A QTL detected in an interspecific pear population confers stable fire blight resistance across different environments and genetic backgrounds

Fire blight, caused by the bacterium Erwinia amylovora (Burrill) Winslow et al., is one of the most serious diseases of pear. The development of pear cultivars with a durable resistance is extremely important for effective control of fire blight and is a key objective of most pear breeding programs throughout the world. We phenotyped seedlings from the interspecific pear population PEAR3 (PremP003, P. × bretschneideri × P. communis) × ‘Moonglow’ (P. communis) for fire blight resistance at two different geographic locations, in France and New Zealand, respectively, employing two local E. amylovora isolates. Using a genetic map constructed with single nucleotide polymorphism (SNP) and microsatellite (SSR) markers previously developed for this segregating population, we detected a major quantitative trait locus (QTL) on linkage group (LG)2 of ‘Moonglow’ (R ² = 12.9–34.4 %), which was stable in both environments. We demonstrated that this QTL co-localizes with another major QTL for fire blight resistance previously detected in ‘Harrow Sweet’ and that the two favorable (i.e., resistant) alleles were not identical by descent. We also identified some smaller effect (R ² = 8.1–14.8 %) QTLs derived from the susceptible parent PEAR3. We propose SNP and SSR markers linked to the large effect QTL on LG2 as candidates for marker-assisted breeding for fire blight resistance in pear.     

QTL mapping for bacterial wilt resistance in peanut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis> L.)

Bacterial wilt (BW) caused by Ralstonia solanacearum is a serious, global, disease of peanut (Arachis hypogaea L.), but it is especially destructive in China. Identification of DNA markers linked to the resistance to this disease will help peanut breeders efficiently develop resistant cultivars through molecular breeding. A F₂ population, from a cross between disease-resistant and disease-susceptible cultivars, was used to detect quantitative trait loci (QTL) associated with the resistance to this disease in the cultivated peanut. Genome-wide SNPs were identified from restriction-site-associated DNA sequencing tags using next-generation DNA sequencing technology. SNPs linked to disease resistance were determined in two bulks of 30 resistant and 30 susceptible plants along with two parental plants using bulk segregant analysis. Polymorphic SSR and SNP markers were utilized for construction of a linkage map and for performing the QTL analysis, and a moderately dense linkage map was constructed in the F₂ population. Two QTL (qBW-1 and qBW-2) detected for resistance to BW disease were located in the linkage groups LG1 and LG10 and account for 21 and 12 % of the bacterial wilt phenotypic variance. To confirm these QTL, the F₈ RIL population with 223 plants was utilized for genotyping and phenotyping plants by year and location as compared to the F₂ population. The QTL qBW-1 was consistent in the location of LG1 in the F₈ population though the QTL qBW-2 could not be clarified due to fewer markers used and mapped in LG10. The QTL qBW-1, including four linked SNP markers and one SSR marker within 14.4-cM interval in the F₈, was closely related to a disease resistance gene homolog and was considered as a candidate gene for resistance to BW. QTL identified in this study would be useful to conduct marker-assisted selection and may permit cloning of resistance genes. Our study shows that bulk segregant analysis of genome-wide SNPs is a useful approach to expedite the identification of genetic markers linked to disease resistance traits in the allotetraploidy species peanut.     

Identification of candidate genes at the <Emphasis Type="Italic">Dp-fl</Emphasis> locus conferring resistance against the rosy apple aphid <Emphasis Type="Italic">Dysaphis plantaginea</Emphasis>

The cultivated apple is susceptible to several pests including the rosy apple aphid (RAA; Dysaphis plantaginea Passerini), control of which is mainly based on chemical treatments. A few cases of resistance to aphids have been described in apple germplasm resources, laying the basis for the development of new resistant cultivars by breeding. The cultivar ‘Florina’ is resistant to RAA, and recently, the Dp-fl locus responsible for its resistance was mapped on linkage group 8 of the apple genome. In this paper, a chromosome walking approach was performed by using a ‘Florina’ bacterial artificial chromosome (BAC) library. The walking started from the available tightly linked molecular markers flanking the resistance region. Various walking steps were performed in order to identify the minimum tiling path of BAC clones covering the Dp-fl region from both the “resistant” and “susceptible” chromosomes of ‘Florina’. A genomic region of about 279 Kb encompassing the Dp-fl resistance locus was fully sequenced by the PacBio technology. Through the development of new polymorphic markers, the mapping interval around the resistance locus was narrowed down to a physical region of 95 Kb. The annotation of this sequence resulted in the identification of four candidate genes putatively involved in the RAA resistance response.     

