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Main conclusion226 CcCYP450 genes were identified at the genomic level and were classified into 45 clades based on phylogenetic analysis. CcCYP75B165 gene was found that might play important roles in the biosynthesis of flavonoids in pigeon pea, and was significantly induced by methyl jasmonate (MeJA).The cytochrome P450 mono-oxygenase (CYP450) superfamily plays a key role in the flavonoid biosynthesis pathway and resists different kinds of stresses. Several CYP450 genes have been identified to be involved in the biosynthesis of crop protection agents. However, the CcCYP450 genes from pigeon pea have not been identified. Here, 226 CcCYP450 genes were identified at the genomic level by analysing the gene structure, distribution on chromosomes, gene duplication, and conserved motifs and were classified into 45 clades based on phylogenetic analysis. RNA-seq analysis revealed clear details of CcCYP450 genes that varied with time of MeJA (methyl jasmonate) induction. Among them, six CcCYP450 subfamily genes were found that might play important roles in the biosynthesis of flavonoids in pigeon pea. The overexpression of CcCYP75B165 in pigeon pea significantly induced the accumulation of genistin and downregulated the contents of cajaninstilbene acid, apigenin, isovitexin, and genistein and the expression of flavonoid synthase genes. This study provides theoretical guidance and plant genetic resources for cultivating new pigeon pea varieties with high flavonoid contents and exploring the molecular mechanisms of the biosynthesis of flavonoids under MeJA treatment.

Summary Pigeon pea (Cajanus cajan) is an important orphan crop mainly grown by smallholder farmers in India and Africa. Here, we present the first pigeon pea pangenome based on 89 accessions mainly from India and the Philippines, showing that there is significant genetic diversity in Philippine individuals that is not present in Indian individuals. Annotation of variable genes suggests that they are associated with self‐fertilization and response to disease. We identified 225 SNPs associated with nine agronomically important traits over three locations and two different time points, with SNPs associated with genes for transcription factors and kinases. These results will lead the way to an improved pigeon pea breeding programme.

Pigeon pea hairy root cultures (PPHRCs) have been proven to be a promising alternative for the production of health-beneficial phenolic compounds, such as the most important health-promoting compound, i.e., cajaninstilbene acid (CSA). In this study, PPHRCs were cocultured with live Aspergillus fungi for further improving phenolic productivity via biological elicitation. Aspergillus oryzae CGMCC 3.951 (AO 3.951) was found to be the optimal fungus that could achieve the maximum increment of CSA (10.73-fold increase) in 42-day-old PPHRCs under the inoculum size of mycelia 0.50% and cocultivation time 36 h. More precisely, the contents of CSA in hairy roots and culture media after fungal elicitation increased by 9.87- and 62.18-fold over control, respectively. Meanwhile, the contents of flavonoid glycosides decreased, while aglycone yields increased upon AO 3.951 elicitation. Moreover, AO 3.951 could trigger the oxidative stress and pathogen defense response thus activating the expression of biosynthesis- and ABC transporter-related genes, which contributed to the intracellular accumulation and extracellular secretion of phenolic compounds (especially CSA) in PPHRCs. And PAL2, 4CL2, STS1, and I3′H were likely to be the potential key enzyme genes regulating the biosynthesis of CSA, and ABCB11X1-1, ABCB11, and ABCG24X2 were closely related to the transmembrane transport of CSA. Overall, the cocultivation approach could make PPHRCs more commercially attractive for the production of high-value phenolic compounds such as CSA and flavonoid aglycones in nutraceutical/medicinal fields. And the elucidation of crucial biosynthesis and transport genes was important for systematic metabolic engineering aimed at increasing CSA productivity.Key points• Cocultivation of PPHRCs and live fungi was to enhance CSA production and secretion.• PPHRCs augmented CSA productivity 10.73-fold when cocultured with AO 3.951 mycelia.• Several biosynthesis and transport genes related to CSA production were clarified.

Background and aims In Malawi, strategies are being sought to boost maize production through improvements in soil fertility. This study assessed the impact of intercropping maize (Zea mays) with pigeon pea (Cajanus cajan) in Lixisols of Malawi on yield, biological N fixation, soil aggregation, and P forms within soil aggregates. Methods Maize and pigeon pea were grown intercropped in pots, with varying degrees of root interaction in order to understand the relative importance of biochemical versus physical rhizospheric interactions. Following harvest, soils were separated into aggregate fractions using wet-sieving, and the nutrient content of all fractions was assessed. Results The proportion of macroaggregates and microaggregates increased by 52 and 111%, respectively, in the intercropping treatment compared to sole maize, which significantly increased organic P storage in the microaggregates of intercropped compared to sole maize (84 versus 29 mg P kg⁻¹, respectively). Biologically fixed N increased from 89% in the sole pigeon pea to 96% in the intercropped system. Conclusions Intercropping maize with pigeon pea can have a significant and positive impact on soil structure as well as nutrient storage in these high P-sorbing soils. This is caused primarily by physical root contact and to a lesser degree by biochemical activities.

