2018年第五周小麦文献推荐（2.4）

1 The goat grass genome’s role in wheat improvement

Nature plants上面的一篇点评，通讯作者是何中虎老师。

The recently published reference genome of Aegilops tauschii provides new insights into the originator of the D genome donor of hexaploid wheat. This will be a foundation for exploring the genomic diversity underpinning adaptive traits in wheat, and ultimately advance wheat improvement efforts.

2 Identification of QTL conferring resistance to stripe rust (Puccinia striiformis f. sp. hordei) and leaf rust (Puccinia hordei) in barley using nested association mapping (NAM)

The biotrophic rust fungi Puccinia hordei and Puccinia striiformis are important barley pathogens with the potential to cause high yield losses through an epidemic spread. The identification of QTL conferring resistance to these pathogens is the basis for targeted breeding approaches aiming to improve stripe rust and leaf rust resistance of modern cultivars. Exploiting the allelic richness of wild barley accessions proved to be a valuable tool to broaden the genetic base of resistance of barley cultivars. In this study, SNP-based nested association mapping (NAM) was performed to map stripe rust and leaf rust resistance QTL in the barley NAM population HEB-25, comprising 1,420 lines derived from BC1S3 generation. By scoring the percentage of infected leaf area, followed by calculation of the area under the disease progress curve and the average ordinate during a two-year field trial, a large variability of resistance across and within HEB-25 families was observed. NAM based on 5,715 informative SNPs resulted in the identification of twelve and eleven robust QTL for resistance against stripe rust and leaf rust, respectively. Out of these, eight QTL for stripe rust and two QTL for leaf rust are considered novel showing no overlap with previously reported resistance QTL. Overall, resistance to both pathogens in HEB-25 is most likely due to the accumulation of numerous small effect loci. In addition, the NAM results indicate that the 25 wild donor QTL alleles present in HEB-25 strongly differ in regard to their individual effect on rust resistance. In future, the NAM concept will allow to select and combine individual wild barley alleles from different HEB parents to increase rust resistance in barley. The HEB-25 results will support to unravel the genetic basis of rust resistance in barley, and to improve resistance against stripe rust and leaf rust of modern barley cultivars.

3 Phosphorus Alters Starch Morphology and Gene Expression Related to Starch Biosynthesis and Degradation in Wheat Grain

Phosphorus is an essential plant macronutrient which profoundly affects the yield and quality of wheat starch. In this study, scanning electron microscopy showed that P fertilizer amount (0, 46, and 92 kg P ha−1) had no significant effect on the shape of starch granules in wheat (cv. Xindong 20) grain. However, confocal laser scanning microscopy with 3-(4-carboxybenzoyl) quinoline-2-carboxaldehyde and methanolic merbromin stains indicated that P amount influenced the microstructure of the starch granules. Starch granules from the 46 kg P ha−1 treatment released significantly more reducing sugars than those from the 0 and 92 kg P ha−1 treatments during digestion with alpha-amylase and amyloglucosidase digestion. Phosphorus application (especially the 46 kg P ha−1 treatments) significantly increased the relative expression of genes related to starch synthesis (especially during early to mid-grain filling) and starch degradation (especially during mid- and late grain filling). Phosphorus application also increased the transcript abundance of amylase genes at the periphery of the endosperm. We propose that P application, especially the 46 kg P ha−1 treatment, enhanced channels in wheat starch granules. These channels facilitated the transport of substances required for starch biosynthesis, thus increasing starch accumulation in wheat endosperm. These results provide insight into the potential mechanisms through which P influences the microstructure and biosynthesis of wheat starch.

