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Sucrose content is a crucial indicator of quality and flavor in peanut seed, and there is a lack of clarity on the molecular basis of sucrose metabolism in peanut seed. In this context, we performed a comprehensive comparative transcriptome study on the samples collected at seven seed development stages between a high-sucrose content variety (ICG 12625) and a low-sucrose content variety (Zhonghua 10). The transcriptome analysis identified a total of 8334 genes exhibiting significantly different abundances between the high- and low-sucrose varieties. We identified 28 differentially expressed genes (DEGs) involved in sucrose metabolism in peanut and 12 of these encoded sugars will eventually be exported transporters (SWEETs). The remaining 16 genes encoded enzymes, such as cell wall invertase (CWIN), vacuolar invertase (VIN), cytoplasmic invertase (CIN), cytosolic fructose-bisphosphate aldolase (FBA), cytosolic fructose-1,6-bisphosphate phosphatase (FBP), sucrose synthase (SUS), cytosolic phosphoglucose isomerase (PGI), hexokinase (HK), and sucrose-phosphate phosphatase (SPP). The weighted gene co-expression network analysis (WGCNA) identified seven genes encoding key enzymes (CIN, FBA, FBP, HK, and SPP), three SWEET genes, and 90 transcription factors (TFs) showing a high correlation with sucrose content. Furthermore, upon validation, six of these genes were successfully verified as exhibiting higher expression in high-sucrose recombinant inbred lines (RILs). Our study suggested the key roles of the high expression of SWEETs and enzymes in sucrose synthesis making the genotype ICG 12625 sucrose-rich. This study also provided insights into the molecular basis of sucrose metabolism during seed development and facilitated exploring key candidate genes and molecular breeding for sucrose content in peanuts.
Weitao Li; Li Huang; Nian Liu; Manish Pandey; Yuning Chen; Liangqiang Cheng; Jianbin Guo; Bolun Yu; Huaiyong Luo; Xiaojing Zhou; Dongxin Huai; Weigang Chen; Liying Yan; Xin Wang; Yong Lei; Rajeev Varshney; Boshou Liao; Huifang Jiang. Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts. International Journal of Molecular Sciences 2021, 22, 7266 .
AMA StyleWeitao Li, Li Huang, Nian Liu, Manish Pandey, Yuning Chen, Liangqiang Cheng, Jianbin Guo, Bolun Yu, Huaiyong Luo, Xiaojing Zhou, Dongxin Huai, Weigang Chen, Liying Yan, Xin Wang, Yong Lei, Rajeev Varshney, Boshou Liao, Huifang Jiang. Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts. International Journal of Molecular Sciences. 2021; 22 (14):7266.
Chicago/Turabian StyleWeitao Li; Li Huang; Nian Liu; Manish Pandey; Yuning Chen; Liangqiang Cheng; Jianbin Guo; Bolun Yu; Huaiyong Luo; Xiaojing Zhou; Dongxin Huai; Weigang Chen; Liying Yan; Xin Wang; Yong Lei; Rajeev Varshney; Boshou Liao; Huifang Jiang. 2021. "Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts." International Journal of Molecular Sciences 22, no. 14: 7266.
The groundnut breeding program at International Crops Research Institute for the Semi-Arid Tropics routinely performs marker-based early generation selection (MEGS) in thousands of segregating populations. The existing MEGS includes planting of segregating populations in fields or glasshouses, label tagging, and sample collection using leaf-punch from 20–25 day old plants followed by genotyping with 10 single nucleotide polymorphisms based early generation selection marker panels in a high throughput genotyping (HTPG) platform. The entire process is laborious, time consuming, and costly. Therefore, in order to save the time of the breeder and to reduce the cost during MEGS, we optimized a single seed chipping (SSC) process based MEGS protocol and deployed on large scale by genotyping >3000 samples from ongoing groundnut breeding program. In SSC-based MEGS, we used a small portion of cotyledon by slicing-off the posterior end of the single seed and transferred to the 96-deep well plate for DNA isolation and genotyping at HTPG platform. The chipped seeds were placed in 96-well seed-box in the same order of 96-well DNA sampling plate to enable tracking back to the selected individual seed. A high germination rate of 95–99% from the chipped seeds indicated that slicing of seeds from posterior end does not significantly affect germination percentage. In addition, we could successfully advance 3.5 generations in a year using a low-cost rapid generation turnover glass-house facility as compared to routine practice of two generations in field conditions. The integration of SSC based genotyping and rapid generation advancement (RGA) could significantly reduce the operational requirement of person-hours and expenses, and save a period of 6–8 months in groundnut genetics and breeding research.
Sejal Parmar; Dnyaneshwar Deshmukh; Rakesh Kumar; Surendra Manohar; Pushpesh Joshi; Vinay Sharma; Sunil Chaudhari; Murali Variath; Sunil Gangurde; Rajaguru Bohar; Prashant Singam; Rajeev Varshney; Pasupuleti Janila; Manish Pandey. Single Seed-Based High-Throughput Genotyping and Rapid Generation Advancement for Accelerated Groundnut Genetics and Breeding Research. Agronomy 2021, 11, 1226 .
AMA StyleSejal Parmar, Dnyaneshwar Deshmukh, Rakesh Kumar, Surendra Manohar, Pushpesh Joshi, Vinay Sharma, Sunil Chaudhari, Murali Variath, Sunil Gangurde, Rajaguru Bohar, Prashant Singam, Rajeev Varshney, Pasupuleti Janila, Manish Pandey. Single Seed-Based High-Throughput Genotyping and Rapid Generation Advancement for Accelerated Groundnut Genetics and Breeding Research. Agronomy. 2021; 11 (6):1226.
Chicago/Turabian StyleSejal Parmar; Dnyaneshwar Deshmukh; Rakesh Kumar; Surendra Manohar; Pushpesh Joshi; Vinay Sharma; Sunil Chaudhari; Murali Variath; Sunil Gangurde; Rajaguru Bohar; Prashant Singam; Rajeev Varshney; Pasupuleti Janila; Manish Pandey. 2021. "Single Seed-Based High-Throughput Genotyping and Rapid Generation Advancement for Accelerated Groundnut Genetics and Breeding Research." Agronomy 11, no. 6: 1226.
Rice grain shape and nutritional quality traits have high economic value for commercial production of rice and largely determine the market price, besides influencing the global food demand for high-quality rice. Detection, mapping and exploitation of quantitative trait loci (QTL) associated with kernel elongation and grain quality in Basmati rice is considered as an efficient strategy for improving the kernel elongation and grain quality trait in rice varieties. Genetic information in rice for most of these traits is scanty and needed interventions through the use of molecular markers. A recombinant inbred lines (RIL) population consisting of 130 lines generated from the cross involving Basmati 370, a superior quality Basmati variety and Pusa Basmati 1121, a Basmati derived variety were used to map the QTLs for 9 important grain quality and yield related traits. Correlation studies showed that various components of yield show a significant positive relationship with grain yield. A genetic map was constructed using 70 polymorphic simple sequence repeat (SSR) markers spanning a genetic distance of 689.3 cM distributed over 12 rice chromosomes. Significant variation was observed and showed transgressive segregation for grain quality traits in RIL population. A total of 20 QTLs were identified associated with nine yield and quality traits. Epistatic interactions were also identified for grain quality related traits indicating complex genetic nature inheritance. Therefore, the identified QTLs and flanking marker information could be utilized in the marker-assisted selection to improve kernel elongation and nutritional grain quality traits in rice varieties.
