Multiple alleles for resistance and susceptibility modulate the defense response in the interaction of tetraploid potato (<Emphasis Type="Italic">Solanum tuberosum</Emphasis>) with <Emphasis Type="Italic">Synchytrium endobioticum</Emphasis> pathotypes 1, 2, 6 and 18

The obligate biotrophic, soil-borne fungus Synchytrium endobioticum causes wart disease of potato (Solanum tuberosum), which is a serious problem for crop production in countries with moderate climates. S. endobioticum induces hypertrophic cell divisions in plant host tissues leading to the formation of tumor-like structures. Potato wart is a quarantine disease and chemical control is not possible. From 38 S. endobioticum pathotypes occurring in Europe, pathotypes 1, 2, 6 and 18 are the most relevant. Genetic resistance to wart is available but only few current potato varieties are resistant to all four pathotypes. The phenotypic evaluation of wart resistance is laborious, time-consuming and sometimes ambiguous, which makes breeding for resistance difficult. Molecular markers diagnostic for genes for resistance to S. endobioticum pathotypes 1, 2, 6 and 18 would greatly facilitate the selection of new, resistant cultivars. Two tetraploid half-sib families (266 individuals) segregating for resistance to S. endobioticum pathotypes 1, 2, 6 and 18 were produced by crossing a resistant genotype with two different susceptible ones. The families were scored for five different wart resistance phenotypes. The distribution of mean resistance scores was quantitative in both families. Resistance to pathotypes 2, 6 and 18 was correlated and independent from resistance to pathotype 1. DNA pools were constructed from the most resistant and most susceptible individuals and screened with genome wide simple sequence repeat (SSR), inverted simple sequence region (ISSR) and randomly amplified polymorphic DNA (RAPD) markers. Bulked segregant analysis identified three SSR markers that were linked to wart resistance loci (Sen). Sen1-XI on chromosome XI conferred partial resistance to pathotype 1, Sen18-IX on chromosome IX to pathotype 18 and Sen2/6/18-I on chromosome I to pathotypes 2,6 and 18. Additional genotyping with 191 single nucleotide polymorphism (SNP) markers confirmed the localization of the Sen loci. Thirty-three SNP markers linked to the Sen loci permitted the dissection of Sen alleles that increased or decreased resistance to wart. The alleles were inherited from both the resistant and susceptible parents.     

A new leaf rust resistance gene <Emphasis Type="Italic">Lr79</Emphasis> mapped in chromosome 3BL from the durum wheat landrace Aus26582

Key message

A new leaf rust resistance gene Lr79 has been mapped in the long arm of chromosome 3B and a linked marker was identified for marker-assisted selection.

Abstract

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

     

Fine mapping of the rosy apple aphid resistance locus <Emphasis Type="Italic">Dp-fl</Emphasis> on linkage group 8 of the apple cultivar ‘Florina’

Rosy apple aphid (Dysaphis plantaginea), is one of the major insect pests of apple, causing serious physical and economic damage to fruit production. A dominant resistance gene Dp-fl was previously mapped at the bottom of linkage group LG8 from the cultivar ‘Florina’, linked to the SSR CH01h10. The development of additional genetic markers mapping closer to Dp-fl was needed to position the gene accurately and to improve the effectiveness of marker-assisted breeding (MAB). The aims of this study were to identify single nucleotide polymorphisms (SNPs) in the region of Dp-fl and to position these SNPs relative to Dp-fl. To generate a fine map of the Dp-fl interval, a total of 191 plants segregating for resistance and derived from four different populations were tested with temperature-switch PCR (TSP) markers developed for SNPs located in the region of CH01h10. All the plants were phenotypically evaluated for aphid resistance and those data compared with the genetic data. These efforts resulted in positioning the Dp-fl resistance locus in a genetic interval corresponding to a physical distance of about 330 kb on the ‘Golden Delicious’ genome. The new markers were tested on several apple founder cultivars in order to test the specificity of the SNPs and, thus, the best markers for the MAB were identified. Finally, the 330-kb interval was analyzed for the identification of coding sequences and putative candidate genes for D. plantaginea resistance were identified.     

