Genome-wide association mapping for LLS resistance in a MAGIC population of groundnut (Arachis hypogaea L.).

KEY MESSAGE: The identified 30 functional nucleotide polymorphisms or genic SNP markers would offer essential information for marker-assisted breeding in groundnut. A genome-wide association study (GWAS) on component traits of LLS resistance in an eight-way multiparent advance generation intercross (MAGIC) population of groundnut in the field and in a light chamber (controlled conditions) was performed via an Affymetrix 48 K single-nucleotide polymorphism (SNP) 'Axiom Arachis' array. Multiparental populations with high-density genotyping enable the detection of novel alleles. In total, five quantitative trait loci (QTLs) with marker - log10(p value) scores ranging from 4.25 to 13.77 for the incubation period (IP) and six QTLs with marker - log10(p value) scores ranging from 4.33 to 10.79 for the latent period (LP) were identified across the A- and B-subgenomes. A total of 62 markers‒trait associations (MTAs) were identified across the A- and B-subgenomes. Markers for LLS scores and the area under the disease progression curve (AUDPC) recorded for plants in the light chamber and under field conditions presented - log10 (p value) scores ranging from 4.22 to 27.30. The highest number of MTAs (six) was identified on chromosomes A05, B07 and B09. Out of a total of 73 MTAs, 37 and 36 MTAs were detected in subgenomes A and B, respectively. Taken together, these results suggest that both subgenomes have equal potential genomic regions contributing to LLS resistance. A total of 30 functional nucleotide polymorphisms or genic SNP markers were detected, among which eight genes were found to encode leucine-rich repeat (LRR) receptor-like protein kinases and putative disease resistance proteins. These important SNPs can be used in breeding programmes for the development of cultivars with improved disease resistance.

Spatiotemporal assessment of post-harvest mycotoxin contamination in rural North Indian food systems.

The spatiotemporal trends in aflatoxin B1 (AFB1), fumonisin B1 (FB1), and deoxynivalenol (DON) accumulation were analyzed in a range of food commodities (maize, groundnut, pearl millet, rice, and wheat) in village settings in Unnao, Uttar Pradesh, India. Samples (n = 1549) were collected across six communities and six time points spanning a calendar year and were analyzed for mycotoxins using enzyme-linked immunosorbent assays. AFB1 and FB1 were common across surveyed villages, with moderate to high detection rates (45-75%) observed across commodities. AFB1 levels in maize and groundnuts and FB1 levels in maize and pearl millet frequently exceeded regulatory threshold levels of 15 µg/kg (AFB1) and 2 µg/g (FB1). DON was analyzed in wheat, with 3% of samples yielding detectable levels and none exceeding 1 µg/g. In rice, AFB1 levels were highest in the bran and husk and lower in the kernel. Commodity type significantly influenced AFB1 detection status, while commodity type, season, and visual quality influenced samples' legal status. Storage characteristics and household socioeconomic status indicators did not have significant effects on contamination. No significant effects of any variables on FB1 detection or legal status were observed. Data on mycotoxin contamination, combined with data on local dietary intake, were used to estimate spatiotemporal mycotoxin exposure profiles. Estimated seasonal per capita exposure levels for AFB1 (5.4-39.3 ng/kg body weight/day) and FB1 (~0-2.4 µg/kg body weight/day) exceeded provisional maximum tolerable daily intake levels (1 ng/kg body weight/day for AFB1 and 2 µg/kg body weight/day for FB1) in some seasons and locations. This study demonstrates substantial dietary mycotoxin exposure risk in Unnao food systems and serves as an evidentiary foundation for participatory food safety intervention in the region.

Genetic diversity, population structure and validation of SSR markers linked to Sw-5 and I-2 genes in tomato germplasm.

Tomato is the world's second largest cultivated vegetable crop. Tomato spotted wilt virus (TSWV) and fusarium wilt (FW) are the two major biotic stresses in India limiting tomato production. Identification and utilization of resistant lines to realize the full genetic potential of varieties for yield gain is an eco-friendly approach. The present research work involved genetic diversity study of 48 genotypes, augmented from different exotic, and indigenous sources belonging to three species using SSR markers. A total of 195 alleles were generated by employing 84 polymorphic markers. The PIC value was ranged from 0.12 to 0.93. Two sub-populations (K = 2) were revealed by model based structure analysis. The cluster analysis using the UPGMA method classified the genotypes into 6 clusters. Pusa Ruby, EC-310310 and EC-620452 were found to be highly diverse. Molecular characterization of 48 genotypes with SSR markers divulged seven genotypes with Sw-5 gene and nine genotypes with I-2 gene showing resistance to TSWV and FW, respectively and further, on artificial screening, they were found to be phenotypically resistant. Out of 195 alleles generated from 84 polymorphic SSR markers, 43 alleles from 26 SSR markers were identified with positive average allele effect distributed across nine chromosomes and positive average allele effect was identified for the average weight of the fruit, the number of fruits formed per plant, and fusarium wilt PDI score. Fruit weight and fruit yield per plant registered a significant and positive correlations. The identified genotypes with varied backgrounds and performances will be very useful as diversified sources in resistant breeding programs of tomato. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01037-8.

Peanuts that keep aflatoxin at bay: a threshold that matters.