Madhvi Sharma; Sunil S Gangurde; Romesh K Salgotra; Bupesh Kumar; Anil K Singh; Manish K Pandey. Genetic mapping for grain quality and yield-attributed traits in Basmati rice using SSR-based genetic map. Journal of Biosciences 2021, 46, 1 -14.
AMA StyleMadhvi Sharma, Sunil S Gangurde, Romesh K Salgotra, Bupesh Kumar, Anil K Singh, Manish K Pandey. Genetic mapping for grain quality and yield-attributed traits in Basmati rice using SSR-based genetic map. Journal of Biosciences. 2021; 46 (3):1-14.
Chicago/Turabian StyleMadhvi Sharma; Sunil S Gangurde; Romesh K Salgotra; Bupesh Kumar; Anil K Singh; Manish K Pandey. 2021. "Genetic mapping for grain quality and yield-attributed traits in Basmati rice using SSR-based genetic map." Journal of Biosciences 46, no. 3: 1-14.
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.
Pooja Soni; Arun Pandey; Spurthi Nayak; Manish Pandey; Priya Tolani; Sarita Pandey; Hari Sudini; Prasad Bajaj; Jake Fountain; Prashant Singam; Baozhu Guo; Rajeev Varshney. Global Transcriptome Profiling Identified Transcription Factors, Biological Process, and Associated Pathways for Pre-Harvest Aflatoxin Contamination in Groundnut. Journal of Fungi 2021, 7, 413 .
AMA StylePooja Soni, Arun Pandey, Spurthi Nayak, Manish Pandey, Priya Tolani, Sarita Pandey, Hari Sudini, Prasad Bajaj, Jake Fountain, Prashant Singam, Baozhu Guo, Rajeev Varshney. Global Transcriptome Profiling Identified Transcription Factors, Biological Process, and Associated Pathways for Pre-Harvest Aflatoxin Contamination in Groundnut. Journal of Fungi. 2021; 7 (6):413.
Chicago/Turabian StylePooja Soni; Arun Pandey; Spurthi Nayak; Manish Pandey; Priya Tolani; Sarita Pandey; Hari Sudini; Prasad Bajaj; Jake Fountain; Prashant Singam; Baozhu Guo; Rajeev Varshney. 2021. "Global Transcriptome Profiling Identified Transcription Factors, Biological Process, and Associated Pathways for Pre-Harvest Aflatoxin Contamination in Groundnut." Journal of Fungi 7, no. 6: 413.
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.
Sunil Gangurde; Spurthi Nayak; Pushpesh Joshi; Shilp Purohit; Hari Sudini; Annapurna Chitikineni; Yanbin Hong; Baozhu Guo; Xiaoping Chen; Manish Pandey; Rajeev Varshney. Comparative Transcriptome Analysis Identified Candidate Genes for Late Leaf Spot Resistance and Cause of Defoliation in Groundnut. International Journal of Molecular Sciences 2021, 22, 4491 .
AMA StyleSunil Gangurde, Spurthi Nayak, Pushpesh Joshi, Shilp Purohit, Hari Sudini, Annapurna Chitikineni, Yanbin Hong, Baozhu Guo, Xiaoping Chen, Manish Pandey, Rajeev Varshney. Comparative Transcriptome Analysis Identified Candidate Genes for Late Leaf Spot Resistance and Cause of Defoliation in Groundnut. International Journal of Molecular Sciences. 2021; 22 (9):4491.
Chicago/Turabian StyleSunil Gangurde; Spurthi Nayak; Pushpesh Joshi; Shilp Purohit; Hari Sudini; Annapurna Chitikineni; Yanbin Hong; Baozhu Guo; Xiaoping Chen; Manish Pandey; Rajeev Varshney. 2021. "Comparative Transcriptome Analysis Identified Candidate Genes for Late Leaf Spot Resistance and Cause of Defoliation in Groundnut." International Journal of Molecular Sciences 22, no. 9: 4491.
The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other -omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).
Vinay Sharma; Prateek Gupta; Kagolla Priscilla; Sharan Kumar; Bhagyashree Hangargi; Akash Veershetty; Devade Ramrao; Srinivas Suresh; Rahul Narasanna; GajananA Naik; Anirudh Kumar; Baozhu Guo; Weijian Zhuang; Rajeev Varshney; Manish Pandey; Rakesh Kumar. Metabolomics Intervention Towards Better Understanding of Plant Traits. Cells 2021, 10, 346 .
AMA StyleVinay Sharma, Prateek Gupta, Kagolla Priscilla, Sharan Kumar, Bhagyashree Hangargi, Akash Veershetty, Devade Ramrao, Srinivas Suresh, Rahul Narasanna, GajananA Naik, Anirudh Kumar, Baozhu Guo, Weijian Zhuang, Rajeev Varshney, Manish Pandey, Rakesh Kumar. Metabolomics Intervention Towards Better Understanding of Plant Traits. Cells. 2021; 10 (2):346.
Chicago/Turabian StyleVinay Sharma; Prateek Gupta; Kagolla Priscilla; Sharan Kumar; Bhagyashree Hangargi; Akash Veershetty; Devade Ramrao; Srinivas Suresh; Rahul Narasanna; GajananA Naik; Anirudh Kumar; Baozhu Guo; Weijian Zhuang; Rajeev Varshney; Manish Pandey; Rakesh Kumar. 2021. "Metabolomics Intervention Towards Better Understanding of Plant Traits." Cells 10, no. 2: 346.
A deep understanding of the genetic control of drought tolerance and iron deficiency tolerance is essential to hasten the process of developing improved varieties with higher tolerance through genomics-assisted breeding. In this context, an improved genetic map with 1205 loci was developed spanning 2598.3 cM with an average 2.2 cM distance between loci in the recombinant inbred line (TAG 24 × ICGV 86031) population using high-density 58K single nucleotide polymorphism (SNP) “Axiom_Arachis” array. Quantitative trait locus (QTL) analysis was performed using extensive phenotyping data generated for 20 drought tolerance- and two iron deficiency tolerance-related traits from eight seasons (2004–2015) at two locations in India, one in Niger, and one in Senegal. The genome-wide QTL discovery analysis identified 19 major main-effect QTLs with 10.0–33.9% phenotypic variation explained (PVE) for drought tolerance- and iron deficiency tolerance- related traits. Major main-effect QTLs were detected for haulm weight (20.1% PVE), SCMR (soil plant analytical development (SPAD) chlorophyll meter reading, 22.4% PVE), and visual chlorosis rate (33.9% PVE). Several important candidate genes encoding glycosyl hydrolases; malate dehydrogenases; microtubule-associated proteins; and transcription factors such as MADS-box, basic helix-loop-helix (bHLH), NAM, ATAF, and CUC (NAC), and myeloblastosis (MYB) were identified underlying these QTL regions. The putative function of these genes indicated their possible involvement in plant growth, development of seed and pod, and photosynthesis under drought or iron deficiency conditions in groundnut. These genomic regions and candidate genes, after validation, may be useful to develop molecular markers for deploying genomics-assisted breeding for enhancing groundnut yield under drought stress and iron-deficient soil conditions.
