QTL mapping of stripe,leaf and stem rust resistance genes in a Kariega × Avocet S doubled haploid wheat population

Adult plant resistance to stripe (yellow) rust in the wheat cultivar Kariega has previously been ascribed to a major quantitative trait locus (QTL) on each of chromosomes 2B and 7D, along with a number of minor QTL. We have extended both the size of the cv. Kariega × cv. Avocet S mapping population, and the marker coverage within it, by assembling a set of Diversity Array Technology (DArT) markers. This has allowed for the analysis of the genetic basis of the adult plant and seedling resistances to stripe, leaf and stem rust present in the two mapping population parents. The stripe rust reactions of the segregating material were assessed in both field (three scoring dates) and greenhouse experiments. The chromosome 2B QTL became more important than the Lr34/Yr18 complex on chromosome 7D as the plants aged. As the infection progressed, the two QTL explained an increasing proportion of the variance for percentage leaf area infected. The cv. Kariega allele at the minor chromosome 4A QTL had a consistent effect on the severity of stripe rust infection and the overall plant reaction at the earlier scoring dates, but lost importance as the disease progressed. Several rust resistances were detected using an improved greenhouse-based test.     

Powdery mildew resistance and Lr34/Yr18 genes for durable resistance to leaf and stripe rust cosegregate at a locus on the short arm of chromosome 7D of wheat

The incorporation of effective and durable disease resistance is an important breeding objective for wheat improvement. The leaf rust resistance gene Lr34 and stripe rust resistance gene Yr18 are effective at the adult plant stage and have provided moderate levels of durable resistance to leaf rust caused by Puccinia triticina Eriks. and to stripe rust caused by Puccinia striiformis Westend. f. sp. tritici. These genes have not been separated by recombination and map to chromosome 7DS in wheat. In a population of 110 F₇ lines derived from a Thatcher × Thatcher isogenic line with Lr34/Yr18, field resistance to leaf rust conferred by Lr34 and to stripe rust resistance conferred by Yr18 cosegregated with adult plant resistance to powdery mildew caused by Blumeria graminis (DC) EO Speer f. sp. tritici. Lr34 and Yr18 were previously shown to be associated with enhanced stem rust resistance and tolerance to barley yellow dwarf virus infection. This chromosomal region in wheat has now been linked with resistance to five different pathogens. The Lr34/Yr18 phenotypes and associated powdery mildew resistance were mapped to a single locus flanked by microsatellite loci Xgwm1220 and Xgwm295 on chromosome 7DS.     

Genetics of resistance to yellow rust in PBW343 × Kenya Kudu recombinant inbred line population and mapping of a new resistance gene YrKK

Yellow or stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of common wheat (Triticum aestivum L.) worldwide. A recombinant inbred line (RIL) population, derived from the cross PBW343 × Kenya Kudu, was phenotyped for yellow rust reaction in the field at the CIMMYT research station near Toluca, Mexico, during 2010 and 2011. Segregation results indicated the presence of a race-specific resistance gene, temporarily designated as YrKK, in Kenya Kudu that conferred immunity to adult plants in field trials, despite conferring only slight reductions in seedling reactions in greenhouse tests with three Mexican pathotypes. A minimum of four minor genes having additive effects also segregated in the population and were likely derived from both parents. A total of 635 simple sequence repeat (SSR) primers were screened for polymorphism surveys on the parents, and resistant (YrKK-possessing RILs) and susceptible (YrKK-lacking RILs) bulks identified four polymorphic markers. These markers were located on the short arm of chromosome 2B. Genotyping of the entire RIL population identified Xgwm148 and Xwmc474 as the most closely linked proximal and distal flanking SSR markers, with respective genetic distances of 3.6 and 1.8 cM from YrKK. Four yellow rust resistance genes (Yr27, Yr31, Yr41, and YrP81) are located on chromosome 2BS; however, their specificity to pathogen pathotypes and host reactions in seedling and adult plants indicate that YrKK is a new resistance gene.     

