Effectiveness of TaDreb-B1 and 1-FEH w3 KASP Markers in Spring and Winter Wheat Populations for Marker-Assisted Selection to Improve Drought Tolerance

Due to the advances in DNA markers, kompetitive allele-specific PCR (KASP) markers could accelerate breeding programs and genetically improve drought tolerance. Two previously reported KASP markers, TaDreb-B1 and 1-FEH w3, were investigated in this study for the marker-assisted selection (MAS) of drought tolerance. Two highly diverse spring and winter wheat populations were genotyped using these two KASP markers. The same populations were evaluated for drought tolerance at seedling (drought stress) and reproductive (normal and drought stress) growth stages. The single-marker analysis revealed a high significant association between the target allele of 1-FEH w3 and drought susceptibility in the spring population, while the marker-trait association was not significant in the winter population. The TaDreb-B1 marker did not have any highly significant association with seedling traits, except the sum of leaf wilting in the spring population. For field experiments, SMA revealed very few negative and significant associations between the target allele of the two markers and yield traits under both conditions. The results of this study revealed that the use of TaDreb-B1 provided better consistency in improving drought tolerance than 1-FEH w3.

Screening Spring Wheat Genotypes for TaDreb-B1 and Fehw3 Genes under Severe Drought Stress at the Germination Stage Using KASP Technology

Drought stress is a major yield-limiting factor throughout the world in wheat (Triticum aestivum L.), causing losses of up to 80% of the total yield. The identification of factors affecting drought stress tolerance in the seedling stage is especially important to increase adaptation and accelerate the grain yield potential. In the current study, 41 spring wheat genotypes were tested for their tolerance to drought at the germination stage under two different polyethylene glycol concentrations (PEG) of 25% and 30%. For this purpose, twenty seedlings from each genotype were evaluated in triplicate with a randomized complete block design (RCBD) in a controlled growth chamber. The following nine parameters were recorded: germination pace (GP), germination percentage (G%), number of roots (NR), shoot length (SL), root length (RL), shoot-root length ratio (SRR), fresh biomass weight (FBW), dry biomass weight (DBW), and water content (WC). An analysis of variance (ANOVA) revealed highly significant differences (p < 0.01) among the genotypes, treatments (PEG25%, PEG30%) and genotypes × treatment interaction, for all traits. The broad-sense heritability (H2) estimates were very high in both concentrations. They ranged from 89.4 to 98.9% under PEG25% and from 70.8 to 98.7% under PEG30%. Citr15314 (Afghanistan) was among the best performing genotypes under both concentrations for most of the germination traits. Two KASP markers for TaDreb-B1 and Fehw3 genes were used to screen all genotypes and to study the effect of these on drought tolerance at the germination stage. All genotypes with Fehw3 (only) showed a better performance for most traits under both concentrations compared to other genotypes having TaDreb-B1 or having both genes. To our knowledge, this work is the first report showing the effect of the two genes on germination traits under severe drought stress conditions.

Genetic Variation in Common Bunt Resistance in Synthetic Hexaploid Wheat

Common bunt (caused by Tilletia caries and T. Foetida) is a major wheat disease. It occurs frequently in the USA and Turkey and damages grain yield and quality. Seed treatment with fungicides is an effective method to control this disease. However, using fungicides in organic and low-income fields is forbidden, and planting resistant cultivars are preferred. Due to the highly effective use of fungicides, little effort has been put into breeding resistant genotypes. In addition, the genetic diversity for this trait is low in modern wheat germplasm. Synthetic wheat genotypes were reported as an effective source to increase the diversity in wheat germplasm. Therefore, a set of 25 synthetics that are resistant to the Turkish common bunt race were evaluated against the Nebraska common bunt race. Four genotypes were found to be very resistant to Nebraska's common bunt race. Using differential lines, four isolines carrying genes, Bt10, Bt11, Bt12, and Btp, were found to provide resistance against both Turkish and Nebraska common bunt races. Genotypes carrying any or all of these four genes could be used as a source of resistance in both countries. No correlation was found between common bunt resistance and some agronomic traits, which suggests that common bunt resistance is an independent trait.

Novel Single-Nucleotide Variants for Morpho-Physiological Traits Involved in Enhancing Drought Stress Tolerance in Barley

Barley (Hordeum vulgare L.) thrives in the arid and semi-arid regions of the world; nevertheless, it suffers large grain yield losses due to drought stress. A panel of 426 lines of barley was evaluated in Egypt under deficit (DI) and full irrigation (FI) during the 2019 and 2020 growing seasons. Observations were recorded on the number of days to flowering (NDF), total chlorophyll content (CH), canopy temperature (CAN), grain filling duration (GFD), plant height (PH), and grain yield (Yield) under DI and FI. The lines were genotyped using the 9K Infinium iSelect single nucleotide polymorphisms (SNP) genotyping platform, which resulted in 6913 high-quality SNPs. In conjunction with the SNP markers, the phenotypic data were subjected to a genome-wide association scan (GWAS) using Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK). The GWAS results indicated that 36 SNPs were significantly associated with the studied traits under DI and FI. Furthermore, eight markers were significant and common across DI and FI water regimes, while 14 markers were uniquely associated with the studied traits under DI. Under DI and FI, three (11_10326, 11_20042, and 11_20170) and five (11_20099, 11_10326, 11_20840, 12_30298, and 11_20605) markers, respectively, had pleiotropic effect on at least two traits. Among the significant markers, 24 were annotated to known barley genes. Most of these genes were involved in plant responses to environmental stimuli such as drought. Overall, nine of the significant markers were previously reported, and 27 markers might be considered novel. Several markers identified in this study could enable the prediction of barley accessions with optimal agronomic performance under DI and FI.

Combined GWAS and QTL mapping revealed candidate genes and SNP network controlling recovery and tolerance traits associated with drought tolerance in seedling winter wheat

To date, very little research on drought tolerance has been conducted at the seedling stage in winter wheat. In this study, two types of traits, namely tolerance and recovery traits, associated with drought tolerance were scored in biparental mapping population (BPP) and association mapping population (A-set). The results of this study revealed no or weak significant correlation between the two types of traits. Based on GWAS and QTL mapping analyses, all QTLs associated with recovery traits were completely different from those associated with tolerance traits except one QTL in each population that was found to be associated with one tolerance trait and one recovery trait. The analysis of SNP and gene networks confirmed the results of combined GWAS and QTL mapping. One SNP marker located on the 2B chromosome (S2B_26494801) was found to be associated with recovery traits in both populations. The results of this study provided new information on understanding and improving drought tolerance in winter wheat.

