakarya, Turkey in 2017–2019. This germplasm was grouped into four categories based on leaf rust reaction: 31 resistant (R), 27 moderately resistant (MR), 37 intermediate (M) and 25 moderately susceptible (MS) entries. Lr genes were postulated based on tests using pathotypes with known virulence profiles and molecular markers. The most frequent Lr genes alone or in combination were Lr10 (31 entries), Lr26 (24), Lr9 (23), Lr1 (18), Lr17 (11), Lr34 (11) and Lr19 (7). Genes Lr1, Lr9, Lr10 and Lr17 reduced the leaf rust severity to M or MS across environments. The presence of Lr26 alone or in combination with other major genes reduced the leaf rust severity to MR-M in Omsk and R in Sakarya. The only gene with the large effect on leaf rust was Lr19, which provided a high level of resistance at all sites both alone and in combination with Lr26. Leaf rust severity in 52 entries with adult plant resistance (APR) was compared to 68 entries possessing effective seedling resistance genes. The leaf rust severity in entries with APR compared to seedling resistance was similar at low infection pressure at Sakarya, 2018 and Omsk, 2019. However, at higher leaf rust infection pressure at Omsk in 2017 and 2018, Almaty in 2019, there was a clear advantage for the germplasm possessing major genes. High level of stem rust infection in Omsk in 2019 confirmed effectiveness of the Sr31/Lr26 gene. A set of 33 genotypes was selected combining resistance to leaf and stem rust with superior agronomic performance. [ABSTRACT FROM AUTHOR]

Key message: GWAS identified 36 potentially new loci for wheat stem water-soluble carbohydrate (WSC) contents and 13 pleiotropic loci affecting WSC and thousand-kernel weight. Five KASP markers were developed and validated. Water-soluble carbohydrates (WSC) reserved in stems contribute significantly to grain yield (GY) in wheat. However, knowledge of the genetic architecture underlying stem WSC content (SWSCC) is limited. In the present study, 166 diverse wheat accessions from the Yellow and Huai Valleys Winter Wheat Zone of China and five other countries were grown in four well-watered environments. SWSCC at 10 days post-anthesis (10DPA), 20DPA and 30DPA, referred as WSC10, WSC20 and WSC30, respectively, and thousand-kernel weight (TKW) were assessed. Correlation analysis showed that TKW was significantly and positively correlated with WSC10 and WSC20. Genome-wide association study was performed on SWSCC and TKW with 373,106 markers from the wheat 660 K and 90 K SNP arrays. Totally, 62 stable loci were detected for SWSCC, with 36, 24 and 19 loci for WSC10, WSC20 and WSC30, respectively; among these, 36 are potentially new, 16 affected SWSCC at two or three time-points, and 13 showed pleiotropic effects on both SWSCC and TKW. Linear regression showed clear cumulative effects of favorable alleles for increasing SWSCC and TKW. Genetic gain analyses indicated that pyramiding favorable alleles of SWSCC had simultaneously improved TKW. Kompetitive allele-specific PCR markers for five pleiotropic loci associated with both SWSCC and TKW were developed and validated. This study provided a genome-wide landscape of the genetic architecture of SWSCC, gave a perspective for understanding the relationship between WSC and GY and explored the theoretical basis for co-improvement of WSC and GY. It also provided valuable loci and markers for future breeding. [ABSTRACT FROM AUTHOR]

Key message: We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding. [ABSTRACT FROM AUTHOR]

Key message: Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued. [ABSTRACT FROM AUTHOR]