4 Enhancement of Germination, Seedling Growth, and Oxidative Metabolism of Barley under Simulated Acid Rain Stress by Exogenous Trehalose

This study investigated the effects of simulated acid rain on germination, seedling growth, and oxidative metabolism in barley (Hordeum vulgare L.). Barley seeds were separately soaked in trehalose solutions of 5, 10, and 15 mM concentration or distilled water (the control). Results showed inhibited seed germination, increased foliar damage, decreased chlorophyll content, damaged roots, and delayed seedlings growth in barley when exposed to acid rain at pH 3.0. Although the treatment with acid rain increased the activities of peroxidase, catalase, and plasma membrane H+-ATPase, membrane permeability and malondialdehyde content still increased significantly. However, the addition of exogenous trehalose significantly alleviated the negative effect of acid rain on growth inhibition of barley and increased total leaf chlorophyll due to an increase of chlorophyll a content. Trehalose also increased catalase and peroxidase activity, which led to an increase in the antioxidant capacity and a balance in production and scavenging of free radicals. Plasma membrane H+-ATPase activities of roots and leaves also increased with trehalose and maintained stable pH of the cytoplasm of roots and leaf cells under low pH. The 10 mM trehalose pretreatment was enough to alleviative the negative effects of acid rain in barley

5 Genome-Wide Comparative Analysis of Flowering-Related Genes in Arabidopsis, Wheat, and Barley

Early flowering is an important trait influencing grain yield and quality in wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) in short-season cropping regions. However, due to large and complex genomes of these species, direct identification of flowering genes and their molecular characterization remain challenging. Here, we used a bioinformatic approach to predict flowering-related genes in wheat and barley from 190 known Arabidopsis (Arabidopsis thaliana (L.) Heynh.) flowering genes. We identified 900 and 275 putative orthologs in wheat and barley, respectively. The annotated flowering-related genes were clustered into 144 orthologous groups with one-to-one, one-to-many, many-to-one, and many-to-many orthology relationships. Our approach was further validated by domain and phylogenetic analyses of flowering-related proteins and comparative analysis of publicly available microarray data sets for in silico expression profiling of flowering-related genes in 13 different developmental stages of wheat and barley. These further analyses showed that orthologous gene pairs in three critical flowering gene families (PEBP, MADS, and BBX) exhibited similar expression patterns among 13 developmental stages in wheat and barley, suggesting similar functions among the orthologous genes with sequence and expression similarities. The predicted candidate flowering genes can be confirmed and incorporated into molecular breeding for early flowering wheat and barley in short-season cropping regions.

6 Genomic, Biochemical, and Modeling Analyses of Asparagine Synthetases from Wheat

Asparagine synthetase activity in cereals has become an important issue with the discovery that free asparagine concentration determines the potential for formation of acrylamide, a probably carcinogenic processing contaminant, in baked cereal products. Asparagine synthetase catalyses the ATP-dependent transfer of the amino group of glutamine to a molecule of aspartate to generate glutamate and asparagine. Here, asparagine synthetase-encoding polymerase chain reaction (PCR) products were amplified from wheat (Triticum aestivum) cv. Spark cDNA. The encoded proteins were assigned the names TaASN1, TaASN2, and TaASN3 on the basis of comparisons with other wheat and cereal asparagine synthetases. Although very similar to each other they differed slightly in size, with molecular masses of 65.49, 65.06, and 66.24 kDa, respectively. Chromosomal positions and scaffold references were established for TaASN1, TaASN2, and TaASN3, and a fourth, more recently identified gene, TaASN4. TaASN1, TaASN2, and TaASN4 were all found to be single copy genes, located on chromosomes 5, 3, and 4, respectively, of each genome (A, B, and D), although variety Chinese Spring lacked a TaASN2 gene in the B genome. Two copies of TaASN3 were found on chromosome 1 of each genome, and these were given the names TaASN3.1 and TaASN3.2. The TaASN1, TaASN2, and TaASN3 PCR products were heterologously expressed in Escherichia coli (TaASN4 was not investigated in this part of the study). Western blot analysis identified two monoclonal antibodies that recognized the three proteins, but did not distinguish between them, despite being raised to epitopes SKKPRMIEVAAP and GGSNKPGVMNTV in the variable C-terminal regions of the proteins. The heterologously expressed TaASN1 and TaASN2 proteins were found to be active asparagine synthetases, producing asparagine and glutamate from glutamine and aspartate. The asparagine synthetase reaction was modeled using SNOOPY® software and information from the BRENDA database to generate differential equations to describe the reaction stages, based on mass action kinetics. Experimental data from the reactions catalyzed by TaASN1 and TaASN2 were entered into the model using Copasi, enabling values to be determined for kinetic parameters. Both the reaction data and the modeling showed that the enzymes continued to produce glutamate even when the synthesis of asparagine had ceased due to a lack of aspartate.

