Unravelling the novel genetic diversity and marker-trait associations of corn leaf aphid resistance in wheat using microsatellite markers.

The study was conducted to identify novel simple sequence repeat (SSR) markers associated with resistance to corn aphid (CLA), Rhopalosiphum maidis L. in 48 selected bread wheat (Triticum aestivum L.) and wild wheat (Aegilops spp. & T. dicoccoides) genotypes during two consecutive cropping seasons (2018-19 and 2019-20). A total of 51 polymorphic markers containing 143 alleles were used for the analysis. The frequency of the major allele ranged from 0.552 (Xgwm113) to 0.938 (Xcfd45, Xgwm194 and Xgwm526), with a mean of 0.731. Gene diversity ranged from 0.116 (Xgwm526) to 0.489 (Xgwm113), with a mean of 0.354. The polymorphic information content (PIC) value for the SSR markers ranged from 0.107 (Xgwm526) to 0.370 (Xgwm113) with a mean of 0.282. The results of the STRUCTURE analysis revealed the presence of four main subgroups in the populations. Analysis of molecular variance (AMOVA) showed that the between-group difference was around 37 per cent of the total variation contributed to the diversity by the whole germplasm, while 63 per cent of the variation was attributed between individuals within the group. A general linear model (GLM) was used to identify marker-trait associations, which detected a total of 23 and 27 significant new marker-trait associations (MTAs) at the p < 0.01 significance level during the 2018-19 and 2019-20 crop seasons, respectively. The findings of this study have important implications for the identification of molecular markers associated with CLA resistance. These markers can increase the accuracy and efficiency of aphid-resistant germplasm selection, ultimately facilitating the transfer of resistance traits to desirable wheat genotypes.

Boosting wheat yield, profitability and NUE with prilled and nano urea in conservation tillage.

Rice-wheat production in the Indo-gangetic plains (IGPs) of India faces major concerns such as depleting resources, rice residue burning, excessive fertilizer use, and decreasing nitrogen use efficiency. These issues threaten sustainable crop production in the future. Therefore, a field study was conducted during the winter seasons of 2020-21 and 2021-22 to evaluate the effect of combined conventional and nano fertilizers on nitrogen application just before or after irrigation to improve wheat productivity, profitability and NUE under conservation tillage. The study evaluated eight treatment combinations of nitrogen application through conventionally applied urea (46% N) and foliar applied nano urea (4% N) under zero tillage with rice residue retention. Results revealed that growth, physiological indices, yield, and quality parameters were enhanced with the application of 150 kg N/ha in three equal splits as basal and just before 1st and 2nd irrigation alone (T2) or along with a spray of nano urea (T5) compared to other treatments. T5 recorded 7.2%, 8.5%, and 7.8% more plant dry matter, number of tillers, and grain yield, respectively, over the conventional practice of applying 150 kg N/ha in three equal splits as basal and 7-10 days after 1st and 2nd irrigation (T3, farmers practice). Although, T2 showed similar results to T5, T5 recorded significantly higher gross ($2542/ha) and net returns ($1279/ha) than the other treatments. However, the benefit-cost ratio of T2 and T5 was same (2.01). A significant and positive correlation coefficient between grain yield and physiological parameters such as CCI and NDVI confirmed that increasing the nitrogen dose enhanced the chlorophyll content, greenness, and plant vigor. Based on the results, it can be concluded that applying 150 kg N/ha in three equal splits as basal and just before 1st and 2nd irrigation under conservation agriculture, along with a single spray of nano urea (4% N) at 60-65 days after sowing, can improve growth, yield attributes, wheat yield, and NUE compared to farmers practice (T3) in India.

Identification of Novel QTLs/Defense Genes in Spring Wheat Germplasm Panel for Seedling and Adult Plant Resistance to Stem Rust and Their Validation Through KASP Marker Assays.

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.

Dataset of phenotyping recombinant inbred lines population of wheat under heat stress conditions.

