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Roots are the main sensing organ, initiating multiple signaling pathways in response to abiotic factors, including nutrients, drought, and salt stress. A focus on improving the root system architecture is a key strategy to mitigate these stresses in wheat crop. In the present study, a diversity panel comprising indigenous landraces and historical cultivars from Pakistan was characterized for the root system architecture (RSA) and important loci were identified using a genome‐wide association study (GWAS). RSA of the diversity panel was characterized 30 days after sowing in brunch tubes, and root images were taken. A high‐throughput root imaging analysis using Rhizovision software was performed by setting the scale to extract the eight RSA traits and four plant biomass‐related traits. GWAS identified 323 association signals for 12 root and biomass traits present on all wheat chromosomes, while the most important and reliable genetic loci (based on pleotropic loci and candidate genes) were identified on chromosomes 2A, 2B, 5A, 5D, 6A, 7B, and 7D for RSA. SNP annotation and transcriptome profiling identified nine candidate genes regulating the RSA and plant biomass traits, including ROOTLESS WITH UNDETECTABLE MERISTEM1, MYB TRANSCRIPTION FACTOR4, BRASSINOSTEROID INSENSITIVE1, SLENDER RICE1, AUXIN‐RESPONSIVE FACTOR25, SCARECROW, NARROW LEAF2, PIN‐FORMED1 AND PHOSPHATE TRANSCRIPTION FACTOR1. This study provided pre‐breeding information for deep‐rooting genotypes and associated markers that will accelerate the incorporation of such traits in breeding. [ABSTRACT FROM AUTHOR]

We evaluated root system architecture (RSA) of a set of 58 historical spring wheat cultivars from Pakistan representing 105 years of selection breeding. The evaluations were carried out under control and water-limited conditions using a high-throughput phenotyping system coupled with RhizoVision Explorer software. The cultivars were classified into three groups based on release year as cultivars released pre-1965, released between 1965 and 2000, and cultivars released post-2000. Under water-limited conditions a decline in 20 out of 25 RSA component traits was observed in pre-1965 cultivars group. Whereas cultivars released after the 1965, so-called green revolution period, showed a decline in 17 traits with significant increments in root length, depth, and steep angle frequency which are important root traits for resource-uptake under water-limited conditions. Similarly, cultivars released after 2000 indicated an increase in the number of roots, depth, diameter, surface area, and steep angle frequency. The coefficient of correlation analysis showed a positive correlation between root depth and yield-related traits under water-limited conditions. We also investigated the effects of green-revolution genes (Rht1) and some phenology-related genes such as DRO1, TaMOR, TaLTPs, TaSus-2B on RSA and identified significant associations of these genes with important root traits. There was strong selection pressure on DRO1 gene in cultivated wheat indicating the allele fixed in modern wheat cultivars is different from landraces. The expression of DRO1, and TaMOR were retrieved from an RNAseq experiment, and results were validated using qRT-PCR. The highest expression of DRO1 and TaMOR was found in Chakwal-50, a rainfed cultivar released in 2008, and MaxiPak-65 released in 1965. We conclude that there is a positive historic change in RSA after 1965 that might be attributed to genetic factors associated with favored RSA traits. Furthermore, we suggest root depth and steep angle as promising traits to withstand water-limited environments and may have implications in selection for breeding. [ABSTRACT FROM AUTHOR]

Crop wild resources are excellent sources of new genetic variation for resilience against climate extremes. However, detailed characterization of the desirable phenotypes is essential before using these crop wild resources in breeding programs. This current study was, therefore, conducted to investigate the water stress responses of eight wild Elymus species and two wheat cultivars. The experiment was carried out under varying levels of osmotic stress induced by polyethylene glycol and progressive water stress through different field capacities. Water stress significantly reduced both physiological and biochemical traits compared to control, ranging from7.1% (protein content) to 34.5% (chlorophyll) under moderate stress and 9.1-45.8% under severe stress. The anatomical features were also affected under progressive water stress, including a reduction in xylem vessel diameter (7.92 and 16.50%), phloem length (4.36 and 7.18%), vascular bundle length (3.09 and 6.04%), and ground tissue thickness (2.36 and 5.52%), respectively. Conclusively, Elymus borianus (endemic to Swat, Pakistan), E. russelli, E. caninus, E. longioristatus, and E. dauhuricus outperformed the check wheat cultivar, Pirsabak 2005, which is a rainfed variety. The results revealed that Elymus species belonging to the tertiary gene pool of bread wheat could be an excellent drought tolerance source for use in a breeding program. [ABSTRACT FROM AUTHOR]