7 Comparative Transcriptome Profiles of Near-Isogenic Hexaploid Wheat Lines Differing for Effective Alleles at the 2DL FHB Resistance QTL

Fusarium head blight (FHB), caused by the fungus Fusarium graminearum, represents one of the major wheat diseases worldwide, determining severe yield losses and reduction of grain quality due to the accumulation of mycotoxins. The molecular response associated with the wheat 2DL FHB resistance QTL was mined through a comprehensive transcriptomic analysis of the early response to F. graminearum infection, at 3 days post-inoculation, in spikelets and rachis. The analyses were conducted on two near isogenic lines (NILs) differing for the presence of the 2DL QTL (2-2618, resistant 2DL+ and 2-2890, susceptible null). The general response to fungal infection in terms of mRNAs accumulation trend was similar in both NILs, even though involving an higher number of DEGs in the susceptible NIL, and included down-regulation of the primary and energy metabolism, up-regulation of enzymes implicated in lignin and phenylpropanoid biosynthesis, activation of hormons biosynthesis and signal transduction pathways and genes involved in redox homeostasis and transcriptional regulation. The search for candidate genes with expression profiles associated with the 2DL QTL for FHB resistance led to the discovery of processes differentially modulated in the R and S NILs related to cell wall metabolism, sugar and JA signaling, signal reception and transduction, regulation of the redox status and transcription factors. Wheat FHB response-related miRNAs differentially regulated were also identified as putatively implicated in the superoxide dismutase activities and affecting genes regulating responses to biotic/abiotic stresses and auxin signaling. Altered gene expression was also observed for fungal non-codingRNAs. The putative targets of two of these were represented by the wheat gene WIR1A, involved in resistance response, and a gene encoding a jacalin-related lectin protein, which participate in biotic and abiotic stress response, supporting the presence of a cross-talk between the plant and the fungus.

这篇文章有漏引嫌疑，通过转录组研究2DL QTL已经有几篇了，这篇又引用了几篇呢。。。。

8 Impact of Timing and Method of Virus Inoculation on the Severity of Wheat Streak Mosaic Disease

Wheat streak mosaic virus (WSMV), transmitted by the wheat curl mite Aceria tosichella, frequently causes significant yield loss in winter wheat throughout the Great Plains of the United States. A field study was conducted in the 2013–14 and 2014–15 growing seasons to compare the impact of timing of WSMV inoculation (early fall, late fall, or early spring) and method of inoculation (mite or mechanical) on susceptibility of winter wheat cultivars Mace (resistant) and Overland (susceptible). Relative chlorophyll content, WSMV incidence, and yield components were determined. The greatest WSMV infection occurred for Overland, with the early fall inoculations resulting in the highest WSMV infection rate (up to 97%) and the greatest yield reductions relative to the control (up to 94%). In contrast, inoculation of Mace resulted in low WSMV incidence (1 to 28.3%). The findings from this study indicate that both method of inoculation and wheat cultivar influenced severity of wheat streak mosaic; however, timing of inoculation also had a dramatic influence on disease. In addition, mite inoculation provided much more consistent infection rates and is considered a more realistic method of inoculation to measure disease impact on wheat cultivars.

