Septoria Speckled Leaf Blotch Research Articles

Barley diseases and their management- an Indian perspective

Barley is an important coarse cereal, cultivated in Rabi season, particularly in the states of Uttar Pradesh, Rajasthan, Madhya Pradesh, Bihar, Punjab, Haryana, Himachal Pradesh and Jammu & Kashmir. Currently, it covers an area of about 0.66 million hectares under rainfed and irrigated crop. Seventy percent produce is used for cattle and poultry feed, 25% in industries for manufacturing malt and malt extracts and rest 5% for human consumption. The straw is also used for animal feed, bedding and to cover roofs of houses. Barley grains demand is increasing continuously because of its various uses and high nutritive value. Therefore, a substantial yield gain will be needed over the next several decades. A number of biotic and abiotic factors pose a challenge to increase production of barley. Barley diseases prominently rusts, net blotch, spot blotch, Septoria speckled leaf blotch, stripe disease, powdery mildew, barley yellow dwarf, and molya disease are the major biotic constraints in enhancing the barley grain production. Other diseases like black point and smuts, are important from the industrial point of view because these deteriorate the quality of malt and beer. This review seeks to provide an overview of different barley diseases and their management. Doi.org/10.25174/2249-4065/2018/83844

Association Mapping of Septoria Speckled Leaf Blotch Resistance in U.S. Barley Breeding Germplasm

Septoria speckled leaf blotch (SSLB) is a sporadic but important disease of barley (Hordeum vulgare) in the Upper Midwest region of the United States and Prairie Provinces of Canada that is caused primarily by Septoria passerinii. Most of the widely grown cultivars in the region are susceptible to the disease. To identify and map SSLB resistance loci in U.S. barley breeding germplasm, we employed an association mapping approach using 3,840 breeding lines and cultivars and nearly 3,000 single-nucleotide polymorphism markers previously mapped to the seven barley chromosomes. SSLB infection responses (IRs) were assayed on seedling plants in the greenhouse using a 0-to-5 scale. From the analysis of four yearly panels consisting of 960 lines each, four quantitative trait loci (QTL) for SSLB resistance were identified: one on chromosome 1H (Rsp-qtl-H_12_31144), one on chromosome 3H (Rsp-qtl-3H_12_31488), and two on chromosome 6H (Rsp-qtl-6H_11_21032 and Rsp-qtl-6H_11_10064). Individual resistance QTL reduced the mean IR from 9 to 38% compared with lines lacking any resistance alleles. However, the combination of all four resistance QTL together reduced the mean IR by 83%. The markers found associated with these QTL will be valuable for programs utilizing marker-assisted selection for SSLB resistance.

Novel Septoria Speckled Leaf Blotch Resistance Loci in a Barley Doubled-Haploid Population

The genetics of resistance to Septoria speckled leaf blotch (SSLB), caused by Septoria passerinii, was studied in the Leger × CIho9831 barley doubled-haploid population. The 140 lines in the population segregated as 102 resistant and 38 susceptible, approximating a 3:1 ratio. A recombination map was developed using diversity arrays technology and other molecular markers. Quantitative trait locus (QTL) analysis demonstrated that resistance is primarily conferred either by having the CIho9831 allele at a QTL on 6HS or by having the CIho9831 allele at both of two QTLs on 3H and 2HL. In addition, ≈1/16 of the lines were resistant for unidentified reasons. This model predicts a resistant/susceptible ratio of 11:5, which fits the phenotypic observations. Minor QTLs were detected on 2HS and 1H. DNA sequences of linked markers suggest that the 6HS, 3H, and 2HS QTLs are part of resistance gene clusters and that the 6HS and 3H QTLs share homology. The 6HS QTL is identical to or closely linked to the SSLB resistance locus Rsp4 and the 1H QTL to the Rsp2 or Rsp3 locus. The 3H and 2HS QTLs are unique and offer new opportunities for pyramiding resistance genes through marker-assisted breeding for resistance to S. passerinii.

