Genome-wide association mapping for field spot blotch resistance in South Asian spring wheat genotypes.

Spot blotch caused by Bipolaris sorokiniana ((Sacc.) Shoemaker) (teleomorph: Cochliobolus sativus [Ito and Kuribayashi] Drechsler ex Dastur) is an economically important disease of warm and humid regions. The present study focused on identifying resistant genotypes and single-nucleotide polymorphism (SNP) markers associated with spot blotch resistance in a panel of 174 bread spring wheat lines using field screening and genome-wide association mapping strategies. Field experiments were conducted in Agua Fria, Mexico, during the 2019-2020 and 2020-2021 cropping seasons. A wide range of phenotypic variation was observed among genotypes tested during both years. Twenty SNP markers showed significant association with spot blotch resistance on 15 chromosomes, namely, 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7B. Of these, two consistently significant SNPs on 5A, TA003225-0566 and TA003225-1427, may represent a new resistance quantitative trait loci. Further, in the proximity of Tsn1 on 5B, AX-94435238 was the most stable and consistent in both years. The identified genomic regions could be deployed to develop spot blotch-resistant genotypes, particularly in the spot blotch-vulnerable wheat growing areas.

Genome-Wide Association Study Reveals Novel Powdery Mildew Resistance Loci in Bread Wheat.

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

Assessment of Indian wheat germplasm for Septoria nodorum blotch and tan spot reveals new QTLs conferring resistance along with recessive alleles of Tsn1 and Snn3.

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

Genome-wide association mapping of genomic regions associated with drought stress tolerance at seedling and reproductive stages in bread wheat.

Understanding the genetic architecture of drought stress tolerance in bread wheat at seedling and reproductive stages is crucial for developing drought-tolerant varieties. In the present study, 192 diverse wheat genotypes, a subset from the Wheat Associated Mapping Initiative (WAMI) panel, were evaluated at the seedling stage in a hydroponics system for chlorophyll content (CL), shoot length (SLT), shoot weight (SWT), root length (RLT), and root weight (RWT) under both drought and optimum conditions. Following that, a genome-wide association study (GWAS) was carried out using the phenotypic data recorded during the hydroponics experiment as well as data available from previously conducted multi-location field trials under optimal and drought stress conditions. The panel had previously been genotyped using the Infinium iSelect 90K SNP array with 26,814 polymorphic markers. Using single as well as multi-locus models, GWAS identified 94 significant marker-trait associations (MTAs) or SNPs associated with traits recorded at the seedling stage and 451 for traits recorded at the reproductive stage. The significant SNPs included several novel, significant, and promising MTAs for different traits. The average LD decay distance for the whole genome was approximately 0.48 Mbp, ranging from 0.07 Mbp (chromosome 6D) to 4.14 Mbp (chromosome 2A). Furthermore, several promising SNPs revealed significant differences among haplotypes for traits such as RLT, RWT, SLT, SWT, and GY under drought stress. Functional annotation and in silico expression analysis revealed important putative candidate genes underlying the identified stable genomic regions such as protein kinases, O-methyltransferases, GroES-like superfamily proteins, NAD-dependent dehydratases, etc. The findings of the present study may be useful for improving yield potential, and stability under drought stress conditions.

Genetics and breeding for resistance against four leaf spot diseases in wheat (Triticum aestivum L.).

In wheat, major yield losses are caused by a variety of diseases including rusts, spike diseases, leaf spot and root diseases. The genetics of resistance against all these diseases have been studied in great detail and utilized for breeding resistant cultivars. The resistance against leaf spot diseases caused by each individual necrotroph/hemi-biotroph involves a complex system involving resistance (R) genes, sensitivity (S) genes, small secreted protein (SSP) genes and quantitative resistance loci (QRLs). This review deals with resistance for the following four-leaf spot diseases: (i) Septoria nodorum blotch (SNB) caused by Parastagonospora nodorum; (ii) Tan spot (TS) caused by Pyrenophora tritici-repentis; (iii) Spot blotch (SB) caused by Bipolaris sorokiniana and (iv) Septoria tritici blotch (STB) caused by Zymoseptoria tritici.

Harnessing High Yield Potential in Wheat (Triticum aestivum L.) under Climate Change Scenario.