Increasing global temperature has adverse effects on crop health and productivity at both seedling and reproductivity stages. It is paramount to develop heat tolerant wheat cultivars able to sustain under high and fluctuating temperature conditions. An experiment was conducted to characterize 194 historical wheat cultivars of Pakistan under high temperature at seedling stage to identify loci associated with heat tolerance using genome-wide association studies (GWAS). A quantitative trait locus, TaHST1, on chr4A was also characterized to identify the haplotypes at this locus associated with heat tolerance in wheat from Pakistan. Initially, the diversity panel was planted under control conditions (25°C/20°C day and night temperature) in a glass house. At three leaf stage, plants were subjected to heat stress (HS) by increasing temperature (40°C/35°C day and night), while one treatment was kept at control condition. After 7days of HS, data were collected for seedling morphology. Heat stress reduced these traits by 25% (root weight) to 40% (shoot weight), and shoot biomass was largely affected by heat stress. A GWAS model, fixed and random model circulating probability unification (FarmCPU), identified 43 quantitative trait nucleotides (QTNs) on all chromosomes, except chr7B, were associated under both HS and control conditions. Thirteen QTNs were identified in control, while 30 QTNs were identified in HS condition. In total, 24 haplotypes were identified at TaHST1 locus, and most of the heat tolerant genotypes were assigned to Hap-20 and Hap-21. Eleven QTNs were identified within 0.3-3.1Mb proximity of heat shock protein (HSP). Conclusively, this study provided a detailed genetic framework of heat tolerance in wheat at the seedling stage and identify potential genetic regions associated with heat tolerance which can be used for marker assisted selection (MAS) in breeding for heat stress tolerance. [ABSTRACT FROM AUTHOR]

Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan. [ABSTRACT FROM AUTHOR]

Karnal bunt caused by Tilletia indica is a quarantine disease of wheat causing huge economic losses due to the ban on the import of bunted grains. This study was designed to characterize pathogenicity, aggressiveness and genetic diversity of 68 Tilletia indica isolates collected from different geographic regions of Pakistan. Forty-six isolates were tested for their pathogenicity on eight wheat varieties, out of which three were non-aggressive. The coefficient of infection (CI) ranged from 15.73% (PB-25) to 10% (PB-68, PB-60, and PB-43). The isolates collected from central Punjab showed higher infestation compared to other isolates. Among the wheat varieties used for the aggressiveness study, WL-711 showed susceptible reaction with 10.88% CI, while NIFA-Barsat, HD-29, Janbaz, Bakhtawar-92, Tatara, and AARI 2011 showed resistance to the highly resistant response. These isolates were amplified using 31 random amplified polymorphic DNA (RAPD) markers and 32 inter-simple sequence repeat (ISSR) markers for diversity analysis. The principal component analysis (PCA) and analysis of molecular variance (AMOVA) showed greater divergence among isolates collected from Punjab and Khyber Pakhtunkhwa (KPK), with a moderate level of admixture. The isolates from Faisalabad (Punjab) were more aggressive compared to isolates from KPK and were clearly separated based on PCA, indicating the significant genetic distance in the populations. Our findings will assist breeders and pathologists in better understanding the pathogenic variability in Tilletia indica and in subsequent disease management. [ABSTRACT FROM AUTHOR]

It is important to understand the genetic gain achieved through selection of key yield traits for planning future breeding strategies in developing high yielding wheat (Triticum aestivum L.) cultivars. The aim of this study was to characterize the genetic changes and genotype × environment (G×E) interaction by additive main effect and multiplicative interactions (AMMI) for morphological, physiological, and yield component traits under five environments using 24 wheat cultivars released from 1911 to 2016 in Pakistan. There was a significant increase in grain yield (9.03 kg ha−1 yr−1, 0.37%), and plant height was reduced linearly (−0.26 cm yr−1, −0.33%). The traits waxiness, leaf rolling, harvest index, spike length, and grains per spike significantly increased but the gain was only 0.16–0.2% per year. Analysis of variance revealed that genotype, environment, and G×E interaction were highly significant (P <.01) for all traits except relative chlorophyll content, biomass, days to maturity, and number of spikes. Gene‐specific markers identified the durable resistance gene Lr67/Yr46/Sr55/Pm46 in obsolete cultivars as early as 1911, whereas the photoperiod‐insensitive allele Ppd‐D1a and reduced height alleles Rht‐B1b and Rht‐D1b were present only in the post‐1965 cultivars. Diversity analysis based on a 50K single nucleotide polymorphism genotyping array clearly differentiated temporal patterns in 24 cultivars, which was correlated with the agronomic performance of the cultivars. This dataset provided detailed insight into the performance of historical wheat cultivars and could help in devising wheat breeding strategies to focus on the traits contributing to grain yield and have slower rate of genetic progress. Core Ideas: The genetic gain in morphology of Pakistani bread wheat cultivars over 105 yr areas was assessed.Leaf rolling, waxiness, and grains/spikes associated with genetic gains in grain yield were achieved by breeding.The performance and stability of yield and yield‐related traits was analyzed for the different cultivars. [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]