Characterization of aphid resistance loci in black raspberry (<Emphasis Type="Italic">Rubus occidentalis</Emphasis> L.)

Viruses vectored by the aphid Amphorophora agathonica cause decline in black raspberry plant health resulting in a shortened life and poor fruit quality of the infected plantings. New aphid resistant cultivars could increase the longevity of plantings providing growers and processors with consistent fruit production. Recent exploration of the native range of black raspberry identified three sources of aphid resistance: Ag₄ from Ontario (ON), Canada, Ag₅ from Maine (ME), and a third source from Michigan (MI) with no formal designation. The objectives of this study were to assess segregation of these three sources of aphid resistance in populations with single and combined sources and develop markers that can identify each source of resistance. A genetic linkage map constructed for ORUS 4305 placed the ON aphid resistance locus on Rubus linkage group (RLG) 6. Segregation ratios in populations with single and combined sources, and linkage mapping in two populations (ORUS 4304 and ORUS 4812) segregating for the Ag₅ and MI sources, respectively, indicated that these three sources of resistance are each conferred by single dominant genes/alleles that are linked on RLG6. Confirmation of marker association in 16 validation populations identified four markers that could be used to predict resistance; however, none could distinguish between the ON and MI sources. These four markers may be useful for screening populations to enrich the field-planted progeny for aphid resistance. Fine mapping of the resistance loci is needed to develop functional markers at each of the resistance loci to enable pyramiding and durable aphid resistance.     

The gene conferring susceptibility to spot blotch caused by <Emphasis Type="Italic">Cochliobolus sativus</Emphasis> is located at the <Emphasis Type="Italic">Mla</Emphasis> locus in barley cultivar Bowman

Key message

We identified, fine mapped, and physically anchored a dominant spot blotch susceptibility gene Scs6 to a 125 kb genomic region containing the Mla locus on barley chromosome 1H.

Abstract

Spot blotch caused by Cochliobolus sativus is an important disease of barley, but the molecular mechanisms underlying resistance and susceptibility to the disease are not well understood. In this study, we identified and mapped a gene conferring susceptibility to spot blotch caused by the pathotype 2 isolate (ND90Pr) of C. sativus in barley cultivar Bowman. Genetic analysis of F₁ and F₂ progeny as well as F₃ families from a cross between Bowman and ND 5883 indicated that a single dominant gene (designated as Scs6) conferred spot blotch susceptibility in Bowman. Using a doubled haploid (DH) population derived from a cross between Calicuchima-sib (resistant) and Bowman-BC (susceptible), we confirmed that Scs6, contributed by Bowman-BC, was localized at the same locus as the previously identified spot blotch resistance allele Rcs6, which was contributed by Calicuchima-sib and mapped on the short arm of chromosome 1H. Using a genome-wide putative linear gene index of barley (Genome Zipper), 13 cleaved amplified polymorphism markers were developed from 11 flcDNA and two EST sequences and mapped to the Scs6/Rcs6 region on a linkage map constructed with the DH population. Further fine mapping with markers developed from barley genome sequences and F₂ recombinants derived from Bowman?×?ND 5883 and Bowman?×?ND B112 crosses delimited Scs6 in a 125 kb genomic interval harboring the Mla locus on the reference genome of barley cv. Morex. This study provides a foundational step for further cloning of Scs6 using a map-based approach.

     

QTL mapping of Fusarium head blight resistance in three related durum wheat populations

Key message

The QTL Fhb1 was successfully introgressed and validated in three durum wheat populations. The novel germplasm and the QTL detected will support improvement of Fusarium resistance in durum wheat.