Identification and Validation of High LD Hotspot Genomic Regions Harboring Stem Rust Resistant Genes on 1B, 2A (Sr38), and 7B Chromosomes in Wheat

Stem rust caused by Puccinia graminis f. sp. tritici Eriks. is an important disease of common wheat globally. The production and cultivation of genetically resistant cultivars are one of the most successful and environmentally friendly ways to protect wheat against fungal pathogens. Seedling screening and genome-wide association study (GWAS) were used to determine the genetic diversity of wheat genotypes obtained on stem rust resistance loci. At the seedling stage, the reaction of the common stem rust race QFCSC in Nebraska was measured in a set of 212 genotypes from F_3:6 lines. The results indicated that 184 genotypes (86.8%) had different degrees of resistance to this common race. While 28 genotypes (13.2%) were susceptible to stem rust. A set of 11,911 single-nucleotide polymorphism (SNP) markers was used to perform GWAS which detected 84 significant marker-trait associations (MTAs) with SNPs located on chromosomes 1B, 2A, 2B, 7B and an unknown chromosome. Promising high linkage disequilibrium (LD) genomic regions were found in all chromosomes except 2B which suggested they include candidate genes controlling stem rust resistance. Highly significant LD was found among these 59 significant SNPs on chromosome 2A and 12 significant SNPs with an unknown chromosomal position. The LD analysis between SNPs located on 2A and Sr38 gene reveal high significant LD genomic regions which was previously reported. To select the most promising stem rust resistant genotypes, a new approach was suggested based on four criteria including, phenotypic selection, number of resistant allele(s), the genetic distance among the selected parents, and number of the different resistant allele(s) in the candidate crosses. As a result, 23 genotypes were considered as the most suitable parents for crossing to produce highly resistant stem rust genotypes against the QFCSC.

GWAS revealed effect of genotype × environment interactions for grain yield of Nebraska winter wheat

Background

Improving grain yield in cereals especially in wheat is a main objective for plant breeders. One of the main constrains for improving this trait is the G × E interaction (GEI) which affects the performance of wheat genotypes in different environments. Selecting high yielding genotypes that can be used for a target set of environments is needed. Phenotypic selection can be misleading due to the environmental conditions. Incorporating information from phenotypic and genomic analyses can be useful in selecting the higher yielding genotypes for a group of environments.

Results

A set of 270 F_3:6 wheat genotypes in the Nebraska winter wheat breeding program was tested for grain yield in nine environments. High genetic variation for grain yield was found among the genotypes. G × E interaction was also highly significant. The highest yielding genotype differed in each environment. The correlation for grain yield among the nine environments was low (0 to 0.43). Genome-wide association study revealed 70 marker traits association (MTAs) associated with increased grain yield. The analysis of linkage disequilibrium revealed 16 genomic regions with a highly significant linkage disequilibrium (LD). The candidate parents’ genotypes for improving grain yield in a group of environments were selected based on three criteria; number of alleles associated with increased grain yield in each selected genotype, genetic distance among the selected genotypes, and number of different alleles between each two selected parents.

Conclusion

Although G × E interaction was present, the advances in DNA technology provided very useful tools and analyzes. Such features helped to genetically select the highest yielding genotypes that can be used to cross grain production in a group of environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07308-0.

Selection signatures across seven decades of hard winter wheat breeding in the Great Plains of the United States

Classical plant breeding has been instrumental in changing the genetic makeup of crop plants for better ecological adaptation and improved quality. This paper provides insights of the genomic changes effected in hard winter wheat (Triticum aestivum L.) through decades of breeding and selection in the Great Plains of the United States. Population structure and differentiation analyses were conducted on 185 wheat cultivars released from 1943 to 2013. Cultivars were grouped into four distinct clusters using discriminant analysis of principal components (DAPC). One of the clusters was unique in that 15 out of the 18 individuals were recent releases (2000-2010), while 12 of the 18 shared the cultivar 'Jagger' in their genetic background. Jagger carries a 2NS/2AS translocation segment from Aegilops ventricosa, an important segment for resistance to several foliar diseases. Using the outlier approach, Wright's population fixation index (Fst) identified 450 loci that were directionally selected. The largest signature of selection was found on chromosome 2A. Genetic diversity was high while the inbreeding coefficient was low, indicating extensive hybridization and germplasm exchange among breeding programs within the region. Foliar disease pressure and selection for resistance helped shape the microevolution of wheat in the southern Great Plains. The results showed that high genetic diversity remains in hard winter wheat cultivars adapted to the Great Plains of the USA, and modern plant breeding did not cause any sizable reduction in genetic diversity of the crop in this region.

Detailed Genetic Analysis for Identifying QTLs Associated with Drought Tolerance at Seed Germination and Seedling Stages in Barley

Drought induces several challenges for plant development, growth, and production. These challenges become more severe, in particular, in arid and semiarid countries like Egypt. In terms of production, barley ranks fourth after wheat, maize, and rice. Seed germination and seedling stages are critical stages for plant establishment and growth. In the current study, 60 diverse barley genotypes were tested for drought tolerance using two different treatments: control (0-PEG) and drought (20%-PEG). Twenty-two traits were estimated for seed germination and seedling parameters. All traits were reduced under drought stress, and a significant variation was found among genotypes under control and stress conditions. The broad-sense heritability estimates were very high under both control and drought for all traits. It ranged from 0.63 to 0.97 under the control condition and from 0.89 to 0.97 under drought, respectively. These high heritabilities suggested that genetic improvement of drought tolerance in barley at both stages is feasible. The principal component analysis revealed that root-related parameters account for the largest portion of phenotypic variation in this collection. The single-marker analysis (SMA) resulted in 71 quantitative trait loci (QTLs) distributed across the seven chromosomes of barley. Thirty-three QTLs were detected for root-length-related traits. Many hotspots of QTLs were detected for various traits. Interestingly, some markers controlled many traits in a pleiotropic manner; thus, they can be used to control multiple traits at a time. Some QTLs were constitutive, i.e., they are mapped under control and drought, and targeting these QTLs makes the selection for drought tolerance a single-step process. The results of gene annotation analysis revealed very potential candidate genes that can be targeted to select for drought tolerance.

Insights into the Genetic Architecture of Bran Friability and Water Retention Capacity, Two Important Traits for Whole Grain End-Use Quality in Winter Wheat

Bran friability (particle size distribution after milling) and water retention capacity (WRC) impact wheat bran functionality in whole grain milling and baking applications. The goal of this study was to identify genomic regions and underlying genes that may be responsible for these traits. The Hard Winter Wheat Association Mapping Panel, which comprised 299 lines from breeding programs in the Great Plains region of the US, was used in a genome-wide association study. Bran friability ranged from 34.5% to 65.9% (median, 51.1%) and WRC ranged from 159% to 458% (median, 331%). Two single-nucleotide polymorphisms (SNPs) on chromosome 5D were significantly associated with bran friability, accounting for 11-12% of the phenotypic variation. One of these SNPs was located within the Puroindoline-b gene, which is known for influencing endosperm texture. Two SNPs on chromosome 4A were tentatively associated with WRC, accounting for 4.6% and 4.4% of phenotypic variation. The favorable alleles at the SNP sites were present in only 15% (friability) and 34% (WRC) of lines, indicating a need to develop new germplasm for these whole-grain end-use quality traits. Validation of these findings in independent populations will be useful for breeding winter wheat cultivars with improved functionality for whole grain food applications.

