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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.

To facilitate selective breeding of polyphenol-rich peanuts, we looked for mass spectrometry-based proteomic evidence, investigating a subset of recombinant inbred lines (RILs) developed by the Australian peanut breeding program. To do this, we used label-free shotgun proteomics for protein and peptide quantitation, statistically analyzed normalized spectral abundance factors using R-package, as well as assayed important antioxidants. Results revealed statistically significant protein expression changes in 82 proteins classified between high or low polyphenols expressing RILs. Metabolic changes in polyphenol-rich RIL p27-362 point towards increased enzymatic breakdown of sugars and phenylalanine biosynthesis. The study revealed phenylpropanoid pathway overexpression resulting in increased polyphenols biosynthesis. Overexpression of antioxidant enzymes such as catalase, by 73.4 fold was also observed. A strong metabolic correlation exists with the observed phenotypic traits. Peanut RIL p27-362 presents a superior nutritional composition with antioxidant-rich peanut phenotype and could yield commercial profits. Data are available via ProteomeXchange with identifier PXD015493.

Five peanut ( Arachis hypogaea L.) genotypes with diverse antioxidant capacity were quantitatively profiled for p -coumaric acid, salicylic acid, resveratrol, and daidzein. The co-eluting compounds, caffeic/vanillic acid and ferulic/sinapic acid, were quantified on caffeic acid equivalent and ferulic acid equivalent bases, respectively. The HPLC analysis established significant genotypic differences ( P p -coumaric acid, 44–53% of the ferulic/sinapic acid, 71–89% of the salicylic acid, 59–68% of the resveratrol, and 89–97% of the daidzein in raw peanut kernels were present in bound forms. D147-p8-6F and Sutherland were sister-lines (derived from the same F2 plant) that had high foliar disease tolerance, high antioxidant capacity, and similar phytochemical profiles, which was consistent with associations between phytoalexin production and genetically determined disease resistance made by previous researchers. Principal components analysis linked high antioxidant capacity with a combination of phytochemicals that were not directly correlated in bivariate analysis (e.g., resveratrol was negatively correlated with caffeic/vanillic and p -coumaric acid) and that were not delineated by genotype.

The potential to select for antioxidant traits in peanut ( Arachis hypogaea L.) kernels by conventional plant breeding was investigated by oxygen radical absorbance capacity (ORAC) assay of (a) 32 full-season maturity genotypes grown at Kairi Research Station in 2008/09; and (b) a subset of ten genotypes with diverse antioxidant capacities grown in five different production regions in Queensland in 2009/10 and 2010/11. There were significant levels of variation of more than 25% relative standard deviation (RSD) in antioxidant capacity among the 32 tested genotypes; and that genotype, environment, and genotype-by-environment (G × E) interaction all significantly ( P

The effects of plant growth conditions on concentrations of proteins, including allergens, in peanut ( Arachis hypogaea L.) kernels are largely unknown. Peanuts (cv. Walter) were grown at five sites (Taabinga, Redvale, Childers, Bundaberg, and Kairi) covering three commercial growing regions in Queensland, Australia. Differences in temperature, rainfall, and solar radiation during the growing season were evaluated. Kernel yield varied from 2.3 t/ha (Kairi) to 3.9 t/ha (Childers), probably due to differences in solar radiation. Crude protein appeared to vary only between Kairi and Childers, whereas Ara h 1 and 2 concentrations were similar in all locations. 2D-DIGE revealed significant differences in spot volumes for only two minor protein spots from peanuts grown in the five locations. Western blotting using peanut-allergic serum revealed no qualitative differences in recognition of antigens. It was concluded that peanuts grown in different growing regions in Queensland, Australia, had similar protein compositions and therefore were unlikely to show differences in allergenicity.

