Category Archives: ORIGINAL ARTICLE

Diversity of Colletotrichum species causing anthracnose on three oak species (Quercus acutissima, Q. mongolica and Q. variabilis) in China

Posted on 25 July 2023 by

The pathogenic species diversity of Colletotrichum on Quercus species from seven locations was assessed by morphological and phylogenetic analyses of ITS, gapdh, chs-1, act and tub2 sequences; nine species were identified.

Abstract

Anthracnose of oak (Quercus) caused by Colletotrichum spp. is one of the most common diseases in oak forests. To investigate the species diversity of Colletotrichum associated with oak anthracnose, symptomatic leaf samples of three oak species (Q. acutissima, Q. mongolica and Q. variabilis) were collected from Anhui, Hainan, Henan, Shaanxi and Shandong Provinces, Inner Mongolia Autonomous Region, and Beijing City in China from 2019 to 2022. A total of 219 Colletotrichum isolates were obtained and identified by morphological and phylogenetic analyses of the rDNA internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (gapdh), chitin synthase 1 (chs-1), actin (act) and β-tubulin (tub2) sequences. Nine species were identified: C. fioriniae (two isolates, 0.9%), C. camellia-japonicae (two isolates, 0.9%), C. karstii (three isolates, 1.4%), C. quercicola (two isolates, 0.9%), C. aenigma (three isolates, 1.4%), C. endophyticum (two isolates, 0.9%), C. fructicola (68 isolates, 31.1%), C. gloeosporioides sensu stricto (74 isolates, 33.8%) and C. siamense (63 isolates, 28.8%). Pathogenicity was confirmed using Koch's postulates, which showed that five species (C. camellia-japonicae, C. endophyticum, C. fructicola, C. gloeosporioides s. s. and C. siamense) caused Q. acutissima anthracnose, four species (C. karstii, C. fructicola, C. gloeosporioides s. s. and C. siamense) caused Q. mongolica anthracnose and six species (C. fioriniae, C. quercicola, C. aenigma, C. fructicola, C. gloeosporioides s. s. and C. siamense) caused Q. variabilis anthracnose. This study demonstrates the pathogenic species diversity of Colletotrichum on Q. acutissima, Q. mongolica and Q. variabilis.

Meta‐analysis of the genetics of resistance to Fusarium head blight and deoxynivalenol accumulation in barley and considerations for breeding

Posted on 23 July 2023 by

Abstract

Fusarium head blight (FHB) or scab is a devastating disease of barley that severely reduces the yield and quality of the grain. Additionally, mycotoxins produced by the causal Fusarium species can contaminate harvested grain, resulting in food safety concerns and further economic losses. In the Upper Midwest region of the United States, Fusarium graminearum is the primary causal agent, and deoxynivalenol (DON) is the main mycotoxin associated with Fusarium infection. Deployment of resistant cultivars is an important component of an integrated strategy to manage this disease. Unfortunately, few good sources of FHB resistance have been identified from the evaluation of large collections of Hordeum germplasm. Over the past 25 years, many barley mapping populations have been developed with selected resistance sources to identify the number, chromosomal position and allelic effect of quantitative trait loci (QTL) contributing to FHB resistance and DON accumulation. To consolidate the genetic data generated from 14 mapping studies that included 22 bi- or tri-parental mapping populations and three genome-wide association (GWAS) mapping panels, a consensus map was constructed that includes 4145 SNP, SSR, RFLP and AFLP markers. A meta-analysis based on this consensus map revealed 96 QTL for FHB resistance and 57 for DON accumulation scattered across the barley genome. Many of the QTL explained a low percentage (<10%) of variation for the traits and were often found significant in only one or a few environments in multi-year/multi-location field trials. Moreover, many of the FHB/DON QTL mapped to chromosomal positions coincided with various agro-morphological traits that could influence the level of disease (e.g. heading date, height, spike density, and spike angle), raising the important question of whether the former are true resistance factors or are simply the result of pleiotropy with the latter. Considering the magnitude of effect, consistency of detection across environments and independence from agro-morphological traits, only three of 96 QTL for FHB and five of 57 QTL for DON were considered priority targets for marker-assisted selection (MAS). In spite of the challenge for having a limited number of useful QTL for breeding, genomic selection holds promise for increasing the efficiency of developing FHB-resistant barley cultivars, an essential component of the overall management strategy for the disease.