Heat stress is a genetically complex and physiologically diverse phenomenon. To overcome the effect of heat stress identification of genomic locations associated with heat stress tolerance is essential. This article provides the dataset of phenotyping used in the research article entitled "Mapping QTLs for grain yield components in wheat under heat stress". The presented data included the phenotyping of the 249 RIL population of F8 and F9 generations under timely and late sown conditions during the 2013-14 and 2014-15 crop seasons, respectively. The RIL population was derived from the cross between HUW510 and HD2808 wheat genotypes. A total of eight agronomic traits were subjected to phenotype and the heat susceptibility index (HSI) of these traits was estimated to identify the effect of heat stress on the parents and RIL population. The presented dataset could be utilized to understand the genetic basis for heat stress tolerance in wheat.

Dataset of nine agronomic traits in bread wheat phenotyped under irrigated and rain-fed environments.

Higher yield and broad adaptation to drought-prone environments are key targets of wheat breeding programs. This can be achieved through a complete knowledge of the genetic architecture of yield and its related traits. This brief article provides analysed mean data used in the research article entitled "QTL mapping for nine drought-responsive agronomic traits in bread wheat under irrigated and rain-fed environments" (Gahlaut et al., 2017). Phenotypic data were recorded on nine important agronomic traits on a doubled haploid (DH) mapping population derived from the cross Kukri/Excalibur. For recording this data, the mapping population was grown during three crop seasons (2010-11 to 2012-13) at four separate locations in India, both under irrigated and rain-fed environments. This dataset is valuable for wheat breeders to better understand the genetic basis of drought tolerance in wheat.

Genome-Wide Association Study Reveals Genomic Regions Associated With Ten Agronomical Traits in Wheat Under Late-Sown Conditions.

Poor understanding of the genetic and molecular basis of heat tolerance component traits is a major bottleneck in designing heat tolerant wheat cultivars. The impact of terminal heat stress is generally reported in the case of late sown wheat. In this study, our aim was to identify genomic regions for various agronomic traits under late sown conditions by using genome-wide association approach. An association mapping panel of 205 wheat accessions was evaluated under late sown conditions at three different locations in India. Genotyping of the association panel revealed 15,886 SNPs, out of which 11,911 SNPs with exact physical locations on the wheat reference genome were used in association analysis. A total of 69 QTLs (10 significantly associated and 59 suggestive) were identified for ten different traits including productive tiller number (17), grain yield (14), plant height (12), grain filling rate (6), grain filling duration (5), days to physiological maturity (4), grain number (3), thousand grain weight (3), harvest index (3), and biomass (2). Out of these associated QTLs, 17 were novel for traits, namely PTL (3), GY (2), GFR (6), HI (3) and GNM (3). Moreover, five consistent QTLs across environments were identified for GY (4) and TGW (1). Also, 11 multi-trait SNPs and three hot spot regions on Chr1Ds, Chr2BS, Chr2DS harboring many QTLs for many traits were identified. In addition, identification of heat tolerant germplasm lines based on favorable alleles HD2888, IC611071, IC611273, IC75240, IC321906, IC416188, and J31-170 would facilitate their targeted introgression into popular wheat cultivars. The significantly associated QTLs identified in the present study can be further validated to identify robust markers for utilization in marker-assisted selection (MAS) for development of heat tolerant wheat cultivars.

Heterologous expression and characterization of novel manganese superoxide dismutase (Mn-SOD) - A potential biochemical marker for heat stress-tolerance in wheat (Triticum aestivum).