Abstract

Durum wheat (Triticum durum Desf.) is particularly susceptible to Fusarium head blight (FHB) and breeding for resistance is hampered by limited genetic variation within this species. To date, resistant sources are mainly available in a few wild relative tetraploid wheat accessions. In this study, the effect of the well-known hexaploid wheat (Triticum aestivum L.) quantitative trait locus (QTL) Fhb1 was assessed for the first time in durum wheat. Three F7-RIL mapping populations of about 100 lines were developed from crosses between the durum wheat experimental line DBC-480, which carries an Fhb1 introgression from Sumai-3, and the European T. durum cultivars Karur, Durobonus and SZD1029K. The RILs were evaluated in field experiments for FHB resistance in three seasons using spray inoculation and genotyped with SSR as well as genotyping-by-sequencing markers. QTL associated with FHB resistance were identified on chromosome arms 2BL, 3BS, 4AL, 4BS, 5AL and 6AS at which the resistant parent DBC-480 contributed the positive alleles. The QTL on 3BS was detected in all three populations centered at the Fhb1 interval. The Rht-B1 locus governing plant height was found to have a strong effect in modulating FHB severity in all populations. The negative effect of the semi-dwarf allele Rht-B1b on FHB resistance was compensated by combining with Fhb1 and additional resistance QTL. The successful deployment of Fhb1 in T. durum was further substantiated by assessing type 2 resistance in one population. The efficient introgression of Fhb1 represents a significant step forward for enhancing FHB resistance in durum wheat.

     

Characterisation and mapping of adult plant stripe rust resistance in wheat accession Aus27284

Key message

A new adult plant stripe rust resistance gene, Yr80, was identified in a common wheat landrace Aus27284. Linked markers were developed and validated for their utility in marker-assisted selection.

Abstract

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the most important constraints to global wheat production. The identification and characterisation of new sources of host plant resistance enrich the gene pool and underpin deployment of resistance gene pyramids in new cultivars. Aus27284 exhibited resistance at the adult plant stage against predominant Pst pathotypes and was crossed with a susceptible genotype Avocet S. A recombinant inbred line (RIL) population comprising 121 lines was developed and tested in the field at three locations in 2016 and two in 2017 crop seasons. Monogenic segregation for adult plant stripe rust response was observed among the Aus27284/Avocet S RIL population and the underlying locus was temporarily designated YrAW11. Bulked-segregant analysis using the Infinium iSelect 90K SNP wheat array placed YrAW11 in chromosome 3B. Kompetitive allele specific PCR (KASP) primers were designed for the linked SNPs and YrAW11 was flanked by KASP_65624 and KASP_53292 (3 cM) proximally and KASP_53113 (4.9 cM) distally. A partial linkage map of the genomic region carrying YrAW11 comprised nine KASP and two SSR markers. The physical position of KASP markers in the pseudomolecule of chromosome 3B placed YrAW11 in the long arm and the location of markers gwm108 and gwm376 in the deletion bin 3BL2-0.22 supported this conclusion. As no other stripe rust resistance locus has been reported in chromosome 3BL, YrAW11 was formally designated Yr80. Marker KASP_ 53113 was polymorphic among 94% of 81 Australian wheat cultivars used for validation.

     

Characterizing the pathotype structure of barley powdery mildew and effectiveness of resistance genes to this pathogen in Kazakhstan

Background

Powdery mildew of barley is a wind-borne and obligate biotrophic pathogen, which ranks among the most widespread barley pathogens worldwide. However, purposeful research towards studying the structure of the barley powdery mildew populations, of their virulence and of effectiveness of certain resistance genes against the infection was not conducted in Kazakhstan till present time. This paper is the first to describe characteristics of the pathotype structure of Blumeria graminis f.sp. hordei (Bgh) population and effectiveness of resistance genes in two regions of barley cultivation in the republic.

Results

One hundred and seven isolates of Bgh were obtained from seven populations occurring on cultivated barley at two geographically locations in Kazakhstan during 2015 and 2016. Their virulence frequency was determined on 17 differential lines Pallas. All isolates were virulent on the resistance gene Mla8 and avirulent for the resistance genes Mla9, Mla1 + MlaAl2, Mla6 + Mla14, Mla13 + MlRu3, Mla7 + MlNo3, Mla10 + MlDu2, Mla13 + MlRu3 and Mlo-5. The frequencies of isolates overcoming the genes Mla3, Mla22, Mlat Mlg + MlCP and Mla12 + MlEm2 were 0.0–33.33%, and frequencies of isolates overcoming the genes Mlra, Mlk, MlLa and Mlh ranged from 10.0 to 78.6%. Based on reactions of differential lines possessing the genes Mla22, Mlra, Mlk, Mlat, MlLa and Mlh, pathotypes were identified. In total, 23 pathotypes with virulence complexity ranging from 1 to 6 were identified. During both years in all populations of South Kazakhstan and Zhambyl regions pathotypes 24 and 64 mainly prevailed.