Validated methods to measure the essential mineral composition of food matrices are needed to satisfy the analytical requirements of product development, quality control, and food regulatory authorities. We investigated the use of inductively coupled plasma–optical emission spectroscopy (ICP–OES) and -mass spectrometry (ICP-MS), with and without the use of a dynamic reaction cell (DRC), to analyse 15 essential minerals in peanut kernels. We validated methods for Ca, Cu, Fe, K, Mg, Mn, Mo, P, and Zn analyses; however further tests are needed for validation of the B, Co, Cr, Na, Ni, and Se analyses. ICP–OES was applied to a study of genotypic variation among 56 breeding lines grown in the Australian peanut improvement program. We found promising levels of genotypic variation (>10%) in essential mineral traits, especially Ca (18–23%) and Mn (24%). Further investigation of the plant breeding potential for mineral traits may aid in the future development of peanut cultivars with enhanced micronutrients.

The use of near infrared reflectance spectroscopy (NIRS) to evaluate the nutritional quality of peanut kernels has potential applications in plant breeding as a rapid, non-destructive tool for seed/plant selection, and in quality control. We investigated the feasibility of applying NIRS to the estimation of essential mineral composition in peanut kernels using two sample sets: A, comprising 56 diverse genotypes (N = 163); and B, comprising nine genotypes grown in five distinct environments (N = 156). Essential mineral composition was analyzed by inductively coupled plasma-optical emission spectroscopy (ICP-OES) and -mass spectrometry (ICP-MS). Calibration models were developed by partial least squares (PLS) regression, and explored a variety of data pre-treatments. Models allowing approximate estimation of K (RPDCV 2.25, r CV 2 0.800, RPDP 2.22) and Mg (RPDCV 2.24, r CV 2 0.786, RPDP 1.74), and to a lesser extent Ca (RPDCV 1.85, r CV 2 0.649, RPDP 1.52) and P (RPDCV 1.77, r CV 2 0.634, RPDP 1.65), were developed for Set B, but poorer calibrations were obtained for Set A. This level of accuracy does not allow accurate prediction, but permits approximate quantification that may be useful in plant improvement programs for screening breeding populations. The results are remarkable because NIRS is rarely applied to analytes present at such low concentrations, especially inorganic constituents that are not inherently NIR-absorbent. Further analysis of more diverse peanut samples is warranted to confirm batch-to-batch accuracy and to improve the robustness of calibrations.

The concentrations of 15 essential minerals (B, Ca, Co, Cr, Cu, Fe, K, Mg, Mn, Mo, Na, Ni, P, Se, and Zn) in kernels of nine diverse peanut genotypes, which were cultivated in five distinct growing environments, were analyzed by inductively coupled plasma-optical emission spectroscopy (ICP-OES) and -mass spectrometry (ICP-MS). The effects of genotype, environment, and genotype-by-environment (G × E) interactions were significant (P0.05) for all elements excluding Cr. Genetic control of mineral composition was demonstrated by large (P0.05) genotypic differences in Ca, Mo, K, Na, and P contents, and clustering of some genotypes in environment-centered principal components analysis (PCA) along axes comprising both macro (Ca, Mg, P, and K)- and microelements (Co, Cu, Fe, Mn, and Zn). Mo and Na concentrations were strongly influenced (P0.05) by the growing environment, with very high levels measured in samples from Bundaberg. The results confirm that that there is breeding potential for several important minerals in peanuts, although significant G × E interactions will complicate the response to selection. From a practical viewpoint, combining genetic improvement with agronomic management may be a useful strategy to consistently achieve desirable mineral concentrations in peanut kernels.

