Characterization of Quantitative Trait Loci for Leaf Rust Resistance from CI 13227 in Three Winter Wheat Populations.

Leaf rust is a widespread foliar wheat disease causing substantial yield losses worldwide. Slow-rusting is "adult plant" resistance that significantly slows epidemic development and thereby reduces yield loss. Wheat accession CI 13227 was previously characterized as having slow-rusting resistance. To validate the quantitative trait loci (QTL) and develop diagnostic markers for slow rusting resistance in CI 13227, a new population of recombinant inbred lines (RILs) of CI 13227 × Everest was evaluated for latent period (LP), final severity (FS), area under disease progress curve (AUDPC), and infection type (IT) in greenhouses and genotyped using genotyping-by-sequencing (GBS). Four QTL were identified on chromosome arms 2BL, 2DS, 3BS, and 7BL, explaining 6.82 to 28.45% of the phenotypic variance for these traits. Seven kompetitive allele specific polymorphism (KASP) markers previously reported to be linked to the QTL in two other CI 13227 populations were validated. In addition, the previously reported QLr.hwwg-7AL was remapped to 2BL (renamed QLr.hwwg-2BL) after adding new markers in this study. Phenotypic data showed that the RILs harboring two or three of the QTL had a significantly longer LP. QLr.hwwg-2DS on 2DS showed a major effect on all rust resistance traits and was finely mapped to a 2.7 Mb interval by two newly developed flanking markers from exome capture. Three disease-resistance genes and two transporter genes were identified as the putative candidates for QLr.hwwg-2DS. The validated QTL can be used as slow rusting resistance resources and the markers developed in this study will be useful for marker-assisted selection.

Identifying novel sources of resistance to wheat stem sawfly in five wild wheat species.

BACKGROUND: The wheat stem sawfly (WSS, Cephus cinctus) is a major pest of wheat (Triticum aestivum) and can cause significant yield losses. WSS damage results from stem boring and/or cutting, leading to the lodging of wheat plants. Although solid-stem wheat genotypes can effectively reduce larval survival, they may have lower yields than hollow-stem genotypes and show inconsistent solidness expression. Because of limited resistance sources to WSS, evaluating diverse wheat germplasm for novel resistance genes is crucial. We evaluated 91 accessions across five wild wheat species (Triticum monococcum, T. urartu, T. turgidum, T. timopheevii, and Aegilops tauschii) and common wheat cultivars (T. aestivum) for antixenosis (host selection) and antibiosis (host suitability) to WSS. Host selection was measured as the number of eggs after adult oviposition, and host suitability was determined by examining the presence or absence of larval infestation within the stem. The plants were grown in the greenhouse and brought to the field for WSS infestation. In addition, a phylogenetic analysis was performed to determine the relationship between the WSS traits and phylogenetic clustering. RESULTS: Overall, Ae. tauschii, T. turgidum and T. urartu had lower egg counts and larval infestation than T. monococcum, and T. timopheevii. T. monococcum, T. timopheevii, T. turgidum, and T. urartu had lower larval weights compared with T. aestivum. CONCLUSION: This study shows that wild relatives of wheat could be a valuable source of alleles for enhancing resistance to WSS and identifies specific germplasm resources that may be useful for breeding. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

QTL Pyramiding Provides Marginal Improvement in 2NvS-Based Wheat Blast Resistance.

Wheat blast, caused by the fungus Magnaporthe oryzae Triticum pathotype (MoT), is a devastating disease affecting South America, Bangladesh, and Zambia. Resistance to wheat blast has strongly relied on the 2NvS translocation; however, newer MoT isolates have increased aggressiveness, threatening the 2NvS translocation's effectiveness and durability. To identify genomic regions associated with wheat blast resistance, we performed a quantitative trait loci (QTL) mapping study using 187 double-haploid (DH) lines from a cross between the Brazilian wheat cultivars 'TBIO Alvorada' and 'TBIO Sossego', which are moderately resistant and susceptible to blast, respectively. The DH population was evaluated in a greenhouse in Brazil and Bolivia, and field conditions in Bolivia. Contrasting models best explained the relationship between traits evaluated according to differences in disease levels and the presence of the 2NvS. A large effect-locus, derived from 'TBIO Sossego', was identified on chromosome 2AS, which was confirmed to be 2NvS translocation and explained 33.5 to 82.4% of the phenotypic variance. Additional significant loci were identified on 5AL, 1DS, 4DS, 5DL, and 6DL chromosome arms with phenotypic variance <6%, but they were not consistent across trait-environment combinations. QTL pyramiding analyses showed that some specific loci had an additive effect when combined with the 2NvS, suggesting that stacking multiple loci may be an effective strategy to help manage wheat blast. The markers associated with the 2NvS can be used as dominant diagnostic markers for this alien translocation. Additional characterization of these loci using a broader set of MoT isolates is critical to validate their effectiveness against current MoT populations.