Pyr-miR171f-targeted <Emphasis Type="Italic">PyrSCL6</Emphasis> and <Emphasis Type="Italic">PyrSCL22</Emphasis> genes regulate shoot growth by responding to IAA signaling in pear

MicroRNA171 (miR171) is a highly conserved miRNA family, crucial for plant growth and development, and has been reported in Arabidopsis thaliana and tomato (Solanum lycopersicum), but the role of miR171 has not been explored in pear. In this study, an effort was made to decipher the mechanism underlying dwarf in ‘Zhongai 3’, of which the shoot length and shoot growth rate during the growing season were much less than those of the vigorous cultivar ‘Zaosu’, and the same for the indole-3-acetic acid (IAA) content in shoot tips after May 22, 2016. We identified a member of the miR171 family, which was most sensitive to IAA and targeted two genes conformed by 5′-RACE, and we named Pyr-miR171f. The two targets were named as PyrSCL6 and PyrSCL22, and contained a GRAS-conserved domain and encoded nucleus proteins. Quantitative RT-PCR analysis revealed that Pyr-miR171f was more abundant in ‘Zaosu’ shoot tips than in ‘Zhongai 3’ shoot tips, whereas the PyrSCL6 and PyrSCL22 mRNAs were more abundant in ‘Zhongai 3’ shoot tips than in ‘Zaosu’ shoot tips. The abundance of Pyr-miR171f and PyrSCL6 and PyrSCL22 mRNAs increased, but the trends were opposite between Pyr-miR171f and its target mRNAs in tissue culture seedlings treated by IAA. Our results suggest that IAA-induced miR171f negatively regulates the IAA signaling cascade via the GRAS pathway to maintain apical dominance. This work reveals a role for the miR171-SCL pathway in the dwarfing of ‘Zhongai 3’, and provides a theoretical basis for dwarf pear breeding.     

QTLs for susceptibility to <Emphasis Type="Italic">Stemphylium vesicarium</Emphasis> in pear

Brown spot is one of the most serious fungal diseases that can affect pear fruits and leaves in the Po valley (Italy). Stemphylium vesicarium is the causal agent of this disease, and several antifungal treatments, repeated throughout the period between bloom and harvest, are needed to control its spread. Many of the most important pear cultivars (such as ‘Abbé Fétel’) are very susceptible to this fungus, while others (such as ‘Bartlett’ and its mutated sports) are known to be resistant. Our research aimed to develop molecular markers linked to this trait. To this end, 92 seedlings derived from an ‘Abbé Fétel’?×?‘Max Red Bartlett’ cross were evaluated for resistance to S. vesicarium for two consecutive years by artificial inoculation with conidia on detached leaves and fruits under controlled conditions in greenhouse. The extent of the lesions was recorded at different time points. A major QTL for susceptibility was located at the lower end of linkage group 15 of ‘Abbé Fétel’. This region was saturated with three SSR markers, and the putative position of a susceptibility gene was also estimated by the single gene mapping approach. This putative gene was located at 2 cM far from the lower end of the linkage group. Molecular markers tightly associated to this locus represent a first step towards the development of MAS (marker-assisted selection) to support the selection of new pear genotypes more resistant to brown spot.     