Heat stress causes oxidative bursts damaging the organelles and nascent proteins. Plants have inherited antioxidant defense system to neutralize the effect of reactive oxygen species. Superoxide dismutase provides first line of defense against the HS by regulating the accumulation of peroxide radicals inside the cells. Here, we report identification and cloning of putative manganese superoxide dismutase (Mn-SOD) gene of ~733 nt from wheat cv. HD2985 through de novo assembly. The gene was observed to localize on Chr 6D with a mitochondrial targeting peptide sequence and iron/manganese domain. We predicted 147 homologs of Mn-SOD in eukaryotes with diverse speciation nodes. A recombinant Mn-SOD protein of ~25.5 kDa was purified through heterologous expression system. Kinetics assay of recombinant protein showed optimum pH of 8.0, optimum temperature of 35 °C and Km and Vmax values of 1.51 µM and 9.45 U/mg proteins, respectively. Maximum expression and activity of Mn-SOD was observed in leaves from Raj3765, as compared to stem and spike during milky-ripe stage under differential HS. In gel activity assay showed the appearance of all the three isoforms of SOD in thermotolerant cv. under HS. Mn-SOD, being active at pivotal position, can be also used as potential biochemical marker in wheat breeding program.

Drought tolerance in Triticum aestivum L. genotypes associated with enhanced antioxidative protection and declined lipid peroxidation.

Drought is one of the major constraints in wheat production and causes a huge loss at grain-filling stage. In this study we highlighted the response of different wheat genotypes under drought stress at the grain-filling stage. Field experiments were conducted to evaluate 72 wheat (Triticum aestivum L.) genotypes under two water regimes: irrigated and drought condition. Four wheat genotypes, two each of drought tolerant (IC36761A, IC128335) and drought-susceptible category (IC335732 and IC138852) were selected on the basis of agronomic traits and drought susceptibility index (DSI), to understand their morphological, biochemical and molecular basis of drought stress tolerance. Among agronomic traits, productive tillers followed by biomass had high percent reduction under drought stress, thus drought stress had a great impact. Antioxidant activity (AO), total phenolic and proline content were found to be significantly higher in IC128335 genotype. Differential expression pattern of transcription factors of ten genes revealed that transcription factor qTaWRKY2 followed by qTaDREB, qTaEXPB23 and qTaAPEX might be utilized for developing wheat varieties resistant to drought stress. Understanding the role of TFs would be helpful to decipher the molecular mechanism involved in drought stress. Identified genotypes (IC128335 and IC36761A) may be useful as parental material for future breeding program to generate new drought-tolerant varieties.

Exploring the traits for lodging tolerance in wheat genotypes: a review.

The rising population entails enhancement in wheat productivity to ensure substantial food supply which often get hindered by various biotic and abiotic stresses. Lodging, due to rain and high velocity wind causes significant economic and yield losses in cereals. Hence, lodging is emerging as a major hurdle to achieve the required yield targets. Various morphological, biochemical, anatomical and genetic traits contribute to produce a plant competent enough to bear lodging stress. Hence, in this review, we intend to elaborate the cause and impact relationship of lodging and tried to link lodging tolerance traits to field practices to minimize the losses. Because of the complex nature of lodging phenomenon, it is still obscure to identify best correlated traits to screen genotype in breeding programmes. However, the genotypes with best correlated traits like plant height, culm wall thickness should be introduced/selected in breeding programmes to inculcate lodging tolerance in a high yielding variety as in recent era lodging tolerance is a key factor to enhance productivity and farmer's income as well.

Correction: Characterising variation in wheat traits under hostile soil conditions in India.

[This corrects the article DOI: 10.1371/journal.pone.0179208.].

Variation in grain Zn concentration, and the grain ionome, in field-grown Indian wheat.