Key message: Recent technological advances in wheat genomics provide new opportunities to uncover genetic variation in traits of breeding interest and enable genome-based breeding to deliver wheat cultivars for the projected food requirements for 2050. There has been tremendous progress in development of whole-genome sequencing resources in wheat and its progenitor species during the last 5 years. High-throughput genotyping is now possible in wheat not only for routine gene introgression but also for high-density genome-wide genotyping. This is a major transition phase to enable genome-based breeding to achieve progressive genetic gains to parallel to projected wheat production demands. These advances have intrigued wheat researchers to practice less pursued analytical approaches which were not practiced due to the short history of genome sequence availability. Such approaches have been successful in gene discovery and breeding applications in other crops and animals for which genome sequences have been available for much longer. These strategies include, (i) environmental genome-wide association studies in wheat genetic resources stored in genbanks to identify genes for local adaptation by using agroclimatic traits as phenotypes, (ii) haplotype-based analyses to improve the statistical power and resolution of genomic selection and gene mapping experiments, (iii) new breeding strategies for genome-based prediction of heterosis patterns in wheat, and (iv) ultimate use of genomics information to develop more efficient and robust genome-wide genotyping platforms to precisely predict higher yield potential and stability with greater precision. Genome-based breeding has potential to achieve the ultimate objective of ensuring sustainable wheat production through developing high yielding, climate-resilient wheat cultivars with high nutritional quality. [ABSTRACT FROM AUTHOR]

Background and aims: Chromium (Cr) toxicity is a rapidly increasing environmental concern and poses a major threat to plant growth as well as food chain. This study was carried out to screen spring wheat diversity panel against Cr toxicity to assess yield reduction, grain contamination extents and genomic regions associated with tolerance to Cr toxicity.Methods: The diversity panel was planted in control and Cr stress (26 mg Cr/kg soil) in paved plots, and several morphological and physiological traits were recorded. Wheat 90 K Infinium iSelect SNP array was used to identify genomic regions underpinning tolerance to Cr toxicity.Results: Some wheat cultivars (Khosar-95, Miraj-08, Millet-11, Sarsabaz and NARC-11) had Cr concentration within international edible threshold limit (1 ppm), but showed greater reduction to grain yield (63–95%) due to higher leaf Cr concentrations (2.35–8.95 ppm). Contrastingly, wheat cultivars Auqab-00 and Pakistan-13 had lower yield reduction up to 9% and 39%, respectively but had higher concentration of Cr in seeds (2.1 and 3.5 ppm, respectively). Genome-wide association studies identified 71 loci linked with yield related traits under Cr stress and 48 loci for differences between control and Cr stress treatments. Further, gene ontology of trait-associated SNPs revealed proteins with significant importance in plant development and tolerance against heavy metal stress.Conclusion: To our knowledge, this is the first study for identification of genomic regions linked to Cr stress, suggesting that this could be useful to identify complex architecture of genetic factors as well as molecular breeding opportunities for tolerance to Cr stress. [ABSTRACT FROM AUTHOR]

Key message: We identified 27 stable loci associated with agronomic traits in spring wheat using genome-wide association analysis, some of which confirmed previously reported studies. GWAS peaks identified in regions where no QTL for grain yield per se has been mapped to date, provide new opportunities for gene discovery and creation of new cultivars with desirable alleles for improving yield and yield stability in wheat. Abstract: We undertook large-scale genetic analysis to determine marker-trait associations (MTAs) underlying agronomic and physiological performance in spring wheat using genome-wide association studies (GWAS). Field trials were conducted at seven sites in three countries (Sudan, Egypt, and Syria) over 2-3 years in each country. Twenty-five agronomic and physiological traits were measured on 188 wheat genotypes. After correcting for population structure and relatedness, a total of 245 MTAs distributed over 66 loci were associated with agronomic traits in individual and mean performance across environments respectively; some of which confirmed previously reported loci. Of these, 27 loci were significantly associated with days to heading, thousand kernel weight, grain yield, spike length, and leaf rolling for mean performance across environments. Despite strong QTL by environment interactions, eight of the loci on chromosomes 1A, 1D, 5A, 5D, 6B, 7A, and 7B had pleiotropic effects on days to heading and yield components (TKW, SM, and SNS). The winter-type alleles at the homoeologous VRN1 loci significantly increased days to heading and grain yield in optimal environments, but decreased grain yield in heat prone environments. Top 20 high-yielding genotypes, ranked by additive main effects and multiplicative interaction (AMMI), had low kinship relationship and possessed 4-5 favorable alleles for GY MTAs except two genotypes, Shadi-4 and Qafzah-11/Bashiq-1-2. This indicated different yield stability mechanisms due to potentially favorable rare alleles that are uncharacterized. Our results will enable wheat breeders to effectively introgress several desirable alleles into locally adapted germplasm in developing wheat varieties with high yield stability and enhanced heat tolerance. [ABSTRACT FROM AUTHOR]