Genome-wide analysis and characterization of molecular evolution of the <Emphasis Type="Italic">HCT</Emphasis> gene family in pear (<Emphasis Type="Italic">Pyrus bretschneideri</Emphasis>)

Lignin is a major component of stone cells in pear fruit, which significantly affects fruit quality. Hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT), a recently discovered enzyme in plants, is an important gene that participates in the formation of lignin. Although HCT gene cloning and expression patterns have been studied in several species, including pear, there is still no extensive genome-wide bioinformatics analysis on the whole gene family, and the evolutionary history of HCT gene family is still unknown. A total of 82 HCT genes were identified in pear, most of which have one or two exons, and all with the conserved HXXXD motif and transferase domains. Based on the structural characteristics and phylogenetic analysis of these sequences, the HCT gene family genes could be classified into four main groups. Structural analysis also revealed that 25 % of HCT genes share a MYB binding site. Expansion of the HCT gene family mostly occurred before the divergence between Arabidopsis and Rosaceae, with whole-genome duplication or segmental duplication events playing the most important role in the expansion of the HCT gene family in pear. At the same time, purifying selection also played a critical role in the evolution of HCT genes. Five of the 82 HCT genes were verified by qRT-PCR to correspond to the pattern of stone cell formation during pear fruit development. The genome-wide identification, chromosome localization, gene structures, synteny, and expression analyses of pear HCT genes provide an overall insight into HCT gene family and their potential involvement in growth and development of stone cells.     

<Emphasis Type="Italic">ALDH2</Emphasis> genes are negatively correlated with natural deastringency in Chinese PCNA persimmon (<Emphasis Type="Italic">Diospyros kaki</Emphasis> Thunb.)

Chinese pollination-constant and non-astringent persimmon (C-PCNA) has important application values in the genetic improvement of PCNA for its trait of natural deastringency controlled by a single dominant gene. However, the key genes and the regulatory networks are still not fully understood. The process of C-PCNA natural deastringency may be associated with the acetaldehyde-mediated coagulation of soluble tannins, but the functions of ALDH2 genes related to the metabolism of acetaldehyde are not clear. In this work, three types of persimmon cultivars, ‘Eshi 1’ and ‘Luotian Tianshi’ (C-PCNA type), ‘Youhou’ (J-PCNA type), and ‘Mopanshi’ (non-PCNA type), were sampled. Two members of ALDH2 family genes, DkALDH2a and DkALDH2b, were isolated from ‘Eshi 1’ persimmon fruit. Gene expression patterns indicated that they may be involved in “coagulation effect”, which leads to natural deastringency in C-PCNA persimmon fruit. Transient expression in ‘Eshi 1’ leaves further demonstrated that their expression can reduce the consumption of soluble tannins and inhibit the astringency removal process. Therefore, DkALDH2a and DkALDH2b are negatively correlated with natural deastringency in C-PCNA persimmon.     

Development of SSR markers linked to QTL reducing leaf hair density and grapevine downy mildew resistance in <Emphasis Type="Italic">Vitis vinifera</Emphasis>

Dense leaf hairs of grapevines have been known to act as a preexisting defense structure for preventing the incidence of grapevine downy mildew, because the pathogen, Plasmopara viticola, needs water to invade grapevines, and water is repelled by a hydrophobic surface due to dense leaf hairs. In the present study, we performed regression analyses of downy mildew resistance with leaf hair density using hybrids of Vitis labrusca origin and confirmed the effect of leaf hairs. Reducing the repelling effect of leaf hairs by detergent application canceled the effect of leaf hair, which confirmed the hypothesis. Thereafter, based on QTL analyses in the population of V. vinifera ‘Muscat of Alexandria’ × the interspecific hybrid ‘Campbell Early,’ we identified a major locus in linkage group (LG) 5 of ‘Muscat of Alexandria’ controlling leaf hair density. This locus was previously reported as a small effect QTL for downy mildew resistance, however we found that the locus had high LOD scores explaining 71.9%–78.5% of the phenotypic variance of leaf hairs. Moreover, this locus was detected as a QTL for downy mildew resistance. The effect of this locus was confirmed in two other hybrid populations. Finally, we could successfully identify three traditional V. vinifera table grapes ‘Muscat of Alexandria,’ ‘Katta Kurgan,’ and ‘Parkent’ as the origin of the allele linked to hairlessness by defining the SSR haplotypes. The use of this locus for marker-assisted selections would be a promising strategy for producing grapevines with resistance by preexisting defense structure.     