9 A Genome-Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race-Specific Genes in North American Spring Wheat

Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. triticihistorically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in contemporary North American spring wheat, genome-wide association analysis (GWAS) was conducted on an association mapping panel comprised of 250 elite lines. The lines were evaluated in separate nurseries each inoculated with a different P. graminis f. sp. tritici race for 3 years (2013, 2015, and 2016) at Rosemount, Minnesota allowing the evaluation of race-specificity separate from the effect of environment. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNPs chip were used to perform association analysis. We observed often negative and sometimes weak correlations between responses to different races that highlighted the abundance of race-specific resistance and the inability to predict the response of the lines across races. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes (Sr6, Sr7a, and Sr9b) except for race QFCSC where a strong association was detected on chromosome arm 1AL. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, Sr25, Sr31, and Sr57 (Lr34) in this germplasm based on phenotypic and marker data. We found over half of the panel possessed three or more Sr genes, and most commonly included various combinations of Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, and Sr57. Most of these genes confer resistance to specific P. graminis f. sp. tritici races accounting for the prevalent stem rust resistance in North American spring wheat.

10 Identification and Expression Analysis of Wheat TaGF14 Genes

The 14-3-3 gene family members play key roles in various cellular processes. However, little is known about the numbers and roles of 14-3-3 genes in wheat. The aims of this study were to identify TaGF14 numbers in wheat by searching its whole genome through blast, to study the phylogenetic relationships with other plant species and to discuss the functions of TaGF14s. The results showed that common wheat harbored 20 TaGF14 genes, located on wheat chromosome groups 2, 3, 4, and 7. Out of them, eighteen TaGF14s are non-ε proteins, and two wheat TaGF14 genes, TaGF14i and TaGF14f, are ε proteins. Phylogenetic analysis indicated that these genes were divided into six clusters: cluster 1 (TaGF14d, TaGF14g, TaGF14j, TaGF14h, TaGF14c, and TaGF14n); cluster 2 (TaGF14k); cluster 3 (TaGF14b, TaGF14l, TaGF14m, and TaGF14s); cluster 4 (TaGF14a, TaGF14e, and TaGF14r); cluster 5 (TaGF14i and TaGF14f); and cluster 6 (TaGF14o, TaGF14p, TaGF14q, and TaGF14t). Tissue-specific gene expressions suggested that all TaGF14s were likely constitutively expressed, except two genes, i.e., TaGF14p and TaGF14f. And the highest amount of TaGF14transcripts were observed in developing grains at 20 days post anthesis (DPA), especially for TaGF14j and TaGF14l. After drought stress, five genes, i.e., TaGF14c, TaGF14d, TaGF14g, TaGF14h, and TaGF14j, were up-regulated expression under drought stress for both 1 and 6 h, suggesting these genes played vital role in combating against drought stress. However, all the TaGF14s were down-regulated expression under heat stress for both 1 and 6 h, indicating TaGF14smay be negatively associated with heat stress by reducing the expression to combat heat stress or through other pathways. These results suggested that cluster 1, e.g., TaGF14j, may participate in the whole wheat developing stages, e.g., grain-filling (starch biosynthesis) and may also participate in combating against drought stress. Subsequently, a homolog of TaGF14j, TaGF14-JM22, were cloned by RACE and used to validate its function. Immunoblotting results showed that TaGF14-JM22 protein, closely related to TaGF14d, TaGF14g, and TaGF14j, can interact with AGP-L, SSI, SSII, SBEIIa, and SBEIIb in developing grains, suggesting that TaGF14s located on group 4 may be involved in starch biosynthesis. Therefore, it is possible to develop starch-rich wheat cultivars by modifying TaGF14s.

11 Towards a genetic road map of wheat-processing quality

The elucidation of wheat-quality genetics may be seen metaphorically as a road map to greater knowledge, and also as an interlocking jigsaw puzzle. Major genes relevant to the attributes needed for wheat-processing quality have been identified, namely, protein content, grain hardness, milling yield, dough strength, dough extensibility, baking quality, starch-paste viscosity and nutritional value.