Key message : We developed and validated a robust marker toolkit for high-throughput and cost-effective screening of a large number of functional genes in wheat. Abstract: Functional markers (FMs) are the most valuable markers for crop breeding programs, and high-throughput genotyping for FMs could provide an excellent opportunity to effectively practice marker-assisted selection while breeding cultivars. Here we developed and validated kompetitive allele-specific PCR (KASP) assays for genes that underpin economically important traits in bread wheat including adaptability, grain yield, quality, and biotic and abiotic stress resistances. In total, 70 KASP assays either developed in this study or obtained from public databases were validated for reliability in application. The validation of KASP assays were conducted by (a) comparing the assays with available gel-based PCR markers on 23 diverse wheat accessions, (b) validation of the derived allelic information using phenotypes of a panel comprised of 300 diverse cultivars from China and 13 other countries, and (c) additional testing, where possible, of the assays in four segregating populations. All KASP assays being reported were significantly associated with the relevant phenotypes in the cultivars panel and bi-parental populations, thus revealing potential application in wheat breeding programs. The results revealed 45 times superiority of the KASP assays in speed than gel-based PCR markers. KASP has recently emerged as single-plex high-throughput genotyping technology; this is the first report on high-throughput screening of a large number of functional genes in a major crop. Such assays could greatly accelerate the characterization of crossing parents and advanced lines for marker-assisted selection and can complement the inflexible, high-density SNP arrays. Our results offer a robust and reliable molecular marker toolkit that can contribute towards maximizing genetic gains in wheat breeding programs. [ABSTRACT FROM AUTHOR]

The important role of germins (GER) and genes coding for germin-like proteins (GLP) in responses against various stresses in both homologous and heterologous systems is well validated. This review summarizes the work on their functional validation using various biotechnological approaches. The genes are widely expressed during a specific period of plant growth and development, and exhibit a pattern of evolutionary subfunctionalization at both the intracellular and whole plant level. Their applications against various biotic and abiotic stresses, especially against fungal pathogens, are enormous. Although the validation of these proteins against various stresses has led to the development of commercially and agronomically important transgenic plants, much work is still needed to exploit this ever-expanding repertoire of genes and deploy them for commercial use. Historical progress of genetic engineering in GERs and GLPs is reviewed, and future prospects for their potential role in crop improvement are highlighted. [ABSTRACT FROM AUTHOR]

The TGW6 gene encodes a novel indole-3-acetic acid-glucose hydrolase and plays a significant role in improving thousand grain weight (TGW) and yield in rice. In the current study, a TGW6 ortholog from bread wheat chromosome 3AL was isolated and designated as TaTGW6-A1. Sequencing and alignment analysis showed that the cloned TaTGW6-A1 consists of a 987-bp intronless open reading frame. Three single-nucleotide polymorphisms (SNPs) were identified between cultivars with higher and lower TGW, forming two haplotypes, TaTGW6-A1a and TaTGW6-A1b. A derived cleaved amplified polymorphic sequence marker, TaTGW6-A1-CAPS, was developed to differentiate the two haplotypes. Linkage analysis using the wheat 90K iSelect SNP array mapped TaTGW6-A1-CAPS at 18 cM from BobWhite_c47304_56 in a RIL population derived from Zhou 8425B/Chinese Spring. A QTL for yield at the TaTGW6-A1 locus explained 17.4 % of the phenotypic variance in average yield over four environments. Association analysis on 242 Chinese and foreign cultivars indicated that TaTGW6-A1 was significantly associated with TGW. The cumulative frequency of the TaTGW6-A1a allele associated with higher TGW was approximately 80 %, indicating that the TaTGW6-A1a allele was positively selected in wheat breeding. In conclusion, TaTGW6-A1 in conjunction with its molecular marker may contribute as a valuable gene in improving yield potential in wheat. [ABSTRACT FROM AUTHOR]

