Special Issue "Healthy Food Development through Genetic Changes during Crop Domestication"

A special issue of Agronomy (ISSN 2073-4395).

Deadline for manuscript submissions: closed (30 June 2018)

Special Issue Editors

Guest Editor
Assoc. Prof. Dr. Petr SMYKAL

Department of Botany, Faculty of Sciences, Palacky University in Olomouc, Slechtitelu 27783 71 OLOMOUC, Czech Republic
Website | E-Mail
Phone: +420 583 382 127
Interests: genetic diversity; plant domestication; legumes phylogeny; seed dormancy; pod dehiscence; pea diversity and domestication
Co-Guest Editor
Dr. Eric von Wettberg

Plant & Soil Science, College of Agriculture and Life Sciences, Jeffords Hall 63 Carrigan Drive, Burlington, VT 05405-0082, USA
Website | E-Mail
Phone: +(802) 656-2630
Interests: Genetics, Genomics, Domestication, Crop Breeding, Evolution, Ecology

Special Issue Information

Dear Colleagues,

We invite you to contribute to the Special Issue, "Healthy Food Development through Genetic Changes during Crop Domestication".

The origin of agriculture was one of the key points in human history, and a central part of this was the evolution of new plant forms, domesticated crops. The process of crop domestication began 10,000 years ago in the transition of early humans, from hunter/gatherers to pastoralists/farmers. The transformation of wild plants into crop plants can be viewed as an accelerated evolution, the result of human and natural selection. These domestication-triggered changes represent adaptations to cultivation and human harvesting, accompanied by genetic changes. Common sets of traits have been recorded for unrelated crops, named domestication syndrome. These include loss of germination inhibition and increases in seed sizes, linked to successful early growth of planted seeds. In most crops where the seed or fruit is consumed, humans have domesticated wild plants in two important ways: Selected for seeds that are not dispersed widely as they are in wild plants, and seeds that will germinate rapidly when sown in cultivated fields, making a species dependent on farmers, and, in turn, allows farmer to harvest. At the same time, this process introduced the diversity bottleneck which affects the agronomic potential of today´s crops.

This Special Issue aims to collate current knowledge on crop domestication, including (but not limited to) the following issues: Genetic and phenotypic aspects of domestication, geography and timeframe, impact on crop productivity today and scenarios for future.

Analysis of past domestication events is also very informative today in light of climate change and modern crop breeding required to ensure global food security.

We welcome the following article types: Original research, reviews, and opinions.

Assoc. Prof. Dr. Petr Symkal
Dr. Eric von Wettberg
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • agriculture
  • domestication
  • crop improvement
  • farming
  • food security
  • genetic diversity
  • neolitic revolution
  • plant breeding

Published Papers (7 papers)

View options order results:
result details:
Displaying articles 1-7
Export citation of selected articles as:

Editorial

Jump to: Research, Review, Other

Open AccessEditorial The Impact of Genetic Changes during Crop Domestication on Healthy Food Development
Received: 28 February 2018 / Revised: 4 March 2018 / Accepted: 5 March 2018 / Published: 7 March 2018
Cited by 1 | PDF Full-text (157 KB) | HTML Full-text | XML Full-text

