Identification and mapping of resistance to stem rust in the European winter wheat cultivars Spark and Rialto

A mapping population of 126 doubled haploid (DH) lines derived from a cross between the English winter wheat cultivars Spark and Rialto was evaluated for response to Puccinia graminis f. sp. tritici in the greenhouse and in artificially inoculated field plots at two locations over 3 years (2011, 2012 and 2013). Genetic analysis indicated the involvement of two seedling genes (Sr5 and Sr31, contributed by Rialto) and three adult plant resistance genes. QTL analyses of field data showed the involvement of three consistent effects QTL on chromosome arms 1BS (contributed by Rialto), and 3BS and chromosome 5A (contributed by Spark) in the observed resistance to stem rust. These QTLs explained average phenotypic variation of 78.5, 9.0 and 5.9 %, respectively. With the presence of virulence for Sr5 and absence of Sr31 virulence in the field, the QTL detected on 1BS (QSr.sun-1BS) was attributed to the major seedling resistance gene Sr31. The QTL located on chromosome arm 3BS (QSr.sun-3BS) was closely associated with SSR marker gwm1034, and the QTL detected on 5A (QSr.sun-5A) was closely linked with SSR marker gwm443. DH lines carrying the combination of QSr.sun-3BS and QSr.sun-5A exhibited lower stem rust responses indicating the additive effects of the two APR genes in reducing disease severity. The markers identified in this study can be useful in pyramiding these QTLs with other major or minor genes and marker assisted selection for stem rust resistance in wheat.     

High-resolution mapping reveals linkage between genes in common bean cultivar Ouro Negro conferring resistance to the rust,anthracnose, and angular leaf spot diseases

Key message

Co-segregation analysis and high-throughput genotyping using SNP, SSR, and KASP markers demonstrated genetic linkage between Ur-14 and Co-3 ⁴ /Phg-3 loci conferring resistance to the rust, anthracnose and angular leaf spot diseases of common bean.

Abstract

Rust, anthracnose, and angular leaf spot are major diseases of common bean in the Americas and Africa. The cultivar Ouro Negro has the Ur-14 gene that confers broad spectrum resistance to rust and the gene cluster Co-3 ⁴ /Phg-3 containing two tightly linked genes conferring resistance to anthracnose and angular leaf spot, respectively. We used co-segregation analysis and high-throughput genotyping of 179 F_2:3 families from the Rudá (susceptible) × Ouro Negro (resistant) cross-phenotyped separately with races of the rust and anthracnose pathogens. The results confirmed that Ur-14 and Co-3 ⁴ /Phg-3 cluster in Ouro Negro conferred resistance to rust and anthracnose, respectively, and that Ur-14 and the Co-3 ⁴ /Phg-3 cluster were closely linked. Genotyping the F_2:3 families, first with 5398 SNPs on the Illumina BeadChip BARCBEAN6K_3 and with 15 SSR, and eight KASP markers, specifically designed for the candidate region containing Ur-14 and Co-3 ⁴ /Phg-3, permitted the creation of a high-resolution genetic linkage map which revealed that Ur-14 was positioned at 2.2 cM from Co-3 ⁴ /Phg-3 on the short arm of chromosome Pv04 of the common bean genome. Five flanking SSR markers were tightly linked at 0.1 and 0.2 cM from Ur-14, and two flanking KASP markers were tightly linked at 0.1 and 0.3 cM from Co-3 ⁴ /Phg-3. Many other SSR, SNP, and KASP markers were also linked to these genes. These markers will be useful for the development of common bean cultivars combining the important Ur-14 and Co-3 ⁴ /Phg-3 genes conferring resistance to three of the most destructive diseases of common bean.

     

A <Emphasis Type="Italic">bean common mosaic virus</Emphasis> (BCMV)-resistance gene is fine-mapped to the same region as <Emphasis Type="Italic">Rsv1</Emphasis>-<Emphasis Type="Italic">h</Emphasis> in the soybean cultivar Suweon 97

Key message

In the soybean cultivar Suweon 97, BCMV-resistance gene was fine-mapped to a 58.1-kb region co-localizing with the Soybean mosaic virus (SMV)-resistance gene, Rsv1-h raising a possibility that the same gene is utilized against both viral pathogens.