MYB transcription factor is one of the largest gene families in plants and plays critical roles in plant growth and development, as well as resistance to biotic and abiotic stress. However, the function of MYB genes in pigeon pea (Cajanus cajan) remains largely unknown. Here, 30 R2R3-MYB which involved flavonoid and lignin biosynthesis were identified in the pigeon pea genome and were classified into five groups based on phylogenetic analysis. Simultaneously, another 122 key enzyme genes from biosynthetic pathways of flavonoid and lignin were identified and all of them were mapped on 11 chromosomes with the co-linearity relationship. Among these genes, the intron/exon organization and motif compositions were conserved and they have undergone a strong purifying selection and tandem duplications during evolution. Expression profile analysis demonstrated most of these genes were expressed in different tissues and responded significantly to MeJA, RNA-seq analysis revealed clear details of genes varied with time of induction. Ten key genes from the phenylpropanoid pathway were selected to further verify whether they responded to induction under different abiotic stress conditions (UV-B, cold, heat, salt, drought, and GA3). This study elaborates on potential regulatory relationships between R2R3-MYB genes and some key genes involved in flavonoid and lignin biosynthesis under MeJA treatment, as well as adding to the understanding of improving abiotic stress tolerance and regulating the secondary metabolism in woody crops. A simplified discussion model for the different regulation networks involved with flavonoid and lignin biosynthesis in pigeon pea is proposed.

Cadmium pollution of soil restricts growth and yield of crop plants. Arbuscular mycorrhizae play significant roles in imparting tolerance to Cd toxicity by establishing symbiotic association with the host plants species. The present study therefore evaluated the effects of four arbuscular mycorrhizal fungal species (AMF), i.e. Claroideoglomus claroideum (AM1), Claroideoglomus etunicatum (AM2), Funneliformis mosseae (AM3) and Rhizoglomus intraradices (AM4), in modulating physiological and molecular attributes of Cd-stressed (Cd – 0, 50 mg/kg) Cajanus cajan (L.) Millsp. (pigeon pea) plants. Application of Cd reduced growth (more in roots than shoots), nitrogen fixing potential and yield. It also led to generation of reactive oxygen species as well as membrane leakiness. AMF supplementations improved growth, nutrient acquisition, rhizobial symbiosis, reduced oxidative burden and Cd uptake by enhancing the synthesis of thiols (cysteine, reduced and oxidized glutathione, phytochelatins, non-protein thiols). Activity of glutathione reductase increased significantly in AMF inoculated plants which imparted redox balance by improving GSH/GSSG ratio in roots and shoots. Quantitative RT-PCR analysis displayed abundance of transcripts encoding two metal chelator genes; metallothionein ( CcMT1 ) and phytochelatin synthase1 (isoforms CcPCS1X1 , CcPCS1X2 and CcPCS1X4 ) which expressed more in roots than leaves of Cd-stressed AMF plants. Moreover, expression level of CcMT1 was more intense than CcPCS1 indicating higher ability of MTs to combat Cd stress than PCS. R. intraradices was the most efficient in inducing the expression of metal responsive genes than other three species suggesting its promising role in the amelioration of Cd toxicity in pigeon pea.

Pigeon pea is the second most important grain legume in India, primarily grown under rainfed conditions. Any changes in agro-climatic conditions will have a profound influence on the productivity of pigeon pea (Cajanus cajan) yield and, as a result, the total pulse production of the country. In this context, weather-based crop yield prediction will enable farmers, decision-makers, and administrators in dealing with hardships. The current study examines the application of the stepwise linear regression method, supervised machine learning algorithms (support vector machines (SVM) and random forest (RF)), shrinkage regression approaches (least absolute shrinkage and selection operator (LASSO) or elastic net (ENET)), and artificial neural network (ANN) model for pigeon pea yield prediction using long-term weather data. Among the approaches, ANN resulted in a higher coefficient of determination (R2 = 0.88–0.99), model efficiency (0.88–1.00) with subsequent lower normalised root mean square error (nRMSE) during calibration (1.13–12.55%), and validation (0.33–21.20%) over others. The temperature alone or its interaction with other weather parameters was identified as the most influencing variables in the study area. The Pearson correlation coefficients were also determined for the observed and predicted yield. Those values also showed ANN as the best model with correlation values ranging from 0.939 to 0.999 followed by RF (0.955–0.982) and LASSO (0.880–0.982). However, all the approaches adopted in the study were outperformed the statistical method, i.e. stepwise linear regression with lower error values and higher model efficiency. Thus, these approaches can be effectively used for precise yield prediction of pigeon pea over different districts of Karnataka in India.