Research

Jump to: Editorial, Review, Other

Open AccessArticle Morphological Assessment of Cultivated and Wild Amaranth Species Diversity
Agronomy 2018, 8(11), 272; https://doi.org/10.3390/agronomy8110272
Received: 7 October 2018 / Revised: 31 October 2018 / Accepted: 9 November 2018 / Published: 21 November 2018
PDF Full-text (573 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Amaranthus L. is genus of C4 dicotyledonous herbaceous plants comprising approximately 70 species, with three subgenera, which contains both cultivated and wild types, where cultivated ones are used for food grains, leafy vegetables, potential forages and ornamentals. Grain amaranth are pseudocereals from three
[...] Read more.
Amaranthus L. is genus of C4 dicotyledonous herbaceous plants comprising approximately 70 species, with three subgenera, which contains both cultivated and wild types, where cultivated ones are used for food grains, leafy vegetables, potential forages and ornamentals. Grain amaranth are pseudocereals from three species domesticated in North and South America and are notable for containing high amount of protein and minerals and balanced amino acid in their small seeds. Genetic diversity analysis of amaranths is important for development of core set of germplasm with widely diverse population and effective utilization of plant genetic resources. In this study, we evaluated a germplasm collection of 260 amaranth accessions from United State Department of Agriculture (USDA) and 33 accessions from Seed Savers’ Exchange (SSE). We evaluated morphological traits like blade pigmentation, blade shape, petiole pigmentation, branching index, flower color, stem color, inflorescence density, inflorescence shape, terminal inflorescence attitude, plant height and yield characteristics across all 293 accessions. We compared clustering within the USDA and SSE collection and across both collections. Data analysis of morphological data showed significant difference of petiole pigmentation, stem color, blade pigmentation, blade shape and flower color across different clusters of accessions of USDA unlike among different clusters of SSE where we found significant difference of only blade pigmentation, blade shape and flower color. The relationship depicted by neighbor-joining dendogram using the morphological markers was consistent with some but not all of the differences observed between species. Some divisions were found between cultivated and weedy amaranths that was substantiated by morphological characteristics but no separation of South and Central American species was observed. Substantial phenotypic plasticity limits the use of morphological analysis for phylogenetic analysis but does show that important morphological traits such as inflorescence type and plant architecture can cross species boundaries. Similarly, color variants for leaves, flowers and seeds are not exclusive to one cluster in our study nor to one species and can be used widely for breeding any of the cultigens, but not to species identification. Our findings will help in germplasm conservation of grain amaranths and facilitate in this crop’s improvement. It will also help on developing effective breeding programs involving different plant characteristics and morphological traits of Amaranths. Full article
Figures

Figure 1

Open AccessArticle Origin and Distribution of the VRN-A1 Exon 4 and Exon 7 Haplotypes in Domesticated Wheat Species
Agronomy 2018, 8(8), 156; https://doi.org/10.3390/agronomy8080156
Received: 5 July 2018 / Revised: 8 August 2018 / Accepted: 17 August 2018 / Published: 20 August 2018
PDF Full-text (2495 KB) | HTML Full-text | XML Full-text
Abstract
The high adaptive potential of modern wheat to a wide range of environmental conditions is determined by genetic changes during domestication. Genetic diversity in VRN1 genes is a key contributor to this adaptability. Previously, the association between the transitions C->T within the fourth
[...] Read more.
The high adaptive potential of modern wheat to a wide range of environmental conditions is determined by genetic changes during domestication. Genetic diversity in VRN1 genes is a key contributor to this adaptability. Previously, the association between the transitions C->T within the fourth and seventh exons of VRN-A1, the distinguishing pair haplotypes Ex4C/Ex4T and Ex7C/Ex7T, and the modulation of such agronomically valuable traits as the vernalization requirement duration, frost tolerance and flowering time of wheat have been shown. However, this polymorphism was analyzed in only a few cultivars of Triticum aestivum L., and not in other wheat species. In the present study, VRN-A1 exon 4 and exon 7 were investigated in six tetraploid and five hexaploid wheat species carrying different VRN-A1 alleles. An allele-specific polymerase chain reaction (PCR) assay was optimized to identify the VRN-A1 exon 7 haplotypes. It was found that polymorphism of the VRN-A1 exon 7 originated in wild tetraploid wheat of Triticum dicoccoides Körn, while the mutant exon 4 of this gene originated later in domesticated hexaploid wheat of T. aestivum. Both these polymorphisms are found in all hexaploid wheat species. Analysis of the VRN-A1 exon 4 and exon 7 haplotype combinations found that intact exon 7 and mutant exon 4 are associated with analogous types of exon 4 and 7, respectively. With the exclusion of the Vrn-A1c (IL369) and Vrn-A1j alleles, identified only in hexaploid wheat, all dominant VRN-A1 alleles carry intact exons 4 and 7 (Ex4C/7C haplotype). The Ex4C/4T/7T haplotype was detected in numerous accessions of hexaploid wheat and is associated with the presence of multiple copies of VRN-A1. Overall, modern domesticated hexaploid wheat T. aestivum includes most possible combinations of the VRN-A1 exon 4 and exon 7 haplotypes among polyploid wheat, which are present in different proportions. This contributes to the high adaptive potential to a broad range of environmental conditions and facilitates the widespread distribution of this species throughout the world. Full article
Figures