Greater rate of nitrogen fertilizer application increases root rot caused by Phytophthora cinnamomi and P. plurivora in container‐grown rhododendron

Posted on 19 July 2023 by

Application of nitrogen accelerated Phytophthora root rot disease symptoms in rhododendron plants inoculated with Phytophthora cinnamomi and P. plurivora.

Abstract

Phytophthora root rot, caused by many Phytophthora species, decreases the health of rhododendrons produced in nurseries. Optimizing nitrogen (N) fertilizer is often used to improve nursery stock quality, but there is little information on how N fertilizers influence root rot caused by these pathogens. To understand the impact of N fertilizer and pathogen species on root rot development, rhododendrons were grown with no (0 g N/pot), low (1.04 g N/pot) or high (3.12 g N/pot) rates of N and inoculated with either P. cinnamomi or P. plurivora. Noninoculated plants at low and high N rates had greater biomass, leaf greenness and enhanced N, potassium, magnesium, phosphorus, sulphur and manganese uptake compared to plants grown with no N. When either Phytophthora species was present, N application increased aboveground disease symptoms (wilting, chlorosis, reduced stomatal conductance and biomass), but had no effect on root rot severity belowground. In addition, P. cinnamomi restricted uptake of several nutrients while P. plurivora had less influence on nutrient uptake. Nurseries frequently apply high amounts of N to promote fast growth. However, our results show that this can exacerbate root rot when P. cinnamomi or P. plurivora is present. Although decreasing N can reduce the number of overtly symptomatic plants, this may conversely increase the risk for selling apparently asymptomatic plants with low levels of infection. Additional studies are needed to determine how N fertilization influences Phytophthora root rot for a broader range of rhododendron cultivars and nursery crop species.

Genetic variants associated with leaf spot disease resistance in oil palm (Elaeis guineensis): A genome‐wide association study

Posted on 17 July 2023 by

Genome-wide association study using a diverse genetic background of the oil palm population reveals associated genes contributing to leaf spot disease resistance.

Abstract

Leaf spot is considered as a common disease of oil palm, caused primarily by Curvularia spp. fungi. This disease mainly affects the early stages of oil palm and if not adequately controlled can cause plant death. Among the methods available to control the disease, breeding resistant varieties is the most economically effective and promising strategy. A genome-wide association study for leaf spot resistance was conducted on 210 individual tenera palms from seven different (origin) crosses. These palms were subsequently infected with Curvularia spp. pathogenic inoculum in a nursery trial located in an endemic area. The area under the disease progress curve was used as a phenotypic measure. In addition, a genotyping-by-sequencing (GBS) approach was used to obtain the genotyping data of each individual. We found two loci, at chromosome 2 and chromosome 13, that were significantly associated with leaf spot disease resistance. Six genetic variants at the two loci (five variants at chromosome 2 and one variant at chromosome 13) surpassed the threshold for genome-wide significance (p < 10⁶). These loci are linked with three widely known disease-related genes, namely, resistance gene analogue 3 (RGA3), resistance gene analogue 4 (RGA4) and receptor-like protein 9a (RLP9a). The loci identified here can be used for marker-assisted selection when developing leaf spot disease-resistant oil palm varieties.

Genetic characterization and prevalence of Pseudomonas syringae strains from sweet cherry orchards in New Zealand

Posted on 14 July 2023 by

The study identified prevalent Pseudomonas syringae strains in New Zealand cherry orchards, with P. syringae pv. syringae as the predominant pathovar in Central Otago, providing valuable insights for future epidemiology research.

