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Agronomy
Special Issues
Crop Domestication and Evolution
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Crop Domestication and Evolution

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (20 August 2020) | Viewed by 35442

Special Issue Editors

Prof. David Marks

E-Mail Website
Guest Editor
University of Minnesota, St Paul, MN 55108 USA.
Dr. Ratan Chopra

E-Mail Website
Guest Editor
University of Minnesota, St Paul, MN 55108 USA.
Dr. Katherine Frels

E-Mail Website
Guest Editor
University of Minnesota, St Paul, MN 55108 USA.

Special Issue Information

Dear Colleagues,

Sustainable intensification of existing agricultural land is required due to the growing world population and threats to the health of landscapes and ecosystems. While there are many proposed approaches for intensifying agriculture, one new option based on next-generation genomic and phenotypic technologies is the domestication of new crop species that can be used in the temporal intensification of traditional cropping systems or grown in marginal or contaminated soils. The domestication of new crops requires an understanding of the genetic structure of the species and the agronomic practices required to implement these new species into cropping systems.

This Special Issue will focus on highlighting the knowledge required to domesticate a new crop species. Topics can include genetic diversity, agronomic practices, genomics, and breeding. We welcome reviews or perspectives related to the essential traits for domestication and the approaches required to domesticate a new crop.

Prof. David Marks
Dr. Ratan Chopra
Dr. Katherine Frels
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 submissions that pass pre-check are 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 2600 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

  • genetic diversity
  • agronomy
  • breeding, genomics
  • crop domestication
  • agricultural intensification

Published Papers (7 papers)

