Category Archives: ORIGINAL ARTICLE

Integrating de novo QTL‐seq and linkage mapping to identify quantitative trait loci conditioning physiological resistance and avoidance to white mold disease in dry bean

Posted on 21 August 2023 by

Abstract

White mold (WM), caused by the ubiquitous fungus Sclerotinia sclerotiorum, is a devastating disease that limits production and quality of dry bean globally. In the present study, classic linkage mapping combined with QTL-seq were employed in two recombinant inbred line (RIL) populations, “Montrose”/I9365-25 (M25) and “Raven”/I9365-31 (R31), with the initial goal of fine-mapping QTL WM5.4 and WM7.5 that condition WM resistance. The RILs were phenotyped for WM reactions under greenhouse (straw test) and field environments. The general region of WM5.4 and WM7.5 were reconfirmed with both mapping strategies within each population. Combining the results from both mapping strategies, WM5.4 was delimited to a 22.60–36.25 Mb interval in the heterochromatic regions on Pv05, while WM7.5 was narrowed to a 0.83 Mb (3.99–4.82 Mb) region on the Pv07 chromosome. Furthermore, additional QTL WM2.2a (3.81–7.24 Mb), WM2.2b (11.18–17.37 Mb, heterochromatic region), and WM2.2c (23.33–25.94 Mb) were mapped to a narrowed genomic interval on Pv02 and WM4.2 in a 0.89 Mb physical interval at the distal end of Pv04 chromosome. Gene models encoding gibberellin 2-oxidase proteins regulating plant architecture are likely candidate genes associated with WM2.2a resistance. Nine gene models encoding a disease resistance protein (quinone reductase family protein and ATWRKY69) found within the WM5.4 QTL interval are putative candidate genes. Clusters of 13 and 5 copies of gene models encoding cysteine-rich receptor-like kinase and receptor-like protein kinase-related family proteins, respectively, are potential candidate genes associated with WM7.5 resistance and most likely trigger physiological resistance to WM. Acquired knowledge of the narrowed major QTL intervals, flanking markers, and candidate genes provides promising opportunities to develop functional molecular markers to implement marker-assisted selection for WM resistant dry bean cultivars.

k‐mer‐based GWAS enhances the discovery of causal variants and candidate genes in soybean

Posted on 18 August 2023 by

Abstract

Genome-wide association studies (GWAS) are powerful statistical methods that detect associations between genotype and phenotype at genome scale. Despite their power, GWAS frequently fail to pinpoint the causal variant or the gene controlling a given trait in crop species. Assessing genetic variants other than single-nucleotide polymorphisms (SNPs) could alleviate this problem. In this study, we tested the potential of structural variant (SV)- and k-mer-based GWAS in soybean by applying these methods as well as conventional SNP/indel-based GWAS to 13 traits. We assessed the performance of each GWAS approach based on loci for which the causal genes or variants were known from previous genetic studies. We found that k-mer-based GWAS was the most versatile approach and the best at pinpointing causal variants or candidate genes. Moreover, k-mer-based analyses identified promising candidate genes for loci related to pod color, pubescence form, and resistance to Phytophthora sojae. In our dataset, SV-based GWAS did not add value compared to k-mer-based GWAS and may not be worth the time and computational resources invested. Despite promising results, significant challenges remain regarding the downstream analysis of k-mer-based GWAS. Notably, better methods are needed to associate significant k-mers with sequence variation. Our results suggest that coupling k-mer- and SNP/indel-based GWAS is a powerful approach for discovering candidate genes in crop species.

In silico prediction and analysis of transmembrane‐coiled‐coil resistance gene analogues in 27 Brassicaceae species

Posted on 18 August 2023 by

A total of 6788 transmembrane-coiled-coil (TM-CCs) genes identified across 28 Brassicaceae species may play roles in plant defence and help improve crop disease resistance.