Canola quality affects second (<Emphasis Type="Italic">Brevicoryne brassicae</Emphasis>) and third (<Emphasis Type="Italic">Diaeretiella rapae</Emphasis>) trophic levels

Biological control agents can be used as a complementary control measure that can be combined with resistant host plants to control pests. In this study, the effects of different canola cultivars (Karaj-1, Karaj-2, Karaj-3, Licord, Okapi, Opera, RGS₀₀₃, Sarigol, Talaye and Zarfam) on the performance and life table parameters of the cabbage aphid, Brevicoryne brassicae, and its parasitoid, Diaeretiella rapae, were determined under laboratory conditions. Total fecundity of the cabbage aphid differed with cultivar, with the highest value (59.41 nymphs per female) of this parameter observed on Opera and the lowest (1.67) observed on RGS₀₀₃. The highest and lowest intrinsic rates of increase (r) of the cabbage aphid were observed on Opera (0.331 day^?1) and RGS₀₀₃ (? 0.242 day^?1) cultivars, respectively, suggesting these to be the most susceptible and most resistant cultivars to this pest. However, because the aphid did not settle and feed well on RGS₀₀₃, it was not possible to determine demographic parameters for its parasitoid. Consequently, the Okapi cultivar, which was the most resistant cultivar to the cabbage aphid after RGS₀₀₃, was used in this study to assess the parasitoid wasp. The parasitoid’s intrinsic rate of increase (r) varied from 0.426 day^?1 on the susceptible cultivar (Opera) to 0.341 day^?1 on the resistant canola cultivar Okapi. Aphid performance decreased 93% on the resistant canola cultivar, while parasitoid performance decreased only 20% on the resistant cultivar compared to more susceptible cultivar.     

Rapid identification of QTLs underlying resistance to <Emphasis Type="Italic">Cucumber mosaic virus</Emphasis> in pepper (<Emphasis Type="Italic">Capsicum frutescens</Emphasis>)

Key message

Next-generation sequencing enabled a fast discovery of QTLs controlling CMV resistant in pepper. The gene CA02g19570 as a possible candidate gene of qCmr2.1 was identified for resistance to CMV in pepper.

Abstract

Cucumber mosaic virus (CMV) is one of the most important viruses infecting pepper, but the genetic basis of CMV resistance in pepper is elusive. In this study, we identified a candidate gene for CMV resistance QTL, qCmr2.1 through SLAF-seq. Segregation analysis in F₂, BC₁ and F_2:3 populations derived from a cross between two inbred lines ‘PBC688’ (CMV-resistant) and ‘G29’ (CMV-susceptible) suggested quantitative inheritance of resistance to CMV in pepper. Genome-wide comparison of SNP profiles between the CMV-resistant and CMV-susceptible bulks constructed from an F₂ population identified two QTLs, designated as qCmr2.1 on chromosome 2 and qCmr11.1 on chromosome 11 for resistance to CMV in PBC688, which were confirmed by InDel marker-based classical QTL mapping in the F₂ population. As a major QTL, joint SLAF-seq and traditional QTL analysis delimited qCmr2.1 to a 330 kb genomic region. Two pepper genes, CA02g19570 and CA02g19600, were identified in this region, which are homologous with the genes LOC104113703, LOC104248995, LOC102603934 and LOC101248357, which were predicted to encode N-like protein associated with TMV-resistant in Solanum crops. Quantitative RT-PCR revealed higher expression levels of CA02g19570 in CMV resistance genotypes. The CA02g19600 did not exhibit obvious regularity in expression patterns. Higher relative expression levels of CA02g19570 in PBC688 and F₁ were compared with those in G29 during days after inoculation. These results provide support for CA02g19570 as a possible candidate gene of qCmr2.1 for resistance to CMV in pepper.