GWAS: Fast-forwarding gene identification and characterization in temperate Cereals: lessons from Barley - A review

Understanding the genetic complexity of traits is an important objective of small grain temperate cereals yield and adaptation improvements. Bi-parental quantitative trait loci (QTL) linkage mapping is a powerful method to identify genetic regions that co-segregate in the trait of interest within the research population. However, recently, association or linkage disequilibrium (LD) mapping using a genome-wide association study (GWAS) became an approach for unraveling the molecular genetic basis underlying the natural phenotypic variation. Many causative allele(s)/loci have been identified using the power of this approach which had not been detected in QTL mapping populations. In barley (Hordeum vulgare L.), GWAS has been successfully applied to define the causative allele(s)/loci which can be used in the breeding crop for adaptation and yield improvement. This promising approach represents a tremendous step forward in genetic analysis and undoubtedly proved it is a valuable tool in the identification of candidate genes. In this review, we describe the recently used approach for genetic analyses (linkage mapping or association mapping), and then provide the basic genetic and statistical concepts of GWAS, and subsequently highlight the genetic discoveries using GWAS. The review explained how the candidate gene(s) can be detected using state-of-art bioinformatic tools.

Perspectives on Low Temperature Tolerance and Vernalization Sensitivity in Barley: Prospects for Facultative Growth Habit

One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known and 10 novel QTL/genes were identified for LTT-assessed as winter survival in 10 field tests and mapped using a GWAS meta-analysis. FR-H1, FR-H2, and FR-H3 were major drivers of LTT, and candidate genes were identified for FR-H3. The principal determinants of vernalization sensitivity were VRN-H1, VRN-H2, and PPD-H1. VRN-H2 deletions conferred insensitive or intermediate sensitivity to vernalization. A subset of accessions with maximum LTT were identified as a resource for allele mining and further characterization. Facultative types comprised a small portion of the GWAS panel but may be useful for developing germplasm with this growth habit.

Determining the Efficacy of a Hybridizing Agent in Wheat (Triticum aestivum L.)

Hybrid wheat (Triticum spp.) has the potential to boost yields and enhance production under changing climates to feed the growing global population. Production of hybrid wheat seed relies on male sterility, the blocking of pollen production, to prevent self-pollination. One method of preventing self-pollination in the female plants is to apply a chemical hybridizing agent (CHA). However, some combinations of CHA and genotypes have lower levels of sterility, resulting in decreased hybrid purity. Differences in CHA efficacy are a challenge in producing hybrid wheat lines for commercial and experimental use. Our primary research questions were to estimate the levels of sterility for wheat genotypes treated with a CHA and determine the best way to analyze differences. We applied the CHA sintofen (1-(4-chlorphyl)-1,4-dihydro-5-(2-methoxyethoxy)-4-oxocinnoline-3-carboxylic acid; Croisor 100) to 27 genotypes in replicate. After spraying, we counted seed in bagged female heads to evaluate CHA efficacy and CHA-by-genotype interaction. Using logit and probit models with a threshold of 7 seeds, we found differences among genotypes in 2015. Sterility was higher in 2016 and fewer genotypic differences were found. When CHA-induced sterilization is less uniform as in 2015, zero-inflated and hurdle count models were superior to standard mixed models. These models calculate mean seed number and fit data with limit-bounded scales collected by agronomists and plant breeders to compare genotypic differences. These analyses can assist in selecting parents and identifying where additional optimization of CHA application needs to occur. There is little work in the literature examining the relationship between CHAs and genotypes, making this work fundamental to the future of hybrid wheat breeding.

Marker-Trait Associations for Enhancing Agronomic Performance, Disease Resistance, and Grain Quality in Synthetic and Bread Wheat Accessions in Western Siberia

Exploiting genetically diverse lines to identify genes for improving crop performance is needed to ensure global food security. A genome-wide association study (GWAS) was conducted using 46,268 SNP markers on a diverse panel of 143 hexaploid bread and synthetic wheat to identify potential genes/genomic regions controlling agronomic performance (yield and 26 yield-related traits), disease resistance, and grain quality traits. From phenotypic evaluation, we found large genetic variation among the 35 traits and recommended five lines having a high yield, better quality, and multiple disease resistance for direct use in a breeding program. From a GWAS, we identified a total of 243 significant marker-trait associations (MTAs) for 35 traits that explained up to 25% of the phenotypic variance. Of these, 120 MTAs have not been reported in the literature and are potentially novel MTAs. In silico gene annotation analysis identified 116 MTAs within genes and of which, 21 MTAs were annotated as a missense variant. Furthermore, we were able to identify 23 co-located multi-trait MTAs that were also phenotypically correlated to each other, showing the possibility of simultaneous improvement of these traits. Additionally, most of the co-located MTAs were within genes. We have provided genomic fingerprinting for significant markers with favorable and unfavorable alleles in the diverse set of lines for developing elite breeding lines from useful trait-integration. The results from this study provided a further understanding of genetically complex traits and would facilitate the use of diverse wheat accessions for improving multiple traits in an elite wheat breeding program.

Principal variable selection to explain grain yield variation in winter wheat from features extracted from UAV imagery

BACKGROUND

Automated phenotyping technologies are continually advancing the breeding process. However, collecting various secondary traits throughout the growing season and processing massive amounts of data still take great efforts and time. Selecting a minimum number of secondary traits that have the maximum predictive power has the potential to reduce phenotyping efforts. The objective of this study was to select principal features extracted from UAV imagery and critical growth stages that contributed the most in explaining winter wheat grain yield. Five dates of multispectral images and seven dates of RGB images were collected by a UAV system during the spring growing season in 2018. Two classes of features (variables), totaling to 172 variables, were extracted for each plot from the vegetation index and plant height maps, including pixel statistics and dynamic growth rates. A parametric algorithm, LASSO regression (the least angle and shrinkage selection operator), and a non-parametric algorithm, random forest, were applied for variable selection. The regression coefficients estimated by LASSO and the permutation importance scores provided by random forest were used to determine the ten most important variables influencing grain yield from each algorithm.

RESULTS

Both selection algorithms assigned the highest importance score to the variables related with plant height around the grain filling stage. Some vegetation indices related variables were also selected by the algorithms mainly at earlier to mid growth stages and during the senescence. Compared with the yield prediction using all 172 variables derived from measured phenotypes, using the selected variables performed comparable or even better. We also noticed that the prediction accuracy on the adapted NE lines (r = 0.58-0.81) was higher than the other lines (r = 0.21-0.59) included in this study with different genetic backgrounds.

CONCLUSIONS

With the ultra-high resolution plot imagery obtained by the UAS-based phenotyping we are now able to derive more features, such as the variation of plant height or vegetation indices within a plot other than just an averaged number, that are potentially very useful for the breeding purpose. However, too many features or variables can be derived in this way. The promising results from this study suggests that the selected set from those variables can have comparable prediction accuracies on the grain yield prediction than the full set of them but possibly resulting in a better allocation of efforts and resources on phenotypic data collection and processing.