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

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

13 Fitness traits of deoxynivalenol and nivalenol-producing Fusarium graminearum species complex strains from wheat

Fusarium graminearum of the 15-acetyl(A)deoxynivalenol(DON) chemotype is the main cause of Fusarium head blight (FHB) of wheat in south of Brazil. However, 3-ADON and nivalenol(NIV) chemotypes in other members of the species complex have been found in wheat. To improve our understanding of the pathogen biology and ecology, we assessed a range of fitness-related traits in a sample of 30 strains representatives of 15-ADON (F. graminearum), 3-ADON (F. cortaderiae and F. austroamericanum) and NIV (F. meridionale and F. cortaderiae). These included: perithecia formation on three cereal-based substrates, mycelial growth at two suboptimal temperatures, sporulation and germination, pathogenicity towards a susceptible and a moderately resistant cultivar and sensitivity to tebuconazole. The most important trait favoring F. graminearum was a two times higher sexual fertility (> 40% PPI = perithecia production index) than the other species (< 30% PPI); PPI varied among substrates (maize > rice > wheat). In addition, sensitivity to tebuconazole appeared lower in F. graminearum which had the only strain with EC50 > 1 ppm. In the pathogenicity assays, the DON-producers were generally more aggressive (1.5 to 2 × higher final severity) towards the two cultivars, with 3-ADON or 15-ADON leading to higher area under the severity curve than the NIV strains in the susceptible and moderately resistant cv., respectively. There was significant variation among strains of a same species with regards asexual fertility (mycelial growth, macroconidia production and germination), which suggested a strain- rather than a species-specific difference. These results contribute new knowledge to improve our understanding of the pathogen-related traits that may explain the dominance of certain members of the species complex in specific wheat agroecosystems.

14 The future of CRISPR technologies in agriculture

Conventional plant breeding is unlikely to meet increasing food demands and other environmental challenges. By contrast, CRISPR technology is erasing barriers to genome editing and could revolutionize plant breeding. However, to fully benefit from the CRISPR revolution, we should focus on resolving its technical and regulatory uncertainties.

15 Asparagine synthetase genes (AsnS1 and AsnS2) in durum wheat: structural analysis and expression under nitrogen stress

Wheat is one of the most widely grown cereal crops based on the amount of calories it provides in the human diet. Durum wheat (Triticum turgidum ssp. durum) is largely used for production of pasta and other products. In order to use genetic knowledge to improve the understanding of N-use efficiency, we carried out, for the first time in durum wheat, the isolation and the characterization of four members of the asparagine synthetase (AsnS) gene family. Phylogenetic inference clustered the Ttu-AsnS1 (1.1 and 1.2) and Ttu-AsnS2 (2.1 and 2.2) genes in AsnS gene class I, which is present in monocots and dicots. Class I genes underwent a subsequent duplication leading to the formation of two subgroups. Plants of Svevo cultivar were grown under N-stress conditions and expression of the four AsnS genes was investigated at three developmental stages (seedling, booting, and late milk development), crucial for N absorption, assimilation and remobilization. AsnS1 genes were down-regulated in N-stressed roots, stems and leaves during seedling growth and booting, but seemed to play a role in N remobilization in flag leaves during grain filling. AsnS2 genes were scarcely expressed in roots, stems, and leaves. In N-stressed spikes there was no differential expression in any of the genes. The genes were mapped in silico using a durum wheat SNP map, assigning Ttu-AsnS1 genes to chromosome 5 and Ttu-AsnS2 to chromosome 3. These findings provide a better understanding of the role of ASN genes in response to N stress in durum wheat.

16 A new opening for wheat seed production

Crop plant domestication has targeted a variety of traits, including synchronous development of ovules and stamens to maximize fertilization and seed production. In wheat, with its autogamous, or self-fertilizing, flowers, this is very attractive for guaranteeing yield but extremely frustrating for a researcher trying to cross individuals of distinct genotypes, and even more so for a breeder trying to generate hybrids. Now, Okada et al. (2017) have provided a turning point by characterizing the developmental physiology of wheat florets opening after a few days post-anthesis (‘second opening’). This additional opportunity for pollination facilitates out-crossing, and provides a method to further understand the regulation of wheat flower architecture and development.