Wheat is a major staple food crop for food security in India and South Asia. The current rate (0.8-1.2%) of genetic gain in wheat is significantly shorter than the 2.4% needed to meet future demand. The changing climate and increased yield loss due to factors such as terminal heat stress necessitate the need for climate-resilient practices to sustain wheat production. At ICAR-Indian Institute of Wheat and Barley Research in Karnal, Haryana, India, a new High Yield Potential Trial (HYPT) was conceptualized and subsequently conducted at six locations in the highly productive North Western Plain Zone (NWPZ). An attempt was made to harness higher wheat yields through the best pipeline genotypes suitable for early sowing and modified agronomic practices to explore the feasibility of a new approach that is profitable to farmers. The modified agronomic practices included like early sowing, application of 150% recommended dose of fertilizers, and two sprays of growth regulators (Chlormaquate chloride and Tebuconazole) to prevent lodging. The mean yield in the HYPT was 19.4% superior compared to the best trials conducted during the normal sowing time. A highly positive and significant correlation of grain yield with grain filling duration (0.51), biomass (0.73), harvest index (0.75), normalized difference vegetation Index (0.27), chlorophyll content index (0.32), and 1000-grain weight (0.62) was observed. An increased return of USD 201.95/ha was realized in the HYPT when compared to normal sowing conditions. This study proves that new integrated practices have the potential to provide the best profitable yields in wheat in the context of climate change.

New Genomic Regions Identified for Resistance to Spot Blotch and Terminal Heat Stress in an Interspecific Population of Triticum aestivum and T. spelta.

Wheat is one of the most widely grown and consumed food crops in the world. Spot blotch and terminal heat stress are the two significant constraints mainly in the Indo-Gangetic plains of South Asia. The study was undertaken using 185 recombinant lines (RILs) derived from the interspecific hybridization of 'Triticum aestivum (HUW234) × T. spelta (H+26)' to reveal genomic regions associated with tolerance to combined stress to spot blotch and terminal heat. Different physiological (NDVI, canopy temperature, leaf chlorophyll) and grain traits (TGW, grain size) were observed under stressed (spot blotch, terminal heat) and non-stressed environments. The mean maturity duration of RILs under combined stress was reduced by 12 days, whereas the normalized difference vegetation index (NDVI) was 46.03%. Similarly, the grain size was depleted under combined stress by 32.23% and thousand kernel weight (TKW) by 27.56% due to spot blotch and terminal heat stress, respectively. The genetic analysis using 6734 SNP markers identified 37 significant loci for the area under the disease progress curve (AUDPC) and NDVI. The genome-wide functional annotation of the SNP markers revealed gene functions such as plant chitinases, NB-ARC and NBS-LRR, and the peroxidase superfamily Cytochrome P450 have a positive role in the resistance through a hypersensitive response. Zinc finger domains, cysteine protease coding gene, F-box protein, ubiquitin, and associated proteins, play a substantial role in the combined stress of spot blotch and terminal heat in bread wheat, according to genomic domains ascribed to them. The study also highlights T. speltoides as a source of resistance to spot blotch and terminal heat tolerance.

Variation in Grain Zinc and Iron Concentrations, Grain Yield and Associated Traits of Biofortified Bread Wheat Genotypes in Nepal.

Wheat (Triticum aestivum L.) is one of the major staples in Nepal providing the bulk of food calories and at least 30% of Fe and Zn intake and 20% of dietary energy and protein consumption; thus, it is essential to improve its nutritional quality. To select high-yielding genotypes with elevated grain zinc and iron concentration, the sixth, seventh, eighth, and ninth HarvestPlus Yield Trials (HPYTs) were conducted across diverse locations in Nepal for four consecutive years: 2015-16, 2016-17, 2017-18, and 2018-19, using 47 biofortified and 3 non-biofortified CIMMYT-bred, bread wheat genotypes: Baj#1, Kachu#1, and WK1204 (local check). Genotypic and spatial variations were found in agro-morphological traits; grain yield and its components; and the grain zinc and iron concentration of tested genotypes. Grain zinc concentration was highest in Khumaltar and lowest in Kabre. Likewise, grain iron concentration was highest in Doti and lowest in Surkhet. Most of the biofortified genotypes were superior for grain yield and for grain zinc and iron concentration to the non-biofortified checks. Combined analyses across environments showed moderate to high heritability for both Zn (0.48-0.81) and Fe (0.46-0.79) except a low heritability for Fe observed for 7th HPYT (0.15). Grain yield was positively correlated with the number of tillers per m2, while negatively correlated with days to heading and maturity, grain iron, grain weight per spike, and thousand grain weight. The grain zinc and iron concentration were positively correlated, suggesting that the simultaneous improvement of both micronutrients is possible through wheat breeding. Extensive testing of CIMMYT derived high Zn wheat lines in Nepal led to the release of five biofortified wheat varieties in 2020 with superior yield, better disease resistance, and 30-40% increased grain Zn and adaptable to a range of wheat growing regions in the country - from the hotter lowland, or Terai, regions to the dry mid- and high-elevation areas.