Genetic diversity and population structure analysis of synthetic and bread wheat accessions in Western Siberia

Recurrent selection and intercrossing between best of the best parents in each generation of breeding cycle resulted in a narrower genetic diversity in elite wheat (Triticum aestivum L.) germplasm. Therefore, we investigated diverse source of 143 synthetic and bread wheat accessions for identifying potentially rich genetic resources for improving the genetic diversity in wheat. This study identified 47,526 genotyping-by-sequencing-derived SNP markers that were nearly evenly distributed across three genomes of wheat. The population structure analysis identified three distinct clusters (Japan synthetics, CIMMYT synthetics, and bread wheat) of wheat genotypes on the basis of type and geographical origin of wheat accessions. Population differentiation using analysis of molecular variance indicated 21% of the total genetic variance among subgroups and the remainder within subgroups. This study also identified that the Japan synthetic group was the most divergent group compared with other subgroups. The genetic diversity comparisons between synthetic and bread wheat lines showed that the gene diversity of synthetic wheat was 33% higher than bread wheat accessions, indicating the potential use of these lines for broadening the genetic diversity of modern wheat cultivars. The results from this study will be helpful in further understanding genomic features of wheat and facilitate their use in wheat breeding programs.

Molecular marker dissection of stem rust resistance in Nebraska bread wheat germplasm

Stem rust (caused by Puccinia graminis f. sp. tritici) is a major disease of wheat. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, a set of 330 genotypes representing two nurseries (DUP2015 and TRP2015) were evaluated for resistance to a Nebraska stem rust race (QFCSC) in two replications. The TRP2015 nursery was also evaluated for its resistance to an additional 13 stem rust races. The analysis of variance revealed significant variation among genotypes in both populations for stem rust resistance. Nine stem rust genes, Sr6, Sr31, Sr1RS^Amigo, Sr24, Sr36, SrTmp, Sr7b, Sr9b, and Sr38, were expected and genotyped using gene-specific markers. The results of genetic analysis confirmed the presence of seven stem rust resistance genes. One genotype (NE15680) contained target alleles for five stem rust resistance genes and had a high level of stem rust resistance against different races. Single marker analysis indicated that Sr24 and Sr38 were highly significantly associated with stem rust resistance in the DUP2015 and TRP2015 nurseries, respectively. Linkage disequilibrium analysis identified the presence of 17 SNPs in high linkage with the Sr38-specific marker. These SNPs potentially tagging the Sr38 gene could be used in marker-assisted selection after validating them in additional genetic backgrounds.

Drought Stress Tolerance in Wheat and Barley: Advances in Physiology, Breeding and Genetics Research

Climate change is a major threat to most of the agricultural crops grown in tropical and sub-tropical areas globally. Drought stress is one of the consequences of climate change that has a negative impact on crop growth and yield. In the past, many simulation models were proposed to predict climate change and drought occurrences, and it is extremely important to improve essential crops to meet the challenges of drought stress which limits crop productivity and production. Wheat and barley are among the most common and widely used crops due to their economic and social values. Many parts of the world depend on these two crops for food and feed, and both crops are vulnerable to drought stress. Improving drought stress tolerance is a very challenging task for wheat and barley researchers and more research is needed to better understand this stress. The progress made in understanding drought tolerance is due to advances in three main research areas: physiology, breeding, and genetic research. The physiology research focused on the physiological and biochemical metabolic pathways that plants use when exposed to drought stress. New wheat and barley genotypes having a high degree of drought tolerance are produced through breeding by making crosses from promising drought-tolerant genotypes and selecting among their progeny. Also, identifying genes contributing to drought tolerance is very important. Previous studies showed that drought tolerance is a polygenic trait and genetic constitution will help to dissect the gene network(s) controlling drought tolerance. This review explores the recent advances in these three research areas to improve drought tolerance in wheat and barley.

Drought Stress Tolerance in Wheat and Barley: Advances in Physiology, Breeding and Genetics Research

Climate change is a major threat to most of the agricultural crops grown in tropical and sub-tropical areas globally. Drought stress is one of the consequences of climate change that has a negative impact on crop growth and yield. In the past, many simulation models were proposed to predict climate change and drought occurrences, and it is extremely important to improve essential crops to meet the challenges of drought stress which limits crop productivity and production. Wheat and barley are among the most common and widely used crops due to their economic and social values. Many parts of the world depend on these two crops for food and feed, and both crops are vulnerable to drought stress. Improving drought stress tolerance is a very challenging task for wheat and barley researchers and more research is needed to better understand this stress. The progress made in understanding drought tolerance is due to advances in three main research areas: physiology, breeding, and genetic research. The physiology research focused on the physiological and biochemical metabolic pathways that plants use when exposed to drought stress. New wheat and barley genotypes having a high degree of drought tolerance are produced through breeding by making crosses from promising drought-tolerant genotypes and selecting among their progeny. Also, identifying genes contributing to drought tolerance is very important. Previous studies showed that drought tolerance is a polygenic trait and genetic constitution will help to dissect the gene network(s) controlling drought tolerance. This review explores the recent advances in these three research areas to improve drought tolerance in wheat and barley.

Correction to: Genetic diversity and genetic variation in morpho-physiological traits to improve heat tolerance in Spring barley

The correct spelling of the third author's surname is Elakhdar and his current address is Agri-Bio Research Laboratory, Kyushu University, Motooka 744, Japan. The correct address for the fourth author is Agri-Bio Research Laboratory, Kyushu University, Motooka 744, Japan.

Genetic architecture of common bunt resistance in winter wheat using genome-wide association study

BACKGROUND

Common bunt (caused by Tilletia caries and T. foetida) has been considered as a major disease in wheat (Triticum aestivum) following rust (Puccinia spp.) in the Near East and is economically important in the Great Plains, USA. Despite the fact that it can be easily controlled using seed treatment with fungicides, fungicides often cannot or may not be used in organic and low-input fields. Planting common bunt resistant genotypes is an alternative.

RESULTS

To identify resistance genes for Nebraska common bunt race, the global set of differential lines were inoculated. Nine differential lines carrying nine different genes had 0% infected heads and seemed to be resistant to Nebraska race. To understand the genetic basis of the resistance in Nebraska winter wheat, a set of 330 genotypes were inoculated and evaluated under field conditions in two locations. Out of the 330 genotypes, 62 genotypes had different degrees of resistance. Moreover, plant height, chlorophyll content and days to heading were scored in both locations. Using genome-wide association study, 123 SNPs located on fourteen chromosomes were identified to be associated with the resistance. Different degrees of linkage disequilibrium was found among the significant SNPs and they explained 1.00 to 9.00% of the phenotypic variance, indicating the presence of many minor QTLs controlling the resistance.

CONCLUSION

Based on the chromosomal location of some of the known genes, some SNPs may be associated with Bt1, Bt6, Bt11 and Bt12 resistance loci. The remaining significant SNPs may be novel alleles that were not reported previously. Common bunt resistance seems to be an independent trait as no correlation was found between a number of infected heads and chlorophyll content, days to heading or plant height.