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Research

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17 pages, 1274 KiB  
Article
Domestication and Spread of Broomcorn Millet (Panicum miliaceum L.) Revealed by Phylogeography of Cultivated and Weedy Populations
by Yue Xu, Minxuan Liu, Chunxiang Li, Fengjie Sun, Ping Lu, Fanshuang Meng, Xinyu Zhao, Mingyue He, Fuzhou Wang, Xingyu Zhu, Xin Zhao and Hui Zhou
Agronomy 2019, 9(12), 835; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy9120835 - 3 Dec 2019
Cited by 10 | Viewed by 3771
Abstract
Cultivated broomcorn millet (Panicum miliaceum L.), one of the most ancient crops, has long been an important staple food in the semiarid regions of Eurasia. Weedy broomcorn millet (Panicum ruderale (Kitag.) Chang comb. Nov.), the companion weed of cultivated broomcorn millet, [...] Read more.
Cultivated broomcorn millet (Panicum miliaceum L.), one of the most ancient crops, has long been an important staple food in the semiarid regions of Eurasia. Weedy broomcorn millet (Panicum ruderale (Kitag.) Chang comb. Nov.), the companion weed of cultivated broomcorn millet, is also widely distributed throughout Eurasia and can produce fertile offspring by crossing with cultivated broomcorn millet. The evolutionary and genetic relationships between weedy and cultivated broomcorn millets, and the explicit domestication areas and detailed spread routes of this cereal are still unclear. The genetic diversity and population structure of 200 accessions of weedy and cultivated broomcorn millets were explored to elucidate the genetic relationship between weedy and cultivated broomcorn millets, and to trace the explicit domestication areas and detailed spread routes of broomcorn millets by using 23 simple sequence repeats (SSR) markers. Our results show that the weedy populations in China may harbor the ancestral variations that gave rise to the domesticated broomcorn millet. The population structure pattern observed in the wild and domesticated broomcorn millets is consistent with the hypothesis that there may be at least two independent domestication areas in China for the cultivated broomcorn millet, the Loess Plateau and the Northeast China, with both following the westward spread routes. These two westward spread routes of cultivated broomcorn millet coincide exactly with the prehistoric Oasis Route and Steppe Route, respectively. Full article
(This article belongs to the Special Issue Crop Domestication and Evolution)
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13 pages, 2891 KiB  
Article
Domestication in Real Time: The Curious Case of a Trigenomic Sunflower Population
by Jill M. Ekar, Kevin J. Betts, Adam C. Herman, Robert M. Stupar, Donald L. Wyse, Yaniv Brandvain and Michael B. Kantar
Agronomy 2019, 9(11), 704; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy9110704 - 31 Oct 2019
Cited by 2 | Viewed by 3238
Abstract
This study chronicles the ongoing process to domesticate an interspecific trigenomic tetraploid hybrid sunflower derived from a series of interspecific crosses between Helianthus annuus and Helianthus tuberosus. The goal of this process is to develop a perennial oilseed crop that can produce [...] Read more.
This study chronicles the ongoing process to domesticate an interspecific trigenomic tetraploid hybrid sunflower derived from a series of interspecific crosses between Helianthus annuus and Helianthus tuberosus. The goal of this process is to develop a perennial oilseed crop that can produce both high value vegetable oil and continuous ground-cover. Selection has focused on developing an ideotype with the domesticated morphology of H. annuus and the below-ground perennial features of H. tuberosus. The overarching challenge in the process of breeding and domesticating this interspecific perennial sunflower is overcoming obstacles associated with interploid meiosis in order to resolve a chromosomally stable hybrid population. As selection progresses through generations of intermating, there are improvements toward the desired ideotype, but selection efficiency is slowed by apparent antagonisms between annual- and perennial morphological targets and irregular meiosis which is especially problematic in a trigenomic tetraploid. This shows that keys toward perennial crop development through interspecific hybridization will be to capitalize on the abundant phenotypic variation within our population, achieve meiotic stability in order to maximize selection efficiency, and to break genetic correlations between annual and perennial traits. Full article
(This article belongs to the Special Issue Crop Domestication and Evolution)
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9 pages, 876 KiB  
Communication
Genetic Variation and Trait Correlations for Fruit Weight, Firmness and Color Parameters in Wild Accessions of Fragaria chiloensis
by Freddy Mora, Paz E. Zúñiga and Carlos R. Figueroa
Agronomy 2019, 9(9), 506; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy9090506 - 2 Sep 2019
Cited by 9 | Viewed by 8934
Abstract
Fragaria chiloensis is an herbaceous perennial undomesticated species with a high potential for sustainable fruit production in areas where drought and salinity represent a constraint on crop growth and productivity. The present study aimed to examine the genetic variability of fruit weight, firmness [...] Read more.
Fragaria chiloensis is an herbaceous perennial undomesticated species with a high potential for sustainable fruit production in areas where drought and salinity represent a constraint on crop growth and productivity. The present study aimed to examine the genetic variability of fruit weight, firmness and color parameters (L*, a*, b*, Hue angle and Chroma) in wild-collected accessions from south-central Chile. A Bayesian analysis of genetic parameters showed that the traits under study were found to be moderately to highly heritable with estimates from the marginal posterior distributions ranging between 0.26 (firmness) and 0.67 (L*). Interestingly, Hue and Chroma had relatively high values of broad-sense heritability, with the Bayesian credible set: H 2 = 0.53–0.76 and H 2 = 0.42–0.66, respectively. A Bayesian bi-trait analysis showed a positive genetic correlation ( r ^ g = 0.65, probability of the posterior samples <0.05) between fruit weight and Hue, which agreed with the existence of two pleiotropic loci [from simple sequence repeats (SSR) markers FvH4045 and CFACT084 on linkage groups FG3A and FG2A/2B/2C] with probabilities of the posterior estimates of 0.022 and <0.001, respectively. According to the Bayesian credible region, 5 (of 12) correlation estimates were significantly different from zero. Hue and Chroma showed a high and negative genetic correlation ( r ^ g = −0.762), but no significant pleotropic locus. The results are promising and suggest that the genetic variation found among wild populations of F. chiloensis supports the idea of domesticating this crop for sustainable fruit production systems. Full article
