Mapping resistance genes conferring tolerance to RWA (Diuraphis noxia) in barley (Hordeum vulgare)

The Russian wheat aphid (RWA) is one of the most aggressive pests of barley and wheat. The outbreak of RWA occurred in Argentina in 2008 caused serious damage to barley cultivars. The most effective and sustainable method of RWA control is to identify new resistance genes. The purpose of the current research was to map RWA resistance genes in a set of double haploid (DH) lines of the Oregon-Wolfe Barley (OWB) mapping population derived from the cross between OWB_DOM and OWB_REC. The DH and both parental lines were screened for antixenosis, tolerance and antibiosis to RWA. There was significant variation among the DH lines in most of the traits studied. However, only tolerance resulted in significant quantitative trait loci (QTLs) associated with the molecular markers. Two main QTLs were identified. These explained 90 and 79 % of the variability of foliar area and chlorophyll content, respectively, of infested and control plants. The initial and final foliar area and the variation in foliar area were associated with the same molecular markers on chromosome 2H (BmAc0125, Vrs1, BmAc0144f and BmAg0113e). The positive alleles were provided by OWB_DOM. The content of chlorophyll was associated with the marker loci WMC1E8, MWG912, ABC261, MWG2028 and Blp on chromosome 1H, with the positive alleles provided by OWB_REC. Both parents contributed to different tolerance traits, with foliar area and chlorophyll content remaining as the plant traits most affected by aphid feeding. The QTLs found in this population are new RWA resistance loci. A sequence homology search was performed to derive the putative function of the genes linked to the QTLs.     

Mapping and candidate gene identification of loci induced by phytohormones in barley (Hordeum vulgare L.)

Phytohormones, a group of structurally unrelated small molecules are plant-signalling compounds that trigger induced resistance against certain pathogens and herbivores. The hormones jasmonic acid (JA), ABA, salicilic acid (SA) and ethylene (ET) are known to play major roles in regulating plant defence responses. In order to determine the changes in growth and in the chlorophyll content induced by the exogenous application of these elicitors, a set of DH lines of the Oregon-Wolfe Barley mapping population, previously screened to locate aphid resistant genes, was investigated. The aim of the current research was to map the induced defence genes and to reveal the relationship with aphid resistance. There were highly significant differences between controls and hormone treated plants in the aerial fresh and dry weights (AFW, ADW), the foliar area (FA) and the root dry weight (RDW). More than 15 JA and ET-induced lines exceeded the chlorophyll (Ch) values of their controls. Most of the plant traits were associated with the same genetic windows on chromosomes 3H, 5H and 7H in the controls and hormone treated plants. QTL(s) identified on chromosome 3H and 5H explained most of the variation of AFW, ADW, FA and RDW of controls and treated plants. QTL(s) located on chromosome 5H were associated with the variation of chlorophyll contents on JA-treated plants. The Ch in ET and ABA-treated plants was associated with two different regions on chromosome 7H. One of the latter genetic windows also explained the variation of RDW of ET- and ABA-treated plants. A sequence homology search was performed to derive the putative function of the genes linked to the QTLs. Several QTLs were identified located close to aphid resistance genes previously mapped. This is the first report of genes associated with hormone response in barley that could be involved with insect resistance. Those recombinant lines carrying the appropriate alleles could be useful for breeding barley to enlarge the genetic base of defence against stress.     

Developing new markers and QTL mapping for greenbug resistance in sorghum [Sorghum bicolor (L.) Moench]