Conclusions

Obtained data suggest that low similarity of populations Bgh in Kazakhstan to European, African, Australian and South-East Asian populations. The present study provides a foundation for future studies on the pathogenic variability within of Bgh populations in Kazakhstan and addresses the knowledge gap on the virulence structure of Bgh in Central Asia. Complete effectiveness of the resistance genes, for which no corresponding virulence was found, will allow Kazakhstanean breeders to access many modern barley cultivars that those possessing the resistance effectiveness genes.

     

Production of potato breeding material using somatic hybrids between <Emphasis Type="Italic">Solanum tuberosum</Emphasis> L. dihaploids and the wild diploid species <Emphasis Type="Italic">Solanum bulbocastanum</Emphasis> Dunal. from Mexico

An original approach to overcome interspecific incompatibility when backcrossing the tetraploid Solanum tuberosum + S. bulbocastanum somatic hybrids with cultivated potato was realized. This method is based on the decrease in their ploidy using anther culture and involvement of the haploid producer S. phureja IvP35. The feasibility of obtaining a diploid progeny from the somatic hybrids carrying genetic material of the wild species S. bulbocastanum and crossable with S. tuberosum dihaploids was demonstrated.     

High resolution DNA melting markers for identification of <Emphasis Type="Italic">H1</Emphasis>-linked resistance to potato cyst nematode

Although Sequence-Characterized Amplified Region (SCAR) markers linked to the potato H1 locus, which confers resistance to pathotypes Ro1 and Ro4 of the potato cyst nematode (PCN) Globodera rostochiensis, have been reported, robust markers that enable estimation of allele dosage would improve the quality of information obtained from genotyping parental accessions (cultivars/breeding lines) and progeny populations within breeding programmes. With this in mind, we have developed single nucleotide polymorphism (SNP)-based molecular markers flanking the H1 resistance gene, using genomic re-sequence data from five elite tetraploid accessions. The published TG689 and 57R primer sequences were used in a Basic Local Alignment Search Tool (BLAST) examination of the reference potato genome, and SNPs within the vicinity of these primer regions were identified and targeted for designing probe-based High Resolution Melting (HRM) SNP assays. Evaluation of the subsequently developed HRM markers, TG689_1P and 57R_1P, against the publicly available SCAR markers, TG689 and 57R, indicated that the HRM markers enabled more reliable marker-trait association than the SCARs. Additionally, allelic dosage estimates for the H1 locus were also derived using the TG689_1P marker, providing a tool to optimise parental and progeny selections in PCN resistance breeding.     

Rapid identification of an adult plant stripe rust resistance gene in hexaploid wheat by high-throughput SNP array genotyping of pooled extremes

Key message

High-throughput SNP array analysis of pooled extreme phenotypes in a segregating population by KASP marker genotyping permitted rapid, cost-effective location of a stripe rust resistance QTL in wheat.

Abstract

German wheat cultivar “Friedrichswerther” has exhibited high levels of adult plant resistance (APR) to stripe rust in field environments for many years. F_2:3 lines and F₆ recombinant inbred line (RILs) populations derived from a cross between Friedrichswerther and susceptible landrace Mingxian 169 were evaluated in the field in 2013, 2016 and 2017. Illumina 90K iSelect SNP arrays were used to genotype bulked extreme pools and parents; 286 of 1135 polymorphic SNPs were identified on chromosome 6B. Kompetitive Allele-Specific PCR (KASP) markers were used to verify the chromosome region associated with the resistance locus. A linkage map was constructed with 18 KASP-SNP markers, and a major effect QTL was identified within a 1.4 cM interval flanked by KASP markers IWB71602 and IWB55937 in the region 6BL3-0-0.36. The QTL, named QYr.nwafu-6BL, was stable across environments, and explained average 54.4 and 47.8% of the total phenotypic variation in F_2:3 lines and F₆ RILs, respectively. On the basis of marker genotypes, pedigree analysis and relative genetic distance QYr.nwafu-6BL is likely to be a new APR QTL. Combined high-throughput SNP array genotyping of pooled extremes and validation by KASP assays lowers sequencing costs compared to genome-wide association studies with SNP arrays, and more importantly, permits rapid isolation of major effect QTL in hexaploid wheat as well as improving accuracy of mapping in the QTL region. QYr.nwafu-6BL with flanking KASP markers developed and verified in a subset of 236 diverse lines can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.