(This article belongs to the Special Issue Crop Domestication and Evolution)
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18 pages, 2355 KiB  
Article
Characterization of Genetic Resistance to Fusarium Head Blight and Bacterial Leaf Streak in Intermediate Wheatgrass (Thinopyrum intermedium)
by Prabin Bajgain, Xiaofei Zhang, M. Kathryn Turner, Rebecca D. Curland, Brett Heim, Ruth Dill-Macky, Carol A. Ishimaru and James A. Anderson
Agronomy 2019, 9(8), 429; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy9080429 - 3 Aug 2019
Cited by 15 | Viewed by 4141
Abstract
Intermediate wheatgrass (IWG, Thinopyrum intermedium, (Host) Barkworth & D.R. Dewey subsp. intermedium, 2n = 6x = 42) is a novel perennial crop currently undergoing domestication efforts. It offers remarkable ecosystem services and yields higher relative to other perennial grain [...] Read more.
Intermediate wheatgrass (IWG, Thinopyrum intermedium, (Host) Barkworth & D.R. Dewey subsp. intermedium, 2n = 6x = 42) is a novel perennial crop currently undergoing domestication efforts. It offers remarkable ecosystem services and yields higher relative to other perennial grain crops. While IWG is mostly resistant to Fusarium head blight (FHB), identifying genomic regions associated with resistance will help protect the crop from potential disease epidemics. An IWG biparental population of 108 individuals was developed by crossing parents differing in their response to FHB and bacterial leaf streak (BLS). The population was screened for disease reaction over three years using isolates collected from IWG plants in St. Paul, Minnesota, USA. Linkage maps representing the 21 IWG chromosomes were constructed from 4622 Single Nucleotide Polymorphism (SNP) markers, with one SNP at every 0.74 cM. Interval mapping identified 15 quantitative trait loci (QTL) associated with FHB resistance and 11 with BLS resistance. Models with two or three QTL combinations reduced FHB disease severity by up to 15%, and BLS by up to 17%. When markers associated with FHB resistance were used as cofactors in genomic selection models, trait predictive ability improved by 24–125%. These genomic regions and genetic markers associated with FHB and BLS resistance can also be used to safeguard annual cereal grains through gene introgression and selective breeding. Full article
(This article belongs to the Special Issue Crop Domestication and Evolution)
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11 pages, 2140 KiB  
Article
Structure and Genetic Diversity of Nine Important Landraces of Capsicum Species Cultivated in the Yucatan Peninsula, Mexico
by Lucero del C. López Castilla, René Garruña Hernández, Crescencio de la Cruz Castillo Aguilar, Aida Martínez-Hernández, Matilde Margarita Ortiz-García and Rubén H. Andueza-Noh
Agronomy 2019, 9(7), 376; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy9070376 - 14 Jul 2019
Cited by 16 | Viewed by 4972
Abstract
Mexico has a wealth of Capsicum species, which has led to the development of a large number of chili pepper landraces. A great wealth of Capsicum germplasm can be found in southern Mexico in the Yucatan Peninsula, an important area of diversification of [...] Read more.
Mexico has a wealth of Capsicum species, which has led to the development of a large number of chili pepper landraces. A great wealth of Capsicum germplasm can be found in southern Mexico in the Yucatan Peninsula, an important area of diversification of Capsicum annuum. Specifically, in the western Yucatan Peninsula, three of the five domesticated species of Capsicum (C. annuum, C. chinense and C. frutescens) have been reported. However, information on their genetic diversity, conservation status and potential use is lacking. To generate useful information toward the sustainable use, management and conservation of these species, we evaluated the structure, diversity and genetic relationships of nine accessions of Capsicum spp., of major importance cultivated in the western Yucatan Peninsula using 42 ISSR loci. The results indicated that these accessions consisted of three genetic groups that were defined by the respective species of each accession. The level of genetic diversity was moderate and distributed mainly among accessions. The ISSR markers detected a high level of polymorphism and allowed the genetic differentiation of the C. annuum complex. The results indicated that the accessions collected in the western Yucatan Peninsula constitute a valuable genetic resource that can be used in genetic improvement and conservation programs. Full article
(This article belongs to the Special Issue Crop Domestication and Evolution)
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11 pages, 2966 KiB  
Article
Genetic Diversity of Field Pennycress (Thlaspi arvense) Reveals Untapped Variability and Paths Toward Selection for Domestication
by Katherine Frels, Ratan Chopra, Kevin M. Dorn, Donald L. Wyse, M. David Marks and James A. Anderson
Agronomy 2019, 9(6), 302; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy9060302 - 11 Jun 2019
Cited by 18 | Viewed by 5937
Abstract
Evaluation of genetic diversity within wild populations is an essential process for improvement and domestication of new crop species. This process involves evaluation of population structure and individual accessions based on genetic markers, growth habits, and geographic collection area. In this study, accessions [...] Read more.
Evaluation of genetic diversity within wild populations is an essential process for improvement and domestication of new crop species. This process involves evaluation of population structure and individual accessions based on genetic markers, growth habits, and geographic collection area. In this study, accessions of field pennycress were analyzed to identify population structure and variation in germplasm available for breeding. A total of 9157 genome-wide single nucleotide polymorphisms (SNPs) were identified among the 121 accessions analyzed, and linkage disequilibrium based pruning resulted in 3497 SNPs. Bayesian cluster analysis was implemented in STRUCTURE v2.3.4 to identify four population groups. These groups were confirmed based on principal components analysis and geographic origins. Pairwise diversity among accessions was evaluated and revealed considerable genetic variation. Notably, a subset of accessions from Armenia with exceptional genetic variation was identified. This survey is the first to report significant genetic diversity among pennycress accessions and explain some of the phenotypic differences previously observed in the germplasm. Understanding variation in pennycress accessions will be a crucial step for selection, breeding, and domestication of a new cash cover crop for cold climates. Full article
(This article belongs to the Special Issue Crop Domestication and Evolution)
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Review