Manish K. Pandey; Sunil S. Gangurde; Vinay Sharma; Santosh K. Pattanashetti; Gopalakrishna K. Naidu; Issa Faye; Falalou Hamidou; Haile Desmae; Ndjido Ardo Kane; Mei Yuan; Vincent Vadez; Shyam N. Nigam; Rajeev K. Varshney. Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut. Genes 2020, 12, 37 .
AMA StyleManish K. Pandey, Sunil S. Gangurde, Vinay Sharma, Santosh K. Pattanashetti, Gopalakrishna K. Naidu, Issa Faye, Falalou Hamidou, Haile Desmae, Ndjido Ardo Kane, Mei Yuan, Vincent Vadez, Shyam N. Nigam, Rajeev K. Varshney. Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut. Genes. 2020; 12 (1):37.
Chicago/Turabian StyleManish K. Pandey; Sunil S. Gangurde; Vinay Sharma; Santosh K. Pattanashetti; Gopalakrishna K. Naidu; Issa Faye; Falalou Hamidou; Haile Desmae; Ndjido Ardo Kane; Mei Yuan; Vincent Vadez; Shyam N. Nigam; Rajeev K. Varshney. 2020. "Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut." Genes 12, no. 1: 37.
Aflatoxin-affected groundnut or peanut presents a major global health issue to both commercial and subsistence farming. Therefore, understanding the genetic and molecular mechanisms associated with resistance to aflatoxin production during host–pathogen interactions is crucial for breeding groundnut cultivars with minimal level of aflatoxin contamination. Here, we performed gene expression profiling to better understand the mechanisms involved in reduction and prevention of aflatoxin contamination resulting from Aspergillus flavus infection in groundnut seeds. RNA sequencing (RNA-Seq) of 16 samples from different time points during infection (24 h, 48 h, 72 h and the 7th day after inoculation) in U 4-7-5 (resistant) and JL 24 (susceptible) genotypes yielded 840.5 million raw reads with an average of 52.5 million reads per sample. A total of 1779 unique differentially expressed genes (DEGs) were identified. Furthermore, comprehensive analysis revealed several pathways, such as disease resistance, hormone biosynthetic signaling, flavonoid biosynthesis, reactive oxygen species (ROS) detoxifying, cell wall metabolism and catabolizing and seed germination. We also detected several highly upregulated transcription factors, such as ARF, DBB, MYB, NAC and C2H2 in the resistant genotype in comparison to the susceptible genotype after inoculation. Moreover, RNA-Seq analysis suggested the occurrence of coordinated control of key pathways controlling cellular physiology and metabolism upon A. flavus infection, resulting in reduced aflatoxin production.
Pooja Soni; Spurthi N. Nayak; Rakesh Kumar; Manish K. Pandey; Namita Singh; Hari K. Sudini; Prasad Bajaj; Jake C. Fountain; Prashant Singam; Yanbin Hong; Xiaoping Chen; Weijian Zhuang; Boshou Liao; Baozhu Guo; Rajeev K. Varshney. Transcriptome Analysis Identified Coordinated Control of Key Pathways Regulating Cellular Physiology and Metabolism upon Aspergillus flavus Infection Resulting in Reduced Aflatoxin Production in Groundnut. Journal of Fungi 2020, 6, 370 .
AMA StylePooja Soni, Spurthi N. Nayak, Rakesh Kumar, Manish K. Pandey, Namita Singh, Hari K. Sudini, Prasad Bajaj, Jake C. Fountain, Prashant Singam, Yanbin Hong, Xiaoping Chen, Weijian Zhuang, Boshou Liao, Baozhu Guo, Rajeev K. Varshney. Transcriptome Analysis Identified Coordinated Control of Key Pathways Regulating Cellular Physiology and Metabolism upon Aspergillus flavus Infection Resulting in Reduced Aflatoxin Production in Groundnut. Journal of Fungi. 2020; 6 (4):370.
Chicago/Turabian StylePooja Soni; Spurthi N. Nayak; Rakesh Kumar; Manish K. Pandey; Namita Singh; Hari K. Sudini; Prasad Bajaj; Jake C. Fountain; Prashant Singam; Yanbin Hong; Xiaoping Chen; Weijian Zhuang; Boshou Liao; Baozhu Guo; Rajeev K. Varshney. 2020. "Transcriptome Analysis Identified Coordinated Control of Key Pathways Regulating Cellular Physiology and Metabolism upon Aspergillus flavus Infection Resulting in Reduced Aflatoxin Production in Groundnut." Journal of Fungi 6, no. 4: 370.
Aflatoxin production by isolates of Aspergillus flavus varies, ranging from highly toxigenic to completely atoxigenic. Several mechanisms have been identified which regulate aflatoxin production including medium carbon source and oxidative stress. In recent studies, aflatoxin production has been implicated in partially ameliorating oxidative stress in A. flavus. To better understand the role of aflatoxin production in oxidative stress responses, a selection of toxigenic and atoxigenic isolates of A. flavus with moderate to high oxidative stress tolerance were exposed to increasing concentrations of H2O2 in both aflatoxin-conducive and non-conducive media. Mycelial mats were collected for global transcriptome sequencing followed by differential expression, functional prediction, and weighted co-expression analyses. Oxidative stress and medium carbon source had a significant effect on the expression of several secondary metabolite gene clusters including those for aflatoxin, aflatrem, aflavarin, cyclopiazonic acid, and kojic acid. Atoxigenic biological control isolates showed less differential expression under stress than other atoxigenic isolates suggesting expression profiles may be useful in screening. Increasing stress also resulted in regulation of SakA/Hog1 and MpkA MAP kinase signalling pathways pointing to their potential roles in regulating oxidative stress responses. Their expression was also influenced by medium carbon source. These results suggest that aflatoxin production along with that of other mycotoxins may occur as part of a concerted coping mechanism for oxidative stress and its effects in the environment. This mechanism is also regulated by availability of simple sugars and glycolytic compounds for their biosynthesis.