     

Antixenosis and antibiosis response of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis>) to two-spotted spider mite (<Emphasis Type="Italic">Tetranychus urticae</Emphasis>)

The two-spotted spider mite, Tetranychus uticae Koch (Acari: Tetranychidae), is globally one of the most devastating pests that feed on numerous crops, including common bean (Phaseolus vulgaris L.). This study was aimed to evaluate the effects of genotype and morphological attributes of common bean on T. uticae. Forty common bean accessions were used to investigate antixenosis and antibiosis through assessing mite feeding preference and reproduction under laboratory conditions. Three resistant (i.e., 56, 63, 238) and two susceptible (i.e., 182, 236) accessions, along with cultivars Naz (resistant) and Akhtar (susceptible), were used in a life-table study. Both antixenosis and antibiosis mechanism were observed in all of the accessions, albeit a negative correlation occurred. Significant differences were observed for all traits of T. urticae: developmental time of immature stages, reproduction, adult longevity and life-table parameters. Based on the intrinsic rate of increase, the accessions 56, 63, 182, 238, and cv. Naz impose high antibiotic effects on T. urticae. Although significant variation existed among accessions for morphological factors, only glandular trichomes correlated with mite fecundity and feeding preference.     

Identification of <Emphasis Type="Italic">Pm58</Emphasis> from <Emphasis Type="Italic">Aegilops tauschii</Emphasis>

Key message

A novel powdery mildew-resistance gene, designated Pm58, was introgressed directly from Aegilops tauschii to hexaploid wheat, mapped to chromosome 2DS, and confirmed to be effective under field conditions. Selectable KASP? markers were developed for MAS.

Abstract

Powdery mildew caused by Blumeria graminis (DC.) f. sp. tritici (Bgt) remains a significant threat to wheat (Triticum aestivum L.) production. The rapid breakdown of race-specific resistance to Bgt reinforces the need to identify novel sources of resistance. The d-genome species, Aegilops tauschii, is an excellent source of disease resistance that is transferrable to T. aestivum. The powdery mildew-resistant Ae. tauschii accession TA1662 (2n?=?2x?=?DD) was crossed directly with the susceptible hard white wheat line KS05HW14 (2n?=?6x?=?AABBDD) followed by backcrossing to develop a population of 96 BC₂F₄ introgression lines (ILs). Genotyping-by-sequencing was used to develop a genome-wide genetic map that was anchored to the Ae. tauschii reference genome. A detached-leaf Bgt assay was used to screen BC₂F_4:6 ILs, and resistance was found to segregate as a single locus (χ?=?2.0, P value?=?0.157). The resistance gene, referred to as Pm58, mapped to chromosome 2DS. Pm58 was evaluated under field conditions in replicated trials in 2015 and 2016. In both years, a single QTL spanning the Pm58 locus was identified that reduced powdery mildew severity and explained 21% of field variation (P value?<?0.01). KASP? assays were developed from closely linked GBS-SNP markers, a refined genetic map was developed, and four markers that cosegregate with Pm58 were identified. This novel source of powdery mildew-resistance and closely linked genetic markers will support efforts to develop wheat varieties with powdery mildew resistance.

     

Barley 4H QTL confers NFNB resistance to a global set of <Emphasis Type="Italic">P. teres</Emphasis> f. <Emphasis Type="Italic">teres</Emphasis> isolates

Net form net blotch (NFNB), caused by Pyrenophora teres f. teres Drechs., is prevalent in barley-growing regions worldwide. A population of 132 recombinant inbred lines (RILs) developed from a cross of the barley varieties ‘Falcon’ and ‘Azhul’ were used to evaluate resistance to NFNB due to their differential reactions to isolates of P. teres f. teres from Australia, Canada, Japan, and the USA. Falcon is a six-rowed, hulless feed barley harboring resistance to NFNB, while Azhul is a six-rowed, hulless food barley with high levels of susceptibility to many P. teres f. teres isolates. Seedling disease resistance data were collected on seedlings of parents, RILs, and checks in a growth chamber. The population was genotyped using Illumina’s GoldenGate assay, and quantitative trait loci (QTL) were detected on chromosomes 2H, 3H, 4H, and 6H. We identified a single genetic region on barley chromosome 4H that provided varying levels of resistance to all P. teres f. teres isolates evaluated.     

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.