Snack foods can contribute a high proportion of energy intake to the diet. Peanuts are a snack food rich in unsaturated fatty acids, protein and fibre which have demonstrated satiety effects and may reduce total energy intake, despite their high energy density. This study examined the effects of consuming Hioleic (oleic acid ~75% of total fatty acids) peanuts and regular peanuts (oleic acid ~50% and higher in polyunsaturated fatty acids) compared with a high carbohydrate snack (potato crisps) on satiety and subsequent energy intake. Using a triple crossover study design, 24 participants (61 ± 1 years) consumed isoenergetic amounts (56-84 g) of Hi-oleic or regular peanuts or (60-90 g) potato crisps after an overnight fast. Hunger and satiety were assessed at baseline, 30, 60, 120 and 180 minutes following snack consumption using visual analogue scales, after which a cold buffet meal was freely consumed and energy intake measured. The same snack was consumed on 3 subsequent days with energy intake assessed from dietary records. This protocol was repeated weekly with each snack food. Total energy intake was lower following consumption of Hi-oleic and regular peanuts compared with crisps, both acutely during the buffet meal (−21%; p < .001 and −17%; p < .01) and over the 4 days (−11%; p < .001 and −9%; p < .01). Despite these reductions in energy intake, no differences in perceived satiety were observed. The findings suggest peanuts may be a preferred snack food to include in the diet for maintaining a healthy weight. Refereed/Peer-reviewed

With the aim of increasing peanut production in Australia, the Australian peanut industry has recently considered growing peanuts in rotation with maize at Katherine in the Northern Territory—a location with a semi-arid tropical climate and surplus irrigation capacity. We used the well-validated APSIM model to examine potential agronomic benefits and long-term risks of this strategy under the current and warmer climates of the new region. Yield of the two crops, irrigation requirement, total soil organic carbon (SOC), nitrogen (N) losses and greenhouse gas (GHG) emissions were simulated. Sixteen climate stressors were used; these were generated by using global climate models ECHAM5, GFDL2.1, GFDL2.0 and MRIGCM232 with a median sensitivity under two Special Report of Emissions Scenarios over the 2030 and 2050 timeframes plus current climate (baseline) for Katherine. Effects were compared at three levels of irrigation and three levels of N fertiliser applied to maize grown in rotations of wet-season peanut and dry-season maize (WPDM), and wet-season maize and dry-season peanut (WMDP). The climate stressors projected average temperature increases of 1°C to 2.8°C in the dry (baseline 24.4°C) and wet (baseline 29.5°C) seasons for the 2030 and 2050 timeframes, respectively. Increased temperature caused a reduction in yield of both crops in both rotations. However, the overall yield advantage of WPDM increased from 41% to up to 53% compared with the industry-preferred sequence of WMDP under the worst climate projection. Increased temperature increased the irrigation requirement by up to 11% in WPDM, but caused a smaller reduction in total SOC accumulation and smaller increases in N losses and GHG emission compared with WMDP. We conclude that although increased temperature will reduce productivity and total SOC accumulation, and increase N losses and GHG emissions in Katherine or similar northern Australian environments, the WPDM sequence should be preferable over the industry-preferred sequence because of its overall yield and sustainability advantages in warmer climates. Any limitations of irrigation resulting from climate change could, however, limit these advantages.

Publisher Summary This chapter reviews the characteristics identified for improved drought resistance in two frameworks outlined in Turner (2000) and evaluate the potential of these characteristics to improve breeding efficiency. The first framework, the “Drought-Resistance Framework,” identifies the specific physiological and biochemical characteristics that lead to improved yields in drought-prone environments through drought escape, dehydration postponement, and dehydration tolerance. The second framework “Yield Component Framework” considers yield variation in terms of characteristics affecting water use, water use efficiency, and harvest index. Both frameworks are required if progress is to be made in breeding for drought-prone areas using physiological approaches. In recent years, the development of molecular approaches or methods to identify physiological and biochemical traits in breeding populations potentially has major implications for breeding crops targeted for drought-prone environments, and progress in this area of research is reviewed. However, the focus of this chapter is grain legumes, but it is necessary to draw on studies with cereals and other species to enable critical evaluation of traits and strategies.