Greenbug is a major damaging insect to sorghum production in the United States. Among various virulent greenbug biotypes, biotype I is the most predominant and severe for sorghum. To combat with the damaging pest, greenbug resistant sources were obtained from screening sorghum germplasm collection. This experiment was conducted to identify the genomic regions contributing resistance to greenbug biotype I in a sorghum accession, PI 607900. An F₂ mapping population consisting of 371 individuals developed from a cross of the resistant line with an elite cultivar, BTx623 (susceptible) were tested and scored for their response to greenbug feeding in the greenhouse. Significant differences in resistance were observed between the two parental lines and among their F₂ progeny in response to greenbug feeding at 7, 10, 14 and 21 days after infestation. A linkage map spanning a total length of 729.5 cM across the genome was constructed with 102 polymorphic SSR markers (69 genomic and 33 EST SSRs). Of those microsatellite markers, 48 were newly developed during this study, which are a useful addition for sorghum genotyping and genome mapping. Single marker analysis revealed 29 markers to be significantly associated with the plant response to greenbug feeding damage. The results from interval mapping, composite interval mapping and multiple interval mapping analyses identified four major QTLs for greenbug resistance on chromosome 9. These QTLs collectively accounted for 34–82 % of the phenotypic variance in greenbug resistance. Minor QTLs located on chromosome 3 explained 1 % of the phenotypic variance in greenbug resistance. The major allele for greenbug resistance was on chromosome 9 close to receptor-like kinase Xa21-binding protein 3. These markers are useful to screen more resistant genotypes. Furthermore, the markers tagged to QTL regions can be used to enhance the sorghum breeding program for greenbug resistance through marker-assisted selection and map-based cloning.     

Genetic markers for doubled haploid response in barley

In order to analyse the genetic control of anther culture response in barley, a doubled-haploid (DH) population from the cross between a medium responsive cultivar ‘Dobla’ and the model cultivar ‘Igri’ was produced. A linkage map was constructed with 91 markers. A sub-population of 41 lines was characterised for different components of the anther culture response, and was used for quantitative trait loci (QTL) analysis. The vrs1 locus region on chromosome 2H, which determines inflorescence row type, was coincident with the largest putative QTL for number of embryos (nEMB) and albino plants. A region of chromosome 6H was associated with QTLs for nEMB and green plants. QTLs for number and percentage of green plants were located on the long arm of chromosome 5H. Therefore, new QTLs for main components of barley anther culture response were identified on chromosomes 2H, 5H and 6H, indicating that anther culture response in barley could be controlled by relative few genes of large effect. This work is a useful step towards the identification of new regions on the barley genome that could be associated with fundamental biological process implicated in the anther culture response.     

Quantitative trait loci for scald resistance in barley localized by a non-interval mapping procedure

Three quantitative trait loci (QTL) for scald resistance in barley were identified and mapped in relation to molecular markers using a population of chromosome doubled‐haploid lines produced from the F₁ generation of a cross between the spring barley varieties ‘Alexis’ and ‘Regatta’. Two field experiments were conducted in Denmark and two in Norway to assess disease resistance. The percentage leaf area covered with scald (Rhynchosporium secalis) ranged from 0 to 40% in the 189 doubled‐haploid (DH) lines analysed. One quantitative trait locus was localized in the centromeric region of chromosome 3H, Qryn3, using the MAPQTL program. MAPQTL was unable to provide proper localization of the other two resistance genes and so a non‐interval QTL mapping method was used. One was found to be located distally to markers on chromosome 4H (Qryn4) and the other, Qryn6, was located distally to markers on chromosome 6H. The effects of differences between the Qryn3, Qryn4 and Qryn6 alleles in two barley genotypes for the QTL were estimated to be 8.8%, 7.3% and 7.0%, respectively, of leaf covered by scald. No interactions between the QTLs were found.     

Molecular mapping of greenbug (Schizaphis graminum) resistance gene Rsg1 in barley

The greenbug, Schizaphis graminum (Rondani) is an extremely damaging aphid pest of barley (Hordeum vulgare L.) particularly in the southern Great Plains of the USA. The simply inherited, dominant resistance gene Rsg1 is in all greenbug‐resistant US barley cultivars. In this study, we conducted molecular mapping of Rsg1 using an F_2:3 population derived from a cross between the greenbug‐resistant Post 90*4/R015 and susceptible CI2260 inbred lines. Segregation of host responses to greenbug biotype E infestation confirmed that a single dominant gene is responsible for greenbug resistance in Post 90*4/R015. Simple sequence repeat (SSR) markers evenly distributed along the seven barley chromosomes were employed for the construction of a framework genetic map. Linkage analysis placed the Rsg1 locus in the long arm of chromosome 3H (3HL) flanked by SSR markers Bmag0877 and GBM1420 that were 35 cM apart. Polymorphic single‐nucleotide polymorphism (SNP) markers in 3HL were identified from an Illumina GoldenGate SNP assay and used for targeted mapping to locate Rsg1 to an 8.4‐cM interval. Comparative analysis identified syntenic genomic regions in Brachypodium distachyon chromosome 2, in which 37 putative genes were annotated including a NB‐LRR‐type resistance gene homologue that may be a potential candidate gene for the Rsg1 locus of barley. Results from this study offer a starting point for fine mapping and cloning of this aphid resistance gene in barley.     

