Comparative transcriptome analysis identified candidate genes for late leaf spot resistance and cause of defoliation in groundnut

Late leaf spot (LLS) caused by fungus Nothopassalora personata in groundnut is responsible for up to 50% yield loss. To dissect the complex nature of LLS resistance, comparative transcriptome analysis was performed using resistant (GPBD 4), susceptible (TAG 24) and a resistant introgression line (ICGV 13208) and identified a total of 12,164 and 9954 DEGs (differentially expressed genes) respectively in A- and B-subgenomes of tetraploid groundnut. There were 135 and 136 unique pathways triggered in A- and B-subgenomes, respectively, upon N. personata infection. Highly upregulated putative disease resistance genes, an RPP-13 like (Aradu.P20JR) and a NBS-LRR (Aradu.Z87JB) were identified on chromosome A02 and A03, respectively, for LLS resistance. Mildew resistance Locus (MLOs)-like proteins, heavy metal transport proteins, and ubiquitin protein ligase showed trend of upregulation in susceptible genotypes, while tetratricopeptide repeats (TPR), pentatricopeptide repeat (PPR), chitinases, glutathione S-transferases, purple acid phosphatases showed upregulation in resistant genotypes. However, the highly expressed ethylene responsive factor (ERF) and ethylene responsive nuclear protein (ERF2), and early responsive dehydration gene (ERD) might be related to the possible causes of defoliation in susceptible genotypes. The identified disease resistance genes can be deployed in genomics-assisted breeding for development of LLS resistant cultivars to reduce the yield loss in groundnut

Seed coat mediated resistance against Aspergillus flavus infection in peanut

Toxic metabolites known as aflatoxins are produced via certain species of the Aspergillus genus, specifically A. flavus, A. parasiticus, A. nomius, and A. tamarie. Although various pre- and post-harvest strategies have been employed, aflatoxin contamination remains a major problem within peanut crop, especially in subtropical environments. Aflatoxins are the most well-known and researched mycotoxins produced within the Aspergillus genus (namely Aspergillus flavus) and are classified as group 1 carcinogens. Their effects and etiology have been extensively researched and aflatoxins are commonly linked to growth defects and liver diseases in humans and livestock. Despite the known importance of seed coats in plant defense against pathogens, peanut seed coat mediated defenses against Aspergillus flavus resistance, have not received considerable attention. The peanut seed coat (testa) is primarily composed of a complex cell wall matrix consisting of cellulose, lignin, hemicellulose, phenolic compounds, and structural proteins. Due to cell wall desiccation during seed coat maturation, postharvest A. flavus infection occurs without the pathogen encountering any active genetic resistance from the live cell(s) and the testa acts as a physical and biochemical barrier only against infection. The structure of peanut seed coat cell walls and the presence of polyphenolic compounds have been reported to inhibit the growth of A. flavus and aflatoxin contamination; however, there is no comprehensive information available on peanut seed coat mediated resistance. We have recently reviewed various plant breeding, genomic, and molecular mechanisms, and management practices for reducing A. flavus infection and aflatoxin contamination. Further, we have also proved that seed coat acts as a physical and biochemical barrier against A. flavus infection. The current review focuses specifically on the peanut seed coat cell wall-mediated disease resistance, which will enable researchers to understand the mechanism and design efficient strategies for seed coat cell wall-mediated resistance against A. flavus infection and aflatoxin contamination

Mitigating aflatoxin contamination in groundnut through a combination of genetic resistance and post-harvest management practices

Aflatoxin is considered a “hidden poison” due to its slow and adverse effect on various biological pathways in humans, particularly among children, in whom it leads to delayed development, stunted growth, liver damage, and liver cancer. Unfortunately, the unpredictable behavior of the fungus as well as climatic conditions pose serious challenges in precise phenotyping, genetic prediction and genetic improvement, leaving the complete onus of preventing aflatoxin contamination in crops on post-harvest management. Equipping popular crop varieties with genetic resistance to aflatoxin is key to effective lowering of infection in farmer’s fields. A combination of genetic resistance for in vitro seed colonization (IVSC), pre-harvest aflatoxin contamination (PAC) and aflatoxin production together with pre- and post-harvest management may provide a sustainable solution to aflatoxin contamination. In this context, modern “omics” approaches, including next-generation genomics technologies, can provide improved and decisive information and genetic solutions. Preventing contamination will not only drastically boost the consumption and trade of the crops and products across nations/regions, but more importantly, stave off deleterious health problems among consumers across the globe

An improved Enzyme-Linked Immunosorbent Assay (ELISA) based protocol using seeds for detection of five major peanut allergens Ara h 1, Ara h 2, Ara h 3, Ara h 6, and Ara h 8