Accelerating wheat breeding for end-use quality through association mapping and multivariate genomic prediction.

In hard-winter wheat (Triticum aestivum L.) breeding, the evaluation of end-use quality is expensive and time-consuming, being relegated to the final stages of the breeding program after selection for many traits including disease resistance, agronomic performance, and grain yield. In this study, our objectives were to identify genetic variants underlying baking quality traits through genome-wide association study (GWAS) and develop improved genomic selection (GS) models for the quality traits in hard-winter wheat. Advanced breeding lines (n = 462) from 2015-2017 were genotyped using genotyping-by-sequencing (GBS) and evaluated for baking quality. Significant associations were detected for mixograph mixing time and bake mixing time, most of which were within or in tight linkage to glutenin and gliadin loci and could be suitable for marker-assisted breeding. Candidate genes for newly associated loci are phosphate-dependent decarboxylase and lipid transfer protein genes, which are believed to affect nitrogen metabolism and dough development, respectively. The use of GS can both shorten the breeding cycle time and significantly increase the number of lines that could be selected for quality traits, thus we evaluated various GS models for end-use quality traits. As a baseline, univariate GS models had 0.25-0.55 prediction accuracy in cross-validation and from 0 to 0.41 in forward prediction. By including secondary traits as additional predictor variables (univariate GS with covariates) or correlated response variables (multivariate GS), the prediction accuracies were increased relative to the univariate model using only genomic information. The improved genomic prediction models have great potential to further accelerate wheat breeding for end-use quality.

The Haplotype-Based Analysis of Aegilops tauschii Introgression Into Hard Red Winter Wheat and Its Impact on Productivity Traits.

The introgression from wild relatives have a great potential to broaden the availability of beneficial allelic diversity for crop improvement in breeding programs. Here, we assessed the impact of the introgression from 21 diverse accessions of Aegilops tauschii, the diploid ancestor of the wheat D genome, into 6 hard red winter wheat cultivars on yield and yield component traits. We used 5.2 million imputed D genome SNPs identified by the whole-genome sequencing of parental lines and the sequence-based genotyping of introgression population, including 351 BC1F3:5 lines. Phenotyping data collected from the irrigated and non-irrigated field trials revealed that up to 23% of the introgression lines (ILs) produce more grain than the parents and check cultivars. Based on 16 yield stability statistics, the yield of 12 ILs (3.4%) was stable across treatments, years, and locations; 5 of these lines were also high yielding lines, producing 9.8% more grain than the average yield of check cultivars. The most significant SNP- and haplotype-trait associations were identified on chromosome arms 2DS and 6DL for the spikelet number per spike (SNS), on chromosome arms 2DS, 3DS, 5DS, and 7DS for grain length (GL) and on chromosome arms 1DL, 2DS, 6DL, and 7DS for grain width (GW). The introgression of haplotypes from A. tauschii parents was associated with an increase in SNS, which was positively correlated with a heading date (HD), whereas the haplotypes from hexaploid wheat parents were associated with an increase in GW. We show that the haplotypes on 2DS associated with an increase in the spikelet number and HD are linked with multiple introgressed alleles of Ppd-D1 identified by the whole-genome sequencing of A. tauschii parents. Meanwhile, some introgressed haplotypes exhibited significant pleiotropic effects with the direction of effects on the yield component traits being largely consistent with the previously reported trade-offs, there were haplotype combinations associated with the positive trends in yield. The characterized repertoire of the introgressed haplotypes derived from A. tauschii accessions with the combined positive effects on yield and yield component traits in elite germplasm provides a valuable source of alleles for improving the productivity of winter wheat by optimizing the contribution of component traits to yield.

