Christopher R. Little

Genome-Wide Association Study on Resistance to Stalk Rot Diseases in Grain Sorghum

Stalk rots are important biotic constraints to sorghum production worldwide. Several pathogens may be associated with the disease, but Macrophomina phaseolina and Fusarium thapsinum are recognized as the major causal organisms. The diseases become more aggressive when drought and high-temperature stress occur during grain filling. Progress in genetic improvement efforts has been slow due to lack of effective phenotyping protocol and the strong environmental effect on disease incidence and severity. Deployment of modern molecular tools is expected to accelerate efforts to develop resistant hybrids. This study was aimed at identifying genomic regions associated with resistance to both causal organisms. A sorghum diversity panel consisting of 300 genotypes assembled from different parts of the world was evaluated for response to infection by both pathogens. Community resources of 79,132 single nucleotide polymorphic (SNP) markers developed on the panel were used in association studies using a multi-locus mixed model to map loci associated with stalk rot resistance. Adequate genetic variation was observed for resistance to both pathogens. Structure analysis grouped the genotypes into five subpopulations primarily based on the racial category of the genotypes. Fourteen loci and a set of candidate genes appear to be involved in connected functions controlling plant defense response. However, each associated SNP had relatively small effect on the traits, accounting for 19–30% of phenotypic variation. Linkage disequilibrium analyses suggest that significant SNPs are genetically independent. Estimation of frequencies of associated alleles revealed that durra and caudatum subpopulations were enriched for resistant alleles, but the results suggest complex molecular mechanisms underlying resistance to both pathogens.

Genotypic variation in sorghum [ Sorghum bicolor (L.) Moench] exotic germplasm collections for drought and disease tolerance

Sorghum [Sorghum bicolor (L.) Moench] grain yield is severely affected by abiotic and biotic stresses during post-flowering stages, which has been aggravated by climate change. New parental lines having genes for various biotic and abiotic stress tolerances have the potential to mitigate this negative effect. Field studies were conducted under irrigated and dryland conditions with 128 exotic germplasm and 12 adapted lines to evaluate and identify potential sources for post-flowering drought tolerance and stalk and charcoal rot tolerances. The various physiological and disease related traits were recorded under irrigated and dryland conditions. Under dryland conditions, chlorophyll content (SPAD), grain yield and HI were decreased by 9, 44 and 16%, respectively, compared to irrigated conditions. Genotype RTx7000 and PI475432 had higher leaf temperature and grain yield, however, genotype PI570895 had lower leaf temperature and higher grain yield under dryland conditions. Increased grain yield and optimum leaf temperature was observed in PI510898, IS1212 and PI533946 compared to BTx642 (B35). However, IS14290, IS12945 and IS1219 had decreased grain yield and optimum leaf temperature under dryland conditions. Under irrigated conditions, stalk and charcoal rot disease severity was higher than under dryland conditions. Genotypes IS30562 and 1790E R had tolerance to both stalk rot and charcoal rot respectively and IS12706 was the most susceptible to both diseases. PI510898 showed combined tolerance to drought and Fusarium stalk rot under dryland conditions. The genotypes identified in this study are potential sources of drought and disease tolerance and will be used to develop better adaptable parental lines followed by high yielding hybrids.

Introduction to Fungi

A fungus is a eukaryote that digests food externally and absorbs nutrients directly through its cell walls. Most fungi reproduce by spores and have a body (thallus) composed of microscopic tubular cells called hyphae. Fungi are heterotrophs and, like animals, obtain their carbon and energy from other organisms. Some fungi obtain their nutrients from a living host (plant or animal) and are called biotrophs; others obtain their nutrients from dead plants or animals and are called saprotrophs (saprophytes, saprobes). Some fungi infect a living host, but kill host cells in order to obtain their nutrients; these are called necrotrophs.

Fungal Phyllosphere Communities are Altered by Indirect Interactions Among Trophic Levels

Trophic interactions involving predators, herbivores, and plants have been described in terrestrial systems. However, there is almost no information on the effect of trophic interactions on microbial phyllosphere community abundance, diversity, or structure. In this study, the interaction between a parasitoid, an insect herbivore, and the fungal phyllosphere community is examined. Parasitoid wasps have an indirect negative impact on fungal community diversity. On the citrus phyllosphere, the exotic wasp species, Amitus hesperidum and Encarsia opulenta, may parasitize the citrus blackfly (Aleurocanthus woglumi). If parasitism levels are low, the blackfly may produce significant amounts of honeydew secretions on the surface of the leaf. Honeydew deposition provides a carbon-rich substrate for the development of fungal growth persisting as sooty mold on the leaves. Leaves from sooty mold-infested grapefruit (Citrus paradisi) trees were collected from multiple orchards in south Texas. The effect of different levels of exotic parasite activity, citrus blackfly, and sooty mold infestation on phyllosphere mycobiota community structure and diversity was examined. Our results suggest the presence of the parasitoid may lead to a top–down trophic cascade affecting phyllosphere fungal community diversity and structure. Additionally, persistent sooty mold deposits that have classically been referred to as Capnodium citri (and related asexual morphological forms) actually comprise a myriad of fungal species including many saprophytes and potential fruit and foliar pathogens of citrus.