Aflatoxin contamination in peanuts poses major challenges for vulnerable populations of sub-Saharan Africa and South Asia. Developing peanut varieties to combat preharvest Aspergillus flavus infection and resulting aflatoxin contamination has thus far remained a major challenge, confounded by highly complex peanut-Aspergilli pathosystem. Our study reports achieving a high level of resistance in peanut by overexpressing (OE) antifungal plant defensins MsDef1 and MtDef4.2, and through host-induced gene silencing (HIGS) of aflM and aflP genes from the aflatoxin biosynthetic pathway. While the former improves genetic resistance to A. flavus infection, the latter inhibits aflatoxin production in the event of infection providing durable resistance against different Aspergillus flavus morphotypes and negligible aflatoxin content in several peanut events/lines well. A strong positive correlation was observed between aflatoxin accumulation and decline in transcription of the aflatoxin biosynthetic pathway genes in both OE-Def and HIGS lines. Transcriptomic signatures in the resistant lines revealed key mechanisms such as regulation of aflatoxin synthesis, its packaging and export control, besides the role of reactive oxygen species-scavenging enzymes that render enhanced protection in the OE and HIGS lines. This is the first study to demonstrate highly effective biotechnological strategies for successfully generating peanuts that are near-immune to aflatoxin contamination, offering a panacea for serious food safety, health and trade issues in the semi-arid regions.

Prevalence of groundnut dry root rot (Macrophomina phaseolina (Tassi) Goid.) and its pathogenic variability in Southern India.

Macrophomina phaseolina is the most devastating and emerging threat to groundnut production in India. An increase in average temperature and inconsistent rainfalls resulting from changing climatic conditions are strongly believed to aggravate the disease and cause severe yield losses. The present study aims to conduct a holistic survey to assess the prevalence and incidence of dry root rot of groundnut in major groundnut growing regions of Southern India, viz., Andhra Pradesh, Telangana, Karnataka, and Tamil Nadu. Furthermore, the pathogenic variability was determined using different assays such as morphological, cultural, pathogenic, and molecular assays. Results indicate that disease incidence in surveyed locations ranged from 8.06 to 20.61%. Both temperature and rainfall played a major role in increasing the disease incidence. The pathogenic variability of M. phaseolina isolates differed significantly, based on the percent disease incidence induced on cultivars of JL-24 groundnut and K-6 groundnut. Morphological variations in terms of growth pattern, culture color, sclerotia number, and sclerotia size were observed. The molecular characterization of M. phaseolina isolates done by ITS rDNA region using ITS1 and ITS4 primers yielded approximately 600 bp PCR amplicons, sequenced and deposited in GenBank (NCBI). Molecular variability analysis using SSR primers indicated the genetic variation among the isolates collected from different states. The present investigation revealed significant variations in pathogenic variability among isolates of M. phaseolina and these may be considered important in disease management and the development of resistant cultivars against groundnut dry root rot disease.

Two decades of association mapping: Insights on disease resistance in major crops.

Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.

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.

Exploring aflatoxin contamination and household-level exposure risk in diverse Indian food systems.

The present study sought to identify household risk factors associated with aflatoxin contamination within and across diverse Indian food systems and to evaluate their utility in risk modeling. Samples (n = 595) of cereals, pulses, and oil seeds were collected from 160 households across four diverse districts of India and analyzed for aflatoxin B1 using enzyme-linked immunosorbent assay (ELISA). Demographic information, food and cropping systems, food management behaviors, and storage environments were profiled for each household. An aflatoxin detection risk index was developed based on household-level features and validated using a repeated 5-fold cross-validation approach. Across districts, between 30-80% of households yielded at least one contaminated sample. Aflatoxin B1 detection rates and mean contamination levels were highest in groundnut and maize, respectively, and lower in other crops. Landholding had a positive univariate effect on household aflatoxin detection, while storage conditions, product source, and the number of protective behaviors used by households did not show significant effects. Presence of groundnut, post-harvest grain washing, use of sack-based storage systems, and cultivation status (farming or non-farming) were identified as the most contributive variables in stepwise logistic regression and were used to generate a household-level risk index. The index had moderate classification accuracy (68% sensitivity and 62% specificity) and significantly correlated with village-wise aflatoxin detection rates. Spatial analysis revealed utility of the index for identifying at-risk localities and households. This study identified several key features associated with aflatoxin contamination in Indian food systems and demonstrated that household characteristics are substantially predictive of aflatoxin risk.

Combining High Oleic Acid Trait and Resistance to Late Leaf Spot and Rust Diseases in Groundnut (Arachis hypogaea L.).

High oleic trait, resistance to rust and late leaf spot (LLS) are important breeding objectives in groundnut. Rust and LLS cause significant economic loss, and high oleic trait is an industry preferred trait that enhances economic returns. This study reports marker-assisted selection to introgress high oleic content, resistance to LLS and rust into Kadiri 6 (K 6), a popular cultivar. The alleles for target traits were selected using linked allele-specific, simple sequence repeats and single nucleotide polymorphic markers. The F1s (384), intercrossed F1s (441), BC1F1s (380), BC1F2s (195), and BC1F3s (343) were genotyped to obtain desired allelic combination. Sixteen plants were identified with homozygous high oleic, LLS and rust resistance alleles in BC1F2, which were advanced to BC1F3 and evaluated for disease resistance, yield governing and nutritional quality traits. Phenotyping with Near-Infrared Reflectance Spectroscopy identified three lines (BC1F3-76, BC1F3-278, and BC1F3-296) with >80% oleic acid. The identified lines exhibit high levels of resistance to LLS and rust diseases (score of 3.0-4.0) with preferred pod and kernel features. The selected lines are under yield testing trials in multi-locations for release and commercialization. The lines reported here demonstrated combining high oleic trait with resistance to LLS and rust diseases.