Expression of multiple resistance genes enhances tolerance to environmental stressors in transgenic poplar (Populus × euramericana 'Guariento')

Commercial and non-commercial plants face a variety of environmental stressors that often cannot be controlled. In this study, transgenic hybrid poplar (Populus × euramericana 'Guariento') harboring five effector genes (vgb, SacB, JERF36, BtCry3A and OC-I) were subjected to drought, salinity, waterlogging and insect stressors in greenhouse or laboratory conditions. Field trials were also conducted to investigate long-term effects of transgenic trees on insects and salt tolerance in the transformants. In greenhouse studies, two transgenic lines D5-20 and D5-21 showed improved growth, as evidenced by greater height and basal diameter increments and total biomass relative to the control plants after drought or salt stress treatments. The improved tolerance to drought and salt was primarily attributed to greater instantaneous water use efficiency (WUEi) in the transgenic trees. The chlorophyll concentrations tended to be higher in the transgenic lines under drought or saline conditions. Transformed trees in drought conditions accumulated more fructan and proline and had increased Fv/Fm ratios (maximum quantum yield of photosystem II) under waterlogging stress. Insect-feeding assays in the laboratory revealed a higher total mortality rate and lower exuviation index of leaf beetle [Plagiodera versicolora (Laicharting)] larvae fed with D5-21 leaves, suggesting enhanced insect resistance in the transgenic poplar. In field trials, the dominance of targeted insects on 2-year-old D5-21 transgenic trees was substantially lower than that of the controls, indicating enhanced resistance to Coleoptera. The average height and DBH (diameter at breast height) of 2.5-year-old transgenic trees growing in naturally saline soil were 3.80% and 4.12% greater than those of the control trees, but these increases were not significant. These results suggested that multiple stress-resistance properties in important crop tree species could be simultaneously improved, although additional research is needed to fully understand the relationships between the altered phenotypes and the function of each transgene in multigene transformants.     

Analysis of leaf and stripe rust severities reveals pathotype changes and multiple minor QTLs associated with resistance in an Avocet?×?Pastor wheat population

Leaf rust and stripe rust are important diseases of wheat world-wide and deployment of cultivars with genetic resistance is an effective and environmentally sound control method. The use of minor, additive genes conferring adult plant resistance (APR) has been shown to provide resistance that is durable. The wheat cultivar ‘Pastor’ originated from the CIMMYT breeding program that focuses on minor gene-based APR to both diseases by selecting and advancing generations alternately under leaf rust and stripe rust pressures. As a consequence, Pastor has good resistance to both rusts and was used as the resistant parent to develop a mapping population by crossing with the susceptible ‘Avocet’. All 148 F₅ recombinant inbred lines were evaluated under artificially inoculated epidemic environments for leaf rust (3 environments) and stripe rust (4 environments, 2 of which represent two evaluation dates in final year due to the late build-up of a new race virulent to Yr31) in Mexico. Map construction and QTL analysis were completed with 223 polymorphic markers on 84 randomly selected lines in the population. Pastor contributed Yr31, a moderately effective race-specific gene for stripe rust resistance, which was overcome during this study, and this was clearly shown in the statistical analysis. Linked or pleiotropic chromosomal regions contributing to resistance against both pathogens included Lr46/Yr29 on 1BL, the Yr31 region on 2BS, and additional minor genes on 5A, 6B and 7BL. Other minor genes for leaf rust resistance were located on 1B, 2A and 2D and for stripe rust on 1AL, 1B, 3A, 3B, 4D, 6A, 7AS and 7AL. The 1AL, 1BS and 7AL QTLs are in regions that were not identified previously as having QTLs for stripe rust resistance. The development of uniform and severe epidemics facilitated excellent phenotyping, and when combined with multi-environment analysis, resulted in the relatively large number of QTLs identified in this study.     

Linkage mapping of genes for resistance to leaf,stem and stripe rusts and ω-secalins on the short arm of rye chromosome 1R

Summary The genes controlling resistance to three wheat rusts, viz., leaf rust (Lr26), stem rust (Sr31) and stripe or yellow rust (Yr9), and -secalins (Sec1), located on the short arm of rye chromosome 1R, were mapped with respect to each other and the centromere. Analysis of 214 seeds (or families derived from them) from testcrosses between a 1BL.1RS/1R heterozygote and Chinese Spring ditelocentric 1BL showed no recombination between the genes for resistance to the three rusts, suggesting very tight linkage or perhaps a single complex locus conferring resistance to the three rusts. The rust resistance genes were located 5.4 ± 1.7 cM from the Sec1 locus, which in turn was located 26.1 ± 4.3 cM from the centromere; the gene order being centromere — Sec1 — Lr26/Sr31/Yr9 — telomere. In a second test-cross, using a different 1BL.1RS translocation which had only stem rust resistance (SrR), the above gene order was confirmed despite a very large proportion of aneuploids (45.8%) among the progeny. Furthermore, a map distance of 16.0 ± 4.8 cM was estimated for SrR and the telomeric heterochromatin (C-band) on 1RS. These results suggest that a very small segment of 1RS chromatin is required to maintain resistance to all three wheat rusts. It should be possible but difficult to separate the rust resistance genes from the secalin gene(s), which are thought to contribute to dough stickiness of wheat-rye translocation lines carrying 1RS.     