     

Genome-wide association mapping of spot blotch resistance to three different pathotypes of <Emphasis Type="Italic">Cochliobolus sativus</Emphasis> in the USDA barley core collection

Spot blotch, caused by Cochliobolus sativus, is an economically important disease of barley. To identify genetic loci conferring resistance to three different pathotypes of C. sativus, a worldwide barley core collection (BCC) consisting of 1480 accessions from the USDA National Small Grains Collection were genotyped with the barley 9k Illumina Infinium iSELECT assay and phenotyped at the seedling stage with three C. sativus isolates ND85F (pathotype 1), ND90Pr (pathotype 2), and ND4008 (pathotype 7). Association mapping analysis was performed with the Whole_Panel containing 1480 barley accessions, as well as Two-rowed_Panel and Six-rowed_Panel consisting of 621 two-rowed and 857 six-rowed barley accessions, respectively. For resistance to isolate ND4008, one quantitative trait locus (QTL, QRcs-6H-P7) was detected in all three panels. Three other QTL (QRcs-1H-P7, QRcs-2H-P7, and QRcs-3H-P7) were detected in Whole_Panel, Six-rowed_Panel, and Two-rowed_Panel, respectively. For resistance to isolate ND90Pr, one QTL (QRcs-1H-P2) was identified in the Whole_Panel and the Two-rowed_Panel, and the other QTL (QRcs-6H-P2) was only identified in the Six-rowed_Panel. For resistance to isolate ND85F, three QTL (QRcs-1H-P1, QRcs-3H-P1, QRcs-7H-2-P1) were detected in all three panels, and one QTL (QRcs-7H-1-P1) was only detected in the Two-rowed_Panel. Among the ten QTL detected, four (QRcs-1H-P1, QRcs-3H-P1, QRcs-7H-2-P1, and QRcs-1H-P2) were mapped to chromosome regions containing previously identified QTL for spot blotch resistance, while six (QRcs-1H-P7, QRcs-2H-P7, QRcs-3H-P7, QRcs-6H-P7, QRcs-6H-P2, and QRcs-7H-1-P1) were novel. The SNP markers associated with the QTL identified in this study will be useful for breeding barley cultivars with resistance to multiple pathotypes of C. sativus.     

A major locus for resistance to <Emphasis Type="Italic">Botryosphaeria dothidea</Emphasis> in <Emphasis Type="Italic">Prunus</Emphasis>

Species in the fungal family Botryosphaeriaceae are significant pathogens of peach. The climatic conditions in the Southeastern USA are conducive to the development of peach fungal gummosis (PFG) with an estimated yield reduction of up to 40% in severe cases. Genotypes with resistance to this PFG were identified in interspecific crosses and segregating backcross populations generated using Kansu peach (Prunus kansuensis Rehder), almond [Prunus dulcis (Mill.) D.A. Webb], and peach [Prunus persica (L.) Batsch]. Hybrids were evaluated for four consecutive years in field conditions. Data generated was validated in different environments using clonal replicates of the hybrids. The F₁ and BC₁F₁ segregation population data suggest a dominant allele for PFG resistance originating from almond. Segregation and mapping analysis located the PFG resistance locus on a chimeric linkage groups 6–8 near the leaf color locus. The molecular markers identified will facilitate marker-assisted selection (MAS) and introgression of this resistance trait into commercial peach germplasm.     