Genetic diversity and genetic variation in morpho-physiological traits to improve heat tolerance in Spring barley

Heat stress is one of the abiotic stresses that limit the production and productivity of barley. Understanding the genetic variation, changes in physiological processes and level of genetic diversity existing among genotypes are needed to produce new cultivars not only having a high tolerance to heat stress, but also displaying high yield. To address this challenge, a set of 60 highly homozygous, diverse barley genotypes were evaluated under normal and heat stress conditions in two seasons of 2014/2015 and 2015/2016. Seedling vigor (SV) as a morphological trait was visually scored under normal conditions. Plant height (Ph), days to flowering (DOF), 1000-kernel weight (TKW), grain yield per spike (GYPS), yield per plot (YPP) and biological yield (BY) were measured. Moreover, proline content (ProC), soluble carbohydrate content (SCC), starch content, soluble protein (SP), and amino acid (AA) content as physiological parameters were analyzed from the grains. High genetic variation was observed among genotypes for all traits scored in this study. All traits had high broad-sense heritability estimates ranging from 0.59 (SV) to 0.97 (TKW) for yield traits. Seedling vigor was significantly correlated with all yield traits under both conditions. Among all physiological traits, the increase in ProC and reduction in starch content due to heat stress had significant correlations with the reduction due to heat stress in YPP, GYPS, TKW, and BY. Furthermore, the genetic diversity based on genetic distance (GD) among genotypes was investigated using 206 highly polymorphic SSR marker alleles. The GD ranged from 0.70 to 0.98 indicating that these genotypes are highly and genetically dissimilar. The combination of analyses using molecular markers, genetic variation in yield traits, and changes in physiological traits provided useful information in identifying the tolerant genotypes which can be used to improve heat tolerance in barley through breeding.

Wheat Height Estimation Using LiDAR in Comparison to Ultrasonic Sensor and UAS

As one of the key crop traits, plant height is traditionally evaluated manually, which can be slow, laborious and prone to error. Rapid development of remote and proximal sensing technologies in recent years allows plant height to be estimated in more objective and efficient fashions, while research regarding direct comparisons between different height measurement methods seems to be lagging. In this study, a ground-based multi-sensor phenotyping system equipped with ultrasonic sensors and light detection and ranging (LiDAR) was developed. Canopy heights of 100 wheat plots were estimated five times during a season by the ground phenotyping system and an unmanned aircraft system (UAS), and the results were compared to manual measurements. Overall, LiDAR provided the best results, with a root-mean-square error (RMSE) of 0.05 m and an R² of 0.97. UAS obtained reasonable results with an RMSE of 0.09 m and an R² of 0.91. Ultrasonic sensors did not perform well due to our static measurement style. In conclusion, we suggest LiDAR and UAS are reliable alternative methods for wheat height evaluation.

Genome-Wide Association Study Reveals Novel Genomic Regions for Grain Yield and Yield-Related Traits in Drought-Stressed Synthetic Hexaploid Wheat

Synthetic hexaploid wheat (SHW; 2n = 6x = 42, AABBDD, Triticum aestivum L.) is produced from an interspecific cross between durum wheat (2n = 4x = 28, AABB, T. turgidum L.) and goat grass (2n = 2x = 14, DD, Aegilops tauschii Coss.) and is reported to have significant novel alleles-controlling biotic and abiotic stresses resistance. A genome-wide association study (GWAS) was conducted to unravel these loci [marker⁻trait associations (MTAs)] using 35,648 genotyping-by-sequencing-derived single nucleotide polymorphisms in 123 SHWs. We identified 90 novel MTAs (45, 11, and 34 on the A, B, and D genomes, respectively) and haplotype blocks associated with grain yield and yield-related traits including root traits under drought stress. The phenotypic variance explained by the MTAs ranged from 1.1% to 32.3%. Most of the MTAs (120 out of 194) identified were found in genes, and of these 45 MTAs were in genes annotated as having a potential role in drought stress. This result provides further evidence for the reliability of MTAs identified. The large number of MTAs (53) identified especially on the D-genome demonstrate the potential of SHWs for elucidating the genetic architecture of complex traits and provide an opportunity for further improvement of wheat under rapidly changing climatic conditions.

Genomic Selection in Preliminary Yield Trials in a Winter Wheat Breeding Program

Genomic prediction (GP) is now routinely performed in crop plants to predict unobserved phenotypes. The use of predicted phenotypes to make selections is an active area of research. Here, we evaluate GP for predicting grain yield and compare genomic and phenotypic selection by tracking lines advanced. We examined four independent nurseries of F3:6 and F3:7 lines trialed at 6 to 10 locations each year. Yield was analyzed using mixed models that accounted for experimental design and spatial variations. Genotype-by-sequencing provided nearly 27,000 high-quality SNPs. Average genomic predictive ability, estimated for each year by randomly masking lines as missing in steps of 10% from 10 to 90%, and using the remaining lines from the same year as well as lines from other years in a training set, ranged from 0.23 to 0.55. The predictive ability estimated for a new year using the other years ranged from 0.17 to 0.28. Further, we tracked lines advanced based on phenotype from each of the four F3:6 nurseries. Lines with both above average genomic estimated breeding value (GEBV) and phenotypic value (BLUP) were retained for more years compared to lines with either above average GEBV or BLUP alone. The number of lines selected for advancement was substantially greater when predictions were made with 50% of the lines from the testing year added to the training set. Hence, evaluation of only 50% of the lines yearly seems possible. This study provides insights to assess and integrate genomic selection in breeding programs of autogamous crops.

A comparison between genotyping-by-sequencing and array-based scoring of SNPs for genomic prediction accuracy in winter wheat

The utilization of DNA molecular markers in plant breeding to maximize selection response via marker-assisted selection (MAS) and genomic selection (GS) has revolutionized plant breeding. A key factor affecting GS applicability is the choice of molecular marker platform. Genotyping-by-sequencing scored SNPs (GBS-scored SNPs) provides a large number of markers, albeit with high rates of missing data. Array scored SNPs are of high quality, but the cost per sample is substantially higher. The objectives of this study were 1) compare GBS-scored SNPs, and array scored SNPs for genomic selection applications, and 2) compare estimates of genomic kinship and population structure calculated using the two marker platforms. SNPs were compared in a diversity panel consisting of 299 hard winter wheat (Triticum aestivum L.) accessions that were part of a multi-year, multi-environments association mapping study. The panel was phenotyped in Ithaca, Nebraska for heading date, plant height, days to physiological maturity and grain yield in 2012 and 2013. The panel was genotyped using GBS-scored SNPs, and array scored SNPs. Results indicate that GBS-scored SNPs is comparable to or better than Array-scored SNPs for genomic prediction application. Both platforms identified the same genetic patterns in the panel where 90% of the lines were classified to common genetic groups. Overall, we concluded that GBS-scored SNPs have the potential to be the marker platform of choice for genetic diversity and genomic selection in winter wheat.