QTL mapping of net blotch resistance genes in a doubled-haploid population of six-rowed barley

Net blotch, caused by Pyrenophora teres f. teres, is a damaging foliar disease of barley worldwide. It is important to identify resistance germplasm and study their genetics. 'Chevron', a six-rowed barley used as a parent for the production of a doubled haploid (DH) population for mapping of Fusarium head blight (FHB) resistance, was also found to be resistant to net blotch. To map the resistance genes, the population was evaluated for resistance at the seedling stage in a greenhouse. The resistance data showed a two-peak distribution. Through linkage mapping, one resistance gene, tentatively called Rpt, was located on chromosome 6HS flanked by Xksua3b-Xwg719d, which was also detected by QTL mapping. This QTL explained 64% of the phenotypic variance for the resistance in this DH population. In addition, a minor QTL was found on chromosome 2HS defined by Xcdo786-Xabc156a. 'Chevron' and 'Stander' contributed the resistant alleles of Rpt and the 2HS QTL, respectively. Both QTLs together explained nearly 70% of the phenotypic variance. The markers for these QTLs are useful for marker-assisted selection of net blotch resistance in barley breeding.     

QTL-based analysis of heterosis for number of grains per spike in wheat using DH and immortalized F 2 populations

To map quantitative trait loci (QTL) and heterotic loci (HL) related to grain number per spike (GNS), 168 double haploid (DH) populations derived from Huapei?3?×?Yumai?57 and an immortalized F ₂ population (IF ₂) generated by randomly permutated intermating of these DH populations were investigated. Using inclusive composite interval mapping (ICIM), a total of nine and eight significant QTLs for GNS were detected in three different environments in DH and IF ₂ populations, respectively. QTLs on chromosomes?1A, 2B, 3B, and 6A were observed between two populations. Five QTLs were detected on chromosome?1A. Of these QTLs, QGns1A-1 was a major QTL explaining 31.25?% of phenotypic variation. QGns2B-2 detected on chromosome?2B had the most significant additive effects, explaining 46.75?% of phenotypic variation with the favorable allele contributed by Yumai?57 corresponding to an increase of 5.69?kernels. Mid-parent heterosis of each cross in the IF ₂ population was used to map heterotic quantitative trait loci. A total of 17 HLs were detected. QTLs and HLs on chromosomes?2B and 6A were observed in the IF ₂ population. Three HLs, QHgns1B-2, QHgns2B, and QHgns6A-1, were detected in two environments and expressed stably. These results showed that some intervals on chromosomes?1B, 2B, and 6A play an important role in GNS heterosis in wheat, improving understanding of this phenomenon.     

Segregation distortion in doubled haploid lines of barley (Hordeum vulgare L.) detected by simple sequence repeat (SSR) markers

A total of 147 simple sequence repeat (SSR) markers (including86 barley and 61 wheat microsatellite markers) were tested for their segregation in a doubled haploid (DH) and an F₂ population of barley. The DH population consisted of 71 doubled haploid lines, developed from F₁ plants of a cross between Tadmor and WI2291using isolated microspore culture technique. A genetic linkage map consisting of 43 microsatellite markers was constructed using the DH population. Particularly on chromosome 4H microsatellite markers showed distorted segregation ratios. Segregation of DH lines based on molecular markers were compared with segregation of 92 F₂ lines from the same cross. The proportion of loci deviating from the expected monogenic segregation ratios in the DH population was significantly higher (19/43loci, 44%) than in the F₂ population (7/43 loci, 16%). The deviation was biased towards the WI2291 parent alleles. In line with this observation, WI2291 was found to perform better than Tadmor in regenerating green plantlets with the isolated microspore-culture technique. This revised version was published online in July 2006 with corrections to the Cover Date.     

