Side-effects of domestication: cultivated legume seeds contain similar tocopherols and fatty acids but less carotenoids than their wild counterparts

Domestication and the evolution of crops: variable syndromes, complex genetic architectures, and ecological entanglements

Domestication can be considered a specialized mutualism in which a domesticator exerts control over the reproduction or propagation (fitness) of a domesticated species to gain resources or services. The evolution of crops by human-associated selection provides a powerful set of models to study recent evolutionary adaptations and their genetic bases. Moreover, the domestication and dispersal of crops such as rice, maize, and wheat during the Holocene transformed human social and political organization by serving as the key mechanism by which human societies fed themselves. Here we review major themes and identify emerging questions in three fundamental areas of crop domestication research: domestication phenotypes and syndromes, genetic architecture underlying crop evolution, and the ecology of domestication. Current insights on the domestication syndrome in crops largely come from research on cereal crops such as rice and maize, and recent work indicates distinct domestication phenotypes can arise from different domestication histories. While early studies on the genetics of domestication often identified single large-effect loci underlying major domestication traits, emerging evidence supports polygenic bases for many canonical traits such as shattering and plant architecture. Adaptation in human-constructed environments also influenced ecological traits in domesticates such as resource acquisition rates and interactions with other organisms such as root mycorrhizal fungi and pollinators. Understanding the ecological context of domestication will be key to developing resource-efficient crops and implementing more sustainable land management and cultivation practices.

Hypochaos prevents tragedy of the commons in discrete-time eco-evolutionary game dynamics

While quite a few recent papers have explored game-resource feedback using the framework of evolutionary game theory, almost all the studies are confined to using time-continuous dynamical equations. Moreover, in such literature, the effect of ubiquitous chaos in the resulting eco-evolutionary dynamics is rather missing. Here, we present a deterministic eco-evolutionary discrete-time dynamics in generation-wise non-overlapping population of two types of harvesters-one harvesting at a faster rate than the other-consuming a self-renewing resource capable of showing chaotic dynamics. In the light of our finding that sometimes chaos is confined exclusively to either the dynamics of the resource or that of the consumer fractions, an interesting scenario is realized: The resource state can keep oscillating chaotically, and hence, it does not vanish to result in the tragedy of the commons-extinction of the resource due to selfish indiscriminate exploitation-and yet the consumer population, whose dynamics depends directly on the state of the resource, may end up being composed exclusively of defectors, i.e., high harvesters. This appears non-intuitive because it is well known that prevention of tragedy of the commons usually requires substantial cooperation to be present.

An Integrated Approach for Biofortification of Carotenoids in Cowpea for Human Nutrition and Health

Stress-resilient and highly nutritious legume crops can alleviate the burden of malnutrition and food security globally. Here, we focused on cowpea, a legume grain widely grown and consumed in regions at a high risk of micronutrient deficiencies, and we discussed the past and present research on carotenoid biosynthesis, highlighting different knowledge gaps and prospects for increasing this micronutrient in various edible parts of the crop. The literature survey revealed that, although carotenoids are important micronutrients for human health and nutrition, like in many other pulses, the potential of carotenoid biofortification in cowpea is still underexploited. We found that there is, to some extent, progress in the quantification of this micronutrient in cowpea; however, the diversity in content in the edible parts of the crop, namely, grains, pods, sprouts, and leaves, among the existing cowpea genetic resources was uncovered. Based on the description of the different factors that can influence carotenoid biosynthesis and accumulation in cowpea, we anticipated that an integrated use of omics in breeding coupled with mutagenesis and genetic engineering in a plant factory system would help to achieve a timely and efficient increase in carotenoid content in cowpea for use in the food systems in sub-Saharan Africa and South Asia.

Lupin as a Source of Bioactive Antioxidant Compounds for Food Products

Four species of lupin (white lupin, yellow lupin, blue lupin and Andean lupin) are widely cropped thanks to the excellent nutritional composition of their seeds: high protein content (28-48 g/100 g); good lipid content (4.6-13.5 g/100 g, but up to 20.0 g/100 g in Andean lupin), especially unsaturated triacylglycerols; and richness in antioxidant compounds like carotenoids, tocols and phenolics. Particularly relevant is the amount of free phenolics, highly bioaccessible in the small intestine. However, the typical bitter and toxic alkaloids must be eliminated before lupin consumption, hindering its diffusion and affecting its nutritional value. This review summarises the results of recent research in lupin composition for the above-mentioned three classes of antioxidant compounds, both in non-debittered and debittered seeds. Additionally, the influence of technological processes to further increase their nutritional value as well as the effects of food manufacturing on antioxidant content were scrutinised. Lupin has been demonstrated to be an outstanding raw material source, superior to most crops and suitable for manufacturing foods with good antioxidant and nutritional properties. The bioaccessibility of lupin antioxidants after digestion of ready-to-eat products still emerges as a dearth in current research.

The phenotypic variation mechanisms of Atractylodes lancea post-cultivation revealed by conjoint analysis of rhizomic transcriptome and metabolome

The wild Atractylodes lancea rhizomes have been traditionally used as herbal medicine. As the increasingly exhaustion of wild A. lancea, the artificial cultivation mainly contributed to the medicinal material production. However, besides the phenotypic variation of rhizome phenotypic trait alteration, the qualities of cultivated A. lancea decrease compared with the wild counterpart. To unveil the physiological and molecular mechanism beneath the phenotypic variation, GC-MS-based volatile organic compounds (VOCs) profiling and RNAseq-based transcriptome analysis were conducted. The volatile metabolomics profiling revealed 65 differentially accumulated metabolites (DAMs) while the transcriptomic profiling identified 12 009 differentially expressed unigenes (DEGs) post-cultivation. The volatile active compounds including atractylone, and eudesmol accumulated more in wild rhizome than in the cultivated counterpart, and several unigenes in terpene synthesis were downregulated under cultivated condition. Compared with the wild A. lancea rhizome, the contents of bioactive Jasmonic Acid (JAs) in cultivated A. lancea rhizome were higher, and evidences that JAs negatively regulate the terpenes biosynthesis in the cultivated A. lancea rhizome were also provided. The combinational omics analysis further indicated the high correlation between the ten cultivation-suppressed VOCs and the cultivation-altered genes for sesquiterpenoids biosynthesis in A. lancea. The network of the cultivation-altered transcription factors (TFs) and the ten VOCs suggested TFs (e.g. Arabidopsis ERF13 homologs and WRKY50) are involved in the regulation of terpenes biosynthesis. These results laid a theoretical basis for developing geo-herbalism medicinal plants with "high quality and optimal shape".