Dicamba resistance in kochia from Kansas and Nebraska evolved independently.

BACKGROUND: Evolution and spread of resistance to glyphosate in kochia [Bassia scoparia (L.) A.J. Scott] is a major challenge for the sustainability of glyphosate-resistant crop technology in this region. Dicamba offers a viable option to manage glyphosate-resistant kochia. However, the recent and rapid evolution of dicamba resistance in glyphosate-resistant kochia populations in Kansas (KS), and other states in the USA is a threat to the management of this weed. Our previous research suggests that two distinct mechanisms confer dicamba resistance in KS (KSUR) and NE (CSUR) kochia. CSUR kochia is dicamba-resistant due to a double mutation in an auxin and dicamba coreceptor gene (Aux/IAA16), and CSUR kochia plants show reduced dicamba translocation. However, the mechanism of dicamba resistance in KSUR is not known. The objective of this research was to determine if dicamba resistance in KSUR is due to a different mechanism and therefore evolved independently from CSUR by measuring whether the resistance traits are chromosomally linked. RESULTS: The F1 and F2 progenies from KSUR × CSUR were generated. Single dicamba rate tests were conducted using the F1 and F2 progeny. The results indicate that two different genes confer dicamba resistance in KSUR and CSUR; importantly, these two genes are not linked. CONCLUSION: This research provides evidence that different populations of kochia have independently evolved resistance to dicamba by different mechanisms, and we confirmed that the genes conferring resistance to the same herbicide in different populations are not chromosomally linked.

Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative.

Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop improvement to maximize retention of introgressed diversity across entire genome.

Winter Wheat Yield Response to Plant Density as a Function of Yield Environment and Tillering Potential: A Review and Field Studies.

Wheat (Triticum aestivum L.) grain yield response to plant density is inconsistent, and the mechanisms driving this response are unclear. A better understanding of the factors governing this relationship could improve plant density recommendations according to specific environmental and genetics characteristics. Therefore, the aims of this paper were to: i) execute a synthesis-analysis of existing literature related to yield-plant density relationship to provide an indication of the need for different agronomic optimum plant density (AOPD) in different yield environments (YEs), and ii) explore a data set of field research studies conducted in Kansas (USA) on yield response to plant density to determine the AOPD at different YEs, evaluate the effect of tillering potential (TP) on the AOPD, and explain changes in AOPD via variations in wheat yield components. Major findings of this study are: i) the synthesis-analysis portrayed new insights of differences in AOPD at varying YEs, reducing the AOPD as the attainable yield increases (with AOPD moving from 397 pl m-2 for the low YE to 191 pl m-2 for the high YE); ii) the field dataset confirmed the trend observed in the synthesis-analysis but expanded on the physiological mechanisms underpinning the yield response to plant density for wheat, mainly highlighting the following points: a) high TP reduces the AOPD mainly in high and low YEs, b) at canopy-scale, both final number of heads and kernels per square meter were the main factors improving yield response to plant density under high TP, c) under varying YEs, at per-plant-scale, a compensation between heads per plant and kernels per head was the main factor contributing to yield with different TP.

Resistance to wheat rusts identified in wheat/Amblyopyrum muticum chromosome introgressions.

Wheat (Triticum aestivum L.) rusts are a worldwide production problem. Plant breeders have used genetic resistance to combat these fungi. However, single-gene resistance is rapidly overcome as a result of frequent occurrence of new virulent fungal strains. Thus, a supply of new resistance sources is continually needed, and new resistance sources are limited within hexaploid wheat genetic stocks. Wild relatives are able to be a resource for new resistance genes but are hindered because of chromosome incapability with domesticated wheats. Twenty-eight double-haploid hexaploid wheat/Amblyopyrum muticum (Boiss.) Eig introgression lines, with introgressions covering the majority of the T genome, were evaluated for resistance to Puccinia triticina Erikss., P. graminis Pers.:Pers. f.sp. tritici Erikss. & E. Henning, and P. striiformis Westend. f.sp. tritici Erikss.. At the seedling level, four lines were resistant to races of P. triticina, six lines were resistant to P. graminis, and 15 lines were resistant to P. striiformis. At the adult stage, 16 lines were resistant to P. triticina. Line 355 had resistance to all three rusts and line 161 had resistance to all tested races of P. triticina. Some of these lines will require further work to reduce the size of the introgressed segment; however, lines 92 and 355 have very small fragments and can be used directly as new resistance donors.