Expression patterns of WRKY genes in di-haploid Populus simonii × P. nigra in response to salinity stress revealed by quantitative real-time PCR and RNA sequencing

Key message

Spatio-temporal expression patterns of 13 out of 119 poplar WRKY genes indicated dynamic and tissue-specific roles of WRKY family proteins in salinity stress tolerance.

Abstract

To understand the expression patterns of poplar WRKY genes under salinity stress, 51 of the 119 WRKY genes were selected from di-haploid Populus simonii × P. nigra by quantitative real-time PCR (qRT-PCR). We used qRT-PCR to profile the expression of the top 13 genes under salinity stress across seven time points, and employed RNA-Seq platforms to cross-validate it. Results demonstrated that all the 13 WRKY genes were expressed in root, stem, and leaf tissues, but their expression levels and overall patterns varied notably in these tissues. Regarding overall gene expression in roots, the 13 genes were significantly highly expressed at all six time points after the treatment, reaching the plateau of expression at hour 9. In leaves, the 13 genes were similarly up-regulated from 3 to 12 h in response to NaCl treatment. In stems, however, expression levels of the 13 genes did not show significant changes after the NaCl treatment. Regarding individual gene expression across the time points and the three tissues, the 13 genes can be classified into three clusters: the lowly expressed Cluster 1 containing PthWRKY28, 45 and 105; intermediately expressed Clusters 2 including PthWRKY56, 88 and 116; and highly expressed Cluster 3 consisting of PthWRKY41, 44, 51, 61, 62, 75 and 106. In general, genes in Cluster 2 and 3 displayed a dynamic pattern of “induced amplification—recovering”, suggesting that these WRKY genes and corresponding pathways may play a critical role in mediating salt response and tolerance in a dynamic and tissue-specific manner.     

A linkage map of chickpea (Cicer arietinum L.) based on populations from Kabuli × Desi crosses: location of genes for resistance to fusarium wilt race 0

Two recombinant inbred line (RIL) populations derived from intraspecific crosses with a common parental line (JG62) were employed to develop a chickpea genetic map. Molecular markers, flower colour, double podding, seed coat thickness and resistance to fusarium wilt race 0 (FOC-0) were included in the study. Joint segregation analysis involved a total of 160 markers and 159 RILs. Ten linkage groups (LGs) were obtained that included morphological markers and 134 molecular markers (3 ISSRs, 13 STMSs and 118 RAPDs). Flower colour (B/b) and seed coat thickness (Tt/tt) appeared to be linked to STMS (GAA47). The single-/double-podding locus was located on LG9 jointly with two RAPD markers and STMS TA80. LG3 included a gene for resistance to FOC-0 (Foc0₁/foc0₁) flanked by RAPD marker OPJ20₆₀₀ and STMS marker TR59. The association of this LG with FOC-0 resistance was confirmed by QTL analysis in the CA2139 × JG62 RIL population where two genes were involved in the resistance reaction. The STMS markers enabled comparison of LGs with preceding maps.     

Isolate-specific QTLs of resistance to leaf stripe (<Emphasis Type="Italic">Pyrenophora graminea</Emphasis>) in the 'Steptoe' × 'Morex' spring barley cross

Leaf stripe caused by the fungus Pyrenophora graminea represents a serious threat to grain yield in organically grown barley and in conventional Nordic and Mediterranean districts, for which resistant cultivars are necessary. A medium-density, molecular marker map derived from a 'Steptoe' (partially resistant) x 'Morex' (susceptible) spring barley cross and its derived doubled-haploid mapping population inoculated with the fungus made it possible to identify QTLs of resistance to leaf stripe. In order to investigate isolate-specificity of partial resistance, the 'Steptoe' x 'Morex' segregating population was inoculated with two highly virulent P. graminea isolates, Dg2 and Dg5. The present study demonstrates that partial resistance to leaf stripe of cv 'Steptoe' is governed in part by shared loci and in part by isolate-specific ones. One QTL is common to the resistance for the two isolates, on the long arm of chromosome 2 (2H), two QTLs are linked on chromosome 3 (3H), and the remaining two are isolate-specific, respectively for isolate Dg2 on chromosome 2 (2H) and for isolate Dg5 on chromosome 7 (5H). The QTL in common is that with the major effect on the resistance for each isolate, explaining 18.3% and 30.9% R(2) respectively for Dg2 and Dg5. The isolate-specific QTLs mapped in the 'Steptoe' x 'Morex' barley reference map support the assumption of Parlevliet and Zadoks (1977) that partial resistance may be due to minor gene-for-minor-gene interactions. Map comparisons of the QTLs with the known qualitative resistance genes to leaf stripe, Rdg1 (2H) and Rdg2 (7H), as well as with other QTLs of partial resistance in barley, show that the QTL for resistance to both isolates mapped on the long arm of chromosome 2 (2H) does not coincide with the qualitative Rdg1 gene but is linked to it at about 30 cM. One isolate-specific QTL of resistance to P. graminea, mapped on the short arm of chromosome 2 (2H), is coincident with a QTL for resistance to Pyrenophora teres previously mapped in the 'Steptoe' x 'Morex' cross.     