Drought is one of the most important environmental factors limiting wheat yield in many parts of the world. Progress in breeding to improve drought tolerance has been limited by its high sensitivity to environmental factors, low heritability, and the complexity and size of wheat genome. Two genetically diverse sets of wheat genotypes were evaluated to identify genetic resources maintaining physiological and metabolic stability under osmotic stress. Data on 13 different morphological and physiological traits under control and osmotic stress clearly depicted the superiority of wheat lines derived from synthetic hexaploid wheats (SHWs) as compared to conventional bread wheats. Accordingly, all lines were genotyped with simple sequence repeat (SSR) markers to assess the diversity and identify the marker-trait associations (MTAs). Structure analysis partitioned the germplasm into two sub-populations ( K = 2) based on Δ K and Ln P( D) values. Association mapping was performed using Q + K matrix as covariates by applying mixed linear model (MLM). In total, 39 MTAs over 20 SSR loci were detected by the strict MLM model, which were reduced to 12 MTAs over 6 SSR loci after strict Bonferroni adjustments. MTAs detected under osmotic stress conditions indicated the effectiveness of association mapping to identify loci for different attributes under low-moisture conditions. Conclusively, this study has demonstrated that synthetic-derived wheats harbor valuable alleles that can enrich the genetic base of cultivated wheat and improve its adaptation under water stress conditions. The MTAs detected may have the candidate genes responsible for drought adaptation, thus providing a unique resource which can be manipulated for developing drought-tolerant cultivars. [ABSTRACT FROM AUTHOR]

Boron toxicity is one of the most important environmental stresses prevailing globally, which limits grain production. In wheat, tolerance to boron toxicity has been manipulated around the Bo1 locus on 7BL chromosome. However, there is a need to identify new diversity in other Triticeae to broaden the germplasm base for genetic improvement and greater tolerance durability. Among these resources, Aegilops tauschii (2 n = 2 x = 14; DD) accessions have demonstrated significant outputs with their contribution of novel alleles for various biotic and abiotic stresses influencing traits that add value to wheat improvement. This study demonstrates the performance of 45 D-genome synthetic hexaploids wheats (SHWs) derived from a durum cultivar 'Decoy' for their tolerance to boron toxicity at seedling plus adult stages and validates their diversity at the molecular level. The root and shoot growth suppression as percentage of control was taken as the selection criteria for boron toxicity tolerance. Analysis of variance (ANOVA) exhibited ample variability (at P = 0.0001) among genotypes, treatments, and their interaction. Among 45 SHWs analyzed, 11 were found tolerant at the seedling stage, while 12 were found tolerant during adult plant screening. The different tolerant accessions at seedling and adult plant revealed that the tolerant mechanism was different at both stages. Genetic diversity was investigated using SSR marker specific to chromosome 7D. A total of 38 alleles were amplified with a mean value of 3.8 alleles per marker. Analysis of molecular variance (AMOVA) further established significant genetic diversity among different clusters. The potential genomic regions underlying tolerance to boron toxicity were also highlighted by searching sequences of cereal boron tolerance genes in wheat-specific databases. The wheat genome survey sequence and the draft genome sequence of Ae. tauschii proved to be useful genomic resources that identified five different chromosomal regions highly similar to the available boron tolerant genes in cereals. Conclusively, tolerance to boron toxicity in SHWs, genetic variability among the tolerant accessions based on SSRs, and availability of orthologous copies of boron tolerance genes make SHWs as potent genetic resources for wheat improvement against boron toxicity. [ABSTRACT FROM AUTHOR]