Abstract

Certain soybean cultivars exhibit resistance against soybean mosaic virus (SMV) or bean common mosaic virus (BCMV). Although several SMV-resistance loci have been reported, the understanding of the mechanism underlying BCMV resistance in soybean is limited. Here, by crossing a resistant cultivar Suweon 97 with a susceptible cultivar Williams 82 and inoculating 220 F₂ individuals with a BCMV strain (HZZB011), we observed a 3:1 (resistant/susceptible) segregation ratio, suggesting that Suweon 97 possesses a single dominant resistance gene against BCMV. By performing bulked segregant analysis with 186 polymorphic simple sequence repeat (SSR) markers across the genome, the resistance gene was determined to be linked with marker BARSOYSSR_13_1109. Examining the genotypes of nearby SSR markers on all 220 F₂ individuals then narrowed down the gene between markers BARSOYSSR_13_1109 and BARSOYSSR_13_1122. Furthermore, 14 previously established F_2:3 lines showing crossovers between the two markers were assayed for their phenotypes upon BCMV inoculation. By developing six more SNP (single nucleotide polymorphism) markers, the resistance gene was finally delimited to a 58.1-kb interval flanked by BARSOYSSR_13_1114 and SNP-49. Five genes were annotated in this interval of the Williams 82 genome, including a characteristic coiled-coil nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR, CNL)-type of resistance gene, Glyma13g184800. Coincidentally, the SMV-resistance allele Rsv1-h was previously mapped to almost the same region, thereby suggesting that soybean Suweon 97 likely relies on the same CNL-type R gene to resist both viral pathogens.

     

QTL mapping of downy and powdery mildew resistances in PI 197088 cucumber with genotyping-by-sequencing in RIL population

Key message

Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized.

Abstract

The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line ‘Coolgreen’. Phenotypic data on responses to natural DM and PM infection were collected in multi-year and multi-location replicated field trials. A high-density genetic map with 2780 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing and 55 microsatellite markers was developed, which revealed genomic regions with segregation distortion and mis-assemblies in the ‘9930’ cucumber draft genome. QTL analysis identified 11 and 4 QTL for DM and PM resistances accounting for more than 73.5 and 63.0% total phenotypic variance, respectively. Among the 11 DM resistance QTL, dm5.1, dm5.2, and dm5.3 were major-effect contributing QTL, whereas dm1.1, dm2.1, and dm6.2 conferred susceptibility. Of the 4 QTL for PM resistance, pm5.1 was the major-effect QTL explaining 32.4% phenotypic variance and the minor-effect QTL pm6.1 contributed to disease susceptibility. Three PM QTL, pm2.1, pm5.1, and pm6.1, were co-localized with DM QTL dm2.1, dm5.2, and dm6.1, respectively, which was consistent with the observed linkage of PM and DM resistances in PI 197088. The genetic architecture of DM resistance in PI 197088 and another resistant line WI7120 (PI 330628) was compared, and the potential of using PI 197088 in cucumber breeding for downy and powdery mildew resistances is discussed.

     

Bone marrow mesenchymal stem cell transplantation improves radiation-induced heart injury through DNA damage repair in rat model

Radiotherapy is an effective form of therapy for most thoracic malignant tumors. However, myocardial injury resulting from the high doses of radiation is a severe complication. Here we aimed to study the possibility of reducing radiation-induced myocardial injury with mesenchymal stem cell (MSC) transplantation. We used MSCs extracted from bone marrow (BMSCs) to transplant via the tail vein into a radiation-induced heart injury (RIHI) rat model. The rats were divided into six groups: a Sham group, an IRR (irradiation) group, and four IRR + BMSCs transplantation groups obtained at different time points. After irradiation, BMSC transplantation significantly enhanced the cardiac function in rats. By analyzing the expression of PPAR-α, PPAR-γ, TGF-β, IL-6, and IL-8, we found that BMSC transplantation alleviated radiation-induced myocardial fibrosis and decreased the inflammatory reaction. Furthermore, we found that expression of γ-H2AX, XRCC4, DNA ligase4, and TP53BP1, which are associated with DNA repair, was up-regulated, along with increased secretion of growth factors SDF-1, CXCR4, VEGF, and IGF in rat myocardium in the IRR + BMSCs transplantation groups compared with the IRR group. Thus, BMSC transplantation has the potential to improve RIHI via DNA repair and be a new therapeutic approach for patients with myocardial injury.     

Integration of sudden death syndrome resistance loci in the soybean genome

Key message

Complexity and inconsistencies in resistance mapping publications of soybean sudden death syndrome (SDS) result in interpretation difficulty. This review integrates SDS mapping literature and proposes a new nomenclature system for reproducible SDS resistance loci.