J.C. Fountain; A.K. Pandey; S.N. Nayak; P. Bajaj; H. Wang; V. Kumar; A. Chitikineni; H.K. Abbas; B.T. Scully; R.C. Kemerait; B. Guo; R.K. Varshney. Transcriptional responses of toxigenic and atoxigenic isolates of Aspergillus flavus to oxidative stress in aflatoxin-conducive and non-conducive media. World Mycotoxin Journal 2020, 13, 443 -457.
AMA StyleJ.C. Fountain, A.K. Pandey, S.N. Nayak, P. Bajaj, H. Wang, V. Kumar, A. Chitikineni, H.K. Abbas, B.T. Scully, R.C. Kemerait, B. Guo, R.K. Varshney. Transcriptional responses of toxigenic and atoxigenic isolates of Aspergillus flavus to oxidative stress in aflatoxin-conducive and non-conducive media. World Mycotoxin Journal. 2020; 13 (4):443-457.
Chicago/Turabian StyleJ.C. Fountain; A.K. Pandey; S.N. Nayak; P. Bajaj; H. Wang; V. Kumar; A. Chitikineni; H.K. Abbas; B.T. Scully; R.C. Kemerait; B. Guo; R.K. Varshney. 2020. "Transcriptional responses of toxigenic and atoxigenic isolates of Aspergillus flavus to oxidative stress in aflatoxin-conducive and non-conducive media." World Mycotoxin Journal 13, no. 4: 443-457.
Key message Comparative assessment identified naïve interaction model, and naïve and informed interaction GS models suitable for achieving higher prediction accuracy in groundnut keeping in mind the high genotype × environment interaction for complex traits. Abstract Genomic selection (GS) can be an efficient and cost-effective breeding approach which captures both small- and large-effect genetic factors and therefore promises to achieve higher genetic gains for complex traits such as yield and oil content in groundnut. A training population was constituted with 340 elite lines followed by genotyping with 58 K ‘Axiom_Arachis’ SNP array and phenotyping for key agronomic traits at three locations in India. Four GS models were tested using three different random cross-validation schemes (CV0, CV1 and CV2). These models are: (1) model 1 (M1 = E + L) which includes the main effects of environment (E) and line (L); (2) model 2 (M2 = E + L + G) which includes the main effects of markers (G) in addition to E and L; (3) model 3 (M3 = E + L + G + GE), a naïve interaction model; and (4) model 4 (E + L + G + LE + GE), a naïve and informed interaction model. Prediction accuracy estimated for four models indicated clear advantage of the inclusion of marker information which was reflected in better prediction accuracy achieved with models M2, M3 and M4 as compared to M1 model. High prediction accuracies (> 0.600) were observed for days to 50% flowering, days to maturity, hundred seed weight, oleic acid, [email protected] days, [email protected] days and late leaf [email protected] days, while medium prediction accuracies (0.400–0.600) were obtained for pods/plant, shelling %, and total yield/plant. Assessment of comparative prediction accuracy for different GS models to perform selection for untested genotypes, and unobserved and unevaluated environments provided greater insights on potential application of GS breeding in groundnut.
Manish K. Pandey; Sunil Chaudhari; Diego Jarquin; Pasupuleti Janila; Jose Crossa; Sudam C. Patil; Subramaniam Sundravadana; Dhirendra Khare; Ramesh S. Bhat; Thankappan Radhakrishnan; John M. Hickey; Rajeev K. Varshney. Genome-based trait prediction in multi- environment breeding trials in groundnut. Theoretical and Applied Genetics 2020, 133, 3101 -3117.
AMA StyleManish K. Pandey, Sunil Chaudhari, Diego Jarquin, Pasupuleti Janila, Jose Crossa, Sudam C. Patil, Subramaniam Sundravadana, Dhirendra Khare, Ramesh S. Bhat, Thankappan Radhakrishnan, John M. Hickey, Rajeev K. Varshney. Genome-based trait prediction in multi- environment breeding trials in groundnut. Theoretical and Applied Genetics. 2020; 133 (11):3101-3117.
Chicago/Turabian StyleManish K. Pandey; Sunil Chaudhari; Diego Jarquin; Pasupuleti Janila; Jose Crossa; Sudam C. Patil; Subramaniam Sundravadana; Dhirendra Khare; Ramesh S. Bhat; Thankappan Radhakrishnan; John M. Hickey; Rajeev K. Varshney. 2020. "Genome-based trait prediction in multi- environment breeding trials in groundnut." Theoretical and Applied Genetics 133, no. 11: 3101-3117.
Key message Groundnut has entered now in post-genome era enriched with optimum genomic and genetic resources to facilitate faster trait dissection, gene discovery and accelerated genetic improvement for developing climate-smart varieties. Abstract Cultivated groundnut or peanut (Arachis hypogaea), an allopolyploid oilseed crop with a large and complex genome, is one of the most nutritious food. This crop is grown in more than 100 countries, and the low productivity has remained the biggest challenge in the semiarid tropics. Recently, the groundnut research community has witnessed fast progress and achieved several key milestones in genomics research including genome sequence assemblies of wild diploid progenitors, wild tetraploid and both the subspecies of cultivated tetraploids, resequencing of diverse germplasm lines, genome-wide transcriptome atlas and cost-effective high and low-density genotyping assays. These genomic resources have enabled high-resolution trait mapping by using germplasm diversity panels and multi-parent genetic populations leading to precise gene discovery and diagnostic marker development. Furthermore, development and deployment of diagnostic markers have facilitated screening early generation populations as well as marker-assisted backcrossing breeding leading to development and commercialization of some molecular breeding products in groundnut. Several new genomics applications/technologies such as genomic selection, speed breeding, mid-density genotyping assay and genome editing are in pipeline. The integration of these new technologies hold great promise for developing climate-smart, high yielding and more nutritious groundnut varieties in the post-genome era.
Manish K. Pandey; Arun K. Pandey; Rakesh Kumar; Chogozie Victor Nwosu; Baozhu Guo; Graeme C. Wright; Ramesh S. Bhat; Xiaoping Chen; Sandip K. Bera; Mei Yuan; Huifang Jiang; Issa Faye; Thankappan Radhakrishnan; Xingjun Wang; Xuanquiang Liang; Boshou Liao; Xinyou Zhang; Rajeev K. Varshney; Weijian Zhuang. Translational genomics for achieving higher genetic gains in groundnut. Theoretical and Applied Genetics 2020, 133, 1679 -1702.
AMA StyleManish K. Pandey, Arun K. Pandey, Rakesh Kumar, Chogozie Victor Nwosu, Baozhu Guo, Graeme C. Wright, Ramesh S. Bhat, Xiaoping Chen, Sandip K. Bera, Mei Yuan, Huifang Jiang, Issa Faye, Thankappan Radhakrishnan, Xingjun Wang, Xuanquiang Liang, Boshou Liao, Xinyou Zhang, Rajeev K. Varshney, Weijian Zhuang. Translational genomics for achieving higher genetic gains in groundnut. Theoretical and Applied Genetics. 2020; 133 (5):1679-1702.