Abstract

Bacterial canker of cherry, caused by Pseudomonas syringae pathovars, is a major constraint to cherry growing in New Zealand. The prevalence of strains from cherry orchards in Central Otago, the main growing area for cherries in New Zealand, was studied, to better understand the epidemiology of the disease. Pseudomonas spp. isolates were collected from symptomatic and asymptomatic cherry tissue from 23 commercial cherry orchards in 2015. Isolates were classified into strains belonging to three different taxonomic groups by determining their phylogeny using the gltA gene sequence for all the strains and multilocus sequence analysis (MLSA) of four housekeeping genes for 35 strains. Pathogenicity of all Central Otago strains was tested on immature cherry fruit to support the phylogenetic classification. The two main taxonomic groups were P. syringae pv. syringae (Pss) and P. syringae pv. morsprunorum race 1 (Psm1), in Phylogroup 2 (PG2) and Phylogroup 3 (PG3), respectively. The third group comprised nonpathogenic strains classified as Pseudomonas spp. Strains of Psm1 formed a monophyletic group, representing an almost clonal population. There was more variation detected within strains of Pss, although they were restricted to group PG2d. Nonpathogenic Pseudomonas spp. and pathogenic Pss and Psm1 strains coexisted in the same orchard. It was concluded that Pss is the predominant pathovar in Central Otago. This is the first detailed study of the P. syringae species complex in cherry orchards in New Zealand and provides the basis for future epidemiology studies.

Genetic mapping identified major main‐effect and three co‐localized quantitative trait loci controlling high iron and zinc content in groundnut

Posted on 5 July 2023 by

Abstract

Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine deployment of genomic-assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping population (ICGV 00440 × ICGV 06040;). Genetic mapping and quantitative trait locus (QTL) analysis (474 mapped single-nucleotide polymorphism loci; 1536.33 cM) using 2 seasons of phenotypic data together with genotypic data identified 5 major main-effect QTLs for Fe content. These QTLs exhibited log-of-odds (LOD) scores ranging from 6.5 to 7.4, explaining phenotypic variation (PVE) ranging from 22% (qFe-Ah01) to 30.0% (qFe-Ah14). Likewise, four major main effect QTLs were identified for Zn content, with LOD score ranging from 4.4 to 6.8 and PVE ranging from 21.8% (qZn-Ah01) to 32.8% (qZn-Ah08). Interestingly, three co-localized major and main effect QTLs (qFe-Ah01, qZn-Ah03, and qFe-Ah11) were identified for both Fe and Zn contents. These genomic regions harbored key candidate genes, including zinc/iron permease transporter, bZIP transcription factor, and vacuolar iron transporter which likely play pivotal roles in the accumulation of Fe and Zn contents in seeds. The findings of this study hold potential for fine mapping and diagnostic marker development for high Fe and Zn contents in groundnut.

Breeding evaluation and precise mapping of Fhb8 for Fusarium head blight resistance in wheat (Triticum aestivum)

Posted on 30 May 2023 by

Abstract

The percentage of Fusarium-damaged kernels (FDK) was proposed as a type of Fusarium head blight (FHB) resistance displayed in matured wheat kernels. In this study, Qfdk.nau-7D, a QTL identified in the Wangshuibai genome for its association with FDK, was introduced into FHB-susceptible common wheat line PH691 through marker-assisted selection and backcrossing. Evaluation of two resulted near-isogenic lines (NILs) showed that the contribution of Qfdk.nau-7D interval to lower FDK resulted from its effects on resistance to pathogen infection and to disease spread within the spike. Of a few major agronomic traits evaluated, head length was the only one that made difference between PH691 and the NILs. To reduce the QTL interval, a high-density marker map was constructed using a BC₃F₂ population of 97 plants. Through resistance evaluation of the homozygous recombinant lines in repeated field trials, Qfdk.nau-7D, designated as Fhb8, was placed in a 1.0-cM Xwgrb1500-Xwgrb1559 interval (from 93.9–96.5 Mb in CS) and showed co-segregation with Xwgrb1587. Moreover, it was found that the association of Fhb8 with head length was due to close linkage with spike length QTL HL2.