Changes in the Phenotype of Winter Wheat Varieties Released Between 1920 and 2016 in Response to In-Furrow Fertilizer: Biomass Allocation, Yield, and Grain Protein Concentration.

Plant breeding has increased the yield of winter wheat (Triticum aestivum L.) over decades, and the rate of genetic gain has been faster under high fertility in some countries. However, this response is not universal, and limited information exists on the physiological traits underlying the interaction between varieties and fertilization. Thus, our objectives were to identify the key shifts in crop phenotype in response to selection for yield and quality, and to determine whether historical and modern winter wheat varieties respond differently to in-furrow fertilizer. Factorial field experiments combined eight winter wheat varieties released between 1920 and 2016, and two fertilizer practices [control versus 112 kg ha-1 in-furrow 12 -40-0-10-1 (N-P-K-S-Zn)] in four Kansas environments. Grain yield and grain N-removal increased nonlinearly with year of release, with greater increases between 1966 and 2000. In-furrow fertilizer increased yield by ~300 kg ha-1 with no variety × fertility interaction. Grain protein concentration related negatively to yield, and the residuals of this relationship were unrelated to year of release. Yield increase was associated with changes in thermal time to critical growth stages, as modern varieties had shorter vegetative period and longer grain filling period. Yield gains also derived from more kernels m-2 resultant from more kernels head-1. Historical varieties were taller, had thinner stems, and allocated more biomass to the stem than semidwarf varieties. Yield gains resulted from increases in harvest index and not in biomass accumulation at grain filling and maturity, as shoot biomass was similar among varieties. The allometric exponent (i.e., the slope between log of organ biomass and log of shoot biomass) for grain increased with, and for leaves was unrelated to, year of release. The ability of modern varieties to allocate more biomass to the kernels coupled to an early maturity increased grain yield and grain N-removal over time. However, increases in grain yield were greater than increases in grain N-removal, reducing grain protein concentration in modern varieties.

Physiological Basis of Genotypic Response to Management in Dryland Wheat.

A great majority of dryland wheat producers are reluctant to intensify management due to the assumption that lack of water availability is the most critical factor limiting yield and thus, the response to management intensification would be limited. We conducted on-farm field experiments across three locations and two growing seasons in Kansas using 21 modern winter wheat genotypes grown under either standard (SM) or intensified management (IM) systems. The goals of this study were to (i) determine whether the SM adopted is adequate to reach achievable yields by farmers in the region and (ii) identify differences in responsiveness to IM among a range of modern genotypes. Across all sites-years and genotypes, the IM increased yield by 0.9 Mg ha-1, outyielding the SM system even in the lowest yielding conditions. As expected, the yield response to IM increased with the achievable yield of the environment and genotype. Across all sources of variation, the yield responsiveness to IM was related to increased biomass rather than harvest index, strongly driven by improvements in grain number (and independent of changes in grain weight), and by improvements in N uptake which resulted from greater biomass and shoot N concentration. The IM system generally also increased grain N concentration and decreased the grain N dilution effect from increased yield. Genotypes varied in their response to IM, with major response patterns resulting from the combination of response magnitude (large vs. small) and consistency (variable vs. consistent). Genotypes with high mean response and high variability in the response to IM across years could offer greater opportunities for producers to maximize yield as those genotypes showed greater yield gain from IM when conditions favored their response. For the background conditions evaluated, intensifying management could improve wheat yield in between c. 0.2 and 1.5 Mg ha-1 depending on genotype.

Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program.