Integrating resistance and tolerance for improved evaluation of sorghum lines against Fusarium stalk rot and charcoal rot

Stalk rots are major fungal diseases of sorghum [Sorghum bicolor (L.) Moench] worldwide and cause significant economic loss. Conventionally, the length of stem lesions, produced by Fusarium thapsinum (FT; Fusarium stalk rot) and Macrophomina phaseolina (MP; charcoal rot), are measured to assess the degree of plant resistance. Genotypes with shorter lesion length (LL) are more resistant and expected to exhibit improved yield compared to susceptible genotypes. However, recent reports reveal inconsistent correlations between yield and LL, demonstrating the inadequacy of LL to predict yield under disease pressure. In this study, a new resistance-tolerance index (IndexRT) was used to rank 36 advanced sorghum male sterility maintainers (B-lines). IndexRT was formulated in such a way that a lower index value indicates increased disease resistance and reduced yield loss (i.e., greater tolerance) and vice-versa after infection. When ranked by LL, ARCH11035B, -11025B and -11011B were the best performing lines against Fusarium stalk rot, whereas the same lines ranked 1, 3, and 9, respectively, using IndexRT. Similarly, ARCH11018B, -11010B and -11014B had the lowest LLs respectively against charcoal rot, whereas the same lines were ranked 1, 4, and 30, respectively, based upon IndexRT. The LL- or IndexRT-dependent ranking differences of certain lines such as FT-inoculated ARCH11011B and MP-inoculated ARCH11014B indicated the effectiveness of deploying IndexRT for better evaluating sorghum lines against stalk rot diseases. There was no significant correlation between LL and IndexRT, revealing the independence of the two ranking systems. It is anticipated that this novel stalk rot screening procedure could be deployed by sorghum breeders for improved selection of parental lines.

Analyses of sorghum (Sorghum bicolor (L.) Moench) lines and hybrids in response to early-season planting and cool conditions

Kapanigowda, M., H., Perumal, R., Aiken, R. M., Herald, T. J., Bean, S. R. and Little, C. R. 2013. Analyses of sorghum [ Sorghum bicolor (L.) Moench] lines and hybrids in response to early-season planting and cool conditions. Can. J. Plant Sci. 93: 773-784. Early-season cold tolerance in sorghum contributes to emergence, seedling establishment, and early vegetative growth, and reduces damping-off diseases under chilling conditions. The objectives of this study were to identify cold-tolerant sources and to evaluate and optimize rapid screening techniques under a controlled environment. Field studies involving 48 genotypes, representing phases of the hybrid development process (landraces, elite and advanced breeding lines, recombinant inbred lines (RILs) and hybrids were conducted with early and normal planting dates in 2011 at Hays and Colby, Kansas. Studies under controlled environments were conducted at both locations using 18 genotypes that differ for emergence index (EI) and 30 d after emergence (DAE) shoot biomass based on field studies during 2011. Significant differences among the genotypes were recorded for all seedling traits (emergence percentage, EI, shoot biomass, plant height, and leaf number measured 30 DAE), and agronomic traits (days to 50% flowering, panicle exsertion, panicle length, and plant height at maturity). Eight advanced breeding lines: ARCH10731, ARCH10732, ARCH10736, ARCH10737, ARCH10738, ARCH10739, ARCH10744 and ARCH10749 and one RIL (RTx430/SQR-2) were found to be potential sources of cold tolerance with early EI, higher biomass and relatively early flowering. These genotypes are free from tannin, which helps to increase the feed grain efficiency of livestock, and hence were selected for test hybrid evaluation to assess fertility status, combining ability and yield performance. Significant correlation was observed between EI and biomass during early planting, which indicated that late-emerging genotypes produced greater biomass (30 DAE) compared with early-emerged genotypes. Significant correlation between growth chamber and field study for EI offers a potential and fast preliminary high-throughput screening technique for identification of cold-tolerant sorghum.

Stalk Rot Fungi Affect Leaf Greenness (SPAD) of Grain Sorghum in a Genotype- and Growth-Stage-Specific Manner

Stalk rots are among the most prevalent and destructive sorghum diseases worldwide. Although experimental evidence is limited, delayed postflowering senescence due to the staygreen trait is accepted as a physiological means of stalk rot resistance. Staygreen has been shown to be correlated with chlorophyll content (as measured by a soil and plant analytical development [SPAD] meter). Field experiments were conducted to test the effects of Fusarium stalk rot and charcoal rot on SPAD readings at three developmental stages, to test whether staygreen genotypes are more resilient to stalk-rot-mediated chlorophyll degradation, and to examine the relationships between SPAD and stalk rot resistance and tolerance when plants were inoculated with causal organisms. Staygreen and nonstaygreen lines (two) and hybrids (two) established in the field were inoculated with Fusarium thapsinum, F. proliferatum, F. andiyazi, and Macrophomina phaseolina at 14 days after flowering. SPAD readings were obtained at soft-dough, hard-dough, and physiological maturity. Most pathogens significantly reduced the SPAD of the genotypes over the mock-inoculated control at three developmental stages. The stalk-rot-resistant and staygreen check line, SC599, showed a remarkable feature of negative senescence from soft dough to physiological maturity under disease pressure. Disease severity was significantly and negatively correlated with SPAD at all developmental stages, revealing the potential impact of the staygreen trait on stalk rot resistance. The difference between control and pathogen-treated total seed weight per panicle (i.e., tolerance) was significantly and positively correlated with the difference between control and pathogen-treated SPAD at physiological maturity, demonstrating the ability of staygreen trait to enhance stalk rot tolerance under disease pressure.