Genotype, environment, seeding rate, and top-dressed nitrogen effects on end-use quality of modern Nebraska winter wheat

BACKGROUND

Fine-tuning production inputs such as seeding rate, nitrogen (N), and genotype may improve end-use quality of hard red winter wheat (Triticum aestivium L.) when growing conditions are unpredictable. Studies were conducted at the Agronomy Research Farm (ARF; Lincoln, NE, USA) and the High Plains Agricultural Laboratory (HPAL; Sidney, NE, USA) in 2014 and 2015 in Nebraska, USA, to determine the effects of genotype (6), environment (4), seeding rate (3), and flag leaf top-dressed N (0 and 34 kg N ha^-1 ) on the end-use quality of winter wheat.

RESULTS

End-use quality traits were influenced by environment, genotype, seeding rate, top-dressed N, and their interactions. Mixograph parameters had a strong correlation with grain volume weight and flour yield. Doubling the recommended seeding rate and N at the flag leaf stage increased grain protein content by 8.1% in 2014 and 1.5% in 2015 at ARF and 4.2% in 2014 and 8.4% in 2015 at HPAL.

CONCLUSION

The key finding of this research is that increasing seeding rates up to double the current recommendations with N at the flag leaf stage improved most of the end-use quality traits. This will have a significant effect on the premium for protein a farmer could receive when marketing wheat. © 2017 Society of Chemical Industry.

Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat

Winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) were used to develop a recombinant inbred population with future goals of identifying genomic regions associated with drought tolerance. To precisely map genomic regions, high-density linkage maps are a prerequisite. In this study genotyping-by- sequencing (GBS) was used to construct the high-density linkage map. The map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. The constructed linkage map revealed strong collinearity in marker order across 21 chromosomes with POPSEQ-v2.0, which was based on a high-density linkage map. The reliability of the linkage map for QTL mapping was demonstrated by co-localizing the genes to previously mapped genomic regions for two highly heritable traits, chaff color, and leaf cuticular wax. Applicability of linkage map for QTL mapping of three quantitative traits, flag leaf length, width, and area, identified 21 QTLs in four environments, and QTL expression varied across the environments. Two major stable QTLs, one each for flag leaf length (Qfll.hww-7A) and flag leaf width (Qflw.hww-5A) were identified. The map constructed will facilitate QTL and fine mapping of quantitative traits, map-based cloning, comparative mapping, and in marker-assisted wheat breeding endeavors.

Genetic basis of the very short life cycle of 'Apogee' wheat

Background

‘Apogee’ has a very short life cycle among wheat cultivars (flowering 25 days after planting under a long day and without vernalization), and it is a unique genetic material that can be used to accelerate cycling breeding lines. However, little is known about the genetic basis of the super-short life of Apogee wheat.

Results

In this study, Apogee was crossed with a strong winter wheat cultivar ‘Overland’, and 858 F₂ plants were generated and tested in a greenhouse under constant warm temperature and long days. Apogee wheat was found to have the early alleles for four flowering time genes, which were ranked in the order of vrn-A1 > VRN-B1 > vrn-D3 > PPD-D1 according to their effect intensity. All these Apogee alleles for early flowering showed complete or partial dominance effects in the F₂ population. Surprisingly, Apogee was found to have the same alleles at vrn-A1a and vrn-D3a for early flowering as observed in winter wheat cultivar ‘Jagger.’ It was also found that the vrn-A1a gene was epistatic to VRN-B1 and vrn-D3. The dominant vrn-D3a alone was not sufficient to cause the transition from vegetative to reproductive development in winter plants without vernalization but was able to accelerate flowering in those plants that carry the vrn-A1a or Vrn-B1 alleles. The genetic effects of the vernalization and photoperiod genes were validated in Apogee x Overland F₃ populations.

Conclusion

VRN-A1, VRN-B1, VRN-D3, and PPD-D1 are the major genes that enabled Apogee to produce the very short life cycle. This study greatly advanced the molecular understanding of the multiple flowering genes under different genetic backgrounds and provided useful molecular tools that can be used to accelerate winter wheat breeding schemes.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4239-8) contains supplementary material, which is available to authorized users.

Identification of markers linked to genes for sprouting tolerance (independent of grain color) in hard white winter wheat (HWWW)

KEY MESSAGE

Hard red wheats can donate genes to hard white wheats for tolerance to preharvest sprouting, the effects are quantitative in nature, and may be tracked with previously described DNA markers.

ABSTRACT

Pre-harvest sprouting (PHS) of wheat (Triticum aestivum L.) can negatively impact end-use quality and seed viability at planting. Due to preferences for white over red wheat in international markets, white wheat with PHS tolerance has become increasingly desired for worldwide wheat production. In general, however, red wheat is more tolerant of sprouting than white wheat. The main objective of this study was the identification of PHS tolerance conditioned by genes donated from hard red winter wheat, using markers applicable to the Great Plains hard white wheat gene pool. Three red wheat by white wheat populations, Niobrara/NW99L7068, NE98466/NW99L7068 and Jagalene/NW99L7068 were developed, and white-seeded progenies were analyzed for PHS tolerance and used to identify markers for the trait. In the three populations, marker loci with significant allelic effects were most commonly located on chromosomes of group 2, 3, 4 and 5, though additional markers were detected across the wheat genome. Chromosome 3A was the only chromosome with significant markers in all three populations. Markers were inconsistent across the three populations, and markers linked to tolerance-inducing loci were identified in both tolerant and susceptible parents. Additive effects of marker loci were common. In the present investigation, a wide range of PHS tolerance was observed, even though all lines were fixed for the recently reported positive TaPHS1 allele. PHS tolerance is controlled by additive major gene effects with minor gene effects where variations of minor gene effects were still unclear.

Distribution of Cadmium, Iron, and Zinc in Millstreams of Hard Winter Wheat (Triticum aestivum L.)

Hard winter wheat (Triticum aestivum L.) is a major crop in the Great Plains of the United States, and our previous work demonstrated that wheat genotypes vary for grain cadmium accumulation with some exceeding the CODEX standard (0.2 mg kg(-1)). Previous reports of cadmium distribution in flour milling fractions have not included high cadmium grain. This study measured the distribution of cadmium, zinc, and iron in flour and bran streams from high cadmium (0.352 mg kg(-1)) grain on a pilot mill that produced 12 flour and four bran streams. Recovery in flour was substantially greater for cadmium (50%) than for zinc (31%) or iron (22%). Cadmium, zinc, and iron in the lowest mineral concentration flour stream, representing the purest endosperm fraction, were 52, 22, and 11%, respectively, of initial grain concentration. Our results indicate that, relative to zinc and iron, a greater proportion of cadmium is stored in the endosperm, the source of white flour.