Abstract

Soybean resistance to sudden death syndrome (SDS) is composed of foliar resistance to phytotoxins and root resistance to pathogen invasion. There are more than 80 quantitative trait loci (QTL) and dozens of single nucleotide polymorphisms (SNPs) associated with soybean resistance to SDS. The validity of these QTL and SNPs is questionable because of the complexity in phenotyping methodologies, the disease synergism between SDS and soybean cyst nematode (SCN), the variability from the interactions between soybean genotypes and environments, and the inconsistencies in the QTL nomenclature. This review organizes SDS mapping results and proposes the Rfv (resistance to Fusarium virguliforme) nomenclature based on supporting criteria described in the text. Among ten reproducible loci receiving our Rfv nomenclature, Rfv18-01 is mostly supported by field studies and it co-localizes to the SCN resistance locus rhg1. The possibility that Rfv18-01 is a pleiotropic resistance locus and the concern about Rfv18-01 being confounded with Rhg1 is discussed. On the other hand, Rfv06-01, Rfv06-02, Rfv09-01, Rfv13-01, and Rfv16-01 were identified both by screening soybean leaves against phytotoxic culture filtrates and by evaluating SDS severity in fields. Future phenotyping using leaf- and root-specific resistance screening methodologies may improve the precision of SDS resistance, and advanced genetic studies may further clarify the interactions among soybean genotypes, F. virguliforme, SCN, and environments. The review provides a summary of the SDS resistance literature and proposes a framework for communicating SDS resistance loci for future research considering molecular interactions and genetic breeding for soybean SDS resistance.

     

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

Key message

Four QTLs for adult-plant resistance to powdery mildew were mapped in the Zhou8425B/Chinese Spring population, and a new QTL on chromosome 3B was validated in 103 wheat cultivars derived from Zhou8425B.

Abstract

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-3BS locus 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.

     

A mutant in the <Emphasis Type="Italic">CsDET2</Emphasis> gene leads to a systemic brassinosteriod deficiency and <Emphasis Type="Italic">super compact </Emphasis>phenotype in cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.)

Key message

A novel dwarf cucumber mutant, scp-2, displays a typical BR biosynthesis-deficient phenotype, which is due to a mutation in CsDET2 for a steroid 5-alpha-reductase.

Abstract

Brassinosteroids (BRs) are a group of plant hormones that play important roles in the development of plant architecture, and extreme dwarfism is a typical outcome of BR-deficiency. Most cucumber (Cucumis sativus L.) varieties have an indeterminate growth habit, and dwarfism may have its value in manipulation of plant architecture and improve production in certain production systems. In this study, we identified a spontaneous dwarf mutant, super compact-2 (scp-2), that also has dark green, wrinkle leaves. Genetic analyses indicated that scp-2 was different from two previously reported dwarf mutants: compact (cp) and super compact-1 (scp-1). Map-based cloning revealed that the mutant phenotype was due to two single nucleotide polymorphism and a single-base insertion in the CsDET2 gene that resulted in a missense mutation in a conserved amino acid and thus a truncated protein lacking the conserved catalytic domains in the predicted steroid 5α-reductase protein. Measurement of endogenous hormone levels indicated a reduced level of brassinolide (BL, a bioactive BR) in scp-2, and the mutant phenotype could be partially rescued by the application of epibrassinolide (EBR). In addition, scp-2 mutant seedlings exhibited dark-grown de-etiolation, and defects in cell elongation and vascular development. These data support that scp-2 is a BR biosynthesis-deficient mutant, and that the CsDET2 gene plays a key role in BR biosynthesis in cucumber. We also described the systemic BR responses and discussed the specific BR-related phenotypes in cucumber plants.

     

Molecular mapping of the genomic region conferring resistance to soybean stem canker in Hutcheson soybean

Genetic resistance to soybean stem canker, caused by the fungus Diaporthe phaseolorum var. meridionalis (Dpm), is controlled by five major, dominant, nonallelic genes Rdm1 to Rdm5. A genomic region containing the Rdm4 and Rdm5 genes was first described in Hutcheson soybean, where they were found to confer specific resistance to Argentinean physiological races of Dpm. Here, we report the genetic mapping of Rdm4 and Rdm5 loci using two pheno- and genotypically characterized F_2:3 populations derived from Hutcheson cultivar. The mapping populations were screened with amplified fragment length polymorphism (AFLP) markers using bulk segregant analysis, and with simple sequence repeat (SSR) markers. Linkage analysis indicated that the Rdm4 and Rdm5 resistance loci were located in a genomic region collinear with the molecular linkage group (MLG) A2 (chromosome 8) of the soybean genetic map. The linkage group contains two SSR markers, Sat_162 and Satt233, flanking the Rdm4 and Rdm5 loci. These SSR will be useful to increase the efficiency of selection in breeding programs aimed to incorporate Rdm4 and Rdm5 genes into soybean elite germplasm.     