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16 pages, 2566 KiB  
Review
Domestication of Perennial Flax Using an Ideotype Approach for Oilseed, Cut Flower, and Garden Performance
by David G. Tork, Neil O. Anderson, Donald L. Wyse and Kevin J. Betts
Agronomy 2019, 9(11), 707; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy9110707 - 1 Nov 2019
Cited by 19 | Viewed by 3898
Abstract
Flaxseed (Linum usitatissimum) has recently grown in popularity as a health food due to its high levels of omega-3 fatty acids. Many undomesticated Linum species possess a similar oil profile, in addition to perenniality, and could, therefore, provide similar products in [...] Read more.
Flaxseed (Linum usitatissimum) has recently grown in popularity as a health food due to its high levels of omega-3 fatty acids. Many undomesticated Linum species possess a similar oil profile, in addition to perenniality, and could, therefore, provide similar products in addition to ecosystem services such as soil retention, improvements in water quality, and pollinator services. Many Linum species also possess ornamental qualities, e.g., blue flowers, which could provide added value as a new cut flower crop or garden herbaceous perennial. A perennial flax breeding program will be initiated by screening of Linum accessions for key agronomic and horticultural traits. Herein, we outline an ideotype approach which will enable identification of top herbaceous perennial candidates for domestication based on qualities relevant to oilseed, cut flower, and garden herbaceous perennial crop uses. In this review, we summarize the concept of ideotype breeding as it relates to perennial crop domestication and outline considerations for ideotype design. The tools outlined herein should prove useful to other breeders and especially for undomesticated crops. Whether the ideotype concept is applied as a framework for selection or simply as a means of generating hypotheses, applying this approach can provide structure to breeding programs with complex objectives. Full article
(This article belongs to the Special Issue Crop Domestication and Evolution)
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