We investigated alleles at 31 loci associated with adaptability, yield, and end-use quality in 107 wheat (Triticum aestivum L.) landraces (WLRs) and 121 improved historical wheat cultivars (HWCs) from Pakistan. The WLRs were categorized into two further subgroups: 36 pre-Green-Revolution landraces released as cultivars and 71 geographically spread landraces from all over Pakistan. Alleles VrnA1a, TaGW2-6A-A, TaCKX6-D1b, Pinb-D1b, Psy-A1b, and Wx-D1b were absent in WLRs, whereas ample diversity was observed at all other loci. In HWCs, only Wx-D1b and Glu-A3e were absent among the alleles tested, whereas the alleles Ppd-D1a (90%), Rht-B1b or Rht-D1b (83.4%), TaCwi-A1a (95%), TaGW2-6A-G (76%), TaCKX6-D1a (77.3%), Glu-A1b (66.1%), Glu-D1d (61.3%), Pina-D1b (88.2%), Pinb-D1a (90%), Psy-A1a (66.1%), Psy-B1b (81.8%), Psy-D1a (86.5%), Ppo-A1a (70%), TaZds-D1b (73.9%), TaLox-B1b (80.1%), and Wx-D1a (100%) predominated, indicating significant improvement in adaptability, yield potential, and end-use quality and unconscious selection for favored alleles. Higher frequencies of favored alleles at the TaCwi-A1 and TaCKX6-D1 loci influencing 1000-kernel weight (TKW) in HWCs indicated that selection pressure on these alleles during breeding successfully contributed to cultivar improvement. Wright's pairwise fixation index (Fst) statistics indicated greater genetic divergence between HWC and WLR collections (0.16) than HWC and WLR cultivars (0.14). Population structure based on functional markers (FMs) using principal component analysis partitioned the germplasm into two distinct groups. High genetic divergence and low admixture between HWCs and WLRs indicated limited use of landraces in wheat breeding in Pakistan. Our results suggested these collections as rich reservoirs of alleles and haplotype combinations that may be useful in future breeding programs. [ABSTRACT FROM AUTHOR]

Stripe rust (yellow rust) caused by Puccinia striiformis f. sp. tritici has been an important disease of wheat in the Indian subcontinent since 1786. Currently, it prevails across all the wheat growing areas from north to south in the country. Due to the favourable weather conditions, the northern uplands have been historically hit by the severe disease epidemics. These epidemics caused significant losses to national wheat production. Acquisition of broader virulence pattern by the pathogen poses a serious threat to national agriculture. Although the deployed national wheat varieties have adequate resistance, these are developed around few major genes and are vulnerable to the new evolving strains of the pathogen. Utilisation of race non-specific durable resistance and seedling resistance via gene pyramiding, based on the current virulence scenario of the pathogen should provide sustainable control. This review focuses on the national milestones that recognise the economic significance of the disease and current status of stripe rust and its management in Pakistan. [ABSTRACT FROM AUTHOR]