The development of drought tolerant wheat cultivars has been slow due to lack of understanding the diagnostic physiological parameters associated with improved productivity under water stress. We evaluated responses to PEG induced osmotic stress under hydroponics in D-genome synthetic derived and bread wheat germplasm with the main aim to unravel and identify some promising attributes having role in stress tolerances. Genotypes used in this study differed in their morpho-physiological and biochemical attributes. Tolerant genotypes exhibited the ability to ameliorate harmful effects of PEG induced osmotic stress through better osmotic adjustment achieved through substantial relative water content (RWC), lowered osmotic potential, relatively stable root length having maximum water extraction capacity, significant increase in osmoprotectant concentration and relatively enhanced antioxidant activities. The results clearly revealed the importance of synthetic derivatives over check cultivars and conventional wheats in terms of osmotic stress responses. Interestingly, synthetic-derived advanced lines with Aegilops tauschii in its parentage including AWL-02, AWL-04 and AWL-07 proved superior over the best rainfed check cultivar (Wa-01). It was concluded that synthetic-derived wheats has great potential to improve a range of stress adaptive traits. It could, therefore, be recommended to be a useful strategy for allowing modern bread wheat to become adapted to a wider range of environments in future climate change scenarios. [ABSTRACT FROM AUTHOR]

Stripe rust is recognized as a significant constraint to wheat production worldwide. Sustainable control against this destructive disease is achieved preferably by deploying stripe rust resistance genes ( Yr) in wheat cultivars. To identify new sources of effective Yr genes against stripe rust, the response of 194 wheat amphiploids (AABBAA and AABBAA) to stripe rust at seedling and adult plant stage was evaluated. Among the amphiploids tested at seedling stage, 26 (13.40 %) were classified as resistant (IT 0-3), 9 (4.63 %) intermediate (IT 4-6) and 159 (81.95 %) as susceptible (IT 7-9). Out of 26 seedling-resistant amphiploids 17 (8.76 %) showed resistance at the adult-plant stage. Comparative analysis of amphiploids and their durum parents identified the putative source of Yr resistance. The role of durum cultivar in resistance suppression was observed in many cases. These novel amphiploid (2n = 6x = 42) stocks are derivatives of 20 durum cultivars and accessions of the A and A genome effectively assembled AB genome diversity that is user friendly for maximizing their exploitation for applied agricultural targets. This initial screening facilitates the characterization of these amphiploids for stripe rust resistance breeding goals. [ABSTRACT FROM AUTHOR]

The objective of this study was to identify allelic variations at Glu-1 loci of wheat ( Triticum aestivum L.) advanced lines derived from hybridization of bread wheat and synthetic hexaploid wheats (2n = 6x = 42; AABBDD). Locally adapted wheat genotypes were crossed with synthetic hexaploid wheats. From the 134 different cross combinations made, 202 F advanced lines were selected and their HMW-GS composition was studied using SDS-PAGE. In total, 24 allelic variants and 68 HMW-GS combinations were observed at Glu-A1, Glu-B1, and Glu-D1 loci. In bread wheat, the Glu-D1 locus is usually characterized by subunits 1Dx2+1Dy12 and 1Dx5+1Dy10 with the latter having a stronger effect on bread-making quality. The subunit 1Dx5+1Dy10 was predominantly observed in these advanced lines. The inferior subunit 1Dx2+1Dy12, predominant in adapted wheat germplasm showed a comparative low frequency in the derived advanced breeding lines. Its successful replacement is due to the other better allelic variants at the Glu-D1 locus inherited in these synthetic hexaploid wheats from Aegilops tauschii (2n = 2x = 14; DD). [ABSTRACT FROM AUTHOR]

Improving wheat yield under water limited conditions could be attained if more traits conferring better agronomic performance are brought together in the same genotype. This study was conducted to assess drought tolerance and diversity of a collection of conventional bread wheat (CBW) and synthetic-derived bread wheat (SBW) genotypes. Evaluation was carried out through phenological traits in the field under well-watered and drought stress conditions imposed at pre-anthesis stage for two successive growing seasons during 2010/11 and 2011/12. Association mapping (AM) analysis was used to dissect the genetic basis of drought-adaptive traits using mixed linear model (MLM). In total, 27 marker-trait associations (MTAs) were associated over 23 SSR loci for six phonological traits. There were 12 MTAs confined only to stress treatment, 2 MTAs confined to control environment and 7 MTAs were common in both treatments. The intra-chromosomal position of several of these MTAs coincided with those previously reported whereas there were some unique loci highlighted for drought-adaptive traits that had not been located to date. Opportunities for further wheat improvement are provided by these novel loci based on a marker approach. [ABSTRACT FROM AUTHOR]