Wheat is an important dietary source of zinc (Zn) and other mineral elements in many countries. Dietary Zn deficiency is widespread, especially in developing countries, and breeding (genetic biofortification) through the HarvestPlus programme has recently started to deliver new wheat varieties to help alleviate this problem in South Asia. To better understand the potential of wheat to alleviate dietary Zn deficiency, this study aimed to characterise the baseline effects of genotype (G), site (E), and genotype by site interactions (GxE) on grain Zn concentration under a wide range of soil conditions in India. Field experiments were conducted on a diverse panel of 36 Indian-adapted wheat genotypes, grown on a range of soil types (pH range 4.5-9.5), in 2013-14 (five sites) and 2014-15 (six sites). Grain samples were analysed using inductively coupled plasma-mass spectrometry (ICP-MS). The mean grain Zn concentration of the genotypes ranged from 24.9-34.8 mg kg-1, averaged across site and year. Genotype and site effects were associated with 10% and 6% of the overall variation in grain Zn concentration, respectively. Whilst G x E interaction effects were evident across the panel, some genotypes had consistent rankings between sites and years. Grain Zn concentration correlated positively with grain concentrations of iron (Fe), sulphur (S), and eight other elements, but did not correlate negatively with grain yield, i.e. no yield dilution was observed. Despite a relatively small contribution of genotype to the overall variation in grain Zn concentration, due to experiments being conducted across many contrasting sites and two years, our data are consistent with reports that biofortifying wheat through breeding is likely to be effective at scale given that some genotypes performed consistently across diverse soil types. Notably, all soils in this study were probably Zn deficient and interactions between wheat genotypes and soil Zn availability/management (e.g. the use of Zn-containing fertilisers) need to be better-understood to improve Zn supply in food systems.

Mapping QTLs for grain yield components in wheat under heat stress.

The current perspective of increasing global temperature makes heat stress as a major threat to wheat production worldwide. In order to identify quantitative trait loci (QTLs) associated with heat tolerance, 251 recombinant inbred lines (RILs) derived from a cross between HD2808 (heat tolerant) and HUW510 (heat susceptible) were evaluated under timely sown (normal) and late sown (heat stress) conditions for two consecutive crop seasons; 2013-14 and 2014-15. Grain yield (GY) and its components namely, grain weight/spike (GWS), grain number/spike (GNS), thousand grain weight (TGW), grain filling rate (GFR) and grain filling duration (GFD) were recorded for both conditions and years. The data collected for both timely and late sown conditions and heat susceptibility index (HSI) of these traits were used as phenotypic data for QTL identification. The frequency distribution of HSI for all the studied traits was continuous during both the years and also included transgressive segregants. Composite interval mapping identified total 24 QTLs viz., 9 (timely sown traits), 6 (late sown traits) and 9 (HSI of traits) mapped on linkage groups 2A, 2B, and 6D during both the crop seasons 2013-14 and 2014-15. The QTLs were detected for GWS (6), GNS (6), GFR (4), TGW (3), GY (3) and GFD (2). The LOD score of identified QTLs varied from 3.03 (Qtgns.iiwbr-6D) to 21.01 (Qhsitgw.iiwbr-2A) during 2014-15, explaining 11.2 and 30.6% phenotypic variance, respectively. Maximum no of QTLs were detected in chromosome 2A followed by 6D and 2B. All the QTL detected under late sown and HSI traits were identified on chromosome 2A except for QTLs associated with GFD. Fifteen out of 17 QTL detected on chromosome 2A were clustered within the marker interval between gwm448 and wmc296 and showed tight linkage with gwm122 and these were localized in 49-52 cM region of Somers consensus map of chromosome 2A i.e. within 18-59.56 cM region of chromosome 2A where no QTL related to heat stress were reported earlier. Besides, three consistent QTLs, Qgws.iiwbr-2A, Qgns.iiwbr-2A and Qgns.iiwbr-2A were also detected in all the environments in this region. The nearest QTL detected in earlier studies, QFv/Fm.cgb-2A was approximately 6cM below the presently identified QTLs region, respectively Additionally, QTLs for physiological and phenological traits and plant height under late sown and HSI of these traits were also detected on chromosome 2A. QTL for HSI of plant height and physiological maturity were located in the same genomic region of chromosome 2Awhereas QTLs for physiological and phonological traits under late sown were located 8cM and 33.5 cM below the genomic location associated with grain traits, respectively in consensus map of Somers. This QTL hot-spot region with consistent QTLs could be used to improve heat tolerance after validation.