Dissecting the Genetic Architecture of Phenology Affecting Adaptation of Spring Bread Wheat Genotypes to the Major Wheat-Producing Zones in India.

Spring bread wheat adaptation to diverse environments is supported by various traits such as phenology and plant architecture. A large-scale genome-wide association study (GWAS) was designed to investigate and dissect the genetic architecture of phenology affecting adaptation. It used 48 datasets from 4,680 spring wheat lines. For 8 years (2014-2021), these lines were evaluated for days to heading (DH) and maturity (DM) at three sites: Jabalpur, Ludhiana, and Samastipur (Pusa), which represent the three major Indian wheat-producing zones: the Central Zone (CZ), North-Western Plain Zone (NWPZ), and North-Eastern Plain Zone (NEPZ), respectively. Ludhiana had the highest mean DH of 103.8 days and DM of 148.6 days, whereas Jabalpur had the lowest mean DH of 77.7 days and DM of 121.6 days. We identified 119 markers significantly associated with DH and DM on chromosomes 5B (76), 2B (18), 7D (10), 4D (8), 5A (1), 6B (4), 7B (1), and 3D (1). Our results clearly indicated the importance of the photoperiod-associated gene (Ppd-B1) for adaptation to the NWPZ and the Vrn-B1 gene for adaptation to the NEPZ and CZ. A maximum variation of 21.1 and 14% was explained by markers 2B_56134146 and 5B_574145576 linked to the Ppd-B1 and Vrn-B1 genes, respectively, indicating their significant role in regulating DH and DM. The results provide important insights into the genomic regions associated with the two phenological traits that influence adaptation to the major wheat-producing zones in India.

SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Triticum aestivum L.), an Essential Crop for Food Security.

The pathogenic fungus, Bipolaris sorokiniana, that causes spot blotch (SB) disease of wheat, is a major production constraint in the Eastern Gangetic Plains of South Asia and other warm, humid regions of the world. A recombinant inbred line population was developed and phenotyped at three SB-prone locations in India. The single nucleotide polymorphism (SNP) for SB resistance was identified using a bulked segregant RNA-Seq-based approach, referred to as "BSR-Seq." Transcriptome sequencing of the resistant parent (YS#24), the susceptible parent (YS#58), and their resistant and susceptible bulks yielded a total of 429.67 million raw reads. The bulk frequency ratio (BFR) of SNPs between the resistant and susceptible bulks was estimated, and selection of SNPs linked to resistance was done using sixfold enrichments in the corresponding bulks (BFR >6). With additional filtering criteria, the number of transcripts was further reduced to 506 with 1055 putative polymorphic SNPs distributed on 21 chromosomes of wheat. Based on SNP enrichment on chromosomal loci, five transcripts were found to be associated with SB resistance. Among the five SB resistance-associated transcripts, four were distributed on the 5B chromosome with putative 52 SNPs, whereas one transcript with eight SNPs was present on chromosome 3B. The SNPs linked to the trait were exposed to a tetra-primer ARMS-PCR assay, and an SNP-based allele-specific marker was identified for SB resistance. The in silico study of these five transcripts showed homology with pathogenesis-related genes; the metabolic pathway also exhibits similar results, suggesting their role in the plant defense mechanism.

Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS.

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

Multi-Locus GWAS for Grain Weight-Related Traits Under Rain-Fed Conditions in Common Wheat (Triticum aestivum L.).