Aflatoxins are produced by Aspergillus flavus and A. parasiticus in oil-rich seed and grain crops and are a serious problem in agriculture, with aflatoxin B1 being the most carcinogenic natural compound known. Sexual reproduction in these species occurs between individuals belonging to different vegetative compatibility groups (VCGs). We examined natural genetic variation in 758 isolates of A. flavus, A. parasiticus and A. minisclerotigenes sampled from single peanut fields in the United States (Georgia), Africa (Benin), Argentina (Córdoba), Australia (Queensland) and India (Karnataka). Analysis of DNA sequence variation across multiple intergenic regions in the aflatoxin gene clusters of A. flavus, A. parasiticus and A. minisclerotigenes revealed significant linkage disequilibrium (LD) organized into distinct blocks that are conserved across different localities, suggesting that genetic recombination is nonrandom and a global occurrence. To assess the contributions of asexual and sexual reproduction to fixation and maintenance of toxin chemotype diversity in populations from each locality/species, we tested the null hypothesis of an equal number of MAT1-1 and MAT1-2 mating-type individuals, which is indicative of a sexually recombining population. All samples were clone-corrected using multi-locus sequence typing which associates closely with VCG. For both A. flavus and A. parasiticus, when the proportions of MAT1-1 and MAT1-2 were significantly different, there was more extensive LD in the aflatoxin cluster and populations were fixed for specific toxin chemotype classes, either the non-aflatoxigenic class in A. flavus or the B1-dominant and G1-dominant classes in A. parasiticus. A mating type ratio close to 1∶1 in A. flavus, A. parasiticus and A. minisclerotigenes was associated with higher recombination rates in the aflatoxin cluster and less pronounced chemotype differences in populations. This work shows that the reproductive nature of the population (more sexual versus more asexual) is predictive of aflatoxin chemotype diversity in these agriculturally important fungi., Author Summary Fungal pathogen populations have mixed proportions of vegetative propagation and sexual reproduction ranging from predominantly clonal to varying levels of sexuality. Aflatoxins are the most potent naturally occurring carcinogens known and aflatoxin-producing Aspergillus flavus and A. parasiticus show extensive genetic and mycotoxin diversity. Population genetic studies and experimental matings in the laboratory have revealed the underlying genetic mechanisms and adaptive processes that create and maintain aflatoxin diversity. These studies provided unequivocal evidence of meiosis, crossing over, and aflatoxin heritability, but whether these processes directly influence genetic diversity in nature with respect to aflatoxin formation is not clear. Here, our work with A. flavus, A. parasiticus and A. minisclerotigenes from fields in different continents shows that populations with higher mean recombination rates exhibit less variability in aflatoxin profiles due to genetic intermixing, whereas populations with lower recombination rates have greater variability in aflatoxin profiles due to increased fixation of specific toxin chemotypes. Therefore, sexuality generates novel toxin chemotypes but tends to equalize toxin differences in populations. Our study highlights how an understanding of variation in mating-type frequency, fertility and recombination in these fungi is crucial for the selection of nontoxigenic biocontrol strains for long-term reduction of aflatoxins in target regions.

Publisher Summary Transpiration efficiency (W), which is defined as the ratio of dry matter production to transpiration, is a trait that can contribute to productivity when water resources are scarce. The accurate measurements of crop transpiration in field are difficult, and it has made the demonstration of species and cultivar differences in W difficult. While transpiration may be readily measured in pots in which soil evaporation can be minimized, it is much more difficult to estimate soil evaporation in the field. There is a scope for W improvement in currently grown commercial cultivars. This chapter discusses the results from a series of experiments done to investigate genotypic and environmental variation in W in peanut and its correlation with carbon isotope discrimination (Δ), under both controlled environment and field conditions. The chapter explores the relationship between pod yield and W. It also explores whether W and Δ are heritable characters. Such information is needed before Δ can be recommended as a selection trait for improving W in peanut-breeding programs.