     

Fine mapping of a quantitative resistance gene for gray leaf spot of maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) derived from teosinte (<Emphasis Type="Italic">Z. mays</Emphasis> ssp. <Emphasis Type="Italic">parviglumis</Emphasis>)

Key message

In this study we mapped the QTL Qgls8 for gray leaf spot (GLS) resistance in maize to a ~130 kb region on chromosome 8 including five predicted genes.

Abstract

In previous work, using near isogenic line (NIL) populations in which segments of the teosinte (Zea mays ssp. parviglumis) genome had been introgressed into the background of the maize line B73, we had identified a QTL on chromosome 8, here called Qgls8, for gray leaf spot (GLS) resistance. We identified alternate teosinte alleles at this QTL, one conferring increased GLS resistance and one increased susceptibility relative to the B73 allele. Using segregating populations derived from NIL parents carrying these contrasting alleles, we were able to delimit the QTL region to a ~130 kb (based on the B73 genome) which encompassed five predicted genes.

     

Genetic mapping of <Emphasis Type="Italic">Stb19</Emphasis>, a new resistance gene to <Emphasis Type="Italic">Zymoseptoria tritici</Emphasis> in wheat

Key message

A new and dominant R gene Stb19 is identified from a soft wheat cultivar ‘Lorikeet’ and was mapped on the distal region of chromosome 1DS. Two tightly linked KASP markers were also discovered and validated for molecular-assisted breeding programs.

Abstract

A new R gene, designated as Stb19, provides resistance to Zymoseptoria tritici in wheat. This new dominant gene resides on the short arm of chromosome 1D, exhibiting complete resistance to three Z. tritici isolates, WAI332, WAI251, and WAI161, at the seedling stage. A genetic linkage map, based on an F_2:3 population of ‘Lorikeet’ and ‘Summit,’ found the Stb19 gene at a 9.3 cM region on 1DS, closely linked with two Kompetitive Allele-Specific PCR markers, snp_4909967 and snp_1218021. Further, the two markers were tested and validated in another F_2:3 population and 266 different wheat accessions, which gave over 95% accuracy of resistance/susceptibility prediction. Combined with the physical location of the identified SNPs and the previous evidence of gene order on chromosome 1DS (centromere–Sr45–Sr33–Lr21–telomere), Stb19 is proposed to be located between Sr33 and Lr21. Thus, the newly discovered Stb19 along with the KASP markers represents an increase in genetic resources available for wheat breeding resistance to Z. tritici.

     

<Emphasis Type="Italic">STAYGREEN</Emphasis> (<Emphasis Type="Italic">CsSGR</Emphasis>) is a candidate for the anthracnose (<Emphasis Type="Italic">Colletotrichum orbiculare</Emphasis>) resistance locus <Emphasis Type="Italic">cla</Emphasis> in Gy14 cucumber

Key message

Map-based cloning identified a candidate gene for resistance to the anthracnose fungal pathogen Colletotrichum orbiculare in cucumber, which reveals a novel function for the highly conserved STAYGREEN family genes for host disease resistance in plants.

Abstract

Colletotrichum orbiculare is a hemibiotrophic fungal pathogen that causes anthracnose disease in cucumber and other cucurbit crops. No host resistance genes against the anthracnose pathogens have been cloned in crop plants. Here, we reported fine mapping and cloning of a resistance gene to the race 1 anthracnose pathogen in cucumber inbred lines Gy14 and WI 2757. Phenotypic and QTL analysis in multiple populations revealed that a single recessive gene, cla, was underlying anthracnose resistance in both lines, but WI2757 carried an additional minor-effect QTL. Fine mapping using 150 Gy14?×?9930 recombinant inbred lines and 1043 F₂ individuals delimited the cla locus into a 32 kb region in cucumber Chromosome 5 with three predicted genes. Multiple lines of evidence suggested that the cucumber STAYGREEN (CsSGR) gene is a candidate for the anthracnose resistance locus. A single nucleotide mutation in the third exon of CsSGR resulted in the substitution of Glutamine in 9930 to Arginine in Gy14 in CsSGR protein which seems responsible for the differential anthracnose inoculation responses between Gy14 and 9930. Quantitative real-time PCR analysis indicated that CsSGR was significantly upregulated upon anthracnose pathogen inoculation in the susceptible 9930, while its expression was much lower in the resistant Gy14. Investigation of allelic diversities in natural cucumber populations revealed that the resistance allele in almost all improved cultivars or breeding lines of the U.S. origin was derived from PI 197087. This work reveals an unknown function for the highly conserved STAYGREEN (SGR) family genes for host disease resistance in plants.