Abstract

The Brassicaceae family is composed of a broad range of species, including the economically important crops from Brassica, Raphanus, Camelina and Sinapis genera. The production of Brassicaceae species, particularly the crop members, is threatened by major diseases. However, the impact of diseases can be minimized or even negated by improving disease resistance. Transmembrane-coiled-coil (TM-CC) genes are a type of resistance gene analogue (RGA) that have been proven to play specific roles in resistance to several diseases. Here, TM-CCs have been predicted in 27 genomes from Brassicaceae genera including Arabidopsis, Arabis, Barbarea, Boechera, Brassica, Camelina, Capsella, Cardamine, Eutrema, Leavenworthia, Lepidium, Raphanus, Sinapis, Sisymbrium, Schrenkiella and Thlaspi. The number of TM-CCs varies throughout the studied genomes, as well as between genera, diploids and polyploids, and Brassica genomes and subgenomes. In total, 6788 TM-CCs were identified, with 708 of them predicted with signalling function, 172 colocalized with previously known disease resistance regions and 70 phylogenetically related to cloned resistance genes, indicating the possible functional involvement of TM-CCs in resistance. This study provides a resource for the identification of functional Brassicaceae TM-CCs along with their clustering and duplication patterns and provides a benchmark for further studies investigating TM-CCs.

Unravelling marker trait associations linking nutritional value with pigmentation in rice seed

Posted on 17 August 2023 by

Abstract

While considerable breeding effort has focused on increasing the yields of staple crops such as rice and the levels of micronutrients such as iron and zinc, breeding to address the problems of the double-burden of malnutrition has received less attention. Pigmented rice has higher nutritional value and greater health benefits compared to white rice. However, the genetic associations underlying pericarp coloration and accumulation of nutritionally valuable compounds is still poorly understood. Here we report the targeted genetic analysis of 364 rice accessions, assessing the genetic relationship between pericarp coloration (measured using multi-spectral imaging) and a range of phenolic compounds with potential nutritional and health-promoting characteristics. A genome-wide association study resulted in the identification of over 280 single nucleotide polymorphisms (SNPs) associated with the traits of interest. Many of the SNPs were associated with more than one trait, colocalization occurring between nutritional traits, and nutritional and color-related traits. Targeted association analysis identified 67 SNPs, located within 52 candidate genes and associated with 24 traits. Six haplotypes identified within the genes Rc/bHLH17 and OsIPT5 indicated that these genes have an important role in the regulation of a wide range of phenolic compounds, and not only those directly conferring pericarp color. These identified genetic linkages between nutritionally valuable phenolic compounds and pericarp color present not only a valuable resource for the enhancement of the nutritional value of rice but an easy method of selection of suitable genotypes.

High‐throughput sequencing of maize dwarf mosaic virus from common reed in a wetland

Posted on 17 August 2023 by nHavva Ilbağı, nRick Masonbrink, nW. Allen Millern

Abstract

Common reed is a widespread aquatic grass in wetland areas of Turkey. In reed samples, RNAs with the sequence of the Maize dwarf mosaic virus (MDMV) were found using high-throughput sequencing. The nearly complete genome sequence comprised 9514 nucleotides. It contains a 5′ UTR of at least 145 nucleotides, a 3′ UTR of at least 237 nucleotides, and an ORF encoding a single polyprotein of 3041 amino acid residues. Two partial sequences were 7709 nt and 7858 nt long, respectively. Three reed sequences contained 22 nt, 25 nt, and 80 nt insertions in the 5′UTR, respectively. The coding region of MDMV TR-34 (49%) was more conserved than UTRs (34.3%) compared to Johnsongrass mosaic virus (JGMV), Sugarcane mosaic virus (SCMV), and Sorghum mosaic virus (SrMV). MDMV-TR34 reed isolate shares 91%–53.1% nucleotide identity and 98.2%–49% amino acid sequence similarity with other MDMV and three potyvirus sequences, respectively. Recombination analysis indicated six putative recombination events. In 2020–2022, the survey studies showed that 25 of 260 reed samples were infected with MDMV at the infection rate of 9.6% in Tekirdag province. This result is the first report of the complete nucleotidesequence of MDMV in the common reed, a reservoir host for cereals growing areas in Turkey.