Molecular mapping of a new temperature-sensitive gene <Emphasis Type="Italic">LrZH22</Emphasis> for leaf rust resistance in Chinese wheat cultivar Zhoumai 22

Leaf rust, caused by Puccinia triticina, is one of the most widespread diseases in common wheat globally. The Chinese wheat cultivar Zhoumai 22 is highly resistant to leaf rust at the seedling and adult stages. Seedlings of Zhoumai 22 and 36 lines with known leaf rust resistance genes were inoculated with 13 P. triticina races for gene postulation. The leaf rust response of Zhoumai 22 was different from those of the single gene lines. With the objective of identifying and mapping, the new gene(s) for resistance to leaf rust, F₁, F₂ plants and F_2:3 lines from the cross Zhoumai 22/Chinese Spring were inoculated with Chinese P. triticina race FHDQ at the seedling stage. A single dominant gene, tentatively designated LrZH22, conferred resistance. To identify other possible genes in Zhoumai 22, ten P. triticina races avirulent on Zhoumai 22 were used to inoculate 24 F_2:3 lines. The same gene conferred resistance to all ten avirulent races. A total of 1300 simple sequence repeat (SSR) markers and 36 EST markers on 2BS were used to test the parents, and resistant and susceptible bulks. Resistance gene LrZH22 was mapped in the chromosome bin 2BS1-0.53-0.75 and closely linked to six SSR markers (barc183, barc55, gwm148, gwm410, gwm374 and wmc474) and two EST markers (BF202681 and BE499478) on chromosome arm 2BS. The two closest flanking SSR loci were Xbarc55 and Xgwm374 with genetic distances of 2.4 and 4.8 cM from LrZH22, respectively. Six designated genes (Lr13, Lr16, Lr23, Lr35, Lr48 and Lr73) are located on chromosome arm 2BS. In seedling tests, LrZH22 was temperature sensitive, conferring resistance at high temperatures. The reaction pattern of Zhoumai 22 was different from that of RL 4031 (Lr13), RL 6005 (Lr16) and RL 6012 (Lr23), Lr35 and Lr48 are adult-plant resistance genes, and Lr73 is not sensitive to the temperature. Therefore, LrZH22 is likely to be a new leaf rust resistance gene or allele.     

Genome-Wide Identification of the Dicer-Like,Argonaute, and RNA-Dependent RNA Polymerase Gene Families in Cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.)

Dicer, Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) comprise the core components of RNA-induced silencing complexes, which trigger RNA silencing. Here, we performed a complete analysis of the cucumber Dicer-like, AGO, and RDR gene families including the gene structure, genomic localization, and phylogenetic relationships among family members. We identified seven CsAGO genes, five CsDCL genes, and eight CsRDR genes in cucumber. Based on phylogenetic analysis, each of these genes families was categorized into three or four clades. The orthologs of CsAGOs, CsDCLs, and CsRDRs were identified in apple, peach, wild strawberry, foxtail millet, and maize, and the evolutionary relationships among the orthologous gene pairs were investigated. We also investigated the expression levels of CsAGOs, CsDCLs, and CsRDRs in various cucumber tissues. All CsAGOs were relatively higher upregulated in leaves and tendrils than in other organs, especially CsAGO1c, CsAGO1d, and CsAGO7. All CsDCL genes were relatively higher upregulated in tendrils, with almost no expression detected for CsDCL1, CsDCL4a, or CsDCL4b in other organs. In addition, CsRDR1a, CsRDR2, CsRDR3, and CsRDR6 had relatively higher upregulation in tendrils, whereas almost all CsRDRs were downregulation in other organs. The results of this study will facilitate further studies of gene silencing pathways in cucumber.     

QTL mapping of domestication and diversifying selection related traits in round-fruited semi-wild Xishuangbanna cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L. var. <Emphasis Type="Italic">xishuangbannanesis</Emphasis>)

Key message

QTL analysis revealed 11 QTL underlying flowering time and fruit size variation in the semi-wild Xishuangbanna cucumber, of which, FT6.2 and FS5.2 played the most important roles in determining photoperiod-dependent flowering time and round-fruit shape, respectively.