Advances in CRISPR/Cas9-based research related to soybean [Glycine max (Linn.) Merr] molecular breeding

Soybean [Glycine max (Linn.) Merr] is a source of plant-based proteins and an essential oilseed crop and industrial raw material. The increase in the demand for soybeans due to societal changes has coincided with the increase in the breeding of soybean varieties with enhanced traits. Earlier gene editing technologies involved zinc finger nucleases and transcription activator-like effector nucleases, but the third-generation gene editing technology uses clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). The rapid development of CRISPR/Cas9 technology has made it one of the most effective, straightforward, affordable, and user-friendly technologies for targeted gene editing. This review summarizes the application of CRISPR/Cas9 technology in soybean molecular breeding. More specifically, it provides an overview of the genes that have been targeted, the type of editing that occurs, the mechanism of action, and the efficiency of gene editing. Furthermore, suggestions for enhancing and accelerating the molecular breeding of novel soybean varieties with ideal traits (e.g., high yield, high quality, and durable disease resistance) are included.

Domestication has altered the ABA and gibberellin profiles in developing pea seeds

MAIN CONCLUSION

We showed that wild pea seeds contained a more diverse combination of bioactive GAs and had higher ABA content than domesticated peas. Although the role of abscisic acid (ABA) and gibberellins (GAs) interplay has been extensively studied in Arabidopsis and cereals models, comparatively little is known about the effect of domestication on the level of phytohormones in legume seeds. In legumes, as in other crops, seed dormancy has been largely or entirely removed during domestication. In this study, we have measured the endogenous levels of ABA and GAs comparatively between wild and domesticated pea seeds during their development. We have shown that wild seeds contained more ABA than domesticated ones, which could be important for preparing the seeds for the period of dormancy. ABA was catabolised particularly by an 8´-hydroxylation pathway, and dihydrophaseic acid was the main catabolite in seed coats as well as embryos. Besides, the seed coats of wild and pigmented cultivated genotypes were characterised by a broader spectrum of bioactive GAs compared to non-pigmented domesticated seeds. GAs in both seed coat and embryo were synthesized mainly by a 13-hydroxylation pathway, with GA29 being the most abundant in the seed coat and GA20 in the embryos. Measuring seed water content and water loss indicated domesticated pea seeds´ desiccation was slower than that of wild pea seeds. Altogether, we showed that pea domestication led to a change in bioactive GA composition and a lower ABA content during seed development.

Recent progress in molecular genetics and omics-driven research in seed biology

Elucidating the mechanisms that control seed development, metabolism, and physiology is a fundamental issue in biology. Michel Caboche had long been a catalyst for seed biology research in France up until his untimely passing away last year. To honour his memory, we have updated a review written under his coordination in 2010 entitled "Arabidopsis seed secrets unravelled after a decade of genetic and omics-driven research". This review encompassed different molecular aspects of seed development, reserve accumulation, dormancy and germination, that are studied in the lab created by M. Caboche. We have extended the scope of this review to highlight original experimental approaches implemented in the field over the past decade such as omics approaches aimed at investigating the control of gene expression, protein modifications, primary and specialized metabolites at the tissue or even cellular level, as well as seed biodiversity and the impact of the environment on seed quality.

The nutritional composition of the vegetable soybean (maodou) and its potential in combatting malnutrition

Introduction

Global malnutrition continues to be a canker owing to poor eating habits and over-reliance on the major staple crops. Vegetable soybean (maodou) is gaining popularity globally as an affordable snack and vegetable.

Methods

In this study, we profiled the nutritional composition of 12 soybean cultivars at the vegetable (R6-R7) and mature (R8) stages. We also conducted an RNA-seq analysis during seed development, focusing on key biosynthesis enzymes for quality traits.

Results

The results showed that 100 g of maodou contained 66.54% moisture, 13.49% protein, 7.81% fatty acids, 2.47% soluble sugar, abundant content of minerals, and micronutrients, including folate (462.27 μg FW) and carotenoids (3,935.41 μg FW). Also, the isoflavone content of maodou ranged between 129.26 and 2,359.35 μg/g FW. With regard to the recommended daily allowance, 100 g fresh weight of maodou can contribute 26.98, 115.57, and 11.60% of protein, folate, and zinc, respectively, and significant proportions of other nutrients including linoleic acid (21.16%), linolenic acid (42.96%), zinc (11.60%), and iron (18.01%). On a dry weight basis, maodou has two to six folds higher contents of folate, tocopherol, and carotenoid than the mature soybean. Furthermore, RNA-seq analysis revealed that key biosynthesis enzymes of quality traits are differentially expressed during seed development and may contribute to variations in the content of quality traits at the vegetable and mature stages. Correlation analysis of quality traits at both stages revealed that protein only correlated positively with zinc at the vegetable stage but negatively correlated with total tocopherol and total fatty acid at the mature stage. Complex associations among folates, soluble sugar, and isoflavones were also identified.

Discussion

This study provides insight into the nutritional contents of vegetable soybean and demonstrates that maodou is essential for meeting the nutritional requirements of most countries.