     

Discovery and introgression of the wild sunflower-derived novel downy mildew resistance gene <Emphasis Type="Italic">Pl</Emphasis><Subscript><Emphasis Type="Italic">19</Emphasis></Subscript> in confection sunflower (<Emphasis Type="Italic">Helianthus annuus</Emphasis> L.)

Key message

A new downy mildew resistance gene, Pl ₁₉ , was identified from wild Helianthus annuus accession PI 435414, introduced to confection sunflower, and genetically mapped to linkage group 4 of the sunflower genome.

Abstract

Wild Helianthus annuus accession PI 435414 exhibited resistance to downy mildew, which is one of the most destructive diseases to sunflower production globally. Evaluation of the 140 BC₁F_2:3 families derived from the cross of CMS CONFSCLB1 and PI 435414 against Plasmopara halstedii race 734 revealed that a single dominant gene controls downy mildew resistance in the population. Bulked segregant analysis conducted in the BC₁F₂ population with 860 simple sequence repeat (SSR) markers indicated that the resistance derived from wild H. annuus was associated with SSR markers located on linkage group (LG) 4 of the sunflower genome. To map and tag this resistance locus, designated Pl ₁₉ , 140 BC₁F₂ individuals were used to construct a linkage map of the gene region. Two SSR markers, ORS963 and HT298, were linked to Pl ₁₉ within a distance of 4.7 cM. After screening 27 additional single nucleotide polymorphism (SNP) markers previously mapped to this region, two flanking SNP markers, NSA_003564 and NSA_006089, were identified as surrounding the Pl ₁₉ gene at a distance of 0.6 cM from each side. Genetic analysis indicated that Pl ₁₉ is different from Pl ₁₇ , which had previously been mapped to LG4, but is closely linked to Pl ₁₇ . This new gene is highly effective against the most predominant and virulent races of P. halstedii currently identified in North America and is the first downy mildew resistance gene that has been transferred to confection sunflower. The selected resistant germplasm derived from homozygous BC₂F₃ progeny provides a novel gene for use in confection sunflower breeding programs.

     

Identification and fine mapping of <Emphasis Type="Italic">qWBPH11</Emphasis> conferring resistance to whitebacked planthopper (<Emphasis Type="Italic">Sogatella furcifera</Emphasis> Horvath) in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

The whitebacked planthopper (WBPH), Sogatella furcifera Horvath, is one of the most destructive pests in rice (Oryza sativa L.) production. Host-plant resistance has been considered as an efficient and eco-friendly strategy to reduce yield losses caused by WBPH. In this study, we found that an indica rice cultivar IR54751-2-44-15-24-2 (IR54751) displayed high resistance to WBPH at both seedling and tillering stages. The resistance of IR54751 was mainly contributed by antixenosis and tolerance rather than antibiosis. An F₂ population derived from a cross between IR54751 and a susceptible japonica cultivar 02428 was constructed to detect the quantitative trait loci (QTLs) conferring the resistance to WBPH. In total, four QTLs including qWBPH3.1, qWBPH3.2, qWBPH11, and qWBPH12 were identified and distributed on three different chromosomes. The four QTLs had LOD scores of 3.8, 8.2, 5.8, and 3.9, accounting for 8.2, 21.5, 13.9, and 10.4% of the phenotypic variation, respectively. Except for qWBPH3.1, the resistance alleles of the other three QTLs were all from IR54751. Further, a secondary population harboring only single qWBPH11 locus was developed from the F₂ population by marker-assisted selection. Finally, qWBPH11 was delimited in a 450-kb region between markers DJ53973 and SNP56. The identification of WBPH resistance QTLs and the fine mapping of qWBPH11 will be helpful for cloning resistance genes and breeding resistant rice cultivars.