Abstract

Flowering time and fruit size are two important traits in domestication and diversifying selection in cucumber, but their genetic basis is not well understood. Here we reported QTL mapping results on flowering time and fruit size with F₂ and F_2:3 segregating populations derived from the cross between WI7200, a small fruited, early flowering primitive cultivated cucumber and WI7167, a round-fruited, later flowering semi-wild Xishuangbanna (XIS) cucumber. A linkage map with 267 microsatellite marker loci was developed with 138 F₂ plants. Phenotypic data of male and female flowering time, fruit length and diameter and three other traits (mature fruit weight and number, and seedling hypocotyl length) were collected in multiple environments. Three flowering time QTL, FT1.1, FT5.1 and FT6.2 were identified, in which FT6.2 played the most important role in conferring less photoperiod sensitive early flowering during domestication whereas FT1.1 seemed more influential in regulating flowering time within the cultivated cucumber. Eight consensus fruit size QTL distributed in 7 chromosomes were detected, each of which contributed to both longitudinal and radial growth in cucumber fruit development. Among them, FS5.2 on chromosome 5 exhibited the largest effect on the determination of round fruit shape that was characteristic of the WI7167 XIS cucumber. Possible roles of these flowering time and fruit size QTL in domestication of cucumber and crop evolution of the semi-wild XIS cucumber, as well as the genetic basis of round fruit shape in cucumber are discussed.

     

Adult plant stripe rust resistance gene <Emphasis Type="Italic">Yr71</Emphasis> maps close to <Emphasis Type="Italic">Lr24</Emphasis> in chromosome 3D of common wheat

Australian cultivar Sunco carries three adult plant stripe rust resistance genes. One of these genes corresponded to Yr18 in chromosome 7DS; the second, YrCK, was mapped on chromosome 2D. Here, we describe the characterization of the third adult plant resistance (APR) gene from Sunco. Sunco/2*Avocet S-derived lines SA65 (resistant) and SA67 (susceptible) were crossed and a recombinant inbred line F₆ population was generated. Monogenic segregation among SA65/SA67-derived RIL population was demonstrated and the resistance locus was designated YrSA3. Selective genotyping using an iSelect 90 K Infinium SNP array and SSR markers located YrSA3 on chromosome 3D. Development of KASP markers for SNP loci showing association with YrSA3 allowed construction of a genetic map harboring the resistance gene. Ten KASP markers (KASP_8306, KASP_9142, KASP_10438, KASP_16434, KASP_17207, KASP_20836, KASP_23518, KASP_23615, KASP_57983 and KASP_63653), one SSR marker (gwm114b) and Lr24/Sr24 were mapped 1.8 cM distal to YrSA3. Comparison of marker data indicated that the previously named seedling stripe rust resistance gene Yr45 was located proximal to YrSA3, and therefore the latter was formally designated Yr71. Two recombinants carrying Lr24/Sr24 and Yr71 in combination were identified for use as donor sources in wheat breeding programs. The robustness of gwm114b, KASP_16434, KASP_17207 and KASP_20836 for marker-assisted selection of these genes was demonstrated through tests on 74 Australian wheat cultivars.     

Fine mapping of a male sterility gene <Emphasis Type="Italic">ms</Emphasis>-<Emphasis Type="Italic">3</Emphasis> in a novel cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.) mutant

Key message

The cucumber male sterility gene ms - 3 was fine mapped in a 76 kb region harboring an MMD1 -like gene Csa3M006660 that may be responsible for the male sterile in cucumber.

Abstract

A cucumber (Cucumis sativus L.) male sterile mutant (ms-3) in an advanced-generation inbred line was identified, and genetic analysis revealed that the male sterility trait was controlled by a recessive nuclear gene, ms-3, which was stably inherited. Histological studies suggested that the main cause of the male sterility was defective microsporogenesis, resulting in no tetrad or microspores being formed. Bulked segregant analysis (BSA) and genotyping of an F₂ population of 2553 individuals were employed used to fine map ms-3, which was delimited to a 76 Kb region. In this region, a single non-synonymous SNP was found in the Csa3M006660 gene locus, which was predicted to result in an amino acid change. Quantitative RT-PCR analysis of Csa3M006660 was consistent with the fact that it plays a role in the early development of cucumber pollen. The protein encoded by Csa3M006660 is predicted to be homeodomain (PHD) finger protein, and the high degree of sequence conservation with homologs from a range of plant species further suggested the importance of the ms-3 non-synonymous mutation. The data presented here provide support for Csa3M006660 as the most likely candidate gene for Ms-3.