Chicago/Turabian StyleManish K. Pandey; Arun K. Pandey; Rakesh Kumar; Chogozie Victor Nwosu; Baozhu Guo; Graeme C. Wright; Ramesh S. Bhat; Xiaoping Chen; Sandip K. Bera; Mei Yuan; Huifang Jiang; Issa Faye; Thankappan Radhakrishnan; Xingjun Wang; Xuanquiang Liang; Boshou Liao; Xinyou Zhang; Rajeev K. Varshney; Weijian Zhuang. 2020. "Translational genomics for achieving higher genetic gains in groundnut." Theoretical and Applied Genetics 133, no. 5: 1679-1702.
Spatio‐temporal and developmental stage specific transcriptome analysis play a crucial role in systems biology‐based improvement of any species. In this context, we report here the Arachis hypogaea gene expression atlas (AhGEA) for the world’s widest cultivated subsp. fastigiata based on RNA‐seq data using 20 diverse tissues across five key developmental stages. Approximately 480 million paired‐end filtered reads were generated followed by identification of 81,901 transcripts from an early maturing, high‐yielding, drought tolerant groundnut variety, ICGV 91114. Further, 57,344 genome‐wide transcripts were identified with ≥1 FPKM across different tissues and stages. Our in‐depth analysis of the global transcriptome sheds light into complex regulatory networks namely, gravitropism and photomorphogenesis, seed development, allergens and oil biosynthesis in groundnut. Importantly, interesting insights into molecular basis of seed development and nodulation have immense potential for translational genomics research. We have also identified a set of stable expressing transcripts across the selected tissues, which could be utilized as internal controls in groundnut functional genomics studies. The AhGEA revealed potential transcripts associated with allergens, which upon appropriate validation could be deployed in the coming years to develop consumer‐friendly groundnut varieties. Taken together, the AhGEA touches upon various important and key features of cultivated groundnut and provides a reference for further functional, comparative and translational genomics research for various economically important traits.
Pallavi Sinha; Prasad Bajaj; Lekha T. Pazhamala; Spurthi N. Nayak; Manish K. Pandey; Annapurna Chitikineni; Dongxin Huai; Aamir W. Khan; Aarthi Desai; Huifang Jiang; Weijian Zhuang; Baozhu Guo; Boshou Liao; Rajeev K. Varshney. Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications. Plant Biotechnology Journal 2020, 18, 2187 -2200.
AMA StylePallavi Sinha, Prasad Bajaj, Lekha T. Pazhamala, Spurthi N. Nayak, Manish K. Pandey, Annapurna Chitikineni, Dongxin Huai, Aamir W. Khan, Aarthi Desai, Huifang Jiang, Weijian Zhuang, Baozhu Guo, Boshou Liao, Rajeev K. Varshney. Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications. Plant Biotechnology Journal. 2020; 18 (11):2187-2200.
Chicago/Turabian StylePallavi Sinha; Prasad Bajaj; Lekha T. Pazhamala; Spurthi N. Nayak; Manish K. Pandey; Annapurna Chitikineni; Dongxin Huai; Aamir W. Khan; Aarthi Desai; Huifang Jiang; Weijian Zhuang; Baozhu Guo; Boshou Liao; Rajeev K. Varshney. 2020. "Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications." Plant Biotechnology Journal 18, no. 11: 2187-2200.
Santosh Pattanashetti; Manish K. Pandey; Gopalakrishna K. Naidu; Manish K. Vishwakarma; Omprakash Kumar Singh; Yaduru Shasidhar; Ishwar H. Boodi; Basavaraj D. Biradar; Roma Rani Das; Abhishek Rathore; Rajeev K. Varshney. Identification of quantitative trait loci associated with iron deficiency chlorosis resistance in groundnut ( Arachis hypogaea ). Plant Breeding 2020, 139, 790 -803.
AMA StyleSantosh Pattanashetti, Manish K. Pandey, Gopalakrishna K. Naidu, Manish K. Vishwakarma, Omprakash Kumar Singh, Yaduru Shasidhar, Ishwar H. Boodi, Basavaraj D. Biradar, Roma Rani Das, Abhishek Rathore, Rajeev K. Varshney. Identification of quantitative trait loci associated with iron deficiency chlorosis resistance in groundnut ( Arachis hypogaea ). Plant Breeding. 2020; 139 (4):790-803.
Chicago/Turabian StyleSantosh Pattanashetti; Manish K. Pandey; Gopalakrishna K. Naidu; Manish K. Vishwakarma; Omprakash Kumar Singh; Yaduru Shasidhar; Ishwar H. Boodi; Basavaraj D. Biradar; Roma Rani Das; Abhishek Rathore; Rajeev K. Varshney. 2020. "Identification of quantitative trait loci associated with iron deficiency chlorosis resistance in groundnut ( Arachis hypogaea )." Plant Breeding 139, no. 4: 790-803.
Aflatoxin B1 (AFB1) and aflatoxin B2 (AFB2) are the most common aflatoxins produced by Aspergillus flavus in peanuts, with high carcinogenicity and teratogenicity. Identification of DNA markers associated with resistance to aflatoxin production is likely to offer breeders efficient tools to develop resistant cultivars through molecular breeding. In this study, seeds of 99 accessions of a Chinese peanut mini-mini core collection were investigated for their reaction to aflatoxin production by a laboratory kernel inoculation assay. Two resistant accessions (Zh.h0551 and Zh.h2150) were identified, with their aflatoxin content being 8.11%–18.90% of the susceptible control. The 99 peanut accessions were also genotyped by restriction site-associated DNA sequencing (RAD-Seq) for a genome-wide association study (GWAS). A total of 60 SNP (single nucleotide polymorphism) markers associated with aflatoxin production were detected, and they explained 16.87%–31.70% of phenotypic variation (PVE), with SNP02686 and SNP19994 possessing 31.70% and 28.91% PVE, respectively. Aflatoxin contents of accessions with “AG” (existed in Zh.h0551 and Zh.h2150) and “GG” genotypes of either SNP19994 or SNP02686 were significantly lower than that of “AA” genotypes in the mean value of a three-year assay. The resistant accessions and molecular markers identified in this study are likely to be helpful for deployment in aflatoxin resistance breeding in peanuts.
Bolun Yu; Huifang Jiang; Manish K. Pandey; Li Huang; Dongxin Huai; Xiaojing Zhou; Yanping Kang; Rajeev K. Varshney; Hari K. Sudini; Xiaoping Ren; Huaiyong Luo; Nian Liu; Weigang Chen; Jianbin Guo; Weitao Li; Yingbin Ding; Yifei Jiang; Yong Lei; Boshou Liao. Identification of Two Novel Peanut Genotypes Resistant to Aflatoxin Production and Their SNP Markers Associated with Resistance. Toxins 2020, 12, 156 .