Effect of Debittering with Different Solvents and Ultrasound on Carotenoids, Tocopherols, and Phenolics of Lupinus albus Seeds

Lupin seeds represent a rich nutritional source of bioactive compounds, including antioxidant molecules such as carotenoids, tocopherols, and phenolics. However, before consumption, the lupin seeds must be debittered in order to remove their bitter and toxic alkaloids. This study analyzed the impact on the bioactive compounds of Lupinus albus seeds of a recent time- and water-saving debittering method, which employs alternative washing solutions (0.5% or 1% of either NaCl or citric acid), with or without the assistance of ultrasound. The results were compared with those of two control methods using water or a NaCl solution. The sonication, when it was significant, led to a large loss of bioactive compounds, which was most likely due to its extraction capability. The seeds that were debittered without ultrasound presented high concentrations of tocopherols (172.8-241.3 mg/kg DM), carotenoids (10.9-25.1 mg/kg DM), and soluble-free (106.9-361.1 mg/kg DM), soluble-conjugated (93.9-118.9 mg/kg DM), and insoluble-bound (59.2-156.7 mg/kg DM) phenolics. The soluble-free fraction showed the greatest loss after a prolonged treatment. Overall, debittering with citric acid or NaCl preserved the highest concentration of antioxidant compounds by shortening the treatment time, thus preventing extensive leaching.

Advancing Grain Legumes Domestication and Evolution Studies with Genomics

Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding.

Unintended Consequences of Plant Domestication

Human selection on wild populations mostly favored a common set of plant traits during domestication. This process of direct selection also altered other independent traits that were not directly perceived or desired during crop domestication and improvement. A deeper knowledge of the inadvertent and undesirable phenotypic effects and their underlying genetic causes can help design strategies to mitigate their effects and improve genetic gain in crop plants. We review different factors explaining the negative consequences of plant domestication at the phenotypic and genomic levels. We further describe the genetic causes of undesirable effects that originate from the selection of favorable alleles during plant domestication. In addition, we propose strategies that could be useful in attenuating such effects for crop improvement. With novel -omics and genome-editing tools, it is relatively approachable to understand and manipulate the genetic and biochemical mechanisms responsible for the undesirable phenotypes in domesticated plants.

Unraveling Origin, History, Genetics, and Strategies for Accelerated Domestication and Diversification of Food Legumes

Domestication is a dynamic and ongoing process of transforming wild species into cultivated species by selecting desirable agricultural plant features to meet human needs such as taste, yield, storage, and cultivation practices. Human plant domestication began in the Fertile Crescent around 12,000 years ago and spread throughout the world, including China, Mesoamerica, the Andes and Near Oceania, Sub-Saharan Africa, and eastern North America. Indus valley civilizations have played a great role in the domestication of grain legumes. Crops, such as pigeon pea, black gram, green gram, lablab bean, moth bean, and horse gram, originated in the Indian subcontinent, and Neolithic archaeological records indicate that these crops were first domesticated by early civilizations in the region. The domestication and evolution of wild ancestors into today’s elite cultivars are important contributors to global food supply and agricultural crop improvement. In addition, food legumes contribute to food security by protecting human health and minimize climate change impacts. During the domestication process, legume crop species have undergone a severe genetic diversity loss, and only a very narrow range of variability is retained in the cultivars. Further reduction in genetic diversity occurred during seed dispersal and movement across the continents. In general, only a few traits, such as shattering resistance, seed dormancy loss, stem growth behavior, flowering–maturity period, and yield traits, have prominence in the domestication process across the species. Thus, identification and knowledge of domestication responsive loci were often useful in accelerating new species’ domestication. The genes and metabolic pathways responsible for the significant alterations that occurred as an outcome of domestication might aid in the quick domestication of novel crops. Further, recent advances in “omics” sciences, gene-editing technologies, and functional analysis will accelerate the domestication and crop improvement of new crop species without losing much genetic diversity. In this review, we have discussed about the origin, center of diversity, and seed movement of major food legumes, which will be useful in the exploration and utilization of genetic diversity in crop improvement. Further, we have discussed about the major genes/QTLs associated with the domestication syndrome in pulse crops and the future strategies to improve the food legume crops.

Metabolomic Analysis Identifies Differences Between Wild and Domesticated Chili Pepper Fruits During Development (Capsicum annuum L.)

Capsicum spp. members are a rich source of specialized compounds due to their secondary metabolism. Some metabolic pathways have suffered modifications during the domestication process and improvement of agricultural traits. Here, we compared non-targeted LC-MS profiles from several areas: wild accessions (C. annuum L. var. glabriusculum), domesticated cultivars (C. annuum L.), and the F1 progeny of a domesticated, and a wild accession cross (in both directions) throughout seven stages of fruit development of chili pepper fruits. The main detected differences were in glycerophospholipid metabolism, flavone and flavonol biosynthesis, sphingolipid metabolism, and cutin biosynthesis. The domesticated group exhibited a higher abundance in 12'-apo-β-carotenal, among others capsorubin, and β-tocopherol. Palmitic acid and derivates, terpenoids, and quercitrin were prevalent in the wild accessions. F1 progeny showed a higher abundance of capsaicin, glycol stearate, and soyacerebroside I. This work supports evidence of the side-affectation of trait selection over the metabolism of chili pepper fruit development. Furthermore, it was also observed that there was a possible heterosis effect over the secondary metabolism in the F1 progeny.

Genetic Diversity and Association Analysis for Carotenoid Content among Sprouts of Cowpea (Vigna unguiculata L. Walp)

The development and promotion of biofortified foods plants are a sustainable strategy for supplying essential micronutrients for human health and nutrition. We set out to identify quantitative trait loci (QTL) associated with carotenoid content in cowpea sprouts. The contents of carotenoids, including lutein, zeaxanthin, and β-carotene in sprouts of 125 accessions were quantified via high-performance liquid chromatography. Significant variation existed in the profiles of the different carotenoids. Lutein was the most abundant (58 ± 12.8 mg/100 g), followed by zeaxanthin (14.7 ± 3.1 mg/100 g) and β-carotene (13.2 ± 2.9 mg/100 g). A strong positive correlation was observed among the carotenoid compounds (r ≥ 0.87), indicating they can be improved concurrently. The accessions were distributed into three groups, following their carotenoid profiles, with accession C044 having the highest sprout carotenoid content in a single cluster. A total of 3120 genome-wide SNPs were tested for association analysis, which revealed that carotenoid biosynthesis in cowpea sprouts is a polygenic trait controlled by genes with additive and dominance effects. Seven loci were significantly associated with the variation in carotenoid content. The evidence of variation in carotenoid content and genomic regions controlling the trait creates an avenue for breeding cowpea varieties with enhanced sprouts carotenoid content.