Identification of putative quantitative trait loci associated with a flavonoid related to resistance to cabbage seedpod weevil (Ceutorhynchus obstrictus) in canola derived from an intergeneric cross,Sinapis alba × Brassica napus

Key message

Kaempferol 3- O -sinapoyl-sophoroside 7- O -glucoside was putatively identified as the major component of a characteristic HPLC peak previously correlated with the reduction of cabbage seedpod weevil larval infestation in a novel canola genotype.

Abstract

The cabbage seedpod weevil (Ceutorhynchus obstrictus [Marsham]) (CSPW) is a serious pest of brassicaceous oilseed crops such as canola in both Europe and more recently in North America. At present, the only control strategy against CSPW is the application of insecticides. As an alternative more environmentally-friendly control strategy, we developed novel canola germplasm resistant to weevil attack through introgression of Sinapis alba DNA into Brassica napus by making the wide cross followed by embryo rescue and backcrossing to the B. napus parent. We have previously characterized resistant canola lines by metabolic profiling and were able to correlate reduction of larval infestation to the presence of a characteristic HPLC peak. In this study, we have putatively identified the major component in the peak using mass spectrometry as kaempferol 3-O-sinapoyl-sophoroside 7-O-glucoside (KSSG). We have also identified quantitative trait loci (QTL) associated with this HPLC peak in a mapping population consisting of more than 200 individual doubled haploid (DH) lines derived from a cross between CSW428 (the resistant parent) and SC030686 (the susceptible parent). This QTL accounted for approximately 9.5 % of the phenotypic variation in KSSG content. The observation that only one QTL was identified as surpassing the LOD threshold of 3.0 suggests that both parents may possess the positive alleles for other QTL that have not been detected in our study. This finding also indicates a complex regulatory mechanism for KSSG levels and provides an appropriate explanation for the large transgressive segregation observed in the DH lines of the QTL mapping population.     

Identification and mapping of a major gene (Ft1) involved in fructification time in the interspecific cross Coffea pseudozanguebariae × C. liberica var. Dewevrei: impact on caffeine content and seed weight

Fructification time was studied in the interspecific cross Coffea pseudozanguebariae x C. liberica var. Dewevrei (PSE x DEW). Parental species, F(1) hybrids and offspring of the first backcross generation (BC(1)), consisting of F(1) x PSE (BCPSE) and F(1) x DEW (BCDEW) plants, were observed. Fructification time can be split into two independent visual phases: the full-growth period, from blooming up to the end of fruit growth, and the maturation phase, defined by the green to red color change. Fructification time was found to be an additive trait. The full-growth period showed a bimodal distribution in the BCDEW hybrid, suggesting the involvement of Ft1, a major gene that was mapped on linkage group E. The main effects of Ft1 were to lower caffeine content and 100-seed weight, without any impact on chlorogenic acid, trigonelline and sucrose contents. Two molecular markers were identified that bracket Ft1 and which could be used for early marker-assisted selection.     

Mapping of SnTox3–<Emphasis Type="Italic">Snn3</Emphasis> as a major determinant of field susceptibility to Septoria nodorum leaf blotch in the SHA3/CBRD × Naxos population

Key message

The effect of the SnTox3–Snn3 interaction was documented for the first time under natural infection at the adult plant stage in the field. Co-segregating SNP markers were identified.