Wheat (Triticum aestivum L.), being a staple food crop, is an important nutritional source providing protein and minerals. It is important to fortify staple cereals such as wheat with essential minerals to overcome the problems associated with malnutrition. The experiment was designed to evaluate the status of 11 micronutrients including grain iron (GFe) and zinc (GZn) in 62 wheat cultivars released between 1911 and 2016 in Pakistan. Field trials were conducted over two years and GFe and GZn were quantified by both inductively coupled plasma optical emission spectroscopy (ICP-OES) and energy-dispersive X-ray fluorescence spectrophotometer (EDXRF). The GZn ranged from 18.4 to 40.8 mg/kg by ED-XRF and 23.7 to 38.8 mg/kg by ICP-OES. Similarly, GFe ranged from 24.8 to 44.1 mg/kg by ICP-OES and 26.8 to 36.6 mg/kg by EDEXR. The coefficient of correlation was higher for GZn (r = 0.90), compared to GFe (r = 0.68). Modern cultivars such as Zincol-16 and AAS-2011 showed higher GFe and GZn along with improved yield components. Old wheat cultivars WL-711, C-518 and Pothowar-70, released before 1970, also exhibited higher values of GFe and GZn; however, their agronomic performance was poor. Multivariate analysis using eleven micronutrients (Fe, Zn, Al, Ca, Cu, K, Mg, Mn, Na, Se and P) along with agronomic traits, and genome-wide SNP markers identified the potential cultivar with improved yield, biofortification and wider genetic diversity. Genetic gain analysis identified a significant increase in grain yield (0.4% year−1), while there was negative gain for GFe (−0.11% year−1) and GZn (−0.15% year−1) over the span of 100 years. The Green Revolution Rht-B1 and Rht-D1 genes had a strong association with plant height and grain yield (GY), while semi-dwarfing alleles had a negative effect on GFe and GZn contents. This study provided a valuable insight into the biofortification status of wheat cultivars deployed historically in Pakistan and is a valuable source to initiate a breeding strategy for simultaneous improvement in wheat phenology and biofortification. [ABSTRACT FROM AUTHOR]

A high grain zinc wheat cultivar, Zincol-2016, was released in Pakistan to mitigate mineral malnutrition. Here, we used RNAseq based approach to reveal transcriptional landscape of its developing grains, and to identify genetic variants in zinc (Zn) and iron (Fe) homeostasis genes. Differential gene expression analysis identified 8370 differentially expressed genes (DEGs) over the course of grain filling. The profiling of 265 Fe/Zn homeostasis genes revealed the homeologs of TaNAS9 , TaFER1, TaNAAT2 , TaDMAS, TaZIFL5-A , TaZIFL5-D , TaZIP14-B , TaNRAMP3 , TaVIT1, TaPRI2-D , TabZIPF1-7B , TabZIPF1-7D , TabZIPF2-5A , and TabZIPF2-5B had increased expression in Zincol-2016 relative to other cultivars from expVIP database. The variant calling identified 358 SNPs and 34 InDels in the Fe/Zn homeostasis genes. Two of those SNPs in TaZIP14-B (TraesCS3B02G140400), and TaNAAT2-B (TraesCS1B02G300600), were associated with grain zinc and iron concentrations (GZnC and GFeC) in a diverse panel of 145 wheat cultivars. The Zincol-type alleles of both genes significantly increased GZnC and GFeC by 7.3–8.6% and 5.9–6.3%, respectively. In addition, 8 SNPs causing missense mutation and 2 InDels causing frameshift mutation were found unique to Zincol. The present study forms a basis for understanding the genetic basis of high GZnC and GFeC in Zincol-2016 and can help efforts to biofortify other wheat varieties. [Display omitted] • RNAseq of Zincol-2016 developing grains during grain filling stage was conducted. • Increased expression of several Fe/Zn homeostasis genes was observed in Zincol. • In total 358 SNPs and 34 InDels in known Fe/Zn homeostasis genes were identified. • Comparison with variants data of other wheat cultivars identified 10 unique variants in the Fe/Zn homeostasis genes of Zincol. • Zincol-type alleles of TaZIP14-B and TaNAAT2-B increased grain iron and zinc contents. [ABSTRACT FROM AUTHOR]

Characterization of genomic regions underlying adaptation of landraces can reveal a quantitative genetics framework for local wheat (Triticum aestivum L.) adaptability. A collection of 512 wheat landraces from the eastern edge of the Fertile Crescent in Iran and Pakistan were genotyped using genome-wide single nucleotide polymorphism markers generated by genotyping-by-sequencing. The minor allele frequency (MAF) and the heterozygosity (H) of Pakistani wheat landraces (MAF = 0.19, H = 0.008) were slightly higher than the Iranian wheat landraces (MAF = 0.17, H = 0.005), indicating that Pakistani landraces were slightly more genetically diverse. Population structure analysis clearly separated the Pakistani landraces from Iranian landraces, which indicates two separate adaptability trajectories. The large-scale agro-climatic data of seven variables were quite dissimilar between Iran and Pakistan as revealed by the correlation coefficients. Genome-wide association study identified 91 and 58 loci using agroclimatic data, which likely underpin local adaptability of the wheat landraces from Iran and Pakistan, respectively. Selective sweep analysis identified significant hits on chromosomes 4A, 4B, 6B, 7B, 2D, and 6D, which were colocalized with the loci associated with local adaptability and with some known genes related to flowering time and grain size. This study provides insight into the genetic diversity with emphasis on the genetic architecture of loci involved in adaptation to local environments, which has breeding implications., (© 2021 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)