In wheat, a multi-locus genome-wide association study (ML-GWAS) was conducted for the four grain weight-related traits (days to anthesis, grain filling duration, grain number per ear, and grain weight per ear) using data recorded under irrigated (IR) and rain-fed (RF) conditions. Seven stress-related indices were estimated for these four traits: (i) drought resistance index (DI), (ii) geometric mean productivity (GMP), (iii) mean productivity index (MPI), (iv) relative drought index (RDI), (v) stress tolerance index (STI), (vi) yield index, and (vii) yield stability index (YSI). The association panel consisted of a core collection of 320 spring wheat accessions representing 28 countries. The panel was genotyped using 9,627 single nucleotide polymorphisms (SNPs). The genome-wide association (GWA) analysis provided 30 significant marker-trait associations (MTAs), distributed as follows: (i) IR (15 MTAs), (ii) RF (14 MTAs), and (iii) IR+RF (1 MTA). In addition, 153 MTAs were available for the seven stress-related indices. Five MTAs co-localized with previously reported QTLs/MTAs. Candidate genes (CGs) associated with different MTAs were also worked out. Gene ontology (GO) analysis and expression analysis together allowed the selection of the two CGs, which may be involved in response to drought stress. These two CGs included: TraesCS1A02G331000 encoding RNA helicase and TraesCS4B02G051200 encoding microtubule-associated protein 65. The results supplemented the current knowledge on genetics for drought tolerance in wheat. The results may also be used for future wheat breeding programs to develop drought-tolerant wheat cultivars.

Juvenile Heat Tolerance in Wheat for Attaining Higher Grain Yield by Shifting to Early Sowing in October in South Asia.

Farmers in northwestern and central India have been exploring to sow their wheat much earlier (October) than normal (November) to sustain productivity by escaping terminal heat stress and to utilize the available soil moisture after the harvesting of rice crop. However, current popular varieties are poorly adapted to early sowing due to the exposure of juvenile plants to the warmer temperatures in the month of October and early November. Therefore, a study was undertaken to identify wheat genotypes suited to October sowing under warmer temperatures in India. A diverse collection of 3322 bread wheat varieties and elite lines was prepared in CIMMYT, Mexico, and planted in the 3rd week of October during the crop season 2012-2013 in six locations (Ludhiana, Karnal, New Delhi, Indore, Pune and Dharwad) spread over northwestern plains zone (NWPZ) and central and Peninsular zone (CZ and PZ; designated as CPZ) of India. Agronomic traits data from the seedling stage to maturity were recorded. Results indicated substantial diversity for yield and yield-associated traits, with some lines showing indications of higher yields under October sowing. Based on agronomic performance and disease resistance, the top 48 lines (and two local checks) were identified and planted in the next crop season (2013-2014) in a replicated trial in all six locations under October sowing (third week). High yielding lines that could tolerate higher temperature in October sowing were identified for both zones; however, performance for grain yield was more promising in the NWPZ. Hence, a new trial of 30 lines was planted only in NWPZ under October sowing. Lines showing significantly superior yield over the best check and the most popular cultivars in the zone were identified. The study suggested that agronomically superior wheat varieties with early heat tolerance can be obtained that can provide yield up to 8 t/ha by planting in the third to fourth week of October.

Increased Predictive Accuracy of Multi-Environment Genomic Prediction Model for Yield and Related Traits in Spring Wheat (Triticum aestivum L.).

Genomic selection (GS) has the potential to improve the selection gain for complex traits in crop breeding programs from resource-poor countries. The GS model performance in multi-environment (ME) trials was assessed for 141 advanced breeding lines under four field environments via cross-predictions. We compared prediction accuracy (PA) of two GS models with or without accounting for the environmental variation on four quantitative traits of significant importance, i.e., grain yield (GRYLD), thousand-grain weight, days to heading, and days to maturity, under North and Central Indian conditions. For each trait, we generated PA using the following two different ME cross-validation (CV) schemes representing actual breeding scenarios: (1) predicting untested lines in tested environments through the ME model (ME_CV1) and (2) predicting tested lines in untested environments through the ME model (ME_CV2). The ME predictions were compared with the baseline single-environment (SE) GS model (SE_CV1) representing a breeding scenario, where relationships and interactions are not leveraged across environments. Our results suggested that the ME models provide a clear advantage over SE models in terms of robust trait predictions. Both ME models provided 2-3 times higher prediction accuracies for all four traits across the four tested environments, highlighting the importance of accounting environmental variance in GS models. While the improvement in PA from SE to ME models was significant, the CV1 and CV2 schemes did not show any clear differences within ME, indicating the ME model was able to predict the untested environments and lines equally well. Overall, our results provide an important insight into the impact of environmental variation on GS in smaller breeding programs where these programs can potentially increase the rate of genetic gain by leveraging the ME wheat breeding trials.