AMA StyleBolun Yu, Huifang Jiang, Manish K. Pandey, Li Huang, Dongxin Huai, Xiaojing Zhou, Yanping Kang, Rajeev K. Varshney, Hari K. Sudini, Xiaoping Ren, Huaiyong Luo, Nian Liu, Weigang Chen, Jianbin Guo, Weitao Li, Yingbin Ding, Yifei Jiang, Yong Lei, Boshou Liao. Identification of Two Novel Peanut Genotypes Resistant to Aflatoxin Production and Their SNP Markers Associated with Resistance. Toxins. 2020; 12 (3):156.
Chicago/Turabian StyleBolun Yu; Huifang Jiang; Manish K. Pandey; Li Huang; Dongxin Huai; Xiaojing Zhou; Yanping Kang; Rajeev K. Varshney; Hari K. Sudini; Xiaoping Ren; Huaiyong Luo; Nian Liu; Weigang Chen; Jianbin Guo; Weitao Li; Yingbin Ding; Yifei Jiang; Yong Lei; Boshou Liao. 2020. "Identification of Two Novel Peanut Genotypes Resistant to Aflatoxin Production and Their SNP Markers Associated with Resistance." Toxins 12, no. 3: 156.
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.
Vinay Sharma; Samrat Bhattacharyya; Rakesh Kumar; Ashish Kumar; Fernando Ibañez; Jianping Wang; Baozhu Guo; Hari K. Sudini; Subramaniam Gopalakrishnan; Maitrayee Dasgupta; Rajeev K. Varshney; Manish K. Pandey. Molecular Basis of Root Nodule Symbiosis between Bradyrhizobium and ‘Crack-Entry’ Legume Groundnut (Arachis hypogaea L.). Plants 2020, 9, 276 .
AMA StyleVinay Sharma, Samrat Bhattacharyya, Rakesh Kumar, Ashish Kumar, Fernando Ibañez, Jianping Wang, Baozhu Guo, Hari K. Sudini, Subramaniam Gopalakrishnan, Maitrayee Dasgupta, Rajeev K. Varshney, Manish K. Pandey. Molecular Basis of Root Nodule Symbiosis between Bradyrhizobium and ‘Crack-Entry’ Legume Groundnut (Arachis hypogaea L.). Plants. 2020; 9 (2):276.
Chicago/Turabian StyleVinay Sharma; Samrat Bhattacharyya; Rakesh Kumar; Ashish Kumar; Fernando Ibañez; Jianping Wang; Baozhu Guo; Hari K. Sudini; Subramaniam Gopalakrishnan; Maitrayee Dasgupta; Rajeev K. Varshney; Manish K. Pandey. 2020. "Molecular Basis of Root Nodule Symbiosis between Bradyrhizobium and ‘Crack-Entry’ Legume Groundnut (Arachis hypogaea L.)." Plants 9, no. 2: 276.
Multiparental genetic mapping populations such as nested‐association mapping (NAM) have great potential for investigating quantitative traits and associated genomic regions leading to rapid discovery of candidate genes and markers. To demonstrate the utility and power of this approach, two NAM populations, NAM_Tifrunner and NAM_Florida‐07, were used for dissecting genetic control of 100‐pod weight (PW) and 100‐seed weight (SW) in peanut. Two high‐density SNP‐based genetic maps were constructed with 3341 loci and 2668 loci for NAM_Tifrunner and NAM_Florida‐07, respectively. The quantitative trait locus (QTL) analysis identified 12 and 8 major effect QTLs for PW and SW, respectively, in NAM_Tifrunner, and 13 and 11 major effect QTLs for PW and SW, respectively, in NAM_Florida‐07. Most of the QTLs associated with PW and SW were mapped on the chromosomes A05, A06, B05 and B06. A genomewide association study (GWAS) analysis identified 19 and 28 highly significant SNP–trait associations (STAs) in NAM_Tifrunner and 11 and 17 STAs in NAM_Florida‐07 for PW and SW, respectively. These significant STAs were co‐localized, suggesting that PW and SW are co‐regulated by several candidate genes identified on chromosomes A05, A06, B05, and B06. This study demonstrates the utility of NAM population for genetic dissection of complex traits and performing high‐resolution trait mapping in peanut.
Sunil S. Gangurde; Hui Wang; Shasidhar Yaduru; Manish K. Pandey; Jake C. Fountain; Ye Chu; Thomas Isleib; C. Corley Holbrook; Alencar Xavier; Albert K. Culbreath; Peggy Ozias‐Akins; Rajeev K. Varshney; Baozhu Guo. Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut ( Arachis hypogaea ). Plant Biotechnology Journal 2019, 18, 1457 -1471.
AMA StyleSunil S. Gangurde, Hui Wang, Shasidhar Yaduru, Manish K. Pandey, Jake C. Fountain, Ye Chu, Thomas Isleib, C. Corley Holbrook, Alencar Xavier, Albert K. Culbreath, Peggy Ozias‐Akins, Rajeev K. Varshney, Baozhu Guo. Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut ( Arachis hypogaea ). Plant Biotechnology Journal. 2019; 18 (6):1457-1471.
Chicago/Turabian StyleSunil S. Gangurde; Hui Wang; Shasidhar Yaduru; Manish K. Pandey; Jake C. Fountain; Ye Chu; Thomas Isleib; C. Corley Holbrook; Alencar Xavier; Albert K. Culbreath; Peggy Ozias‐Akins; Rajeev K. Varshney; Baozhu Guo. 2019. "Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut ( Arachis hypogaea )." Plant Biotechnology Journal 18, no. 6: 1457-1471.
The subspecies fastigiata of cultivated groundnut lost fresh seed dormancy (FSD) during domestication and human‐made selection. Groundnut varieties lacking FSD experience precocious seed germination during harvest imposing severe losses. Development of easy‐to‐use genetic markers enables early‐generation selection in different molecular breeding approaches. In this context, one recombinant inbred lines (RIL) population (ICGV 00350 × ICGV 97045) segregating for FSD was used for deploying QTL‐seq approach for identification of key genomic regions and candidate genes. Whole‐genome sequencing (WGS) data (87.93 Gbp) were generated and analysed for the dormant parent (ICGV 97045) and two DNA pools (dormant and nondormant). After analysis of resequenced data from the pooled samples with dormant parent (reference genome), we calculated delta‐SNP index and identified a total of 10,759 genomewide high‐confidence SNPs. Two candidate genomic regions spanning 2.4 Mb and 0.74 Mb on the B05 and A09 pseudomolecules, respectively, were identified controlling FSD. Two candidate genes—RING‐H2 finger protein and zeaxanthin epoxidase—were identified in these two regions, which significantly express during seed development and control abscisic acid (ABA) accumulation. QTL‐seq study presented here laid out development of a marker, GMFSD1, which was validated on a diverse panel and could be used in molecular breeding to improve dormancy in groundnut.
Rakesh Kumar; Pasupuleti Janila; Manish K. Vishwakarma; Aamir W. Khan; Surendra S. Manohar; Sunil S. Gangurde; Murali T. Variath; Yaduru Shasidhar; Manish K. Pandey; Rajeev K. Varshney. Whole‐genome resequencing‐based QTL‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut. Plant Biotechnology Journal 2019, 18, 992 -1003.