QTLs identification of crude fat content in brown rice and its genetic basis analysis using DH and two backcross populations

Fat content is a concern for the enhancement of rice for eating, cooking, and storage qualities. To clarify its genetic mechanism, a double haploid (DH) population derived from anther hybrid F₁ of Zhenshan 97B (indica) and Wuyujing 2 (japonica) and two backcross F₁ (BCF₁) populations, which came from the DH lines backcrossing to two parents, were used to scan quantitative trait loci (QTLs) and dissect gene effects for the crude fat content (CFC) in brown rice. Fourteen QTLs were resolved, distributing on chromosomes 1, 3, and 5–9. Three loci were detected repeatedly in two populations, DH or BCF₁. Among these loci, a major QTL, qCFC5, flanking markers RM87 and RM334, was located on chromosome 5, which was detected simultaneously among three populations. The main QTLs had a major role in controlling CFC in brown rice and were modified by several mini-effect QTLs and epistatic affection. Wenjun Liu and Jing Zeng are contributed equally to this paper.     

Characterization of greenbug resistance in barley

The greenbug [Schizaphis graminum (Rondani)] is an extremely damaging pest of barley (Hordeum vulgare L.), particularly in the southern Great Plains of the USA. Winter barley targeted for production in this region should incorporate resistance to greenbug in the form of the resistance gene Rsg1a (in ‘Post 90′) or Rsg2b (in PI 426756). This study was conducted to fully characterize the resistance profile of these two genes against important greenbug biotypes, and to determine which of the two resistance genes is most effective in protecting barley from the greenbug. Eight barley and four wheat cultivars and germplasms were challenged with six greenbug biotypes and damage ratings were recorded for each combination. In five of the six tests, ‘Post 90’ was significantly more resistant than PI 426756 to greenbug feeding damage. Based on the results presented here, we conclude that the resistance gene, Rsg1a, in ‘Post 90’ is the better choice for use in breeding programmes and will provide better protection than Rsg2b against the greenbug.     

Distorted Segregation for Mildew Resistance in Doubled Haploid Lines of Spring Barley

The mildew reactions of the second generation of doubled haploid (DH) plants, derived from anther culture of crosses among three spring barley lines carrying different Mla mildew resistance alleles and the cv. ‘Pallas’, were analyzed by using a set of three European and one Israeli mildew isolate. The results indicated, (1) a significant level of distortion segregation in favour of resistant DH genotypes, which was possibly due to linkage of mildew resistance genes on chromosome 5 with genes for plant regeneration and (2) various degrees of dominance for the different resistance genes studied as well as the possible action of modifier genes.     

Mapping quantitative trait loci for salt tolerance at germination and the seedling stage in barley (Hordeum vulgare L.)

Quantitative trait loci (QTLs) controlling salt tolerance at germination and the seedling stage in barley (Hordeum vulgare L.) were identified by interval mapping analysis using marker information from two doubled haploid (DH) populations derived from the crosses, Steptoe/Morex and Harrington/TR306. Interval mapping analysis revealed that the QTLs for salt tolerance at germination in the DH lines of Steptoe/Morex were located on chromosomes 4 (4H), 6(6H), and 7(5H), and in the DH lines of Harrington/TR306 on chromosomes 5(1H) and 7(5H). In both DH populations, the most effective QTLs were found at different loci on chromosome 7(5H). Genetic linkage between salt tolerance at germination and abscisic acid (ABA) response was found from QTL mapping. The QTLs for the most effective ABA response at germination were located very close to those for salt tolerance on chromosome 7 (5H) in both crosses. The QTLs for salt tolerance at the seedling stage were located on chromosomes 2(2H), 5(1H), 6(6H), and 7(5H) in the DH lines of Steptoe/Morex, and on chromosome 7(5H) in the DH lines of Harrington/TR 306. Their positions were different from those of QTLs controlling salt tolerance at germination, indicating that salt tolerance at germination and at the seedling stage were controlled by different loci. This revised version was published online in July 2006 with corrections to the Cover Date.     