<I>Zymoseptoria</I> gen. nov.: a new genus to accommodate <I>Septoria-</I>like species occurring on graminicolous hosts

The Mycosphaerella complex is both poly- and paraphyletic, containing several different families and genera. The genus Mycosphaerella is restricted to species with Ramularia anamorphs, while Septoria is restricted to taxa that cluster with the type species of Septoria, S. cytisi, being closely related to Cercospora in the Mycosphaerellaceae. Species that occur on graminicolous hosts represent an as yet undescribed genus, for which the name Zymoseptoria is proposed. Based on the 28S nrDNA phylogeny derived in this study, Zymoseptoria is shown to cluster apart from Septoria. Morphologically species of Zymoseptoria can also be distinguished by their yeast-like growth in culture, and the formation of different conidial types that are absent in Septoria s.str. Other than the well-known pathogens such as Z. tritici, the causal agent of septoria tritici blotch on wheat, and Z. passerinii, the causal agent of septoria speckled leaf blotch of barley, both for which epitypes are designated, two leaf blotch pathogens are also described on graminicolous hosts from Iran. Zymoseptoria brevis sp. nov. is described from Phalaris minor, and Z. halophila comb. nov. from leaves of Hordeum glaucum. Further collections are now required to elucidate the relative importance, host range and distribution of these species.

A novel QTL for Septoria speckled leaf blotch resistance in barley (Hordeum vulgareL.) accession PI 643302 by whole-genome QTL mapping

Septoria speckled leaf blotch (SSLB), caused by Septoria passerinii, is one of the most important foliar diseases of barley (Hordeum vulgare L.) in North America. The primary problem caused by this disease is substantial yield loss. The objective of this study was to determine the chromosomal location of SSLB resistance genes in the barley accession PI 643302. A recombinant inbred line population was developed from the cross Zhenongda 7/PI 643302. PI 643302 is resistant while Zhenongda 7 is susceptible to SSLB. The population was phenotyped for SSLB resistance in five experiments in the greenhouse. A linkage map comprising 113 molecular markers was constructed and simplified composite interval mapping was performed. Two QTLs, designated QrSp-1H and QrSP-2H, were found. QrSp-1H was found on the short arm of chromosome 1H (1HS) in all five experiments and showed a large effect against SSLB. Based on the location of QrSp-1H, it is likely the SSLB resistance gene Rsp2. The QTL QrSp-2H mapped to the distal region on the long arm of chromosome 2H (2HL), had a smaller effect than QrSp-1H, and was also detected consistently in all five experiments. A QTL for SSLB resistance in the same region on chromosome 2H has not been reported previously in either cultivated or wild barley; thus, QrSp-2H is a new QTL for SSLB resistance in barley.

Mapping Net Form Net Blotch and Septoria Speckled Leaf Blotch Resistance Loci in Barley

Septoria speckled leaf blotch (SSLB), caused by Septoria passerinii Sacc., and net form net blotch (NB), caused by Pyrenophora teres f. teres Drechsler, are fungal diseases that decrease the yields of barley in the Upper Midwest. An effective way to manage these diseases is to plant resistant cultivars. To characterize the genetics of resistance to both pathogens, two advanced barley breeding lines, one resistant to NB (M120) and another resistant to SSLB (Sep2-72), were crossed, creating a population of 115 recombinant inbred lines. The two parents and the population were evaluated in three greenhouse seedling assays for each pathogen and for simple-sequence repeat and diversity arrays technology markers. Composite interval mapping revealed two major quantitative trait loci (QTL) associated with NB on chromosome 6H, located in bins 2 and 6. The QTL located in bin 6 explained 19 to 48% of the phenotypic variation and the QTL located in bin 2 explained 25 to 44% of the phenotypic variation. A new locus for resistance to SSLB, Rsp4, was identified on chromosome 6H, located in bins 3 to 4. Mapping these genes in elite breeding germplasm will accelerate the development and utilization of marker-assisted selection to enhance resistance to these diseases.