AMA StyleRakesh Kumar, Pasupuleti Janila, Manish K. Vishwakarma, Aamir W. Khan, Surendra S. Manohar, Sunil S. Gangurde, Murali T. Variath, Yaduru Shasidhar, Manish K. Pandey, Rajeev K. Varshney. Whole‐genome resequencing‐based QTL‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut. Plant Biotechnology Journal. 2019; 18 (4):992-1003.
Chicago/Turabian StyleRakesh Kumar; Pasupuleti Janila; Manish K. Vishwakarma; Aamir W. Khan; Surendra S. Manohar; Sunil S. Gangurde; Murali T. Variath; Yaduru Shasidhar; Manish K. Pandey; Rajeev K. Varshney. 2019. "Whole‐genome resequencing‐based QTL‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut." Plant Biotechnology Journal 18, no. 4: 992-1003.
The primary and secondary metabolites of fungi are critical for adaptation to environmental stresses, host pathogenicity, competition with other microbes, and reproductive fitness. Drought-derived reactive oxygen species (ROS) have been shown to stimulate aflatoxin production and regulate in Aspergillus flavus, and may function in signaling with host plants. Here, we have performed global, untargeted metabolomics to better understand the role of aflatoxin production in oxidative stress responses, and also explore isolate-specific oxidative stress responses over time. Two field isolates of A. flavus, AF13 and NRRL3357, possessing high and moderate aflatoxin production, respectively, were cultured in medium with and without supplementation with 15 mM H2O2, and mycelia were collected following 4 and 7 days in culture for global metabolomics. Overall, 389 compounds were described in the analysis which encompassed 9 biological super-pathways and 47 sub-pathways. These metabolites were examined for differential accumulation. Significant differences were observed in both isolates in response to oxidative stress and when comparing sampling time points. The moderately high aflatoxin-producing isolate, NRRL3357, showed extensive stimulation of antioxidant mechanisms and pathways including polyamines metabolism, glutathione metabolism, TCA cycle, and lipid metabolism while the highly aflatoxigenic isolate, AF13, showed a less vigorous response to stress. Carbohydrate pathway levels also imply that carbohydrate repression and starvation may influence metabolite accumulation at the later timepoint. Higher conidial oxidative stress tolerance and antioxidant capacity in AF13 compared to NRRL3357, inferred from their metabolomic profiles and growth curves over time, may be connected to aflatoxin production capability and aflatoxin-related antioxidant accumulation. The coincidence of several of the detected metabolites in H2O2-stressed A. flavus and drought-stressed hosts also suggests their potential role in the interaction between these organisms and their use as markers/targets to enhance host resistance through biomarker selection or genetic engineering.
Jake C. Fountain; Liming Yang; Manish K. Pandey; Prasad Bajaj; Danny Alexander; Sixue Chen; Robert C. Kemerait; Rajeev K. Varshney; Baozhu Guo. Carbohydrate, glutathione, and polyamine metabolism are central to Aspergillus flavus oxidative stress responses over time. BMC Microbiology 2019, 19, 1 -14.
AMA StyleJake C. Fountain, Liming Yang, Manish K. Pandey, Prasad Bajaj, Danny Alexander, Sixue Chen, Robert C. Kemerait, Rajeev K. Varshney, Baozhu Guo. Carbohydrate, glutathione, and polyamine metabolism are central to Aspergillus flavus oxidative stress responses over time. BMC Microbiology. 2019; 19 (1):1-14.
Chicago/Turabian StyleJake C. Fountain; Liming Yang; Manish K. Pandey; Prasad Bajaj; Danny Alexander; Sixue Chen; Robert C. Kemerait; Rajeev K. Varshney; Baozhu Guo. 2019. "Carbohydrate, glutathione, and polyamine metabolism are central to Aspergillus flavus oxidative stress responses over time." BMC Microbiology 19, no. 1: 1-14.
High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42–0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement. High-quality genome sequence of cultivated peanut comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models provides insights into genome evolution and the genetic mechanisms underlying seed size and leaf resistance in peanut.
Weijian Zhuang; Hua Chen; Meng Yang; Jianping Wang; Manish K. Pandey; Chong Zhang; Wen-Chi Chang; Liangsheng Zhang; Xingtan Zhang; Ronghua Tang; Vanika Garg; Xingjun Wang; Haibao Tang; Chi-Nga Chow; Jinpeng Wang; Ye Deng; Depeng Wang; Aamir W. Khan; Qiang Yang; Tiecheng Cai; Prasad Bajaj; Kangcheng Wu; Baozhu Guo; Xinyou Zhang; Jingjing Li; Fan Liang; Jiang Hu; Boshou Liao; Shengyi Liu; Annapurna Chitikineni; Hansong Yan; Yixiong Zheng; Shihua Shan; Qinzheng Liu; Dongyang Xie; Zhenyi Wang; Shahid Ali Khan; Niaz Ali; Chuanzhi Zhao; Xinguo Li; Ziliang Luo; Shubiao Zhang; Ruirong Zhuang; Ze Peng; Shuaiyin Wang; Gandeka Mamadou; Yuhui Zhuang; Zifan Zhao; Weichang Yu; Faqian Xiong; Weipeng Quan; Mei Yuan; Yu Li; Huasong Zou; Han Xia; Li Zha; Junpeng Fan; Jigao Yu; Wenping Xie; Jiaqing Yuan; Kun Chen; Shanshan Zhao; Wenting Chu; Yuting Chen; Pengchuan Sun; Fanbo Meng; Tao Zhuo; Yuhao Zhao; Chunjuan Li; Guohao He; Yongli Zhao; Congcong Wang; Polavarapu Bilhan KaviKishor; Rong-Long Pan; Andrew H. Paterson; Xiyin Wang; Ray Ming; Rajeev K. Varshney. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature Genetics 2019, 51, 865 -876.