Breeding of Lotus japonicus that can overcome adverse seasonal environment by coupling flowering time and abiotic stresses

Posted on 29 May 2023 by nMeiru Li, nHongqing Lin

Abstract

Manipulation of floral transition may allow for a free change in the duration of plant vegetative and reproductive growth, thus rendering them to avoid adverse seasonal environmental conditions. In this report, we investigated the effect of the stress-inducible promoter RD29A on driving the rice FT ortholog Hd3a expression in Lotus japonicus ‘MG20’ in response to environmental changes. Constitutive overexpression of Hd3a (HOE) in ‘MG20’ hastened its flowering in contrast to non-transformed control (wild type; WT), which did not flower in winter hampered by long days and low temperatures. RD29A promoter had low activity under non-stress conditions and was induced by cold, drought and salinity in transgenic ‘MG20’. Transgenic plants of Hd3a driven by the RD29A promoter (RH) could flower under unfavourable weather conditions that prohibited the flowering of WT plants. In addition, RH transgenic plants exhibited thriving clumps of branching, inflorescence, and pods because of the low temperature-induced expression of Hd3a. These results demonstrate that inducible expression of florigen has the potential to tackle unfavourable weather conditions and boost plant production.

Functional identification of OsMADS6 and OsMADS17 in floral organ development in rice

Posted on 19 May 2023 by nHao Dong, nYingxin Qiu, nTiankang Wang, nShufeng Song, nLi Li, nYixing Lin

Abstract

Rice floral organs are closely related to rice yield and quality, and MADS family genes play an important role in rice floral organ development. In this study, we identified functions of two MADS genes in floral organ development by bioinformatics analysis and CRISPR/Cas9 technology. Our results showed that MADS6 and MADS17 were a pair of highly homologous genes, which had highly similar sequences, motifs and expression profiles. The floral organs of mads6 and mads6/17 mutants were abnormal, whereas mads17 mutants showed no difference with wild type. Collectively, these results reveal that there are functional differentiations between conserved gene MADS6 and MADS17. Our findings provide a theoretical basis for further analysing the function of MADS family homologous genes and unravelling their molecular mechanism and regulatory network.

Multi‐trait genomic selection improves the prediction accuracy of end‐use quality traits in hard winter wheat

Posted on 17 May 2023 by

Abstract

Improvement of end-use quality remains one of the most important goals in hard winter wheat (HWW) breeding. Nevertheless, the evaluation of end-use quality traits is confined to later development generations owing to resource-intensive phenotyping. Genomic selection (GS) has shown promise in facilitating selection for end-use quality; however, lower prediction accuracy (PA) for complex traits remains a challenge in GS implementation. Multi-trait genomic prediction (MTGP) models can improve PA for complex traits by incorporating information on correlated secondary traits, but these models remain to be optimized in HWW. A set of advanced breeding lines from 2015 to 2021 were genotyped with 8725 single-nucleotide polymorphisms and was used to evaluate MTGP to predict various end-use quality traits that are otherwise difficult to phenotype in earlier generations. The MTGP model outperformed the ST model with up to a twofold increase in PA. For instance, PA was improved from 0.38 to 0.75 for bake absorption and from 0.32 to 0.52 for loaf volume. Further, we compared MTGP models by including different combinations of easy-to-score traits as covariates to predict end-use quality traits. Incorporation of simple traits, such as flour protein (FLRPRO) and sedimentation weight value (FLRSDS), substantially improved the PA of MT models. Thus, the rapid low-cost measurement of traits like FLRPRO and FLRSDS can facilitate the use of GP to predict mixograph and baking traits in earlier generations and provide breeders an opportunity for selection on end-use quality traits by culling inferior lines to increase selection accuracy and genetic gains.