17 Unfertilized ovary pushes wheat flower open for cross-pollination

Bread wheat is strongly autogamous; however, an opportunity for outcrossing occurs when self-pollination fails and florets open. The first phase of floret opening at anthesis is short and induced by lodicule turgidity. Some wheat florets re-open post-anthesis for several days, known as the 'second opening', for which the underlying mechanisms are largely unknown. We performed detailed physiological, anatomical, and histological investigations to understand the biological basis of the flower opening process. Wheat florets were observed open when the ovary was unfertilized. Unfertilized ovaries significantly increased in radial size post-anthesis, pushing the lemma and palea apart to open the florets. The absence of fertile pollen was not directly linked to this, but anther filament elongation coincided with initiation of ovary swelling. The pericarp of unfertilized ovaries did not undergo degeneration as normally seen in developing grains, instead pericarp cells remained intact and enlarged, leading to increased ovary radial size. This is a novel role for the ovary pericarp in wheat flower opening, and the knowledge is useful for facilitating cross-pollination in hybrid breeding. Ovary swelling may represent a survival mechanism in autogamous cereals such as wheat and barley, ensuring seed set in the absence of self-fertilization and increasing genetic diversity through cross-pollination.

18 Mapping and validation of a new QTL for adult-plant resistance to powdery mildew in Chinese elite bread wheat line Zhou8425B

Zhou8425B is an elite wheat (Triticum aestivum L.) line widely used as a parent in Chinese wheat breeding programs. Identification of genes for adult-plant resistance (APR) to powdery mildew in Zhou8425B is of high importance for continued controlling the disease. In the current study, the high-density Illumina iSelect 90K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for APR to powdery mildew in 244 recombinant inbred lines derived from the cross Zhou8425B/Chinese Spring. Inclusive composite interval mapping identified QTL on chromosomes 1B, 3B, 4B, and 7D, designated as QPm.caas-1BL.1, QPm.caas-3BS, QPm.caas-4BL.2, and QPm.caas-7DS, respectively. Resistance alleles at the QPm.caas-1BL.1, QPm.caas-3BS, and QPm.caas-4BL.2 loci were contributed by Zhou8425B, whereas that at QPm.caas-7DS was from Chinese Spring. QPm.caas-3BS, likely to be a new APR gene for powdery mildew resistance, was detected in all four environments. One SNP marker closely linked to QPm.caas-3BS was transferred into a semi-thermal asymmetric reverse PCR (STARP) marker and tested on 103 commercial wheat cultivars derived from Zhou8425B. Cultivars with the resistance allele at the QPm.caas-3BSlocus had averaged maximum disease severity reduced by 5.3%. This STARP marker can be used for marker-assisted selection in improvement of the level of powdery mildew resistance in wheat breeding.