     

Characterization of <Emphasis Type="Italic">Lr75</Emphasis>: a partial,broad-spectrum leaf rust resistance gene in wheat

Key message

Here, we describe a strategy to improve broad-spectrum leaf rust resistance by marker-assisted combination of two partial resistance genes. One of them represents a novel partial adult plant resistance gene, named Lr75.

Abstract

Leaf rust caused by the fungal pathogen Puccinia triticina is a damaging disease of wheat (Triticum aestivum L.). The combination of several, additively-acting partial disease resistance genes has been proposed as a suitable strategy to breed wheat cultivars with high levels of durable field resistance. The Swiss winter wheat cultivar ‘Forno’ continues to show near-immunity to leaf rust since its release in the 1980s. This resistance is conferred by the presence of at least six quantitative trait loci (QTL), one of which is associated with the morphological trait leaf tip necrosis. Here, we used a marker-informed strategy to introgress two ‘Forno’ QTLs into the leaf rust-susceptible Swiss winter wheat cultivar ‘Arina’. The resulting backcross line ‘ArinaLrFor’ showed markedly increased leaf rust resistance in multiple locations over several years. One of the introgressed QTLs, QLr.sfr-1BS, is located on chromosome 1BS. We developed chromosome 1B-specific microsatellite markers by exploiting the Illumina survey sequences of wheat cv. ‘Chinese Spring’ and mapped QLr.sfr-1BS to a 4.3 cM interval flanked by the SSR markers gwm604 and swm271. QLr.sfr-1BS does not share a genetic location with any of the described leaf rust resistance genes present on chromosome 1B. Therefore, QLr.sfr-1BS is novel and was designated as Lr75. We conclude that marker-assisted combination of partial resistance genes is a feasible strategy to increase broad-spectrum leaf rust resistance. The identification of Lr75 adds a novel and highly useful gene to the small set of known partial, adult plant leaf rust resistance genes.

     

Physical mapping of NBS-coding resistance genes to the <Emphasis Type="Italic">Me</Emphasis>-gene cluster on chromosome P9 reveals markers tightly linked to the <Emphasis Type="Italic">N</Emphasis> gene for root-knot nematode resistance in pepper

Natural root-knot nematode resistance genes are unique resources to control this major pest in pepper (Capsicum annuum). Although four genes (Me1, Me3, Me7 and N) conferring broad-spectrum resistance were mapped to a cluster in a 28-cm interval on chromosome P9, limited markers targeting this region were available. In the present study, the Me-gene cluster was structurally annotated for resistance genes to develop markers targeting the N gene. As a result, the Me-gene cluster (4.07 Mb in size) was found to contain three resistance gene hotspots. In addition, a SSR maker tightly linked to the N gene (0.8 cM away) was developed for marker-assisted selection in pepper.     

QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods

Key message

QTL mapping using NGS-assisted BSA was successfully applied to an F ₂ population for downy mildew resistance in cucumber. QTLs detected by NGS-assisted BSA were confirmed by conventional QTL analysis.

Abstract

Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the most destructive foliar diseases in cucumber. QTL mapping is a fundamental approach for understanding the genetic inheritance of DM resistance in cucumber. Recently, many studies have reported that a combination of bulked segregant analysis (BSA) and next-generation sequencing (NGS) can be a rapid and cost-effective way of mapping QTLs. In this study, we applied NGS-assisted BSA to QTL mapping of DM resistance in cucumber and confirmed the results by conventional QTL analysis. By sequencing two DNA pools each consisting of ten individuals showing high resistance and susceptibility to DM from a F₂ population, we identified single nucleotide polymorphisms (SNPs) between the two pools. We employed a statistical method for QTL mapping based on these SNPs. Five QTLs, dm2.2, dm4.1, dm5.1, dm5.2, and dm6.1, were detected and dm2.2 showed the largest effect on DM resistance. Conventional QTL analysis using the F₂ confirmed dm2.2 (R ² = 10.8–24 %) and dm5.2 (R ² = 14–27.2 %) as major QTLs and dm4.1 (R ² = 8 %) as two minor QTLs, but could not detect dm5.1 and dm6.1. A new QTL on chromosome 2, dm2.1 (R ² = 28.2 %) was detected by the conventional QTL method using an F₃ population. This study demonstrated the effectiveness of NGS-assisted BSA for mapping QTLs conferring DM resistance in cucumber and revealed the unique genetic inheritance of DM resistance in this population through two distinct major QTLs on chromosome 2 that mainly harbor DM resistance.