Genetic analysis and localization of loci controlling leaf rust resistance of <Emphasis Type="Italic">Triticum aestivum</Emphasis> × <Emphasis Type="Italic">Triticum timopheevii</Emphasis> introgression lines

Introgressive lines resulting from crossing common wheat Triticum aestivum with the tetraploid T. timopheevii are characterized by effective resistance to leaf rust caused by Puccinia triticina Eriks. Molecular analysis using 350 specific simple sequence repeat (SSR) markers determined localization of the T. timopheevii genome in chromosomes 1A, 2A, 2B, 5A, 5B, and 6B. A population of F₂ offspring of crossing hybrid line 842-2 with common wheat cultivar Skala was obtained for mapping the loci controlling leaf rust resistance. Analysis of association of phenotypic and genotypic data by means of simple interval mapping (SIM) and composite interval mapping (CIM) has shown that the resistance of adult plants is determined by two loci in chromosomes 5B and 2A. The major locus QLr.icg-5B, transferred from T. timopheevii chromosome 5G mapped to the interval of microsatellite loci Xgwm408-Xgwm1257 controls 72% of the phenotypic variance of the trait. The other, minor locus QLr.icg-2A located to chromosome 2A at a distance of 10 cM from Xgwm312 accounts for 7% of the trait expression. Microsatellite markers located near these loci may be used for controlling the transfer of agronomically valuable loci when new lines and cultivars are created.     

Graphical genotyping as a method to map <Emphasis Type="Italic">Ny</Emphasis><Subscript><Emphasis Type="Italic">(o,n)sto</Emphasis></Subscript> and <Emphasis Type="Italic">Gpa5</Emphasis> using a reference panel of tetraploid potato cultivars

Key message

The method of graphical genotyping is applied to a panel of tetraploid potato cultivars to visualize haplotype sharing. The method allowed to map genes involved in virus and nematode resistance. The physical coordinates of the amount of linkage drag surrounding these genes are easily interpretable.

Abstract

Graphical genotyping is a visually attractive and easily interpretable method to represent genetic marker data. In this paper, the method is extended from diploids to a panel of tetraploid potato cultivars. Application of filters to select a subset of SNPs allows one to visualize haplotype sharing between individuals that also share a specific locus. The method is illustrated with cultivars resistant to Potato virus Y (PVY), while simultaneously selecting for the absence of the SNPs in susceptible clones. SNP data will then merge into an image which displays the coordinates of a distal genomic region on the northern arm of chromosome 11 where a specific haplotype is introgressed from the wild potato species S. stoloniferum (CPC 2093) carrying a gene (Ny _(o,n)sto ) conferring resistance to two PVY strains, PVY^O and PVY^NTN. Graphical genotyping was also successful in showing the haplotypes on chromosome 12 carrying Ry-f _sto , another resistance gene derived from S. stoloniferum conferring broad-spectrum resistance to PVY, as well as chromosome 5 haplotypes from S. vernei, with the Gpa5 locus involved in resistance against Globodera pallida cyst nematodes. The image also shows shortening of linkage drag by meiotic recombination of the introgression segment in more recent breeding material. Identity-by-descent was found to be a requirement for using graphical genotyping, which is proposed as a non-statistical alternative method for gene discovery, as compared with genome-wide association studies. The potential and limitations of the method are discussed.

     

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.

     

Genetic identification of SNP markers linked to a new grape phylloxera resistant locus in <Emphasis Type="Italic">Vitis cinerea</Emphasis> for marker-assisted selection

Background

Grape phylloxera (Daktulosphaira vitifoliae Fitch) is a major insect pest that negatively impacts commercial grapevine performance worldwide. Consequently, the use of phylloxera resistant rootstocks is an essential component of vineyard management. However, the majority of commercially available rootstocks used in viticulture production provide limited levels of grape phylloxera resistance, in part due to the adaptation of phylloxera biotypes to different Vitis species. Therefore, there is pressing need to develop new rootstocks better adapted to specific grape growing regions with complete resistance to grape phylloxera biotypes.

Results

Grapevine rootstock breeding material, including an accession of Vitis cinerea and V. aestivalis, DRX55 ([M. rotundifolia x V. vinifera] x open pollinated) and MS27-31 (M. rotundifolia specific hybrid), provided complete resistance to grape phylloxera in potted plant assays. To map the genetic factor(s) of grape phylloxera resistance, a F₁ V. cinerea x V. vinifera Riesling population was screened for resistance. Heritability analysis indicates that the V. cinerea accession contained a single allele referred as RESISTANCE TO DAKTULOSPHAIRA VITIFOLIAE 2 (RDV2) that confers grape phylloxera resistance. Using genetic maps constructed with pseudo-testcross markers for V. cinerea and Riesling, a single phylloxera resistance locus was identified in V. cinerea. After validating SNPs at the RDV2 locus, interval and linkage mapping showed that grape phylloxera resistance mapped to linkage group 14 at position 16.7 cM.