Morphomolecular identification and pathogenicity of Colletotrichum species associated with avocado anthracnose in northern Thailand

Posted on 14 August 2023 by nAlireza Armand, nRuvishika S. Jayawardenan

11 Colletotrichum Isolates were identified based on a polyphasic approach from avocado orchards in northern Thailand, and the pathogenicity was assessed for each species on avocado fruits and leaves.

Abstract

Avocado production is restricted globally by the anthracnose disease caused by Colletotrichum species. In Thailand, anthracnose symptoms can be found on avocado leaves and fruits, and it is an important postharvest disease, reducing the shelf life of the fruits and causing huge economic losses. Avocado leaves and fruits showing anthracnose disease were collected from Chiang Rai province, located in northern Thailand, and the Colletotrichum species isolated from the samples were identified based on morphological examination and multigene phylogenetic analyses. Phylogenetic analyses using five loci (ITS, ACT, CHS-1, GAPDH and TUB2) coupled with the morphology of 11 isolates showed that they belonged to four known species of Colletotrichum. Colletotrichum endophytica, C. fructicola and C. siamense are illustrated as new geographical records, and C. henanense is characterized as a new host record. Furthermore, the pathogenicity of these species in avocado fruits and leaves (West Indian variety) has been proven. In addition, this study provides further evidence for the synonymization of C. pandanicola and C. parvisporum with C. siamense.

Overexpression of BnNAC19 in Brassica napus enhances resistance to Leptosphaeria maculans, the blackleg pathogen of canola

Posted on 14 August 2023 by nZhongwei Zou, nW. G. Dilantha Fernandon

Overexpression of BnNAC19 in canola (Brassica napus) can enhance disease resistance against blackleg, caused by Leptosphaeria maculans, providing a valuable genetic resource for disease breeding.

Abstract

Leptosphaeria maculans is a fungal pathogen that causes blackleg disease in canola (Brassica napus), resulting in significant yield and economic losses in Canada and many parts of the world. Plant NAC transcription factors play critical roles in plant development and response to biotic or abiotic stress. In this study, we identified and characterized a BnNAC19 gene from Brassica napus. The overexpression of BnNAC19 in transgenic canola plants contributed to the improvement of seedling resistance against L. maculans. The mycelial growth of a green fluorescent protein-tagged strain of L. maculans and production of pycnidiospores were shown to be inhibited in the transgenic canola plants overexpressing BnNAC19. In addition, the canola transgenic line overexpressing BnNAC19 showed increased disease resistance in the adult plant, which was determined by quantitative resistance. Both increased seedling and adult plant resistance in transgenic canola plants overexpressing BnNAC19 indicate that the BnNAC19 gene plays a positive role against L. maculans. The expression pattern of genes BnNAC19 upstream and downstream of BnNAC19 that participate in plant defence pathways were investigated to elucidate the B. napus resistance mechanisms to L. maculans infection, and hence to aid the long-term blackleg disease-resistant breeding programmes.

Gibbsiella quercinecans, a pathogen with an increasing prevalence: A study on the causative agents of bacterial canker of Persian walnut and oak trees in central provinces of Iran

Posted on 10 August 2023 by nSaman Firouzianbandpey, nPejman Khodaygann

The emerging pathogen Gibbsiella quercinecans was found in walnut and oak trees, posing a threat to Persian walnut cultivation in central provinces of Iran.