One of the biggest challenges for genetic studies on natural or unstructured populations is the unbalanced datasets where individuals are measured at different times and environments. This problem is also common in crop and animal breeding where many individuals are only evaluated for a single year and large but unbalanced datasets can be generated over multiple years. Many wheat breeding programs have focused on increasing bread wheat (Triticum aestivum L.) yield, but processing and end-use quality are critical components when considering its use in feeding the rising population of the next century. The challenges with end-use quality trait improvements are high cost and seed amounts for testing, the latter making selection in early breeding populations impossible. Here we describe a novel approach to identify marker-trait associations within a breeding program using a meta-genome wide association study (GWAS), which combines GWAS analysis from multi-year unbalanced breeding nurseries, in a manner reflecting meta-GWAS in humans. This method facilitated mapping of processing and end-use quality phenotypes from advanced breeding lines (n = 4,095) of the CIMMYT bread wheat breeding program from 2009 to 2014. Using the meta-GWAS we identified marker-trait associations, allele effects, candidate genes, and can select using markers generated in this process. Finally, the scope of this approach can be broadly applied in 'breeding-assisted genomics' across many crops to greatly increase our functional understanding of plant genomes.

Expression of a rice soluble starch synthase gene in transgenic wheat improves the grain yield under heat stress conditions.

Wheat (Triticum aestivum L.) is a temperate cereal with an optimum temperature range of 15-22°C during the grain filling stage. Heat stress is one of the major environmental constraints for wheat production worldwide. Temperatures above 25°C during the grain filling stage significantly reduced wheat yield and quality. This reduction was reported due to the inactivation of the soluble starch synthase, a key heat-labile enzyme in starch transformation of wheat endosperm. To improve wheat productivity under heat stress, the rice soluble starch synthase I, under the control of either a constitutive promoter or an endosperm-specific promoter, was expressed in wheat and the transgenic lines were monitored for expression and the effects on yield-related traits. The results showed that the transgenic wheat events expressed rice soluble starch synthase I at a high level after four generations, and transgenic plants produced grains of greater weight during heat stress. Under heat stress conditions, the thousand kernel weight increased 21-34% in T2 and T3 transgenic plants compared to the non-transgenic control plants. In addition, the photosynthetic duration of transgenic wheat was longer than in non-transgenic controls. This study demonstrated that the engineering of a heat tolerant soluble starch synthase gene can be a potential strategy to improve wheat yield under heat stress conditions.

Quantitative Trait Loci for Slow-Rusting Resistance to Leaf Rust in Doubled-Haploid Wheat Population CI13227 × Lakin.

CI13227 is a U.S. winter wheat line with adult-plant slow-rusting resistance that has been the subject of several studies on the characteristics and components of slow rusting. Previous genetic studies used different populations and approaches and came to different conclusions about the genetic basis of resistance in CI13227. To clarify the situation, a new doubled-haploid (DH) population of CI13227 × Lakin was produced and a linkage map was constructed using 5,570 single-nucleotide polymorphism (SNP) markers derived from wheat 90K SNP assays and 84 simple sequence repeat markers. Three quantitative trait loci (QTL) were identified for three slow-rusting traits on chromosome arms 2DS, 7AL, and 7BL from CI13227. A fourth QTL mapped on chromosome 3BS was from Lakin. The QTL on 2DS, designated QLr.hwwg-2DS, explained 11.2 to 25.6% of the phenotypic variation. It was found in the same position as a slow-rusting QTL in the CI13227 × Suwon 92 population in a previous study and, thus, verified the 2DS QTL. The QTL on chromosome 7BL explained 8.1 and 19.3% of the phenotypic variation and is likely to be Lr68. The other two QTL showed a minor effect on some of the traits evaluated in a single experiment. Flanking SNP closely linked to all QTL were converted to Kompetitive allele-specific polymerase chain reaction markers that can be used in marker-assisted selection to transfer these QTL into adapted wheat cultivars.

Wheat Genotypes With Combined Resistance to Wheat Curl Mite, Wheat Streak Mosaic Virus, Wheat Mosaic Virus, and Triticum Mosaic Virus.