Evaluations of Genomic Prediction and Identification of New Loci for Resistance to Stripe Rust Disease in Wheat (Triticum aestivum L.).

Stripe rust is one of the most destructive diseases of wheat (Triticum aestivum L.), caused by Puccinia striiformis f. sp. tritici (Pst), and responsible for significant yield losses worldwide. Single-nucleotide polymorphism (SNP) diagnostic markers were used to identify new sources of resistance at adult plant stage to wheat stripe rust (YR) in 141 CIMMYT advanced bread wheat lines over 3 years in replicated trials at Borlaug Institute for South Asia (BISA), Ludhiana. We performed a genome-wide association study and genomic prediction to aid the genetic gain by accumulating disease resistance alleles. The responses to YR in 141 advanced wheat breeding lines at adult plant stage were used to generate G × E (genotype × environment)-dependent rust scores for prediction and genome-wide association study (GWAS), eliminating variation due to climate and disease pressure changes. The lowest mean prediction accuracies were 0.59 for genomic best linear unbiased prediction (GBLUP) and ridge-regression BLUP (RRBLUP), while the highest mean was 0.63 for extended GBLUP (EGBLUP) and random forest (RF), using 14,563 SNPs and the G × E rust score results. RF and EGBLUP predicted higher accuracies (∼3%) than did GBLUP and RRBLUP. Promising genomic prediction demonstrates the viability and efficacy of improving quantitative rust tolerance. The resistance to YR in these lines was attributed to eight quantitative trait loci (QTLs) using the FarmCPU algorithm. Four (Q.Yr.bisa-2A.1, Q.Yr.bisa-2D, Q.Yr.bisa-5B.2, and Q.Yr.bisa-7A) of eight QTLs linked to the diagnostic markers were mapped at unique loci (previously unidentified for Pst resistance) and possibly new loci. The statistical evidence of effectiveness and distribution of the new diagnostic markers for the resistance loci would help to develop new stripe rust resistance sources. These diagnostic markers along with previously established markers would be used to create novel DNA biosensor-based microarrays for rapid detection of the resistance loci on large panels upon functional validation of the candidate genes identified in the present study to aid in rapid genetic gain in the future breeding programs.

Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.).

Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon's information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

Target Population of Environments for Wheat Breeding in India: Definition, Prediction and Genetic Gains.

In this study, we defined the target population of environments (TPE) for wheat breeding in India, the largest wheat producer in South Asia, and estimated the correlated response to the selection and prediction ability of five selection environments (SEs) in Mexico. We also estimated grain yield (GY) gains in each TPE. Our analysis used meteorological, soil, and GY data from the international Elite Spring Wheat Yield Trials (ESWYT) distributed by the International Maize and Wheat Improvement Center (CIMMYT) from 2001 to 2016. We identified three TPEs: TPE 1, the optimally irrigated Northwestern Plain Zone; TPE 2, the optimally irrigated, heat-stressed North Eastern Plains Zone; and TPE 3, the drought-stressed Central-Peninsular Zone. The correlated response to selection ranged from 0.4 to 0.9 within each TPE. The highest prediction accuracies for GY per TPE were derived using models that included genotype-by-environment interaction and/or meteorological information and their interaction with the lines. The highest prediction accuracies for TPEs 1, 2, and 3 were 0.37, 0.46, and 0.51, respectively, and the respective GY gains were 118, 46, and 123 kg/ha/year. These results can help fine-tune the breeding of elite wheat germplasm with stable yields to reduce farmers' risk from year-to-year environmental variation in India's wheat lands, which cover 30 million ha, account for 100 million tons of grain or more each year, and provide food and livelihoods for hundreds of millions of farmers and consumers in South Asia.