AMA StyleWeijian Zhuang, Hua Chen, Meng Yang, Jianping Wang, Manish K. Pandey, Chong Zhang, Wen-Chi Chang, Liangsheng Zhang, Xingtan Zhang, Ronghua Tang, Vanika Garg, Xingjun Wang, Haibao Tang, Chi-Nga Chow, Jinpeng Wang, Ye Deng, Depeng Wang, Aamir W. Khan, Qiang Yang, Tiecheng Cai, Prasad Bajaj, Kangcheng Wu, Baozhu Guo, Xinyou Zhang, Jingjing Li, Fan Liang, Jiang Hu, Boshou Liao, Shengyi Liu, Annapurna Chitikineni, Hansong Yan, Yixiong Zheng, Shihua Shan, Qinzheng Liu, Dongyang Xie, Zhenyi Wang, Shahid Ali Khan, Niaz Ali, Chuanzhi Zhao, Xinguo Li, Ziliang Luo, Shubiao Zhang, Ruirong Zhuang, Ze Peng, Shuaiyin Wang, Gandeka Mamadou, Yuhui Zhuang, Zifan Zhao, Weichang Yu, Faqian Xiong, Weipeng Quan, Mei Yuan, Yu Li, Huasong Zou, Han Xia, Li Zha, Junpeng Fan, Jigao Yu, Wenping Xie, Jiaqing Yuan, Kun Chen, Shanshan Zhao, Wenting Chu, Yuting Chen, Pengchuan Sun, Fanbo Meng, Tao Zhuo, Yuhao Zhao, Chunjuan Li, Guohao He, Yongli Zhao, Congcong Wang, Polavarapu Bilhan KaviKishor, Rong-Long Pan, Andrew H. Paterson, Xiyin Wang, Ray Ming, Rajeev K. Varshney. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature Genetics. 2019; 51 (5):865-876.
Chicago/Turabian StyleWeijian Zhuang; Hua Chen; Meng Yang; Jianping Wang; Manish K. Pandey; Chong Zhang; Wen-Chi Chang; Liangsheng Zhang; Xingtan Zhang; Ronghua Tang; Vanika Garg; Xingjun Wang; Haibao Tang; Chi-Nga Chow; Jinpeng Wang; Ye Deng; Depeng Wang; Aamir W. Khan; Qiang Yang; Tiecheng Cai; Prasad Bajaj; Kangcheng Wu; Baozhu Guo; Xinyou Zhang; Jingjing Li; Fan Liang; Jiang Hu; Boshou Liao; Shengyi Liu; Annapurna Chitikineni; Hansong Yan; Yixiong Zheng; Shihua Shan; Qinzheng Liu; Dongyang Xie; Zhenyi Wang; Shahid Ali Khan; Niaz Ali; Chuanzhi Zhao; Xinguo Li; Ziliang Luo; Shubiao Zhang; Ruirong Zhuang; Ze Peng; Shuaiyin Wang; Gandeka Mamadou; Yuhui Zhuang; Zifan Zhao; Weichang Yu; Faqian Xiong; Weipeng Quan; Mei Yuan; Yu Li; Huasong Zou; Han Xia; Li Zha; Junpeng Fan; Jigao Yu; Wenping Xie; Jiaqing Yuan; Kun Chen; Shanshan Zhao; Wenting Chu; Yuting Chen; Pengchuan Sun; Fanbo Meng; Tao Zhuo; Yuhao Zhao; Chunjuan Li; Guohao He; Yongli Zhao; Congcong Wang; Polavarapu Bilhan KaviKishor; Rong-Long Pan; Andrew H. Paterson; Xiyin Wang; Ray Ming; Rajeev K. Varshney. 2019. "The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication." Nature Genetics 51, no. 5: 865-876.
Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.
David J. Bertioli; Jerry Jenkins; Josh Clevenger; Olga Dudchenko; Dongying Gao; Guillermo Seijo; Soraya C. M. Leal-Bertioli; Longhui Ren; Andrew D. Farmer; Manish K. Pandey; Sergio S. Samoluk; Brian Abernathy; Gaurav Agarwal; Carolina Ballén Taborda; Connor Cameron; Jacqueline Campbell; Carolina Chavarro; Annapurna Chitikineni; Ye Chu; Sudhansu Dash; Moaine El Baidouri; Baozhu Guo; Wei Huang; Kyung Do Kim; Walid Korani; Sophie Lanciano; Christopher Lui; Marie Mirouze; Márcio C. Moretzsohn; Melanie Pham; Jin Hee Shin; Kenta Shirasawa; Senjuti Sinharoy; Avinash Sreedasyam; Nathan T. Weeks; Xinyou Zhang; Zheng Zheng; Ziqi Sun; Lutz Froenicke; Erez L. Aiden; Richard Michelmore; Rajeev K. Varshney; C. Corley Holbrook; Ethalinda K. S. Cannon; Brian E. Scheffler; Jane Grimwood; Peggy Ozias-Akins; Steven B. Cannon; Scott A. Jackson; Jeremy Schmutz. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics 2019, 51, 877 -884.
AMA StyleDavid J. Bertioli, Jerry Jenkins, Josh Clevenger, Olga Dudchenko, Dongying Gao, Guillermo Seijo, Soraya C. M. Leal-Bertioli, Longhui Ren, Andrew D. Farmer, Manish K. Pandey, Sergio S. Samoluk, Brian Abernathy, Gaurav Agarwal, Carolina Ballén Taborda, Connor Cameron, Jacqueline Campbell, Carolina Chavarro, Annapurna Chitikineni, Ye Chu, Sudhansu Dash, Moaine El Baidouri, Baozhu Guo, Wei Huang, Kyung Do Kim, Walid Korani, Sophie Lanciano, Christopher Lui, Marie Mirouze, Márcio C. Moretzsohn, Melanie Pham, Jin Hee Shin, Kenta Shirasawa, Senjuti Sinharoy, Avinash Sreedasyam, Nathan T. Weeks, Xinyou Zhang, Zheng Zheng, Ziqi Sun, Lutz Froenicke, Erez L. Aiden, Richard Michelmore, Rajeev K. Varshney, C. Corley Holbrook, Ethalinda K. S. Cannon, Brian E. Scheffler, Jane Grimwood, Peggy Ozias-Akins, Steven B. Cannon, Scott A. Jackson, Jeremy Schmutz. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics. 2019; 51 (5):877-884.
Chicago/Turabian StyleDavid J. Bertioli; Jerry Jenkins; Josh Clevenger; Olga Dudchenko; Dongying Gao; Guillermo Seijo; Soraya C. M. Leal-Bertioli; Longhui Ren; Andrew D. Farmer; Manish K. Pandey; Sergio S. Samoluk; Brian Abernathy; Gaurav Agarwal; Carolina Ballén Taborda; Connor Cameron; Jacqueline Campbell; Carolina Chavarro; Annapurna Chitikineni; Ye Chu; Sudhansu Dash; Moaine El Baidouri; Baozhu Guo; Wei Huang; Kyung Do Kim; Walid Korani; Sophie Lanciano; Christopher Lui; Marie Mirouze; Márcio C. Moretzsohn; Melanie Pham; Jin Hee Shin; Kenta Shirasawa; Senjuti Sinharoy; Avinash Sreedasyam; Nathan T. Weeks; Xinyou Zhang; Zheng Zheng; Ziqi Sun; Lutz Froenicke; Erez L. Aiden; Richard Michelmore; Rajeev K. Varshney; C. Corley Holbrook; Ethalinda K. S. Cannon; Brian E. Scheffler; Jane Grimwood; Peggy Ozias-Akins; Steven B. Cannon; Scott A. Jackson; Jeremy Schmutz. 2019. "The genome sequence of segmental allotetraploid peanut Arachis hypogaea." Nature Genetics 51, no. 5: 877-884.