19 A new leaf rust resistance gene Lr79 mapped in chromosome 3BL from the durum wheat landrace Aus26582

Aus26582, a durum wheat landrace from the A. E. Watkins Collection, showed seedling resistance against durum-specific and common wheat-specific Puccinia triticina (Pt) pathotypes. Genetic analysis using a recombinant inbred line (RIL) population developed from a cross between Aus26582 and the susceptible parent Bansi with Australian Pt pathotype showed digenic inheritance and the underlying loci were temporarily named LrAW2 and LrAW3. LrAW2 was located in chromosome 6BS and this study focused on characterisation of LrAW3 using RILs lacking LrAW2. LrAW3 was incorporated into the DArTseq map of Aus26582/Bansi and was located in chromosome 3BL. Markers linked with LrAW3 were developed from the chromosome survey sequence contig 3B_10474240 in which closely-linked DArTseq markers 1128708and 3948563 were located. Although bulk segregant analysis (BSA) with the 90 K Infinium array identified 51 SNPs associated with LrAW3, only one SNP-derived KASP marker mapped close to the locus. Deletion bin mapping of LrAW3-linked markers located LrAW3 between bins 3BL11-0.85-0.90 and 3BL7-0.63. Since no other all stage leaf rust resistance gene is located in chromosome 3BL, LrAW3 represented a new locus and was designated Lr79. Marker sun786 mapped 1.8 cM distal to Lr79 and Aus26582 was null for this locus. However, the marker can be reliably scored as it also amplifies a monomorphic fragment that serves as an internal control to differentiate the null status of Aus26582 from reaction failure. This marker was validated among a set of durum and common wheat cultivars and was shown to be useful for marker-assisted selection of Lr79 at both ploidy levels.

20 Targeted Haplotype Comparisons between South African Wheat Cultivars Appear Predictive of Pre-harvest Sprouting Tolerance

Pre-harvest sprouting (PHS) has been a serious production constraint for over two decades, especially in the summer rainfall wheat production regions of South Africa. It is a complex genetic trait controlled by multiple genes, which are significantly influenced by environmental conditions. This complicates the accurate prediction of a cultivar's stability in terms of PHS tolerance. A number of reports have documented the presence of major QTL on chromosomes 3A and 4A of modern bread wheat cultivars, which confer PHS tolerance. In this study, the SSR marker haplotype combination of chromosomes 3A and 4A of former and current South African cultivars were compared with the aim to select for improved PHS tolerance levels in future cultivars. A total of 101 wheat cultivars, including a susceptible cultivar and five international tolerant sources, were used in this study. These cultivars and donors were evaluated for their PHS tolerance by making use of a rain simulator. In addition, five seeds of each entry were planted out into seedling trays and leaf material harvested for DNA isolation. A modified CTAB extraction method was used before progressing to downstream PCR applications. Eight SSR markers targeted from the well-characterized 3A and 4A QTL regions associated with PHS tolerance, were used to conduct targeted haplotype analysis. Additionally, recently published KASP SNP markers, which identify the casual SNP mutations within the TaPHS1 gene, were used to genotype the germplasm. The haplotype marker data and phenotypic PHS data were compared across all cultivars and different production regions. A relative change in observed phenotypic variation percentage was obtained per marker allele and across marker haplotype combinations when compared to the PHS susceptible cultivar, Tugela-DN. Clear favorable haplotypes, contributing 40–60% of the variation for PHS tolerance, were identified for QTL 3A and 4A. Initial analyses show haplotype data appear to be predictive of PHS tolerance status and germplasm can now be selected to improve PHS tolerance. These haplotype data are the first of its kind for PHS genotyping in South Africa. In future, this can be used as a tool to predict the possible PHS tolerance range of a new cultivar.

21 Irrigation and Nitrogen Regimes Promote the Use of Soil Water and Nitrate Nitrogen from Deep Soil Layers by Regulating Root Growth in Wheat