Quantitative trait loci for grain yield and yield components in a cross between a six-rowed and a two-rowed barley

Summary The positions of quantitative trait loci (QTL) for yield and yield components were estimated using a 85-point linkage map and phenotype data from a F₁-derived doubled haploid (DH) population of barley. Yield and its components were recorded in two growing seasons. Highly significant QTL effects were found for all traits at several sites in the genome. A major portion of the QTL was found on chromosome 2. The effect of the alleles in locus v on thousand grain weight and kernels per ear explained 70–80% of the genetic variation in the traits. QTL × year interaction was found for grain yield. Several different QTL were found within the two-rowed DH lines compared to those found in the six-rowed DH lines. Epistasis between locus v and several loci for yield and yield components indicates that genes are expressed differently in the two ear types. This may explain the difficulties of selecting high yielding lines from crosses between two-rowed and six-rowed barley.Abbreviations DH doubled haploid - QTL quantitative trait locus/loci - RAPD random amplified polymorphic DNA - RFLP restriction fragment length polymorphism - T. Prentice Tystofte Prentice - V. Gold Vogelsanger Gold     

Grain dormancy QTL identified in a doubled haploid barley population derived from two non-dormant parents

Grain dormancy provides protection against pre-harvest sprouting (PHS) in cereals. Composite interval mapping and association analyses were performed to identify quantitative trait loci (QTL) contributing grain dormancy in a doubled haploid (DH) barley population (ND24260?×?Flagship) consisting of 321 lines genotyped with DArT markers. Harvest-ripe grain collected from three field experiments was germinated over a 7-day period to determine a weighted germination index for each line. DH lines displaying moderate to high levels of grain dormancy were identified; however, both parental lines were non-dormant and displayed rapid germination within the first two?days of testing. Genetic analysis identified two QTL on chromosome 5H that were expressed consistently in each of the three environments. One QTL (donated by Flagship) was located close to the centromeric region of chromosome 5H (qSDFlag), accounting for up to 15% of the phenotypic variation. A second QTL with a larger effect (from ND24260) was detected on chromosome 5HL (qSDND), accounting for up to 35% of the phenotypic variation. qSDFlag and qSDND displayed an epistatic interaction and DH lines that had the highest levels of grain dormancy carried both genes. We demonstrate that qSDND in the ND24260?×?Flagship DH population is positioned proximal and independent to the well-characterised SD2 region that is associated with both high levels of dormancy and inferior malt quality. This indicates that it should be possible to develop cultivars that combine acceptable malting quality and adequate levels of grain dormancy for protection against PHS by utilizing these alternate QTL.     

Differentiating greenbug resistance genes in barley

The greenbug [Schizaphis graminum (Rondani)] is an extremely damaging pest of barley (Hordeum vulgare L), particularly in the southern Great Plains of the USA. Two greenbug resistance genes, Rsg1a (in ‘Post 90’) and Rsg2b (in PI 426756), available for developing resistant barley cultivars, have similar phenotypes when challenged by various greenbug biotypes. This study was conducted to separate these two resistance genes via differential plant reactions to a recently collected field isolate of greenbug. Four barley entries and one wheat germplasm were challenged with two greenbug isolates and damage ratings were recorded for each combination. One greenbug isolate used in this study (TX1) was able to differentiate Rsg1a from Rsg2b through dramatically different plant responses (Rsg2b conferred resistance, Rsg1a did not). The results indicate the potential vulnerability of greenbug resistance genes in barley. Based on these and other reported results, we propose that gene symbol designations for greenbug resistance in barley be changed from Rsg1a to Rsg1 and Rsg2b to Rsg2.     

Genetic regulation of growth and nutrient content under phosphorus deficiency in the wild barley introgression library S42IL

Phosphorus (P) is an important macronutrient required for plant growth and yield formation. Since decades, breeders aim to optimize P efficiency in crops. We studied a set of 47 wild barley (Hordeum vulgare ssp. spontaneum, Hsp) introgression lines (ILs) in hydroponic culture to identify quantitative trait loci (QTLs) improving growth and nutrient content under P deficiency. Applying a mixed model analysis, a total of 91 independent QTLs were located among 39 ILs, of which 64 QTLs displayed trait‐improving Hsp effects. For example, an unknown Hsp allele on barley chromosome 4H increased shoot dry weight under P deficiency in three overlapping ILs by 25.9%. Likewise, an Hsp allele on barley chromosome 6H increased root dry weight under P deficiency in two overlapping ILs by 27.6%. In total, 31 QTLs confirmed Hsp effects already identified in previous field and glasshouse experiments with the same ILs. We conclude that wild barley contains numerous trait‐improving QTL alleles, which are active under P deficiency. In future, the underlying genes can be subjected to cloning and, simultaneously, used in elite barley breeding.     