Chickpea (Cicer arietinum L.) has been traditionally grown in India but is a relatively new export crop in Australia where its cultivation is expanding into new areas. The objective of this study was to identify homoclimes (i.e. similar chickpea-growing environments) in the major chickpea-growing areas of the 2 countries, using the Agricultural Production Systems Simulator (APSIM) chickpea model. The model, which processes climatic, soil, and plant information on a daily time step, was first validated and then used to simulate flowering, maturity, and grain yield of Amethyst, a mid-season cultivar, and Barwon, a full-season cultivar, on low (100 mm), medium (150 mm), and high (190 mm) water-holding capacity soils, using historical climatic data of 67 Australian and 24 Indian locations. The mean of annual outputs of flowering, maturity, and grain yield of the 2 cultivars on 3 soils was then clustered using Ward’s hierarchical complete linkage clustering procedure. At a 90% level of similarity, all the locations could be grouped into 6 homoclime clusters. The Australian locations appeared more diverse as they were present in all the clusters, whereas the Indian locations were present only in clusters 1, 2, and 6. While there were clear geographical patterns of spread of these clusters, in Australia they were not entirely related to latitude. The cluster 1 and 2 locations, which represent the largest chickpea-growing area in Australia, had homoclime locations in common with northern India. The clustering of locations appeared generally consistent with the known adaptation of chickpea in different environments of the 2 countries and therefore suggests that the methodology could be potentially used for complementing conventional approaches of introducing or exchanging germplasm, as well as determining appropriateness of breeding/testing sites.

Aflatoxins are highly carcinogenic mycotoxins produced by two fungi, Aspergillus flavus and A. parasiticus, under specific moisture and temperature conditions before harvest and/or during storage of a wide range of crops including maize. Modelling of interactions between host plant and environment during the season can enable quantification of preharvest aflatoxin risk and its potential management. A model was developed to quantify climatic risks of aflatoxin contamination in maize using principles previously used for peanuts. The model outputs an aflatoxin risk index in response to seasonal temperature and soil moisture during the maize grain filling period using the APSIM’s maize module. The model performed well in simulating climatic risk of aflatoxin contamination in maize as indicated by a significant R2 (P ≤ 0.01) between aflatoxin risk index and the measured aflatoxin B1 in crop samples, which was 0.69 for a range of rainfed Australian locations and 0.62 when irrigated locations were also included in the analysis. The model was further applied to determine probabilities of exceeding a given aflatoxin risk in four non-irrigated maize growing locations of Queensland using 106 years of historical climatic data. Locations with both dry and hot climates had a much higher probability of higher aflatoxin risk compared with locations having either dry or hot conditions alone. Scenario analysis suggested that under non-irrigated conditions the risk of aflatoxin contamination could be minimised by adjusting sowing time or selecting an appropriate hybrid to better match the grain filling period to coincide with lower temperature and water stress conditions.

Measurement or accurate simulation of soil temperature is important for improved understanding and management of peanuts (Arachis hypogaea L.), due to their geocarpic habit. A module of the Agricultural Production Systems Simulator Model (APSIM), APSIM-soiltemp, which uses input of ambient temperature, rainfall and solar radiation in conjunction with other APSIM modules, was evaluated for its ability to simulate surface 5 cm soil temperature in 35 peanut on-farm trials conducted between 2001 and 2005 in the Burnett region (25°36′S to 26°41′S, 151°39′E to 151°53′E). Soil temperature simulated by the APSIM-soiltemp module, from 30 days after sowing until maturity, closely matched the measured values (R2 ≥ 0.80) in the first three seasons (2001–04). However, a slightly poorer relationship (R2 = 0.55) between the observed and the simulated temperatures was observed in 2004–05, when the crop was severely water stressed. Nevertheless, over all the four seasons, which were characterised by a range of ambient temperature, leaf area index, radiation and soil water, each of which was found to have significant effects on soil temperature, a close 1 : 1 relationship (R2 = 0.85) between measured and simulated soil temperatures was observed. Therefore, the pod zone soil temperature simulated by the module can be generally relied on in place of measured input of soil temperature in APSIM applications, such as quantifying climatic risk of aflatoxin accumulation.