Unreasonably high irrigation levels and excessive nitrogen (N) supplementation are common occurrences in the North China Plain that affect winter wheat production. Therefore, a 6-yr-long stationary field experiment was conducted to investigate the effects of irrigation and N regimes on root development and their relationship with soil water and N use in different soil layers. Compared to the non-irrigated treatment (W0), a single irrigation at jointing (W1) significantly increased yield by 3.6–45.6%. With increases in water (W2, a second irrigation at flowering), grain yield was significantly improved by 14.1–45.3% compared to the W1 treatments during the drier growing seasons (2010–2011, 2012–2013, and 2015–2016). However, under sufficient pre-sowing soil moisture conditions, grain yield was not increased, and water use efficiency (WUE) decreased significantly in the W2 treatments during normal precipitation seasons (2011–2012, 2013–2014, and 2014–2015). Irrigating the soil twice inhibited root growth into the deeper soil depth profiles and thus weakened the utilization of soil water and NO3-N from the deep soil layers. N applications increased yield by 19.1–64.5%, with a corresponding increase in WUE of 66.9–83.9% compared to the no-N treatment (N0). However, there was no further increase in grain yield and the WUE response when N rates exceeded 240 and 180 kg N ha−1, respectively. A N application rate of 240 kg ha−1 facilitated root growth in the deep soil layers, which was conducive to utilization of soil water and NO3-N and also in reducing the residual NO3-N. Correlation analysis indicated that the grain yield was significantly positively correlated with soil water storage (SWS) and nitrate nitrogen accumulation (SNA) prior to sowing. Therefore, N rates of 180–240 kg ha−1 with two irrigations can reduce the risk of yield loss that occurs due to reduced precipitation during the wheat growing seasons, while under better soil moisture conditions, a single irrigation at jointing was effective and more economical.

22 Genome-Wide Association Studies and Comparison of Models and Cross-Validation Strategies for Genomic Prediction of Quality Traits in Advanced Winter Wheat Breeding Lines

The aim of the this study was to identify SNP markers associated with five important wheat quality traits (grain protein content, Zeleny sedimentation, test weight, thousand-kernel weight, and falling number), and to investigate the predictive abilities of GBLUP and Bayesian Power Lasso models for genomic prediction of these traits. In total, 635 winter wheat lines from two breeding cycles in the Danish plant breeding company Nordic Seed A/S were phenotyped for the quality traits and genotyped for 10,802 SNPs. GWAS were performed using single marker regression and Bayesian Power Lasso models. SNPs with large effects on Zeleny sedimentation were found on chromosome 1B, 1D, and 5D. However, GWAS failed to identify single SNPs with significant effects on the other traits, indicating that these traits were controlled by many QTL with small effects. The predictive abilities of the models for genomic prediction were studied using different cross-validation strategies. Leave-One-Out cross-validations resulted in correlations between observed phenotypes corrected for fixed effects and genomic estimated breeding values of 0.50 for grain protein content, 0.66 for thousand-kernel weight, 0.70 for falling number, 0.71 for test weight, and 0.79 for Zeleny sedimentation. Alternative cross-validations showed that the genetic relationship between lines in training and validation sets had a bigger impact on predictive abilities than the number of lines included in the training set. Using Bayesian Power Lasso instead of GBLUP models, gave similar or slightly higher predictive abilities. Genomic prediction based on all SNPs was more effective than prediction based on few associated SNPs.

23 Plasma membrane proteome analysis identifies a role of barley Membrane Steroid Binding Protein in root architecture response to salinity

Although physiological consequences of plant growth under saline conditions have been well described, understanding the core mechanisms conferring plant salt adaptation has only started. We target the root plasma membrane (PM) proteomes of two barley varieties, cvs. Steptoe and Morex, with contrasting salinity tolerance. In total, 588 PM proteins were identified by mass spectrometry, of which 182 were either cultivar- or salinity stress-responsive. Three candidate proteins with increased abundance in the tolerant cv. Morex were involved either in sterol-binding (a GTPase-activating protein for the ADP ribosylation factor, ZIGA2, and a membrane steroid binding protein, MSBP) or in phospholipid synthesis (phosphoethanolamine methyltransferase, PEAMT). Overexpression of barley MSBP conferred salinity tolerance to yeast cells, while knock-out of the heterologous AtMSBP1 increased salt sensitivity in Arabidopsis. Atmsbp1 plants showed a reduced number of lateral roots under salinity and root tip-specific expression of barley MSBPin Atmsbp1 complemented this phenotype. In barley, an increased abundance of MSBP correlates with reduced root length and lateral root formation as well as increased levels of auxin under salinity being stronger in the tolerant cv. Morex. Hence, we concluded the involvement of MSBP in phytohormone-directed adaptation of root architecture in response to salinity.