Peanut allergy is an important health concern among many individuals. As there is no effective treatment to peanut allergy, continuous monitoring of peanut-based products, and their sources is essential. Precise detection of peanut allergens is key for identification and development of improved peanut varieties with minimum or no allergens in addition to estimating the levels in peanut-based products available in food chain. The antibody based ELISA protocol along with sample preparation was standardized for Ara h 1, Ara h 2, Ara h 3, Ara h 6, and Ara h 8 to estimate their quantities in peanut seeds. Three different dilutions were optimized to precisely quantify target allergen proteins in peanut seeds such as Ara h 1 (1/1,000, 1/2,000, and 1/4,000), Ara h 2 and Ara h 3 (1/5,000, 1/10,000, and 1/20,000), Ara h 6 (1/40,000, 1/80,000, and 1/1,60,000), and Ara h 8 (1/10, 1/20, and 1/40). These dilutions were finalized for each allergen based on the accuracy of detection by achieving <20% coefficient of variation in three technical replicates. This protocol captured wide variation of allergen proteins in selected peanut genotypes for Ara h 1 (77–46,106 μg/g), Ara h 2 (265–5,426 μg/g), Ara h 3 (382–12,676 μg/g), Ara h 6 (949–43,375 μg/g), and Ara h 8 (0.385–6 μg/g). The assay is sensitive and reliable in precise detection of five major peanut allergens in seeds. Deployment of such protocol allows screening of large scale germplasm and breeding lines while developing peanut varieties with minimum allergenicity to ensure food safety

Harnessing genetic diversity of Wild Arachis species for genetic enhancement of cultivated peanut

Peanut (Arachis hypogaea L.) is an important self-pollinating tetraploid (AABB, 2n = 4x = 40) legume grown for the high-quality edible oil and easily digestible protein in its seeds. Enormous genetic variability is present in the genus Arachis containing 79 wild species and cultivated peanut. Wild species offer significant variability, particularly for biotic and abiotic stresses, and can be used to develop cultivars with enhanced levels of resistance to key stresses. However, utilization of these species requires use of ploidy manipulations, bridge crosses, and embryo or ovule rescue. For efficient use of diploid wild species from section Arachis, several synthetics (amphidiploids and autotetraploids) have been developed using A- and B-genome accessions with high levels of resistance to multiple stresses. These synthetics are used in crossing programs with cultigens to develop prebreeding populations and introgression lines (ILs) with high frequency of useful genes and alleles into good agronomic backgrounds. Evaluation of two such populations derived from ICGV 91114 × ISATGR 121250 (a synthetic derived from A. duranensis Krapov. & W.C. Greg. × A. ipaensis Krapov. & W.C. Greg.) and ICGV 87846 × ISATGR 265-5 (A. kempf-mercadoi W.C. Greg. & C.E. Simpson × A. hoehnei Krapov. & W.C. Greg.) resulted in the identification of ILs with high levels of late leaf spot (LLS) and rust resistance and significant genetic variability for morphoagronomic traits. Genotyping of these ILs with markers linked to rust and LLS resistance provided evidence that introgression of possible novel alleles and resistance sources from different wild species other than the commonly used A. cardenasii Krapov. & W.C. Greg. will be beneficial for peanut improvement

Assessing the prospects of Streptomyces sp. RP1A-12 in managing groundnut stem rot disease caused by Sclerotium rolfsii Sacc

Stem rot of groundnut caused by the soilborne pathogen Sclerotium rolfsii can cause significant yield losses. Biological control of stem rot using actinomycetes is a viable alternative to existing fungicidal management. Though actinomycetes are prolific antibiotic producers, reports pertaining to their use in groundnut disease management are limited. Here, actinomycetes were isolated from groundnut rhizospheric soils and screened for antagonism against S. rolfsii through a dual culture assay. Culture filtrates and crude extracts of the potential candidates were screened further for extracellular antifungal activity and characterized for biocontrol and plant-growth-promoting traits. A promising candidate was tested under greenhouse conditions as whole organism as well as crude extracts. Isolate RP1A-12 exhibited high antagonism against S. rolfsii in dual culture assay (69 % inhibition), culture filtrate assay (78–100 % inhibition at various concentrations) and crude extract assay (100 % inhibition with 1 % crude extracts). Moreover, germination of sclerotia of the test pathogen was inhibited with 1 % crude extracts. Strain RP1A-12 produced hydrogen cyanide, lipase, siderophores and indole acetic acid. Oxalic acid production by S. rolfsii was also inhibited by crude extracts of RP1A-12. In greenhouse studies, RP1A-12 reduced stem rot severity. Overall, our results suggest that isolate RP1A-12 has potential biocontrol capabilities against stem rot pathogen. Molecular characterization based on 16S rRNA gene sequencing of RP1A-12 identified it as a species of Streptomyces, closely related to S. flocculus

Employing Peanut Seed Coat Cell Wall Mediated Resistance Against Aspergillus flavus Infection and Aflatoxin Contamination