Conclusion

The mapping of RDV2 and the validation of markers linked to grape phylloxera resistance provides the basis to breed new rootstocks via marker-assisted selection that improve vineyard performance.

     

Managing potato wart: a review of present research status and future perspective

Key message

Identification of resistance genes to potato wart disease caused by Synchytrium endobioticum is the key for developing diagnostic markers for breeding resistant cultivars. We present an overview on the current knowledge of this host-pathogen system and molecular advances while highlighting future research focus.

Abstract

Potato wart is a quarantined disease of cultivated potato (Solanum tuberosum L.) caused by the obligate biotrophic, soil-borne fungus Synchytrium endobioticum (Schilb.) Perc. Since its discovery by Schilberszky in 1896, the management of wart disease was enabled by research efforts focusing on understanding and classifying the causative agent, its mode of infection, pathogenesis, geographical distribution, detection and chemical control, on developing screening methods for host resistance and on genetic analyses, which led to the development of resistant cultivars. These early successes are currently challenged by new S. endobioticum pathotypes evolving and the increased risk of dissemination by potato tuber trade. New research efforts are therefore required to ensure continuation of effective and sustainable management of the potato wart disease. Advances in molecular biology and genomic tools offer potential for innovations. This review presents an overview on what we know about this complex host-pathogen interaction, highlights recent molecular work and embarks on an outlook towards future research directions.     

QTL-seq and marker development for resistance to <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="Italic">niveum</Emphasis> race 1 in cultivated watermelon

Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. niveum (Fon), is one of the predominant diseases of watermelon. Resistance to Fon race 1 is conferred by a single major quantitative trait locus (QTL), Fo-1.1, but resolution of this region has been poor due to low marker density. In this study, a combination of whole genome resequencing of bulked segregants (QTL-seq analysis) followed by QTL mapping with kompetitive allele specific PCR (KASP) markers developed across Fo-1.1 successfully increased the resolution from 2.03 to 1.56 Mb and 315 kb, respectively. The linkage of the KASP markers to Fon race 1 resistance across a wide range of watermelon germplasm was validated in a set of elite watermelon cultivars. The linked markers described here provide a breeder-friendly toolkit immediately available for high-throughput genotyping in large-scale breeding programs for fine mapping and incorporation of Fon race 1 resistance in watermelon.     

Genome-wide association mapping for seedling and field resistance to <Emphasis Type="Italic">Puccinia striiformis</Emphasis> f. sp. <Emphasis Type="Italic">tritici</Emphasis> in elite durum wheat

Key message

Genome-wide association analysis in tetraploid wheat revealed novel and diverse loci for seedling and field resistance to stripe rust in elite spring durum wheat accessions from worldwide.

Abstract

Improving resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major objective for wheat breeding. To identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using 232 elite durum wheat (Triticum turgidum ssp. durum) lines from worldwide breeding programs. Genotyping with the 90 K iSelect wheat single nucleotide polymorphism (SNP) array resulted in 11,635 markers distributed across the genome. Response to stripe rust infection at the seedling stage revealed resistant and susceptible accessions present in rather balanced frequencies for the six tested races, with a higher frequency of susceptible responses to United States races as compared to Italian races (61.1 vs. 43.1% of susceptible accessions). Resistance at the seedling stage only partially explained adult plant resistance, which was found to be more frequent with 67.7% of accessions resistant across six nurseries in the United States. GWAS identified 82 loci associated with seedling stripe rust resistance, five of which were significant at the false discovery rate adjusted P value <0.1 and 11 loci were detected for the field response at the adult plant stages in at least two environments. Notably, Yrdurum-1BS.1 showed the largest effect for both seedling and field resistance, and is therefore considered as a major locus for resistance in tetraploid wheat. Our GWAS study is the first of its kind for stripe rust resistance in tetraploid wheat and provides an overview of resistance in elite germplasm and reports new loci that can be used in breeding resistant cultivars.