QTL analysis of black rot resistance in cabbage using newly developed EST-SNP markers

One hundred sixty-one EST-SNP markers were newly developed for analysis of QTLs for resistance to black rot caused by Xanthomonas campestris pv. campestris by determining EST sequences of a resistant line obtained from cabbage ‘Early Fuji’ and a susceptible broccoli line. A linkage map consisting of nine linkage groups was constructed with a total of 209 markers, including these new SNP markers and previously reported DNA markers. F₂ plants grown in a field for 1 month were inoculated by spraying bacteria of race 1, and disease severity of each plant was recorded. Three QTLs, i.e., QTL-1, QTL-2, and QTL-3, were detected on linkage group C2, C4 and C5, respectively. QTL-1, which showed the highest LOD score and additive effect, was again detected in another F₂ population used the next year, suggesting QTL-1 to be a major QTL. QTL-2 and QTL-3 could be minor QTLs influenced by environmental factors. The genomic region harboring QTL-1 showed synteny with a region from 5.3 to 7.4 Mb from the short arm end of chromosome 5 of Arabidopsis thaliana, which is rich in TIR-NBS-LRR family genes. The identified SNP markers in QTL-1 are considered to be useful in marker-assisted selection for black rot resistance in Brassica oleracea lines.     

Molecular mapping of QTLs for non-parasitic leaf spot resistance and comparison of half-sib DH populations in spring barley

Quantitative trait loci (QTLs) for resistance against non-parasitic leaf spots (NPLS) were first characterized in a spring barley double haploid population derived from the cross IPZ 24727/Barke (Behn et al., 2004). The aim of the present study was to identify QTLs for NPLS resistance in the half-sibling DH population IPZ 24727/Krona and to compare them with the QTLs of the population IPZ 24727/Barke. An anther culture-derived doubled haploid population of 536 DH lines was developed from the cross IPZ 24727 (resistant)/Krona (susceptible). Field trials were performed over two years in two replications, scoring NPLS and agronomic traits that might interact with NPLS. A molecular linkage map of 1035 cM was constructed based on AFLPs, SSRs and the mlo marker. QTL analyses for NPLS identified three QTLs that accounted for 30% of the phenotypic variation. For comparison of the QTLs from each DH population, a consensus map was generated comprising 277 markers with a length of 1199 cM. In both populations, the QTLs for NPLS mapped to chromosomes 1H, 4H and 7H. A common QTL with a great effect in both populations and over all environments was localized at the mlo locus on chromosome 4H, indicating that the mlo powdery mildew resistance locus has a considerable effect on NPLS susceptibility. The steps necessary to validate the QTLs and to improve the NPLS resistance by breeding were discussed.     

QTL analysis on rice grain appearance quality,as exemplifying the typical events of transgenic or backcrossing breeding

Rice grain shape and yield are usually controlled by multiple quantitative trait loci (QTL). This study used a set of F_9–10 recombinant inbred lines (RILs) derived from a cross of Huahui 3 (Bt/Xa21) and Zhongguoxiangdao, and detected 27 QTLs on ten rice chromosomes. Among them, twelve QTLs responsive for grain shape/ or yield were mostly reproducibly detected and had not yet been reported before. Interestingly, the two known genes involved in the materials, with one insect-resistant Bt gene, and the other disease-resistant Xa21 gene, were found to closely link the QTLs responsive for grain shape and weight. The Bt fragment insertion was firstly mapped on the chromosome 10 in Huahui 3 and may disrupt grain-related QTLs resulting in weaker yield performance in transgenic plants. The introgression of Xa21 gene by backcrossing from donor material into receptor Minghui 63 may also contain a donor linkage drag which included minor-effect QTL alleles positively affecting grain shape and yield. The QTL analysis on rice grain appearance quality exemplified the typical events of transgenic or backcrossing breeding. The QTL findings in this study will in the future facilitate the gene isolation and breeding application for improvement of rice grain shape and yield.