Key message OsLec-RLK overexpression enhances cell signalling and salt stress tolerance in pigeon pea, enhancing seed yield and harvest index and thus, enabling marginal lands to increase food and nutritional security. Lectin Receptor-like kinases (Lec-RLKs) are highly effective cell signaling molecules that counteract various stresses, including salt stress. We engineered pigeon pea by overexpressing OsLec-RLK gene for enhancing salt tolerance. The OsLec-RLK overexpression lines demonstrated superior performance under salt stress, from vegetative to reproductive phase, compared to wild types (WT). The overexpression lines had significantly higher K + /Na +  ratio than WT exposed to 100 mM NaCl. Under salt stress, transgenic lines showed higher levels of chlorophyll, proline, total soluble sugars, relative water content, and peroxidase and catalase activity than WT plants. Membrane injury index and lipid peroxidation were significantly reduced in transgenic lines. Analysis of phenological and yield attributes confirmed that the OsLec-RLK pigeon pea lines maintain plant vigor, with 10.34-fold increase in seed yield (per plant) and 4–5-fold increase in harvest index of overexpression lines, compared to wild type. Meanwhile, the overexpression of  OsLec-RLK up-regulated the expression levels of  histone deacetylase1, acyl CoA, ascorbate peroxidase, peroxidase, glutathione reductase and catalase , which were involved in the K + /Na +  homeostasis pathway. This study showed the potential of OsLec-RLK gene for increasing crop productivity and yields under salt stress and enabling the crops to be grown on marginal lands for increasing food and nutritional security.

Aims: To assess how biochar addition in rainfed conservation agriculture affects short-term transformation, plant uptake, retention of nitrogen (N) in soil, and nitrous oxide (N2O) fluxes in a tropical Arenosol planted to maize. Methods: A ten-day in situ15N pool dilution and N cycling experiment, using tracer amounts (0.1 g m-2) of 15N labeled ammonium (15NH4+), nitrate (15NO3-) or 15N-urea, was carried out seven weeks after planting of maize (Zea mays L.) under conservation agriculture in Zambia, using planting basins without (CA) and with pigeon-pea biochar (BC) addition (4 t ha-1). Results: Pigeon-pea biochar increased soil NO3- concentration, gross nitrification rate, 15N recovery in extractable soil NO3-, and soil moisture. However, effects of biochar on soil N retention and plant N uptake were not significant. Likewise, biochar did not affect N2O fluxes. Conclusions: At low dosage, pigeon pea biochar has a positive effect on gross nitrification rate but does not affect short-term N retention in soil, N2O fluxes, nor does it help increasing the uptake of N by maize.

Warm-season legumes have been receiving increased attention as forage resources in the southern United States and other countries. However, the near infrared spectroscopy (NIRS) technique has not been widely explored for predicting the forage quality of many of these legumes. The objective of this research was to assess the performance of NIRS in predicting the forage quality parameters of five warm-season legumes—guar (Cyamopsis tetragonoloba), tepary bean (Phaseolus acutifolius), pigeon pea (Cajanus cajan), soybean (Glycine max), and mothbean (Vigna aconitifolia)—using three machine learning techniques: partial least square (PLS), support vector machine (SVM), and Gaussian processes (GP). Additionally, the efficacy of global models in predicting forage quality was investigated. A set of 70 forage samples was used to develop species-based models for concentrations of crude protein (CP), acid detergent fiber (ADF), neutral detergent fiber (NDF), and in vitro true digestibility (IVTD) of guar and tepary bean forages, and CP and IVTD in pigeon pea and soybean. All species-based models were tested through 10-fold cross-validations, followed by external validations using 20 samples of each species. The global models for CP and IVTD of warm-season legumes were developed using a set of 150 random samples, including 30 samples for each of the five species. The global models were tested through 10-fold cross-validation, and external validation using five individual sets of 20 samples each for different legume species. Among techniques, PLS consistently performed best at calibrating (R2c = 0.94–0.98) all forage quality parameters in both species-based and global models. The SVM provided the most accurate predictions for guar and soybean crops, and global models, and both SVM and PLS performed better for tepary bean and pigeon pea forages. The global modeling approach that developed a single model for all five crops yielded sufficient accuracy (R2cv/R2v = 0.92–0.99) in predicting CP of the different legumes. However, the accuracy of predictions of in vitro true digestibility (IVTD) for the different legumes was variable (R2cv/R2v = 0.42–0.98). Machine learning algorithms like SVM could help develop robust NIRS-based models for predicting forage quality with a relatively small number of samples, and thus needs further attention in different NIRS based applications.