Molecular Mapping of Rsp1, Rsp2, and Rsp3 Genes Conferring Resistance to Septoria Speckled Leaf Blotch in Barley

ABSTRACT Septoria speckled leaf blotch (SSLB) caused by Septoria passerinii is a common disease in barley. SSLB resistance genes Rsp1, Rsp2, and Rsp3 have previously been identified in the United States Department of Agriculture National Small Grains collection accessions CIho 14300, CIho 4780, and CIho 10644, respectively. Populations of 100 to 120 F(2) individuals were evaluated for SSLB resistance in the greenhouse. Inheritance was evaluated in F(2:3)-derived families in the field. Partial molecular maps for three Rsp genes were constructed on F(2) and F(2:3) families derived from crosses between Robust and the resistant accessions CIho 14300, CIho 4780, and CIho 10644. The resistant locus Rsp1 was mapped to the short arm of chromosome 3H with two flanking diversity arrays technology (DArT) markers, bPb-6978 (8.9 cM) and bPb-9945 (16.3 cM), and two random amplified polymorphic DNA (RAPD) markers, OPC2(441R) (3.0 cM) and UBC285(158R) (4.3 cM). The genes Rsp2 and Rsp3 were positioned on the short arm of barley chromosome 1H with two restriction fragment length polymorphism (RFLP), six DArT, and three RAPD markers. An RFLP marker, MWG938, and an RAPD marker, OPAH5(545C), were tightly associated with Rsp2 at a distance of 0 cM. Five DArT markers spanning the short arm of 1H surrounded Rsp3 at a distance of 2.3 and 5.8 cM, while two RAPD markers-OPBA12(314C) (2.4 cM) in coupling and OPB17(451R) (3.5 cM) in repulsion-flanked Rsp3. Molecular marker data associated with Rsp2 and Rsp3 indicated that the two genes are closely linked on chromosome 1HS. A total of 17 of 154 simple sequence repeats (SSRs) tested were associated with Rsp genes on chromosome 1H and 3H, and they were also integrated into genetic linkage maps of the three F(2) Robust populations. Knowledge about the map position of Rsp genes on barley chromosomes will be useful for breeding for SSLB resistance in barley and eventual gene cloning.

Sequence Tagged Site Markers to Rsp1, Rsp2, and Rsp3 Genes for Resistance to Septoria Speckled Leaf Blotch in Barley

ABSTRACT Five random amplified polymorphic DNA markers, two in coupling (OPAH5(545C), and OPBA12(314C)) and three in repulsion phase (UBC285(158R), OPC2(441R), and OPB17(451R)), closely linked to Rsp genes conferring resistance to Septoria speckled leaf blotch (SSLB), were identified using bulked segregant analysis in three F(2) populations, each containing a Rsp gene. These markers were converted into the sequence tagged site (STS) markers SUBC285, SOPC2, SOPAH5, and SOPBA12. Another STS marker (MWG938) linked to Rsp2 in coupling phase was also identified in an F(2) population from the cross Robust/CIho 4780. The STS markers were tested on a set of 42 resistant and susceptible barley germplasm lines and 98 landraces. The expected sizes of marker fragments associated with each allele at Rsp loci were present in resistant or susceptible accessions. Efficiency of marker-assisted selection (MAS) for Rsp1, Rsp2, and Rsp3 using STS markers were evaluated in three F(23) populations in the greenhouse and the field. Results of testing F(23) progeny demonstrated that the accuracy of MAS was, with one exception, greater than 97% in the greenhouse and in two field locations (90% in the Osnabrock, ND trial for Rsp2). The STS markers closely linked to Rsp genes also identified the SSLB resistance corresponding to Rsp1, Rsp2, or Rsp3 in gene pyramiding F(2) populations. The STS markers tightly linked to Rsp genes may be useful for M and for pyramiding with other genes in barley breeding for SSLB resistance.