Aflatoxins, which have been classified as a group-1 carcinogen are the well-known mycotoxins produced by Aspergillus flavus. Aflatoxins have been linked to liver diseases, acute hepatic necrosis, resulting in cirrhosis or hepatocellular carcinomas due to which it incurs a loss of value in international trade for peanuts contaminated with it. The four main aflatoxins are B1, B2, G1, and G2 of which B1 is predominant. In plants, the cell wall is the primary barrier against pathogen invasion. Cell wall fortifications such as deposition of callose, cellulose, lignin, phenolic compounds and structural proteins help to prevent the pathogen infection. Further, the host cell’s ability to rapidly repair and reinforce its cell walls will result in a reduction of the penetration efficiency of the pathogen. Peanut seed coat acts as a physical and biochemical cell wall barrier against both pre and post-harvest pathogen infection. The structure of seed coat and the presence of polyphenol compounds have been reported to inhibit the growth of A. flavus, however, not successfully employed to develop A. flavus resistance in peanut. A comprehensive understanding of peanut seed coat development and biochemistry will provide information to design efficient strategies for the seed coat mediated A. flavus resistance and Aflatoxin contamination

Peanut seed coat acts as a physical and biochemical barrier against Aspergillus flavus infection

Aflatoxin contamination is a global menace that adversely affects food crops and human health. Peanut seed coat is the outer layer protecting the cotyledon both at pre- and post-harvest stages from biotic and abiotic stresses. The aim of the present study is to investigate the role of seed coat against A. flavus infection. In-vitro seed colonization (IVSC) with and without seed coat showed that the seed coat acts as a physical barrier, and the developmental series of peanut seed coat showed the formation of a robust multilayered protective seed coat. Radial growth bioassay revealed that both insoluble and soluble seed coat extracts from 55-437 line (resistant) showed higher A. flavus inhibition compared to TMV-2 line (susceptible). Further analysis of seed coat biochemicals showed that hydroxycinnamic and hydroxybenzoic acid derivatives are the predominant phenolic compounds, and addition of these compounds to the media inhibited A. flavus growth. Gene expression analysis showed that genes involved in lignin monomer, proanthocyanidin, and flavonoid biosynthesis are highly abundant in 55-437 compared to TMV-2 seed coats. Overall, the present study showed that the seed coat acts as a physical and biochemical barrier against A. flavus infection and its potential use in mitigating the aflatoxin contamination

Global transcriptome profiling identified transcription factors, biological process, and associated pathways for pre-harvest aflatoxin contamination in groundnut

Pre-harvest aflatoxin contamination (PAC) in groundnut is a serious quality concern globally, and drought stress before harvest further exacerbate its intensity, leading to the deterioration of produce quality. Understanding the host–pathogen interaction and identifying the candidate genes responsible for resistance to PAC will provide insights into the defense mechanism of the groundnut. In this context, about 971.63 million reads have been generated from 16 RNA samples under controlled and Aspergillus flavus infected conditions, from one susceptible and seven resistant genotypes. The RNA-seq analysis identified 45,336 genome-wide transcripts under control and infected conditions. This study identified 57 transcription factor (TF) families with major contributions from 6570 genes coding for bHLH (719), MYB-related (479), NAC (437), FAR1 family protein (320), and a few other families. In the host (groundnut), defense-related genes such as senescence-associated proteins, resveratrol synthase, seed linoleate, pathogenesis-related proteins, peroxidases, glutathione-S-transferases, chalcone synthase, ABA-responsive gene, and chitinases were found to be differentially expressed among resistant genotypes as compared to susceptible genotypes. This study also indicated the vital role of ABA-responsive ABR17, which co-regulates the genes of ABA responsive elements during drought stress, while providing resistance against A. flavus infection. It belongs to the PR-10 class and is also present in several plant–pathogen interactions

Molecular basis of root nodule symbiosis between Bradyrhizobium and ‘Crack-Entry’ legume groundnut (Arachis hypogaea L.)

Nitrogen is one of the essential plant nutrients and a major factor limiting crop productivity. To meet the requirements of sustainable agriculture, there is a need to maximize biological nitrogen fixation in different crop species. Legumes are able to establish root nodule symbiosis (RNS) with nitrogen-fixing soil bacteria which are collectively called rhizobia. This mutualistic association is highly specific, and each rhizobia species/strain interacts with only a specific group of legumes, and vice versa. Nodulation involves multiple phases of interactions ranging from initial bacterial attachment and infection establishment to late nodule development, characterized by a complex molecular signalling between plants and rhizobia. Characteristically, legumes like groundnut display a bacterial invasion strategy popularly known as “crack-entry’’ mechanism, which is reported approximately in 25% of all legumes. This article accommodates critical discussions on the bacterial infection mode, dynamics of nodulation, components of symbiotic signalling pathway, and also the effects of abiotic stresses and phytohormone homeostasis related to the root nodule symbiosis of groundnut and Bradyrhizobium. These parameters can help to understand how groundnut RNS is programmed to recognize and establish symbiotic relationships with rhizobia, adjusting gene expression in response to various regulations. This review further attempts to emphasize the current understanding of advancements regarding RNS research in the groundnut and speculates on prospective improvement possibilities in addition to ways for expanding it to other crops towards achieving sustainable agriculture and overcoming environmental challenges