Quality Evaluation Indices for Soybean Oil in Relation to Cultivar, Application of N Fertiliser and Seed Inoculation with Bradyrhizobium japonicum

Soybean ranks second in production and consumption of vegetable oils worldwide and these are expected to continue to increase. The suitability of soybean oil for specific uses is determined by the fatty acid composition from which a number of indices and indicators can be calculated. The aim of this study was to evaluate the indices of nutritional and health-promoting fat in seeds of soybean cultivars grown in 2016–2019 under the influence of varying doses of N and inoculation with Bradyrhizobium japonicum. Omega 3 and Omega 6, unsaturated fatty acids (UFA), saturated fatty acids (SFA), polyunsaturated fatty acids (PUFA), index of desirable fatty acids (DFA), sum of hypercholesterolemic fatty acids (OFA), index of atherogenicity (AI), index of thrombogenicity (TI), oleic desaturation ratio (ODR), linoleic desaturation ratio (LDR), calculated oxidizability value (COX) and the hypocholesterolemic/hypercholesterolemic ratio (HH), saturation fat index (S/P) and ALA/LA, OL/(LA+ALA) ratios and the consumer index (CI) were included. Fat quality indices for soybean seeds were strongly determined by weather conditions. Seeds of the cv. Aldana contained higher amounts of Omega 6 and featured more favourable MUFA/PUFA and OL/(LA+ALA) ratios, while the seeds of the cv. Annushka had more favourable CI and higher ODR, COX and S/P indices. No important differences were observed regarding the effect of nitrogen dose and seed inoculation on the formation of the DFA, OFA, HH, AI, TI and CI indices. The value of the S/P index suggests that higher nitrogen rates (60 kg∙ha−1) and the lack of inoculation treatment produce seeds with a more favourable dietary fatty acid balance.

Revisiting the Domestication Process of African Vigna Species (Fabaceae): Background, Perspectives and Challenges

Legumes are one of the most economically important and biodiverse families in plants recognised as the basis to develop functional foods. Among these, the Vigna genus stands out as a good representative because of its relatively recent African origin as well as its outstanding potential. Africa is a great biodiversity centre in which a great number of species are spread, but only three of them, Vigna unguiculata, Vigna subterranea and Vigna vexillata, were successfully domesticated. This review aims at analysing and valorising these species by considering the perspective of human activity and what effects it exerts. For each species, we revised the origin history and gave a focus on where, when and how many times domestication occurred. We provided a brief summary of bioactive compounds naturally occurring in these species that are fundamental for human wellbeing. The great number of wild lineages is a key point to improve landraces since the domestication process caused a loss of gene diversity. Their genomes hide a precious gene pool yet mostly unexplored, and genes lost during human activity can be recovered from the wild lineages and reintroduced in cultivated forms through modern technologies. Finally, we describe how all this information is game-changing to the design of future crops by domesticating de novo.

Tissue culture-based genetic improvement of fava bean (Vicia faba L.): analysis on previous achievements and future perspectives

Fava bean is an extremely important legume and serves immense potential to function as an ingredient as pulse proteins in human diet. Bearing the proficiency of yielding magnanimous amount of functional and nutritional ingredients, this bean deserves to replace any other leguminous crop too. The instability of fava bean in its yield makes breeding for crop improvement difficult, and its high susceptibility to a number of abiotic and biotic stresses additionally results in unstable yields. The self-incompatibility leads to the formation of a limited genetic pool and shows a slow progress in breeding. The plant is highly recalcitrant, making it an onerous task to micropropagate or regenerate fava beans under in vitro conditions. Another fly in the ointment is the release of phenolic compounds by the plant. There are several endeavours that have been made to establish in vitro regeneration, protoplast culture, and genetic transformation and to genetically improve this plant. Nonetheless there are a number of promising cutting-edge technologies that are yet to be harnessed in order to ensure its comprehensive and sustainable genetic improvement. The in vitro-based technologies of this legume and its untraveled path in the plant tissue culture-mediated approaches can assist further genetic manipulation of this plant species in a smoother manner and at an exponential rate. Creation of a single review comprising all the updates and genetic advancements in fava bean is an absolute necessity of the hour. Thus, the importance of this review remains at the peak as it covers a vast range of information, starting from the basic description to the utmost modern stages of advancement in the selected crop. Overall interpretation of the review is aimed at encouraging readers to focus on almost all possible dimensions of international research, already executed, and is being executed in fava bean, thereby helping to understand the demand and advantages of the crop, even at the molecular level.Key points• Fava bean, commonly known as "poor man's meat", is a protein-rich legume with multiple nutritional and pharmacological benefits.• Its highly recalcitrant response makes in vitro interventions quite challenging for its genetic improvement.• This review delves into biotechnological interventions for its advancements to date and highlights major hurdles and potential research solutions to ensure comprehensive genetic improvement.

Assessing the Fatty Acid, Carotenoid, and Tocopherol Compositions of Seeds from Apple Cultivars (Malus domestica Borkh.) Grown in Norway

Apple production generates large amounts of apple pomace including seeds, leading to high transportation costs, public health hazards and undesirable odor. A new reuse strategy of this kind of waste could solve environmental issues and/or create unconventional sources of health beneficial products. In total, seeds from 75 apple cultivars grown in Norway (both domestic and international) have been analyzed for the first time for oil content and fatty acid profile together with tocopherols and carotenoids quantification in defatted seeds. Seeds from cultivar Håkonseple had the highest oil content (22.10%), with linoleic, oleic acid, and palmitic acid as the most abundant fatty acids. The levels of β-carotene and lycopene carotenoids and α-tocopherol were the highest in defatted seeds of the cultivar Sureple Grøn. Principal component analysis separated cultivars according to the total oil content. The Norwegian apple cultivars Håkonseple, Kviteple, Tolleivseple, Vinterrosenstrips, and Tokheimseple are recommended for obtaining vegetable oil due to their high oil contents, while cultivar Sureple Grøn can be separated due to its high levels of β-carotene, lycopene and total tocopherols.