Discovery of a functional Mycosphaerella teleomorph in the presumed asexual barley pathogen Septoria passerinii

We studied the possibility of a teleomorph associated with the genotypically diverse septoria speckled leaf blotch (SSLB) pathogen of barley, Septoria passerinii. A teleomorph in the genus Mycosphaerella had been predicted previously based on phylogenetic analyses. This prediction was tested with experiments in the Netherlands and the United States by co-inoculating isolates with opposite mating types onto susceptible barley cultivars and monitoring leaves for sexual structures and for the discharge of ascospores. Characterization of putative hybrid progeny by both molecular (AFLP, RAPD, mating type, and ITS sequencing) and phenotypic analyses confirmed that a Mycosphaerella teleomorph of S. passerinii has been discovered approximately 125 years after the description of the anamorph. Progeny had recombinant genotypes of the molecular alleles present in the parents, and the identities of representative progeny isolates as S. passerinii were confirmed by ITS sequencing. A previously unknown sexual cycle explains the high degree of genetic variation among isolates found in nature. The experimental identification of a predicted teleomorph for S. passerinii indicates that cryptic sexual cycles may be common for many other “asexual” fungi with high levels of genotypic diversity.

Breeding Barley for Multiple Disease Resistance in the Upper MidwestRegion of the USA

The Upper Midwest is one of the largest barley production areas in the USA. In this region, diseases can markedly reduce both the yield and quality of the crop. Molecular and classical breeding techniques are being employed to develop cultivars with resistance to five different diseases in the Minnesota barley improvement program. Stem rust and spot blotch have been successfully controlled for many years through the deployment of the major gene Rpg1 and a major effect QTL, respectively. A sequence characterized amplified region (SCAR) marker developed from the sequence of Rpg1 has made marker-assisted selection (MAS) for stem rust resistance highly effective. The major QTL controlling durable adult plant spot blotch resistance was first identified in the Steptoe/Morex population. This QTL was completely suppressed in the Harrington/Morex and Dicktoo/Morex populations, highlighting the importance of genetic background for the expression of resistance. The onset of Fusarium head blight (FHB) in 1993 led to dramatic changes in the focus of the breeding program. Significant resources have been expended to develop populations for mapping resistance QTL and identify closely linked markers for MAS. This is a difficult challenge because FHB resistance is controlled by many QTL with small effects. Sources of resistance to net blotch and Septoria speckled leaf blotch (SSLB) have been identified in a number of barley accessions. These resistances are simply inherited and are being introgressed into elite lines via phenotypic and MAS. Continued progress toward multiple disease resistance will require efficient phenotypic screening, MAS, and utilization of discoveries in barley genomics to manage numerous resistance genes and desirable gene complexes assembled over decades of breeding.  

Molecular Mapping and Marker-Assisted Selection of Genes for Septoria Speckled Leaf Blotch Resistance in Barley

ABSTRACT Septoria speckled leaf blotch (SSLB), caused by Septoria passerinii, has emerged as one of the most important foliar diseases of barley in the Upper Midwest region of the United States. To map and tag genes for SSLB resistance, we developed two populations derived from the resistant accessions CIho 4780 and CIho 10644 and the susceptible malting cv. Foster. Segregation analysis of F(2) plants or F(2:3) families from the Foster/CIho 4780 and Foster/CIho 10644 populations revealed that a single dominant gene conferred resistance at the seedling stage. Bulked segregant analysis identified an amplified fragment length polymorphism marker, E-ACT/M-CAA-170, that co-segregated with the SSLB resistance gene Rsp2 in the Foster/CIho 4780 F(2) population. Southern hybridization analysis with DNA from the wheat/barley addition lines localized E-ACT/M-CAA-170 on the short arm of the barley chromosome 5(1H). Restriction fragment length polymorphism analysis with DNA clones previously mapped to the short arm of chromosome 5(1H) placed Rsp2 at a position flanked by the markers Act8 and ksuD14. A sequence-characterized amplified region (SCAR) marker (E-ACT/M-CAA-170a) was developed that co-segregated with not only Rsp2 in the Foster/CIho 4780 population but also resistance gene Rsp3 in the Foster/CIho 10644 population. This result indicates that Rsp3 is closely linked to Rsp2 on the short arm of chromosome 5(1H). The utility of SCAR marker E-ACT/M-CAA-170a for selecting Rsp2 in two different breeding populations was validated.