Elucidating the genetics of grain yield and stress-resilience in bread wheat using a large-scale genome-wide association mapping study with 55,568 lines.

Wheat grain yield (GY) improvement using genomic tools is important for achieving yield breakthroughs. To dissect the genetic architecture of wheat GY potential and stress-resilience, we have designed this large-scale genome-wide association study using 100 datasets, comprising 105,000 GY observations from 55,568 wheat lines evaluated between 2003 and 2019 by the International Maize and Wheat Improvement Center and national partners. We report 801 GY-associated genotyping-by-sequencing markers significant in more than one dataset and the highest number of them were on chromosomes 2A, 6B, 6A, 5B, 1B and 7B. We then used the linkage disequilibrium (LD) between the consistently significant markers to designate 214 GY-associated LD-blocks and observed that 84.5% of the 58 GY-associated LD-blocks in severe-drought, 100% of the 48 GY-associated LD-blocks in early-heat and 85.9% of the 71 GY-associated LD-blocks in late-heat, overlapped with the GY-associated LD-blocks in the irrigated-bed planting environment, substantiating that simultaneous improvement for GY potential and stress-resilience is feasible. Furthermore, we generated the GY-associated marker profiles and analyzed the GY favorable allele frequencies for a large panel of 73,142 wheat lines, resulting in 44.5 million datapoints. Overall, the extensive resources presented in this study provide great opportunities to accelerate breeding for high-yielding and stress-resilient wheat varieties.

Crosses with spelt improve tolerance of South Asian spring wheat to spot blotch, terminal heat stress, and their combination.

Spot blotch and terminal heat are two of the most important stresses for wheat in South Asia. A study was initiated to explore the use of spelt (Triticum spelta) to improve tolerance to these stresses in spring wheat (T. aestivum). We assessed 185 recombinant inbred lines (RILs) from the cross T. spelta (H + 26) × T. aestivum (cv. HUW234), under the individual stresses and their combination. H + 26 showed better tolerance to the single stresses and also their combination; grain yield in RILs was reduced by 21.9%, 27.7% and 39.0% under spot blotch, terminal heat and their combined effect, respectively. However, phenological and plant architectural traits were not affected by spot blotch itself. Multivariate analysis demonstrated a strong negative correlation between spikelet sterility and grain yield under spot blotch, terminal heat and their combination. However, four recombinant lines demonstrated high performance under both stresses and also under their combined stress. The four lines were significantly superior in grain yield and showed significantly lower AUDPC than the better parent. This study demonstrates the potential of spelt wheat in enhancing tolerance to spot blotch and terminal heat stresses. It also provides comprehensive evidence about the expression of yield and phenological traits under these stresses.

Genetic characterization for lesion mimic and other traits in relation to spot blotch resistance in spring wheat.

Lesion mimic (Lm) mutants display hypersensitive responses (HR) without any pathogen attack; their symptoms are similar to those produced by a pathogen and result in cell death. In wheat, such mutants have been reported to be resistant against leaf rust due to their biotrophic nature. However, Lm mutants tend to encourage spot blotch (SB) disease caused by Bipolarissorokiniana since dead cells facilitate pathogen multiplication. In this study, 289 diverse wheat germplasm lines were phenotyped in three consecutive growing seasons (2012-2015). Genotype data was generated using the Illumina iSelect beadchip assay platform for wheat germplasm lines. A total of 13,589 single-nucleotide polymorphisms (SNPs) were selected andused for further association mapping. Lm was positively associated with Area Under Disease Progress Curve (AUDPC) for SB but negatively with glaucous index (GI), leaf tip necrosis (Ltn) and latent period (LP). Ltn had a negative association with AUDPC and Lm but a positive one with LP. In a genome-wide association study (GWAS), 29 markers were significantly associated with these traits and 27 were an notated. Seven SNP markers associated with Lm were on chromosome 6A; another on 1B was found to be linked with Ltn. Like wise, seven SNP markers were associated with GI; one on chromosome 6A with the others on 6B. Five SNP markers on chromosomes 3B and 3Dwere significantly correlated with LP, while nine SNP markers on chromosomes 5A and 5B were significantly associated with AUDPC for SB. This study is the first to explore the interaction in wheat between Lm mutants and the hemibiotrophic SB pathogen B.sorokiniana.