The effect of plant domestication on host control of the microbiota

Macroorganisms are colonized by microbial communities that exert important biological and ecological functions, the composition of which is subject to host control and has therefore been described as "an ecosystem on a leash". However, domesticated organisms such as crop plants are subject to both artificial selection and natural selection exerted by the agricultural ecosystem. Here, we propose a framework for understanding how host control of the microbiota is influenced by domestication, in which a double leash acts from domesticator to host and host to microbes. We discuss how this framework applies to a plant compartment that has demonstrated remarkable phenotypic changes during domestication: the seed.

Intentional and unintentional selection during plant domestication: herbivore damage, plant defensive traits and nutritional quality of fruit and seed crops

Greater susceptibility to herbivory can arise as an effect of crop domestication. One proposed explanation is that defenses decreased intentionally or unintentionally during the domestication process, but evidence for this remains elusive. An alternative but nonexclusive explanation is presumed selection for higher nutritional quality. We used a metaanalytical approach to examine susceptibility to herbivores in fruit and seed crops and their wild relatives. Our analyses provide novel insights into the mechanisms of increased susceptibility by evaluating whether it can be attributed to either a reduction in herbivore defensive traits, including direct/indirect and constitutive/inducible defenses, or an increase in the nutritional content of crops. The results confirm higher herbivory and lower levels of all types of defenses in crops compared to wild relatives, although indirect defenses were more affected than direct ones. Contrary to expectations, nutritional quality was lower in crops than in wild relatives, which may enhance biomass loss to herbivores if they increase consumption to meet nutritional requirements. Our findings represent an important advance in our understanding of how changes in defensive and nutritional traits following domestication could influence, in combination or individually, crop susceptibility to herbivore attacks.

Chemical Composition, Tocopherol and Carotenoid Content of Seeds from Different Andean Lupin (Lupinus mutabilis) Ecotypes

Andean lupin (Lupinus mutabilis) seeds are appreciated for their high protein and lipid contents and have potential applications as ingredients in food, cosmetic, and pharmaceutical industries. Nevertheless, the information about the seed composition (especially in lipophilic antioxidants) of ecotypes from distinct cropping areas is currently limited. Thus, the aim of the present research was to assess the morphological characteristics, chemical composition, tocopherol and carotenoid contents of the seeds of 33 Andean lupin ecotypes from different Peruvian regions, along with three L. albus, one L. angustifolius and one L. luteus controls. Significant differences were noted among the Andean ecotypes for all analyzed features. The protein, lipid and ash contents were 32.0-46.9, 13.6-18.6 and 2.7-4.4 g/100 g dry matter (DM), respectively. The seeds were rich in tocopherols (172.1-249.8 mg/kg DM; γ-tocopherol was 98% of total tocols) and low in carotenoids (0.69-2.89 mg/kg DM). Debittering increased the tocopherol content (227.0-378.2 mg/kg DM), probably because of the soluble components loss, although the carotenoid concentration remained unchanged. The Andean lupins had higher protein, lipid and tocopherol contents than L. albus and L. angustifolius; the L. luteus values were within the L. mutabilis range. These results suggest that L. mutabilis harbors nutritional characteristics that are well suited to modern food trends.

The History of Lentil (Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions

Protein-rich legumes accompanied carbohydrate-rich cereals since the beginning of agriculture and yet their domestication history is not as well understood. Lentil (Lens culinaris Medik. subsp. culinaris) was first cultivated in Southwest Asia (SWA) 8000-10,000 years ago but archeological evidence is unclear as to how many times it may have been independently domesticated, in which SWA region(s) this may have happened, and whether wild species within the Lens genus have contributed to the cultivated gene pool. In this study, we combined genotyping-by-sequencing (GBS) of 190 accessions from wild (67) and domesticated (123) lentils from the Old World with archeological information to explore the evolutionary history, domestication, and diffusion of lentils to different environments. GBS led to the discovery of 87,647 single-nucleotide polymorphisms (SNPs), which allowed us to infer the phylogeny of genus Lens. We confirmed previous studies proposing four groups within it. The only gene flow detected was between cultivated varieties and their progenitor (L. culinaris subsp. orientalis) albeit at very low levels. Nevertheless, a few putative hybrids or naturalized cultivars were identified. Within cultivated lentil, we found three geographic groups. Phylogenetics, population structure, and archeological data coincide in a scenario of protracted domestication of lentils, with two domesticated gene pools emerging in SWA. Admixed varieties are found throughout their range, suggesting a relaxed selection process. A small number of alleles involved in domestication and adaptation to climatic variables were identified. Both novel mutation and selection on standing variation are presumed to have played a role in adaptation of lentils to different environments. The results presented have implications for understanding the process of plant domestication (past), the distribution of genetic diversity in germplasm collections (present), and targeting genes in breeding programs (future).