Validation of Quantitative Trait Loci for Multiple Disease Resistance in Barley Using Advanced Backcross Lines Developed with a Wild Barley

ABSTRACTQuantitative trait loci (QTLs) for resistance to spot blotch {Cochliobolus sativus (Ito & Kurib.) Drechs. ex Dastur [anamorph: Bipolaris sorokiniana (Sacc. in Sorok.) Shoem.]}, net type net blotch (NTNB, Pyrenophora teres f. teres), Septoria speckled leaf blotch (SSLB, primarily Septoria passerinii Sacc.), and leaf scald [caused by Rhynchosporium secalis (Oudem.) Davis] were previously detected in a recombinant inbred line (RIL) population derived from a cross between the wild barley [Hordeum vulgare subsp. spontaneum (K. Koch) Thell.] accession OUH602 and the two‐rowed malting barley (H vulgare L.) cultivar Harrington. Our objectives in this study were to develop and genetically characterize an advanced backcross (AB) population with OUH602 as the donor parent and Harrington as the recurrent parent, to validate seedling disease resistance QTLs detected in the OUH602/Harrington RIL population, and to identify adult plant spot blotch resistance QTLs. We developed an AB population (BC2F6:8) and genotyped the population with a set of 111 simple sequence repeat (SSR) markers. The estimated donor‐parent genome introgression averaged 11.25%. A QTL analysis of the AB population validated all major QTLs previously identified in the OUH602/Harrington RIL population. No new QTLs for seedling resistance were identified in the AB population, indicating that AB populations do not provide an advantage compared with RIL populations for detecting seedling disease resistance QTLs. A previously unidentified QTL conferring adult plant spot blotch resistance was identified on chromosome 4(4H). The resistance alleles for each of the QTLs were contributed by OUH602. The AB population is a valuable resource for further genetic studies and breeding applications.

Quantitative Trait Loci for Multiple Disease Resistance in Wild Barley

Foliar diseases of barley (Hordeum vulgare L.) such as spot blotch [caused by Cochliobolus sativus (Ito & Kuribayashi) Drechs. ex Dastur], net type net blotch (NTNB; caused by Pyrenophora teres f teres Drechs), Septoria speckled leaf blotch (SSLB; caused by Septoria passerinii Sacc.), leaf scald [caused by Rhynchosporium secalis (Oudem.) J. J. Davis], and powdery mildew (caused by Blumeria graminis f. sp. hordei Em. Marchal) can result in significant yield reductions in many production areas. The wild progenitor of cultivated barley, Hordeum vulgare subsp. spontaneum is well known as a rich source of disease resistance. To determine the location of H. vulgare subsp. spontaneum‐derived alleles for disease resistance, we conducted quantitative trait locus (QTL) analysis of a recombinant inbred line (RIL) population derived from a cross between the resistant H. vulgare subsp. spontaneum accession OUH602 and the two‐rowed malting cultivar Harrington. A total of 151 simple sequence repeats (SSR) markers were mapped into 11 linkage groups, covering 948 cM. Major QTLs for resistance to each disease were identified: one for spot blotch resistance on chromosome 1(7H); three for NTNB resistance on chromosomes 3(3H), 4(4H), and 5(1H); two for SSLB resistance on chromosomes 2(2H) and 6(6H); one for leaf scald resistance on chromosome 5(1H); and two for powdery mildew resistance on chromosomes 4(4H) and 5(1H). Resistance alleles for each QTL were contributed by OUH602, except those for NTNB and powdery mildew resistance on chromosome 5(1H) and chromosome 4(4H), respectively. The two QTLs identified for SSLB resistance are novel. All other QTLs mapped to regions where known resistance QTLs or major resistance genes have been reported. Our results indicate that most of the OUH602‐derived loci are clustered in regions coincident with those described in cultivated barley. These resistance QTLs and their associated markers should be valuable for further exploitation of disease resistance variation in barley improvement.