The wheat curl mite, Aceria tosichella Keifer, (WCM) is a global pest of bread wheat that reduces yields significantly. In addition, WCM carries Wheat streak mosaic virus (WSMV, family Potyviridae, genus Tritimovirus), the most significant wheat virus in North America; High Plains wheat mosaic virus (HPWMoV, genus Emaravirus, formerly High plains virus); and Triticum mosaic virus (TriMV, family Potyviridae, genus Poacevirus). Viruses carried by WCM have reduced wheat yields throughout the U.S. Great Plains for >50 yr, with average yield losses of 2-3% and occasional yield losses of 7-10%. Acaricides are ineffective against WCM, and delayed planting of winter wheat is not feasible. Five wheat breeding lines containing Cmc4, a WCM resistance gene from Aegilops tauschii, and Wsm2, a WSMV resistance gene from wheat germplasm CO960293-2 were selected from the breeding process and assessed for phenotypic reaction to WCM feeding, population increase, and the degree of WSMV, HPWMoV, and TriMV infection. Experiments determined that all five lines are resistant to WCM biotype 1 feeding and population increase, and that two breeding lines contain resistance to WSMV, HPWMoV, and TriMV infection as well. These WCM-, WSMV-, HPWMoV-, and TriMV-resistant genotypes can be used improve management of wheat yield losses from WCM-virus complexes.

Genomic Selection for Processing and End-Use Quality Traits in the CIMMYT Spring Bread Wheat Breeding Program.

Wheat ( L.) cultivars must possess suitable end-use quality for release and consumer acceptability. However, breeding for quality traits is often considered a secondary target relative to yield largely because of amount of seed needed and expense. Without testing and selection, many undesirable materials are advanced, expending additional resources. Here, we develop and validate whole-genome prediction models for end-use quality phenotypes in the CIMMYT bread wheat breeding program. Model accuracy was tested using forward prediction on breeding lines ( = 5520) tested in unbalanced yield trials from 2009 to 2015 at Ciudad Obregon, Sonora, Mexico. Quality parameters included test weight, 1000-kernel weight, hardness, grain and flour protein, flour yield, sodium dodecyl sulfate sedimentation, Mixograph and Alveograph performance, and loaf volume. In general, prediction accuracy substantially increased over time as more data was available to train the model. Reflecting practical implementation of genomic selection (GS) in the breeding program, forward prediction accuracies () for quality parameters were assessed in 2015 and ranged from 0.32 (grain hardness) to 0.62 (mixing time). Increased selection intensity was possible with GS since more entries can be genotyped than phenotyped and expected genetic gain was 1.4 to 2.7 times higher across all traits than phenotypic selection. Given the limitations in measuring many lines for quality, we conclude that GS is a powerful tool to facilitate early generation selection for end-use quality in wheat, leaving larger populations for selection on yield during advanced testing and leading to better gain for both quality and yield in bread wheat breeding programs.

Genome-wide association analysis on pre-harvest sprouting resistance and grain color in U.S. winter wheat.

BACKGROUND: Pre-harvest sprouting (PHS) in wheat can cause substantial reduction in grain yield and end-use quality. Grain color (GC) together with other components affect PHS resistance. Several quantitative trait loci (QTL) have been reported for PHS resistance, and two of them on chromosome 3AS (TaPHS1) and 4A have been cloned. METHODS: To determine genetic architecture of PHS and GC and genetic relationships of the two traits, a genome-wide association study (GWAS) was conducted by evaluating a panel of 185 U.S. elite breeding lines and cultivars for sprouting rates of wheat spikes and GC in both greenhouse and field experiments. The panel was genotyped using the wheat 9K and 90K single nucleotide polymorphism (SNP) arrays. RESULTS: Four QTL for GC on four chromosomes and 12 QTL for PHS resistance on 10 chromosomes were identified in at least two experiments. QTL for PHS resistance showed varied effects under different environments, and those on chromosomes 3AS, 3AL, 3B, 4AL and 7A were the more frequently identified QTL. The common QTL for GC and PHS resistance were identified on the long arms of the chromosome 3A and 3D. CONCLUSIONS: Wheat grain color is regulated by the three known genes on group 3 chromosomes and additional genes from other chromosomes. These grain color genes showed significant effects on PHS resistance in some environments. However, several other QTL that did not affect grain color also played a significant role on PHS resistance. Therefore, it is possible to breed PHS-resistant white wheat by pyramiding these non-color related QTL.