Antioxidant Phytochemicals in Pulses and their Relation to Human Health: A Review

Pulses are a staple food cultivated since ancient times, which play an important role in the human diet. From a nutritional point of view, pulses are very interesting foods as they are rich in proteins, carbohydrates and dietary fibre. Dietary antioxidants are a complex mixture of hydrophilic and lipophilic compounds usually present in foods of plant origin, including pulses. In the present study, the phytochemical composition of selected pulses (common beans, fava beans, lentils, chickpeas, peas and lupins) has been reviewed in terms of their content of antioxidant compounds. The content of hydrosoluble antioxidants (organic acids, phenolic compounds), liposoluble antioxidants (tocopherols, carotenoids) and other compounds which exert antioxidant properties, such as dietary fibre and minerals (zinc, selenium), has been studied, reporting that pulses are an interesting source of these compounds, which have important health benefits, including a preventing role in cardiovascular diseases, anticarcinogenic or neuroprotective properties. It is important to take into account that pulses are not usually consumed raw, but they must be processed before consumption in order to improve their nutritional quality and their palatability, therefore, the effect of different technological and heat treatments (germination, cooking, boiling, extrusion) on the antioxidant compounds present in pulses has been also reviewed. In this regard, it has been observed that as a consequence of processing, the content of phytochemicals with antioxidant properties is usually decreased, but processed pulses maintain relevant amounts of these compounds, preserving their beneficial health effect.

The Effects of Domestication on Secondary Metabolite Composition in Legumes

Legumes are rich in secondary metabolites, such as polyphenols, alkaloids, and saponins, which are important defense compounds to protect the plant against herbivores and pathogens, and act as signaling molecules between the plant and its biotic environment. Legume-sourced secondary metabolites are well known for their potential benefits to human health as pharmaceuticals and nutraceuticals. During domestication, the color, smell, and taste of crop plants have been the focus of artificial selection by breeders. Since these agronomic traits are regulated by secondary metabolites, the basis behind the genomic evolution was the selection of the secondary metabolite composition. In this review, we will discuss the classification, occurrence, and health benefits of secondary metabolites in legumes. The differences in their profiles between wild legumes and their cultivated counterparts will be investigated to trace the possible effects of domestication on secondary metabolite compositions, and the advantages and drawbacks of such modifications. The changes in secondary metabolite contents will also be discussed at the genetic level to examine the genes responsible for determining the secondary metabolite composition that might have been lost due to domestication. Understanding these genes would enable breeding programs and metabolic engineering to produce legume varieties with favorable secondary metabolite profiles for facilitating adaptations to a changing climate, promoting beneficial interactions with biotic factors, and enhancing health-beneficial secondary metabolite contents for human consumption.

Interactions between genetics and environment shape Camelina seed oil composition

BACKGROUND

Camelina sativa (gold-of-pleasure) is a traditional European oilseed crop and emerging biofuel source with high levels of desirable fatty acids. A twentieth century germplasm bottleneck depleted genetic diversity in the crop, leading to recent interest in using wild relatives for crop improvement. However, little is known about seed oil content and genetic diversity in wild Camelina species.

RESULTS

We used gas chromatography, environmental niche assessment, and genotyping-by-sequencing to assess seed fatty acid composition, environmental distributions, and population structure in C. sativa and four congeners, with a primary focus on the crop's wild progenitor, C. microcarpa. Fatty acid composition differed significantly between Camelina species, which occur in largely non-overlapping environments. The crop progenitor comprises three genetic subpopulations with discrete fatty acid compositions. Environment, subpopulation, and population-by-environment interactions were all important predictors for seed oil in these wild populations. A complementary growth chamber experiment using C. sativa confirmed that growing conditions can dramatically affect both oil quantity and fatty acid composition in Camelina.

CONCLUSIONS

Genetics, environmental conditions, and genotype-by-environment interactions all contribute to fatty acid variation in Camelina species. These insights suggest careful breeding may overcome the unfavorable FA compositions in oilseed crops that are predicted with warming climates.

Sokovic M, Barros L, Ferreira ICFR. Chemical Composition and Plant Growth of Centaurea raphanina subsp. mixta Plants Cultivated under Saline Conditions

The aim of this report was to study the effect of salinity (control: 2dS/m, S1: 4 dS/m and S2: 6 dS/m) and harvest time (first harvest on 9 May 2018 and second harvest on 19 April 2018) on the growth and the chemical composition of Centaurea raphanina subsp. mixta plants. The plants of the first harvest were used for the plant growth measurements (fresh weight and moisture content of leaves, rosette diameter, number and thickness of leaves), whereas those of the second harvest were not used for these measurements due to the flowering initiation, which made the leaves unmarketable due to their hard texture. The results of our study showed that C. raphanina subsp. mixta plants can be cultivated under mild salinity (S1 treatment) conditions without severe effects on plant growth and yield, since a more severe loss (27.5%) was observed for the S2 treatment. In addition, harvest time proved to be a cost-effective cultivation practice that allows to regulate the quality of the final product, either in edible form (first harvest) or for nutraceutical and pharmaceutical purposes as well as antimicrobial agents in food products. Therefore, the combination of these two agronomic factors showed interesting results in terms of the quality of the final product. In particular, high salinity (S2 treatment) improved the nutritional value by increasing the fat, proteins and carbohydrates contents in the first harvest, as well as the tocopherols and sugars contents (S1 and S2 treatments, respectively) in the second harvest. In addition, salinity and harvest time affected the oxalic acid content which was the lowest for the S2 treatment at the second harvest. Similarly, the richest fatty acid (α-linolenic acid) increased with increasing salinity at the first harvest. Salinity and harvest time also affected the antimicrobial properties, especially against Staphylococcus aureus, Bacillus cereus and Trichoderma viride, where the extracts from the S1 and S2 treatments showed high effectiveness. In contrast, the highest amounts of flavanones (pinocembrin derivatives) were detected in the control treatment (second harvest), which was also reflected to the highest antioxidant activity (TBARS) for the same treatment. In conclusion, C. raphanina subsp. mixta plants seem to be tolerant to medium salinity stress (S1 treatment) since plant growth was not severely impaired, while salinity and harvesting time affected the nutritional value (fat, proteins, and carbohydrates) and the chemical composition (tocopherols, sugars, oxalic acid, fatty acids), as well as the bioactive properties (cytotoxicity and antimicrobial properties) of the final product.