Sources of resistance to septoria speckled leaf blotch caused by Septoria passerinii in barley

Septoria speckled leaf blotch (SSLB), incited by Septoria passerinii, has reemerged as one of the most serious foliar diseases of barley (Hordeum vulgare) in the Upper Midwest region of the United States over the last decade. The most cost-effective and environmentally safe method of preventing SSLB epidemics is through the use of resistant cultivars. Thus, the objective of this study was to investigate sources of resistance to S. passerinii in barley and to determine the reliability of greenhouse seedling tests for predicting the adult-plant reaction in the field. From a preliminary greenhouse screening of over 250 barley accessions, 78 lines were selected and subsequently evaluated at the seedling (greenhouse) and adult-plant (field) stages for reaction to S. passerinii. All of the major malting (H. vulgare ‘Drummond’, ‘Excel’, ‘Foster’, ‘Lacey’, ‘Legacy’, ‘Morex’, ‘Stander’, ‘Conlon’, and ‘Robust’) and feed (H. vulgare ‘Bowman’, ‘Logan’, and ‘Royal’) cultivars grown in or recommended for the Upper Midwest region of the United States were highly susceptible. Highly significant correlations were detected between the infection response of seedlings in the greenhouse and adult plants in the field. Twenty-nine accessions exhibited resistance at both the seedling and adult-plant stages. The resistant accessions identified in this study were from geographically diverse regions and will be valuable in developing barley cultivars with diverse and broad-based resistance to SSLB.

Diversity and Sources of Multiple Disease Resistance in Hordeum spontaneum.

Hordeum spontaneum, the progenitor of cultivated barley, is known to be a rich source of disease resistance genes. The objective of this study was to assess the diversity of H. spontaneum accessions from Israel and Jordan for their reaction to six fungal pathogens of importance to cultivated barley in the United States and Canada. Overall, a high level of macro-scale (across collection sites) and micro-scale (within a collection site) diversity for disease reaction was found in the 116 accessions of H. spontaneum evaluated at the seedling stage. Additionally, genetic heterozygosity for resistance loci was common in H. spontaneum. The frequency of resistance in accessions from Jordan and Israel was high for Septoria speckled leaf blotch (77 and 98%, respectively), leaf rust (70 and 90%), net blotch (72 and 68%), and powdery mildew (58 and 70%); intermediate for spot blotch (53 and 46%); and low for stem rust (2 and 26%). The level of disease resistance in H. spontaneum was not strongly correlated with any of the weather variables (temperature, precipitation, and humidity) monitored near the collection sites. However, in general, resistance was more often found in germ plasm from mesic (e.g., Mediterranean coast) than in xeric (e.g., Negev Desert) areas. Two H. spontaneum accessions (Shechem 12-32 and Damon 11-11) were resistant to all six pathogens and may be useful parents in programs breeding barley for multiple disease resistance. The high level of diversity and heterozygosity for disease reaction found in this study indicates that H. spontaneum is an extraordinarily rich and largely untapped source of unique disease resistance alleles for cultivated barley improvement.

Inheritance and chromosomal location of Septoria passerinii resistance introgressed from Hordeum bulbosum into Hordeum vulgare

AbstractSeptoria speckled leaf blotch (SSLB), caused by Septoria passerinii, has become one of the most serious diseases of barley in the Upper Midwest region of the USA. The recombinant line 36L5 derived from a backcross of the susceptible barley cultivar ‘Emir’ and a resistant Hordeum bulbosum parent Cb2920/4/Colch was found to be resistant to S. passerinii. Two doubled haploids derived from 36L5 were backcrossed to cv.‘Emir’ to obtain two BCF2 populations for determining the inheritance of resistance to S. passerinii. BCF2 progeny and BCF2:3 families were evaluated at the seedling stage in the greenhouse for reaction to S. passerinii. BCF2 progeny and BCF2:3 families from both crosses segregated 3 : 1 (resistant : susceptible), and 1:2:1 (resistant : segregating : susceptible), respectively, indicating that the H. bulbosum‐derived SSLB resistance is conferred by a single dominant gene. The H. bulbosum introgressions were positioned on chromosome 4HL by genomic and fluorescent in situ hybridizations (GISH and FISH, respectively) and by Southern hybridization with the rye repetitive sequence pSc119.2. These findings indicate that SSLB resistance in H. bulbosum has the potential to be transferred and utilized in barley breeding programs.