Evaluation and Association Mapping of Resistance to Tan Spot and Stagonospora Nodorum Blotch in Adapted Winter Wheat Germplasm

Tan spot and Stagonospora nodorum blotch (SNB), often occurring together, are two economically significant diseases of wheat in the Northern Great Plains of the United States. They are caused by the fungi Pyrenophora tritici-repentis and Parastagonospora nodorum, respectively, both of which produce multiple necrotrophic effectors (NE) to cause disease. In this work, 120 hard red winter wheat (HRWW) cultivars or elite lines, mostly from the United States, were evaluated in the greenhouse for their reactions to the two diseases as well as NE produced by the two pathogens. One P. nodorum isolate (Sn4) and four Pyrenophora tritici-repentis isolates (Pti2, 331-9, DW5, and AR CrossB10) were used separately in the disease evaluations. NE sensitivity evaluation included ToxA, Ptr ToxB, SnTox1, and SnTox3. The numbers of lines that were rated highly resistant to individual isolates ranged from 11 (9%) to 30 (25%) but only six lines (5%) were highly resistant to all isolates, indicating limited sources of resistance to both diseases in the U.S. adapted HRWW germplasm. Sensitivity to ToxA was identified in 83 (69%) of the lines and significantly correlated with disease caused by Sn4 and Pti2, whereas sensitivity to other NE was present at much lower frequency and had no significant association with disease. As expected, association mapping located ToxA and SnTox3 sensitivity to chromosome arm 5BL and 5BS, respectively. A total of 24 potential quantitative trait loci was identified with -log (P value) > 3.0 on 12 chromosomes, some of which are novel. This work provides valuable information and tools for HRWW production and breeding in the Northern Great Plains.

Quantification of Yield Loss Caused by Triticum mosaic virus and Wheat streak mosaic virus in Winter Wheat Under Field Conditions

Triticum mosaic virus (TriMV) and Wheat streak mosaic virus (WSMV) infect winter wheat (Triticum aestivum) in the Great Plains region of the United States. The two viruses are transmitted by wheat curl mites (Aceria tosichella), which also transmit High Plains virus. In a field study conducted in 2011 and 2012, winter wheat cultivars Millennium (WSMV-susceptible) and Mace (WSMV-resistant) were mechanically inoculated with TriMV, WSMV, TriMV+WSMV, or sterile water at the two-leaf growth stage. Chlorophyll meter (soil plant analysis development [SPAD]) readings, area under the SPAD progress curve (AUSPC), grain yield (=yield), yield components (spikes/m², kernels/spike, 1,000-kernel weight), and aerial dry matter were determined. In Millennium, all measured variables were significantly reduced by single or double virus inoculation, with the greatest reductions occurring in the double-inoculated treatment. Among the yield components, the greatest reductions occurred in spikes/m². In Mace, only AUSPC was significantly reduced by the TriMV+WSMV treatment in 2012. There was a significant (P ≤ 0.05), negative linear relationship between SPAD readings and day of year in all inoculation treatments in Millennium and in the TriMV+WSMV treatment in Mace. There were significant (P ≤ 0.05), positive linear relationships between yield and SPAD readings and between yield and aerial dry matter in Millennium but not in Mace. The results from this study indicate that under field conditions, (i) Mace, a WSMV-resistant cultivar, is also resistant to TriMV, and (ii) double inoculation of winter wheat by TriMV and WSMV exacerbates symptom expression and yield loss in a susceptible cultivar.

Genetic dissection of yield and its component traits using high-density composite map of wheat chromosome 3A: bridging gaps between QTLs and underlying genes

Earlier we identified wheat (Triticum aestivum L.) chromosome 3A as a major determinant of grain yield and its component traits. In the present study, a high-density genetic linkage map of 81 chromosome 3A-specific markers was developed to increase the precision of previously identified yield component QTLs, and to map QTLs for biomass-related traits. Many of the previously identified QTLs for yield and its component traits were confirmed and were localized to narrower intervals. Four novel QTLs one each for shoot biomass (Xcfa2262-Xbcd366), total biomass (wPt2740-Xcfa2076), kernels/spike (KPS) (Xwmc664-Xbarc67), and Pseudocercosporella induced lodging (PsIL) were also detected. The major QTLs identified for grain yield (GY), KPS, grain volume weight (GVWT) and spikes per square meter (SPSM) respectively explained 23.2%, 24.2%, 20.5% and 20.2% of the phenotypic variation. Comparison of the genetic map with the integrated physical map allowed estimation of recombination frequency in the regions of interest and suggested that QTLs for grain yield detected in the marker intervals Xcdo549-Xbarc310 and Xpsp3047-Xbarc356 reside in the high-recombination regions, thus should be amenable to map-based cloning. On the other hand, QTLs for KPS and SPSM flanked by markers Xwmc664 and Xwmc489 mapped in the low-recombination region thus are not suitable for map-based cloning. Comparisons with the rice (Oryza sativa L.) genomic DNA sequence identified 11 candidate genes (CGs) for yield and yield related QTLs of which chromosomal location of two (CKX2 and GID2-like) was confirmed using wheat aneuploids. This study provides necessary information to perform high-resolution mapping for map-based cloning and for CG-based cloning of yield QTLs.

Introgression of novel traits from a wild wheat relative improves drought adaptation in wheat

Root architecture traits are an important component for improving water stress adaptation. However, selection for aboveground traits under favorable environments in modern cultivars may have led to an inadvertent loss of genes and novel alleles beneficial for adapting to environments with limited water. In this study, we elucidate the physiological and molecular consequences of introgressing an alien chromosome segment (7DL) from a wild wheat relative species (Agropyron elongatum) into cultivated wheat (Triticum aestivum). The wheat translocation line had improved water stress adaptation and higher root and shoot biomass compared with the control genotypes, which showed significant drops in root and shoot biomass during stress. Enhanced access to water due to higher root biomass enabled the translocation line to maintain more favorable gas-exchange and carbon assimilation levels relative to the wild-type wheat genotypes during water stress. Transcriptome analysis identified candidate genes associated with root development. Two of these candidate genes mapped to the site of translocation on chromosome 7DL based on single-feature polymorphism analysis. A brassinosteroid signaling pathway was predicted to be involved in the novel root responses observed in the A. elongatum translocation line, based on the coexpression-based gene network generated by seeding the network with the candidate genes. We present an effective and highly integrated approach that combines root phenotyping, whole-plant physiology, and functional genomics to discover novel root traits and the underlying genes from a wild related species to improve drought adaptation in cultivated wheat.

Inheritance of grain polyphenol oxidase (PPO) activity in multiple wheat (Triticum aestivum L.) genetic backgrounds

Grain polyphenol oxidase (PPO) activity can cause discoloration of wheat (Triticum aestivum L.) food products. Five crosses (PI 117635/Antelope; Fielder/NW03681; Fielder/Antelope; NW07OR1070/Antelope; NW07OR1066/OR2050272H) were selected to study the genetic inheritance of PPO activity. STS markers, PPO18, PPO29 and STS01, were used to identify lines with putative alleles at the Ppo-A1 and Ppo-D1 loci conditioning low or high PPO activity. ANOVA showed significant genotypic effects on PPO activity (P < 0.0001) in all populations. The generations and generation × genotype effects were not significant in any population. A putative third (null) genotype at Ppo-A1 (no PCR fragments for PPO18) was discovered in NW07OR1066 and NW07OR1070 derived populations, and these had the lowest mean PPO activities. Results demonstrated that both Ppo-A1 and Ppo-D1 loci affect the kernel PPO activity, but the Ppo-A1 has the major effect. In three populations, contrary results were observed to those predicted from previous work with Ppo-D1 alleles, suggesting the markers for Ppo-D1 allele might give erroneous results in some genetic backgrounds or lineages. Results suggest that selection for low or null alleles only at Ppo-A1 might allow development of low PPO wheat cultivars.