Wild and Cultivated Centaurea raphanina subsp. mixta: A Valuable Source of Bioactive Compounds

Centaurea raphanina subsp. mixta (DC.) Runemark is a wild edible species endemic to Greece. This study evaluated the chemical composition and bioactive properties of wild and cultivated C. raphanina subsp. mixta plants. Wild plants had higher nutritional value than cultivated ones, whereas cultivated plants contained more tocopherols. Glucose and sucrose were higher in cultivated plants and trehalose in wild ones. Oxalic and total organic acids were detected in higher amounts in cultivated samples. The main fatty acids were α-linolenic, linoleic and palmitic acid, while wild plants were richer in polyunsaturated fatty acids. Two pinocembrin derivatives were the main phenolic compounds being detected in higher amounts in wild plants. Regarding the antioxidant activity, wild and cultivated plants were more effective in the oxidative haemolysis (OxHLIA) and thiobarbituric acid reactive substances (TBARS) assays, respectively. Moreover, both extracts showed moderate cytotoxicity in non-tumor cell lines (PLP2), while cultivated plants were more effective against cervical carcinoma (HeLa), breast carcinoma (MCF-7) and non-small lung cancer (NCI-H460) cell lines. Finally, wild plants showed higher antimicrobial activity than cultivated plants against specific pathogens. In conclusion, the cultivation of C.raphanina subsp. mixta showed promising results in terms of tocopherols content and antiproliferative effects, however further research is needed to decrease oxalic acid content.

Pod Shattering: A Homologous Series of Variation Underlying Domestication and an Avenue for Crop Improvement

In wild habitats, fruit dehiscence is a critical strategy for seed dispersal; however, in cultivated crops it is one of the major sources of yield loss. Therefore, indehiscence of fruits, pods, etc., was likely to be one of the first traits strongly selected in crop domestication. Even with the historical selection against dehiscence in early domesticates, it is a trait still targeted in many breeding programs, particularly in minor or underutilized crops. Here, we review dehiscence in pulse (grain legume) crops, which are of growing importance as a source of protein in human and livestock diets, and which have received less attention than cereal crops and the model plant Arabidopsis thaliana. We specifically focus on the (i) history of indehiscence in domestication across legumes, (ii) structures and the mechanisms involved in shattering, (iii) the molecular pathways underlying this important trait, (iv) an overview of the extent of crop losses due to shattering, and the effects of environmental factors on shattering, and, (v) efforts to reduce shattering in crops. While our focus is mainly pulse crops, we also included comparisons to crucifers and cereals because there is extensive research on shattering in these taxa.

Significance of Genetic, Environmental, and Pre- and Postharvest Factors Affecting Carotenoid Contents in Crops: A Review

Carotenoids are a diverse group of tetraterpenoid pigments that play indispensable roles in plants and animals. The biosynthesis of carotenoids in plants is strictly regulated at the transcriptional and post-transcriptional levels in accordance with inherited genetic signals and developmental requirements and in response to external environmental stimulants. The alteration in the biosynthesis of carotenoids under the influence of external environmental stimulants, such as high light, drought, salinity, and chilling stresses, has been shown to significantly influence the nutritional value of crop plants. In addition to these stimulants, several pre- and postharvesting cultivation practices significantly influence carotenoid compositions and contents. Thus, this review discusses how various environmental stimulants and pre- and postharvesting factors can be positively modulated for the enhanced biosynthesis and accumulation of carotenoids in the edible parts of crop plants, such as the leaves, roots, tubers, flowers, fruit, and seeds. In addition, future research directions in this context are identified.

Reproductive traits and evolutionary divergence between Mediterranean crops and their wild relatives

Changes in reproductive traits associated with domestication critically determine the evolutionary divergence between crops and their wild relatives, as well as the potential of crop plants to become feral. In this review, we examine the genetic mechanisms of plant domestication and the different types of selection involved, and describe the particularities of domestication of Mediterranean field crops with regard to their reproductive traits, showing illustrative examples. We also explore gene flow patterns between Mediterranean field crops and their wild relatives, along with their ecological, evolutionary and economic implications. Domestication entails multiple selective processes, including direct selection, environmental adaptation and developmental constraints. In contrast to clonal propagation in perennials, sexual reproduction and seed propagation in annuals and biennials have led to a distinct pathway of evolution of reproductive traits. Thus, the initial domestication and further breeding of Mediterranean field crops has brought about changes in reproductive traits, such as higher mean values and variance of seed and fruit sizes, reduced fruit and seed toxicity, non-shattering seeds and loss of seed dormancy. Evolution under domestication is not a linear process, and bi-directional gene flow between wild and crop taxa is a frequent phenomenon. Thus, hybridisation and introgression have played a very important role in determining the genetics of current cultivars. In turn, gene flow from crops to wild relatives can lead to introgression of crop genes into wild populations and potentially alter the characteristics of natural communities. In conclusion, plant evolution under domestication has not only changed the reproductive biology of cultivated taxa, its effects are multifaceted and have implications beyond agriculture.

Seed Carotenoid and Tocochromanol Composition of Wild Fabaceae Species Is Shaped by Phylogeny and Ecological Factors

Carotenoids distribution and function in seeds have been very scarcely studied, notwithstanding their pivotal roles in plants that include photosynthesis and phytohormone synthesis, pigmentation, membrane stabilization and antioxidant activity. Their relationship with tocochromanols, whose critical role in maintaining seed viability has already been evidenced, and with chlorophylls, whose retention in mature seed is thought to have negative effects on storability, remain also unexplored. Here, we aimed at elucidating seed carotenoids relationship with tocochromanols and chlorophylls with regard to phylogenetic and ecological traits and at understanding their changes during germination. The composition and distribution of carotenoids were investigated in seeds of a wide range of wild species across the Fabaceae (the second-most economically important family after the Poaceae). Photosynthetic pigments and tocochromanols were analyzed by HPLC in mature dry seeds of 50 species representative of 5 subfamilies within the Fabaceae (including taxa that represent all continents, biomes and life forms within the family) and at key timepoints during seedling establishment in three species representative of distinct clades. Total-carotenoids content positively correlated with tocopherols in the basal subfamilies Detarioideae, Cercidoideae, and Dialioideae, and with chlorophylls in the Papilionoideae. Papilionoideae lacked tocotrienols and had the highest total-carotenoids, chlorophyll and γ-tocopherol contents. Interestingly, lutein epoxide was present in 72% of the species including several herbs from different subfamilies. Overall, species original from temperate biomes presented higher carotenoids and lower tocochromanols levels than those from tropical biomes. Also shrub species showed higher carotenoids content than herbs and trees. During germination, total content of photosynthetic pigments increased in parallel to changes in relative abundance of carotenoids: zeaxanthin and anteraxanthin decreased and β-carotene augmented. Notably, the highest contents of nutritionally valuable carotenoids were found in Papilionoideae subfamily to which all pulses of socio-economic importance belong. The major differences in carotenoids and tocochromanols composition across the Fabaceae are apparently related to phylogeny in conjunction with ecological traits such as biome and growth form.