New Sources of Resistance in Sorghum (Sorghum bicolor) Germplasm Are Effective Against a Diverse Array of Potyvirus spp.

Sorghum is a host to numerous Potyvirus spp. and its germplasm encompasses a wide range of infection responses to these viruses. We determined how 183 mini-core-collection sorghum germplasm accessions responded to mechanical inoculation with Maize dwarf mosaic virus (MDMV) in growth regimes in which they were maintained at 30°C followed by 16°C for 5 days. Accessions that appeared immune to MDMV in this initial screening were evaluated for their response in a similar temperature maintenance regime to mechanical inoculation with MDMV, Sugarcane mosaic virus strain MDB (SCMV-MDB), Sorghum mosaic virus (SrMV), Zea mosaic virus (ZeMV), and Kansas, Nigerian, and Australian isolates of Johnsongrass mosaic virus (JGMV-KS, -N, and -Aus, respectively). In both experiments, MDMV systemically infected all accessions except international sorghum accession number (IS) 7679 and IS 20740. These accessions also proved resistant to MDMV, SCMV-MDB, SrMV, and JGMV-N but both were susceptible to the JGMV-KS and JGMV-Aus isolates. IS 7679 but not IS 20740 was resistant to infection with ZeMV. These observations suggest that IS 7679 and IS 20740 might serve as new sources of resistance to several Potyvirus spp. that systemically infect sorghum.

Evaluation of Gambian and Malian sorghum germplasm against downy mildew pathogen, Peronosclerospora sorghi, in Mexico and the USA

The recent outbreak of sorghum downy mildew (SDM) in Texas, USA caused by pathotype P3 of Peronosclerospora sorghi, which is resistant to standard fungicide seed treatment, and the subsequent development of a new pathotype, P6, that overcame resistance in some hybrids, has emphasized the importance of continuing to develop new sources with genetic resistance. Eighty-two exotic Gambian and Malian germplasms and 10 sorghum lines commonly used as SDM pathotype differentials were field-evaluated in a randomized complete block design replicated three times at one Mexican location (Ocotlán, Jalisco) in 2004 and 2005, and two USA locations (Louise and New Taiton, TX, USA) in 2005 to identify new sources of SDM resistance. Accessions PI609151 and PI609442 from Mali had high levels of SDM resistance at all locations. Malian accession PI612815 also had a moderate to resistant reaction to SDM in two of the three locations. Accession PI522108 from Gambia was resistant in Mexico but susceptible in Louise, TX, USA. The reaction of the 10 lines used as differentials suggested the presence of a pathotype in Mexico that differed from those in the USA.

Impacts of Fungal Stalk Rot Pathogens on Physicochemical Properties of Sorghum Grain

Stalk rot diseases are among the most ubiquitous and damaging fungal diseases of sorghum (Sorghum bicolor (L.) Moench) worldwide. Although reports of quantitative yield losses to stalk rots are available, the impact of stalk rot on grain quality attributes is unknown. This study was conducted to test whether stalk rot diseases could affect grain mineral (N, P, K; Ca, Mg, Cu, Fe, Mn, and Zn) and macronutrient (protein, fat, and starch) content, ash content, and physical traits (unit grain weight, hardness, and diameter). A field experiment was conducted in 2013 and 2014 with four sorghum genotypes (two hybrids and two lines). Plants from each genotype were inoculated with four stalk rot pathogens (Fusarium andiyazi, F. proliferatum, F. thapsinum, and Macrophomina phaseolina) and mock-inoculated with phosphate-buffered saline (control). Grains collected from infected and control plants were analyzed for macronutrient and ash content using near-infrared reflectance spectroscopy, grain hardness and diameter using the single-kernel characterization system, and mineral content using the Rapid Flow Analyzer (Model RFA-300 for N) and inductively coupled plasma spectrometer (for P, K, Ca, Mg, Cu, Fe, Mn, and Zn). Although stalk rot pathogens significantly reduced unit grain weight, they did not significantly affect grain hardness and diameter and, therefore, may not affect milling quality. Pathogens significantly reduced all macronutrient and most mineral contents across genotypes and environments on a per-unit-grain basis, except N and Mg, which were affected in a genotype- and environment-specific manner, and Fe, which was not significantly affected. Most minerals tested were significantly and negatively correlated with disease severity (lesion length) and total grain weight per panicle. The hybrid tested (Pioneer 84G62) exhibited reduced mineral and macronutritional changes after stalk rot infection, providing insights into the possibility of producing high-yielding, nutritionally stable hybrids under stalk rot disease pressure through dedicated breeding efforts.