Effects of Single and Double Infections of Winter Wheat by Triticum mosaic virus and Wheat streak mosaic virus on Yield Determinants

Triticum mosaic virus (TriMV) is a recently discovered virus infecting wheat (Triticum aestivum) in the Great Plains region of the United States. It is transmitted by wheat curl mites (Aceria tosichella) which also transmit Wheat streak mosaic virus (WSMV) and Wheat mosaic virus. In a greenhouse study, winter wheat 'Millennium' (WSMV susceptible) and 'Mace' (WSMV resistant) were mechanically inoculated with TriMV, WSMV, TriMV+WSMV, or sterile water at the two-leaf growth stage. At 28 days after inoculation, final chlorophyll meter (soil plant analysis development [SPAD]) readings, area under the SPAD progress curve (AUSPC), the number of tillers per plant, shoot and root weight, and total nitrogen and carbon content were determined. In Millennium, all measured variables were significantly reduced by single or double virus infections, with the greatest reductions occurring in the double-infection treatment. In Mace, only final SPAD readings, AUSPC, and total nitrogen were significantly reduced by single or double virus infections. There was a significant (P ≤ 0.05), positive linear relationship between SPAD readings and shoot weight in Millennium but not in Mace. The relationship between total nitrogen and shoot weight was positive, linear, and significant in both cultivars. The results from this study indicate that Mace, a WSMV-resistant cultivar, is also resistant to TriMV, and double infection of winter wheat by TriMV and WSMV exacerbates symptom expression and loss of biomass in susceptible cultivars.

Evaluation of buffalograss genotypes and full-sibs for chinch bug resistance

Fifteen buffalograss, Buchloe dactyloides (Nutt.) Engelm, genotypes and 94 diploid full-sib progeny were evaluated for western chinch bug, Blissus occiduus Barber (Hemiptera: Lygaeidae), resistance in two separate studies. The experimental design for each study was a completely randomized design. Adult chinch bugs were introduced onto caged single clone genotypes and progeny in the greenhouse. Chinch bug damage was assessed using a 1-5 visual damage rating scale with 1 = < or = 10%; 2 = 11-30%; 3 = 31-50%; 4 = 51-70%; and 5 = > or = 70% of the buffalograss leaf area with severe discoloration, or dead tissue. Highly significant differences were found among the genotypes and progeny for chinch bug damage. Among the genotypes, Legacy, Prestige, 184, 196, Bowie, NE 3297, NE 2769, and NE 2768 were moderately resistant with damage ratings of > 1, but < 3, while NE 2990, NE 2838, and 1-57-19 were moderately susceptible with damage ratings of > or = 3, but < 4. Among the progeny, one progeny (MP45) was highly resistant with a chinch bug damage rating of 1.0, 78 progeny (83%) had moderate resistance, with damage ratings of > 1.0 and < 3.0, 13 progeny (14%) were moderately susceptible with damage ratings ranging from 3.0 to 3.9, while only two were highly susceptible with damage ratings of > or = 4.0. The significant variability among genotypes and progeny for chinch bug resistance indicates the ability to improve buffalograss resistance to chinch bugs through selection or hybridization of selected genotypes.

High-density mapping and comparative analysis of agronomically important traits on wheat chromosome 3A

Bread wheat chromosome 3A has been shown to contain genes/QTLs controlling grain yield and other agronomic traits. The objectives of this study were to generate high-density physical and genetic-linkage maps of wheat homoeologous group 3 chromosomes and reveal the physical locations of genes/QTLs controlling yield and its component traits, as well as agronomic traits, to obtain a precise estimate of recombination for the corresponding regions and to enrich the QTL-containing regions with markers. Physical mapping was accomplished by 179 DNA markers mostly representing expressed genes using 41 single-break deletion lines. Polymorphism survey of cultivars Cheyenne (CNN) and Wichita (WI), and a substitution line of CNN carrying chromosome 3A from WI [CNN(WI3A)], with 142 RFLP probes and 55 SSR markers revealed that the extent of polymorphism is different among various group 3 chromosomal regions as well as among the homoeologs. A genetic-linkage map for chromosome 3A was developed by mapping 17 QTLs for seven agronomic traits relative to 26 RFLP and 15 SSR chromosome 3A-specific markers on 95 single-chromosome recombinant inbred lines. Comparison of the physical maps with the 3A genetic-linkage map localized the QTLs to gene-containing regions and accounted for only about 36% of the chromosome. Two chromosomal regions containing 9 of the 17 QTLs encompassed less than 10% of chromosome 3A but accounted for almost all of the arm recombination. To identify rice chromosomal regions corresponding to the particular QTL-containing wheat regions, 650 physically mapped wheat group 3 sequences were compared with rice genomic sequences. At an E value of E < or = 10(-5), 82% of the wheat group 3 sequences identified rice homologs, of which 54% were on rice chromosome 1. The rice chromosome 1 region collinear with the two wheat regions that contained 9 QTLs was about 6.5 Mb.

The use of microsatellite markers for the detection of genetic similarity among winter bread wheat lines for chromosome 3A

Previous studies with chromosome substitution and recombinant inbred chromosome lines identified that chromosome 3A of wheat cv. Wichita contains alleles that influence grain yield, yield components and agronomic performance traits relative to alleles on chromosome 3A of Cheyenne, a cultivar believed to be the founder parent of many Nebraska developed cultivars. This study was carried out to examine the genetic similarity among wheat cultivars based on the variation in chromosome 3A. Forty-eight cultivars, two promising lines and four substitution lines (in duplicate) were included in the study. Thirty-six chromosome 3A-specific and 12 group-3 barley simple sequence repeat (SSR) primer pairs were used. A total of 106 polymorphic bands were scored. Transferability of barley microsatellite markers to wheat was 73%. The coefficient of genetic distance (D) among the genotypes ranged from 0.40 to 0.91 and averaged D=0.66. Cluster analysis by the unweighted pair-group method with arithmetic averages showed one large and one small cluster with eight minor clusters in the large cluster. Several known pedigree relationships largely corresponded with the results of SSR clusters and principal coordinate analysis. Cluster analysis was also carried out by using 22 alleles that separate Wichita 3A from Cheyenne 3A, and three clusters were identified (a small cluster related to Cheyenne of mainly western Nebraska wheat cultivars; a larger, intermediate cluster with many modern Nebraska wheat cultivars; a large cluster related to Wichita with many modern high-yielding or Kansas wheat cultivars). Using three SSR markers that identify known agronomically important quantitative trait loci (QTL) regions, we again separated the cultivars into three main clusters that were related to Cheyenne or Wichita, or had a different 3A lineage. These results suggest that SSR markers linked to agronomically important QTLs are a valuable asset for estimating both genetic similarity for chromosome 3A and how the chromosome has been used in cultivar improvement.