Using RNA Sequencing and In Silico Subtraction to Identify Resistance Gene Analog Markers for Lr16 in Wheat.

Leaf rust, caused by Puccinia triticina Eriks., is one of the most widespread diseases of wheat and breeding for resistance is one of the most effective methods of control. Lr16 is a wheat leaf rust resistance gene (R-gene) that provides resistance at both the seedling and adult stages. Simple-sequence repeat (SSR) markers have been used to map Lr16 to the distal end of chromosome 2B. The objectives of this study were to use RNA sequencing (RNA-seq) and in silico subtraction to identify new R-gene analogs (RGAs) and use them as Lr16 markers. RNA was isolated from the susceptible wheat cultivar Thatcher (Tc) and the resistant Tc isolines TcLr10, TcLr16, TcLr21, and sequenced using Illumina technology. Using in silico subtraction, sequences from the resistant Tc isolines were aligned to a Tc reference expressed sequence tag (EST) set. Sequences not aligning to the Tc reference were assembled into contigs and analyzed using BLASTx to determine putative gene functions. Primer pairs were designed for 181 RGA sequences, of which, 137 amplified in at least one of the parents. A mapping population was developed with 165 F2 lines from a cross between the rust-susceptible cultivar Chinese Spring (CS) and TcLr16. Two RGA markers XTaLr16_RGA266585 and XTaLr16_RGA22128 were identified that mapped proximally 1.2 and 23.8 cM from Lr16, respectively. Three SSR markers Xwmc764, Xwmc661, and Xbarc35 mapped between these two RGA markers at distances of 5.0, 10.9, and 16.1 cM from Lr16, respectively. In silico subtraction is an effective technique for isolating RGAs linked to R-genes of interest.

Response of Aegilops species to drought stress during reproductive stages of development.

Drought stress is an important abiotic factor limiting wheat yield. Thirty-one accessions of Aegilops species belonging to five species were screened to identify species/accessions tolerant to drought stress and to measure traits associated with the tolerance. Plants were grown at full irrigation, 25/19°C day/night temperature and an 18h photoperiod. At anthesis (Feekes 10.5.1), drought stress was imposed by withholding water for 16 days. Controls were continuously irrigated. Drought stress decreased chlorophyll content, grain number, individual grain weight and grain yield by 31, 25, 68 and 76% compared with the control. Aegilops geniculata Roth had greater tolerance to drought stress for yield (48% decline from control) compared with other species (>73% decline from control). The tolerance was associated with higher grain number spike-1 and heavier grains. A. geniculata, GenBank accession number TA 10437, was highly tolerant to drought stress with <20% yield decline and a drought stress susceptibility index (DSI) <0.5, whereas TA 1802, TA 2061, TA 1814, TA 1819 were identified as moderately tolerant to drought stress (20-40% yield decline and DSI<1.0). Our results suggest a presence of genetic variability among Aegilops species that can be utilised in breeding wheat for tolerance to drought stress at reproductive stages.

Effects of drought and high temperature stress on synthetic hexaploid wheat.

Drought and high temperature often occurs simultaneously, causing significant yield losses in wheat (Triticum aestivum L.). The objectives of this study were to: (i) quantify independent and combined effects of drought and high temperature stress on synthetic hexaploid wheat genotypes at anthesis and at 21 days after anthesis; and (ii) determine whether responses to stress varied among genotypes. Four synthetic hexaploid and two spring wheat genotypes were grown from emergence to anthesis (Experiment I) and emergence to 21 days after anthesis (Experiment II), with full irrigation and 21/15°C day/night temperature. Thereafter, four treatments were imposed for 16 days as (a) optimum condition: irrigation+21/15°C, (b) drought stress: withhold irrigation+21/15°C, (c) high temperature stress: irrigation+36/30°C and (d) combined stress: withhold irrigation+36/30°C. Results indicated a decrease in leaf chlorophyll, individual grain weight and grain yield in an increasing magnitude of drought