Figure 1

Open AccessArticle Retrotransposon-Based Genetic Diversity Assessment in Wild Emmer Wheat (Triticum turgidum ssp. dicoccoides)
Agronomy 2018, 8(7), 107; https://doi.org/10.3390/agronomy8070107
Received: 28 March 2018 / Revised: 19 June 2018 / Accepted: 26 June 2018 / Published: 29 June 2018
Cited by 1 | PDF Full-text (3521 KB) | HTML Full-text | XML Full-text
Abstract
Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the wild ancestor of all cultivated tetraploid and hexaploid wheats and harbors a large amount of genetic diversity. This diversity is expected to display eco-geographical patterns of variation, conflating gene flow, and local
[...] Read more.
Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the wild ancestor of all cultivated tetraploid and hexaploid wheats and harbors a large amount of genetic diversity. This diversity is expected to display eco-geographical patterns of variation, conflating gene flow, and local adaptation. As self-replicating entities comprising the bulk of genomic DNA in wheat, retrotransposons are expected to create predominantly neutral variation via their propagation. Here, we have examined the genetic diversity of 1 Turkish and 14 Israeli populations of wild emmer wheat, based on the retrotransposon marker methods IRAP and REMAP. The level of genetic diversity we detected was in agreement with previous studies that were performed with a variety of marker systems assaying genes and other genomic components. The genetic distances failed to correlate with the geographical distances, suggesting local selection on geographically widespread haplotypes (‘weak selection’). However, the proportion of polymorphic loci correlated with the population latitude, which may reflect the temperature and water availability cline. Genetic diversity correlated with longitude, the east being more montane. Principal component analyses on the marker data separated most of the populations. Full article
Figures

Figure 1

Review

Jump to: Editorial, Research, Other

Open AccessReview Pod Shattering: A Homologous Series of Variation Underlying Domestication and an Avenue for Crop Improvement
Agronomy 2018, 8(8), 137; https://doi.org/10.3390/agronomy8080137
Received: 10 June 2018 / Revised: 20 July 2018 / Accepted: 1 August 2018 / Published: 3 August 2018
PDF Full-text (1551 KB) | HTML Full-text | XML Full-text
Abstract
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
[...] Read more.
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. Full article
Figures

Figure 1

Open AccessReview The Impact of Genetic Changes during Crop Domestication
Agronomy 2018, 8(7), 119; https://doi.org/10.3390/agronomy8070119
Received: 11 June 2018 / Revised: 11 July 2018 / Accepted: 12 July 2018 / Published: 14 July 2018
Cited by 1 | PDF Full-text (10109 KB) | HTML Full-text | XML Full-text
Abstract
Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were
[...] Read more.
Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world. Full article
Figures

Figure 1

Other

Jump to: Editorial, Research, Review

Open AccessProject Report The Nutritional Content of Common Bean (Phaseolus vulgaris L.) Landraces in Comparison to Modern Varieties
Agronomy 2018, 8(9), 166; https://doi.org/10.3390/agronomy8090166
Received: 9 July 2018 / Revised: 1 August 2018 / Accepted: 22 August 2018 / Published: 27 August 2018
PDF Full-text (1186 KB) | HTML Full-text | XML Full-text
Abstract
In terms of safe food and a healthy food supply, beans (Phaseolus spp.) are a significant source of protein, carbohydrates, vitamins and minerals especially for poor populations throughout the world. They are also rich in unsaturated fatty acids, such as linoleic and
[...] Read more.
In terms of safe food and a healthy food supply, beans (Phaseolus spp.) are a significant source of protein, carbohydrates, vitamins and minerals especially for poor populations throughout the world. They are also rich in unsaturated fatty acids, such as linoleic and oleic acids. From the past to the present, a large number of breeding studies to increase bean yield, especially the common bean (P. vulgaris L.), have resulted in the registration of many modern varieties, although quality and flavor traits in the modern varieties have been mostly ignored. The aim of the present study, therefore, was to compare protein, fat, fatty acid, and some mineral content such as selenium (Se), zinc (Zn) and iron (Fe) of landraces to modern varieties. The landrace LR05 had higher mineral contents, particularly Se and Zn, and protein than the modern varieties. The landrace LR11 had the highest linoleic acid. The landraces are grown by farmers in small holdings for dual uses, such as both dry seed and snap bean production, and are commercialized with a higher cash price. The landraces of the common bean are, not only treasures that need to be guarded for the future, but also important genetic resources that can be used in bean breeding programs. The results of this study suggest that landraces are essential sources of important nutritional components for food security and a healthy food supply. Full article
Figures

Figure 1

Back to Top