QTL mapping for nine drought-responsive agronomic traits in bread wheat under irrigated and rain-fed environments.

In bread wheat, QTL interval mapping was conducted for nine important drought responsive agronomic traits. For this purpose, a doubled haploid (DH) mapping population derived from Kukri/Excalibur was grown over three years at four separate locations in India, both under irrigated and rain-fed environments. Single locus analysis using composite interval mapping (CIM) allowed detection of 98 QTL, which included 66 QTL for nine individual agronomic traits and 32 QTL, which affected drought sensitivity index (DSI) for the same nine traits. Two-locus analysis allowed detection of 19 main effect QTL (M-QTL) for four traits (days to anthesis, days to maturity, grain filling duration and thousand grain weight) and 19 pairs of epistatic QTL (E-QTL) for two traits (days to anthesis and thousand grain weight). Eight QTL were common in single locus analysis and two locus analysis. These QTL (identified both in single- and two-locus analysis) were distributed on 20 different chromosomes (except 4D). Important genomic regions on chromosomes 5A and 7A were also identified (5A carried QTL for seven traits and 7A carried QTL for six traits). Marker-assisted recurrent selection (MARS) involving pyramiding of important QTL reported in the present study, together with important QTL reported earlier, may be used for improvement of drought tolerance in wheat. In future, more closely linked markers for the QTL reported here may be developed through fine mapping, and the candidate genes may be identified and used for developing a better understanding of the genetic basis of drought tolerance in wheat.

Characterising variation in wheat traits under hostile soil conditions in India.

Intensive crop breeding has increased wheat yields and production in India. Wheat improvement in India typically involves selecting yield and component traits under non-hostile soil conditions at regional scales. The aim of this study is to quantify G*E interactions on yield and component traits to further explore site-specific trait selection for hostile soils. Field experiments were conducted at six sites (pH range 4.5-9.5) in 2013-14 and 2014-15, in three agro-climatic regions of India. At each site, yield and component traits were measured on 36 genotypes, representing elite varieties from a wide genetic background developed for different regions. Mean grain yields ranged from 1.0 to 5.5 t ha-1 at hostile and non-hostile sites, respectively. Site (E) had the largest effect on yield and component traits, however, interactions between genotype and site (G*E) affected most traits to a greater extent than genotype alone. Within each agro-climatic region, yield and component traits correlated positively between hostile and non-hostile sites. However, some genotypes performed better under hostile soils, with site-specific relationships between yield and component traits, which supports the value of ongoing site-specific selection activities.

Physiological traits associated with heat tolerance in bread wheat (Triticum aestivum L.).

Field experiments for evaluating heat tolerance-related physiological traits were conducted for two consecutive years using a mapping population of recombinant inbred lines (RILs) from the cross RAJ4014/WH730. Chlorophyll content (Chl) and chlorophyll fluorescence (CFL) were recorded under timely sown (TS) and late sown (LS) conditions. Late sowing exposes the terminal stage of plants to high temperature stress. Pooled analysis showed that CFL and Chl differed significantly under TS and LS conditions. The mean value of CFL (Fv/Fm) and Chl under both timely and late sown conditions were used as physiological traits for association with markers. Regression analysis revealed significant association of microsatellite markers viz., Xpsp3094 and Xgwm131 with coefficients of determination (R (2)) values for CFL (Fv/Fm) and Chl as 12 and 8 %, respectively. The correlation between thousand grain weight (TGW) with Chl and CFL were 14 and 7 % and correlation between grain wt./spike with Chl and CFL were 15 and 8 %, respectively. The genotypes showing tolerance to terminal heat stress as manifested by low heat susceptibility index (HSI = 0.43) for thousand grain weight, were also found having very low Chl, HSI (-0.52). These results suggest that these physiological traits may be used as a secondary character for screening heat-tolerant genotypes.