Abstract

The cultivation of Persian walnuts in Iran is concentrated in the mountainous regions of Zagros and Alborz, encompassing Kohgiluyeh and Boyer-Ahmad, Isfahan and Fars provinces. Historically, these areas were renowned for their abundant growth of oak trees. However, due to environmental stressors, oak populations in the Zagros region have been declining, leading to an increased risk of diseases caused by new and aggressive pathogens, exacerbated by climate change. Understanding the distribution and association of pathogenic bacteria in the environment, especially for less common or uncommon species, has become crucial. In this study, 80 bacterial strains were isolated from 84 symptomatic walnut and 16 symptomatic oak trees to investigate bacterial canker agents in primary walnut cultivation regions of Iran. Following the hypersensitivity test and pathogenicity assays, 21 strains were classed as ‘Brenneria nigrifluens’ or ‘Brenneria-like’, based on their similarities to the reference strain B. nigrifluens ICMP 20120 using phenotypic techniques and specific primers (F1/C3, B. nigrifluens). Varying biochemical characteristics were exhibited by the ‘Brenneria-like’ group in comparison to the ‘B. nigrifluens’ group. Multilocus sequence analysis was performed using the gyrB, rpoB, infB and atpD genes to determine the taxonomic classification of this group, revealing that it belonged to Gibbsiella quercinecans. The increasing reports of this bacterium from different woodland tree hosts suggest its opportunistic role as an individual causative agent, necessitating monitoring of its host expansion and morbidity.

Evaluation of native isolates of Trichoderma spp. for controlling potato late blight caused by Phytophthora infestans in Nepal

Posted on 10 August 2023 by

Abstract

Late blight, caused by Phytophthora infestans, is the most devastating disease of potato worldwide that can cause up to 100% crop loss under disease conducive conditions. The present study was carried out to evaluate and identify effective Trichoderma isolates against the disease. Thirty-nine isolates of Trichoderma spp. isolated at Nepal Plant Disease and Agro Associates (NPDA), Kathmandu from Likhu areas of Nuwakot, Nepal were screened against P. infestans in detached leaf assay for their efficacy in reducing the lesion size of late blight. Fifteen isolates significantly reduced lesion size by 19%–46% compared with the control (water spray). Of them, top 10 isolates along with Sanjeevni (T. viride), a commercial product were tested in field experiments under natural epiphytotic conditions at Thansing and Dhikure of Likhu Rural Municipality in 2020–2021 and 2022–2023 crop years, respectively. The Trichoderma isolates significantly (p < .001) increased plant growth, tuber yield and reduced disease severity in both years. In 2020–2021, isolates, TL1-2A, TL4-81A and TL5-21A reduced disease severity by 37.3%, 37.2% and 30.4%, respectively. The isolate TL1-2A also significantly increased plant height, ground coverage and tuber yield by 41.2%, 30.3% and 72.3%, respectively compared with the control (water spray). In 2022–2023, TL1-2A reduced disease severity by 40.2% and increased tuber yield by 46.4%. Other isolates, though significantly different from control, did not have satisfactory effect on disease control and tuber yield. In both years, the isolate TL1-2A significantly reduced the disease, and increased plant growth and tuber yield. Thus, TL1-2A isolate can be a potential candidate as a biocontrol agent for the integrated management of potato late blight in Nepal.

RALF‐like peptide improves the colonization of endophytic Colletotrichum tofieldiae through interacting with plant receptor‐like kinase

Posted on 7 August 2023 by

Endophytic Colletotrichum tofieldiae harbours RALF homologues to regulate symbiotic signals and promote hyphae colonization through interacting with FERONIA encoded by plant.

Abstract

Endophytes can colonize a host plant without inducing obvious disease symptoms. Elicitors from endophytes may play important roles in balancing endophyte colonization. We identified a novel endophytic elicitor from Colletotrichum tofieldiae, CtRALF, that has structural and functional characteristics similar to those of rapid alkalinization factor (RALF) peptides in Arabidopsis thaliana. We found that CtRALF can directly interact with the host plant receptor-like kinase FERONIA (FER). The colonization of FER mutant plants by hyphae of C. tofieldiae was obviously reduced compared with that on wild-type plants. Furthermore, the interaction of CtRALF with FER regulated symbiotic signals by triggering calcium waves, inhibiting reactive oxygen species bursts, increasing mitogen-activated protein kinase phosphorylation and reducing the stabilization of MYC2. Collectively, these results suggested that the RALF homologue of endophytes may improve their symbiosis by interacting with host plant-encoded FER.