Convergent and divergent genetic changes in the genome of Chinese and European pigs

Since 10,000 BC, continuous human selection has led to intense genetic and phenotypic changes in pig (Sus scrofa) domestication. Through whole genome analysis of 257 individuals, we demonstrated artificial unidirectional and bidirectional selection as the primary force to shape the convergent and divergent changes between Chinese domestic pigs (CHD) and European domestic pigs (EUD). We identified 31 genes in unidirectional selection regions that might be related to fundamental domestication requirements in pigs. And these genes belong predominantly to categories related to the nervous system, muscle development, and especially to metabolic diseases. In addition, 35 genes, representing different breeding preference, were found under bidirectional selection for the distinct leanness and reproduction traits between CHD and EUD. The convergent genetic changes, contributing physical and morphological adaption, represent the common concerns on pig domestication. And the divergent genetic changes reflect distinct breeding goals between Chinese and European pigs. Using ITPR3, AHR and NMU as examples, we explored and validated how the genetic variations contribute to the phenotype changes.

Legume bioactive compounds: influence of rhizobial inoculation

Legumes consumption has been recognized as beneficial for human health, due to their content in proteins, fiber, minerals and vitamins, and their cultivation as beneficial for sustainable agriculture due to their ability to fix atmospheric nitrogen in symbiosis with soil bacteria known as rhizobia. The inoculation with these baceria induces metabolic changes in the plant, from which the more studied to date are the increases in the nitrogen and protein contents, and has been exploited in agriculture to improve the crop yield of several legumes. Nevertheless, legumes also contain several bioactive compounds such as polysaccharides, bioactive peptides, isoflavones and other phenolic compounds, carotenoids, tocopherols and fatty acids, which makes them functional foods included into the nutraceutical products. Therefore, the study of the effect of the rhizobial inoculation in the legume bioactive compounds content is gaining interest in the last decade. Several works reported that the inoculation of different genera and species of rhizobia in several grain legumes, such as soybean, cowpea, chickpea, faba bean or peanut, produced increases in the antioxidant potential and in the content of some bioactive compounds, such as phenolics, flavonoids, organic acids, proteins and fatty acids. Therefore, the rhizobial inoculation is a good tool to enhance the yield and quality of legumes and further studies on this field will allow us to have plant probiotic bacteria that promote the plant growth of legumes improving their functionality.

Evolutionary Metabolomics Reveals Domestication-Associated Changes in Tetraploid Wheat Kernels

Domestication and breeding have influenced the genetic structure of plant populations due to selection for adaptation from natural habitats to agro-ecosystems. Here, we investigate the effects of selection on the contents of 51 primary kernel metabolites and their relationships in three Triticum turgidum L. subspecies (i.e., wild emmer, emmer, durum wheat) that represent the major steps of tetraploid wheat domestication. We present a methodological pipeline to identify the signature of selection for molecular phenotypic traits (e.g., metabolites and transcripts). Following the approach, we show that a reduction in unsaturated fatty acids was associated with selection during domestication of emmer (primary domestication). We also show that changes in the amino acid content due to selection mark the domestication of durum wheat (secondary domestication). These effects were found to be partially independent of the associations that unsaturated fatty acids and amino acids have with other domestication-related kernel traits. Changes in contents of metabolites were also highlighted by alterations in the metabolic correlation networks, indicating wide metabolic restructuring due to domestication. Finally, evidence is provided that wild and exotic germplasm can have a relevant role for improvement of wheat quality and nutritional traits.

The mechanism of high contents of oil and oleic acid revealed by transcriptomic and lipidomic analysis during embryogenesis in Carya cathayensis Sarg

Background

Hickory (Carya cathayensis Sarg.) accumulates more than 70 % oil and 90 % unsaturated fatty acids with considerably high oleic acid in its mature embryo. The concurrent global trancriptomic and lipidomic analyses provided a framework for better understanding of glycerolipid biosynthesis and metabolism in the hickory nut.

Results

The synthetical regulation of numerous leading lipid-related genes harmonized with the oil accumulation and fatty acid conversion in embryo development. The high level of ACCase correlated positively with fatty acids de novo synthesis, and the synergy of DGAT2 and PDAT promoted the TAG assembly, and oleosins, caleosins and steroleosins were transcribed considerably high for timely energy reserve in oil body. Glycolysis possibly provided sufficient precursors and energy for lipid synthesis. The perfect harmonization of the high level of SAD with low level of FAD2 facilitated the oleic acid accumulation. And the ratio of FATA/FATB or SAD/FATB was proposed for determining the saturated degree of oil. The gene multi-copy event was generated probably for accommodating various survival environments. A thermotolerant defense system including TAG hydrolysis determinants, heat shock proteins, and high ratio of MUFA to PUFA constrained the lipid degradation and provided a guarantee for high lipid content. A batch of potential genes recruited from the co-expression network helps us to understand the lipid synthesis and the response to high temperature better.

Conclusions

The high transcriptional levels of key genes in lipid synthesis promoted the oil accumulation, and the harmonious expression of key ones for unsaturated fatty acids led oleic acid to high levels.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2434-7) contains supplementary material, which is available to authorized users.