Abstract

Parastagonospora nodorum is a necrotrophic pathogen of wheat, causing Septoria nodorum blotch (SNB) affecting both the leaf and glume. P. nodorum is the major leaf blotch pathogen on spring wheat in Norway. Resistance to the disease is quantitative, but several host-specific interactions between necrotrophic effectors (NEs) and host sensitivity (Snn) genes have been identified, playing a major role at the seedling stage. However, the effect of these interactions in the field under natural infection has not been investigated. In the present study, we saturated the genetic map of the recombinant inbred (RI) population SHA3/CBRD?×?Naxos using the Illumina 90 K SNP chip. The population had previously been evaluated for segregation of SNB susceptibility in field trials. Here, we infiltrated the population with the purified NEs SnToxA, SnTox1 and SnTox3, and mapped the Snn3 locus on 5BS based on sensitivity segregation and SNP marker data. We also conducted inoculation and culture filtrate (CF) infiltration experiments on the population with four selected P. nodorum isolates from Norway and North America. Remapping of quantitative trait loci (QTL) for field resistance showed that the SnTox3–Snn3 interaction could explain 24% of the phenotypic variation in the field, and more than 51% of the variation in seedling inoculations. To our knowledge, this is the first time the effect of this interaction has been documented at the adult plant stage under natural infection in the field.

     

Mapping and pyramiding of two major genes for resistance to the brown planthopper (<Emphasis Type="Italic">Nilaparvata lugens</Emphasis> [Stål]) in the rice cultivar ADR52

The brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most serious and destructive pests of rice, and can be found throughout the rice-growing areas of Asia. To date, more than 24 major BPH-resistance genes have been reported in several Oryza sativa ssp. indica cultivars and wild relatives. Here, we report the genetic basis of the high level of BPH resistance derived from an Indian rice cultivar, ADR52, which was previously identified as resistant to the whitebacked planthopper (Sogatella furcifera [Horváth]). An F₂ population derived from a cross between ADR52 and a susceptible cultivar, Taichung 65 (T65), was used for quantitative trait locus (QTL) analysis. Antibiosis testing showed that multiple loci controlled the high level of BPH resistance in this F₂ population. Further linkage analysis using backcross populations resulted in the identification of BPH-resistance (antibiosis) gene loci from ADR52. BPH25 co-segregated with marker S00310 on the distal end of the short arm of chromosome 6, and BPH26 co-segregated with marker RM5479 on the long arm of chromosome 12. To characterize the virulence of the most recently migrated BPH strain in Japan, preliminary near-isogenic lines (pre-NILs) and a preliminary pyramided line (pre-PYL) carrying BPH25 and BPH26 were evaluated. Although both pre-NILs were susceptible to the virulent BPH strain, the pre-PYL exhibited a high level of resistance. The pyramiding of resistance genes is therefore likely to be effective for increasing the durability of resistance against the new virulent BPH strain in Japan.     

A study of the storage proteins in the introgression lines of common wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L. × <Emphasis Type="Italic">T. timopheevii</Emphasis> Zhuk.) Resistant to brown leaf rust

Storage proteins, prolamins, were studied in ten introgression lines of common wheat bred with involvement of Triticum timopheevii (Tt) Zhuk. and five commercial hexaploid wheat cultivars. The lines are resistant to leaf rust. A comparative analysis of the storage proteins in the Triticum aestivum L. (Ta) introgression lines and the parental forms allowed us to (1) detect the active genes of prolamins on the chromosomes homeologous groups 1 and 6 in the introgression lines of T. aestivum and T. timopheevii; (2) clarify their origin; (3) identify the chromosome attribution of the products; (4) estimate the degree of introgression and postulate the introgression mechanisms; and (5) predict the bread-making quality of these introgression lines.     

Polygenic inheritance of resistance to <Emphasis Type="Italic">Cacopsylla pyri</Emphasis> in a <Emphasis Type="Italic">Pyrus communis</Emphasis> × <Emphasis Type="Italic">P. ussuriensis</Emphasis> progeny is explained by three QTLs involving an epistatic interaction

Pear psylla (Cacopsylla pyri) causes severe damage on European pear cultivars, resulting in high yield losses. Its control has become difficult since it developed resistance to a wide range of pesticides, while the number of authorized molecules for pest control has decreased. Identifying pear psylla resistance factors should help breeding new resistant pear cultivars. We analyzed the quantitative resistance to psylla inherited from the genotype NY 10355 derived from Pyrus ussuriensis. Quantitative trait locus (QTL) analysis was carried out after counting the number of nymphs and estimating the nymphal development rate using a free-choice test performed on a large segregating progeny. We mapped two new loci for pear psylla resistance on linkage groups LG01 and LG04 of NY 10355 and confirmed the QTL previously detected on LG17. A strong epistatic interaction between the two QTLs detected on LG01 and LG17 appeared to be a major factor controlling the psylla infestation in the genotype NY 10355.