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Evolutionary Genetics of Plant Crop-Wild Complexes: From Fundamental to Applied...
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Evolutionary Genetics of Plant Crop-Wild Complexes: From Fundamental to Applied Research

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 September 2021) | Viewed by 27727

Special Issue Editors

Dr. Andrés J. Cortés

E-Mail Website
Guest Editor
1. Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro—Las Palmas, Rionegro 054048, Colombia
2. Facultad de Ciencias Agrarias, Departamento de Ciencias Forestales, Universidad Nacional de Colombia—Sede Medellín, Medellín 050034, Colombia
Interests: plant genetics; crop breeding; hybridization; poliploidy; fruit trees
Special Issues, Collections and Topics in MDPI journals
Dr. Amandine Cornille

E-Mail Website
Guest Editor
Centre national de la recherche scientifique, Gif-sur-Yvette, France
Interests: adaptation; introgression; gene flow; conservation; agroforestery; breeding; ecology; domestication; weed; coevolution; pest evolution; endosymbiotic bacteria; citizen science
Dr. Roxana Yockteng

E-Mail Website
Guest Editor
AGROSAVIA (Corporación Colombiana de Investigación Agropecuaria), Tibaitatá 250047, Colombia
Interests: genetic diversity; plant genetics; genomics and transcriptomics; plant–pathogen interaction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The goal of this Special Issue is to summarize basic and applied approaches on the evolutionary genetics of plant crop–wild complexes in order to identify current paradigms, methods, and caveats that are widely being used or currently being developed to study crop–wild complexes. The content of the paper should focus on the hottest topics addressed when investigating genetics and adaptation of crops, their wild relatives, and their abiotic and biotic interactions. We encourage works addressing any of the following topics:

  • Evolutionary genetics of crop wild relatives;
  • Genetic and genomic consequences of domestication;
  • Role of crop–wild gene flow during domestication and adaptation;
  • Evolutionary genetics of undomesticated plants and trees with bio-economic potential;
  • Wild relatives in the improvement of crops and trees.

Dr. Andrés J. Cortés
Dr. Amandine Cornille
Dr. Roxana Yockteng
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. Genes 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

  • crop wild relatives
  • domestication
  • introgression
  • backcrossing
  • hybridization
  • gene flow
  • adaptation
  • conservation
  • genetic diversity
  • breeding

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Published Papers (6 papers)

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Editorial

Jump to: Research, Review

5 pages, 286 KiB  
Editorial
Evolutionary Genetics of Crop-Wild Complexes
by Andrés J. Cortés, Amandine Cornille and Roxana Yockteng
Genes 2022, 13(1), 1; https://doi.org/10.3390/genes13010001 - 21 Dec 2021
Cited by 11 | Viewed by 2872
Abstract
Since Darwin’s time, the role of crop wild relatives (CWR), landraces, and cultivated genepools in shaping plant diversity and boosting food resources has been a major question [...] Full article
(This article belongs to the Special Issue Evolutionary Genetics of Plant Crop-Wild Complexes: From Fundamental to Applied Research)
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Research

Jump to: Editorial, Review

14 pages, 1009 KiB  
Article
Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions
by Ranjita Thapa, Matthew Edwards and Matthew W. Blair
Genes 2021, 12(12), 1849; https://doi.org/10.3390/genes12121849 - 23 Nov 2021
Cited by 11 | Viewed by 2575
Abstract
Amaranthus is a genus of C4 dicotyledonous herbaceous plants, and three New World species have been domesticated to produce grain crops with light colored seed which are classified as pseudo-cereals rich in protein and minerals. A core collection of grain amaranths and immediate [...] Read more.
Amaranthus is a genus of C4 dicotyledonous herbaceous plants, and three New World species have been domesticated to produce grain crops with light colored seed which are classified as pseudo-cereals rich in protein and minerals. A core collection of grain amaranths and immediate precursor species has been established, representing the closest related species. The goal of this study was to evaluate the genetic diversity in that collection of cultivated and wild species, using competitive allele single nucleotide polymorphism markers. A secondary objective was to determine the relationships among the three cultivated species and non-domesticated Amaranthus, while a third objective was to evaluate the utility of the markers in detecting diversity in the 276 genotypes. The markers were found to be highly variable with an average polymorphism information content of 0.365. All markers were bi-allelic; and the major allele frequency ranged from 0.388 to 0.871. Population structure analysis of the cultigens revealed the presence of two sub populations. Phylogeny confirmed that the two Mesoamerican species, Amaranthus cruentus and Amaranthus hypochondriacus, were related and distant from the South American species Amaranthus caudatus, which in turn was very closely clustered with Amaranthus quitensis, even though this is considered a weedy relative. The first pair of species were likely to have inter-crossed, while the latter two likely exist in a wild-cultivated hybrid state. In conclusion, the results of this SNP study provided insights on amaranth cultivars and their relationship to wild species, the probable domestication events leading to the cultivars, and possible crop breeding or germplasm conservation strategies. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Plant Crop-Wild Complexes: From Fundamental to Applied Research)
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21 pages, 4080 KiB  
Article
Opportunities and Challenges to Improve a Public Research Program in Plant Breeding and Enhance Underutilized Plant Genetic Resources in the Tropics
by Ivania Cerón-Souza, Carlos H. Galeano, Katherine Tehelen, Hugo R. Jiménez and Carolina González
Genes 2021, 12(10), 1584; https://doi.org/10.3390/genes12101584 - 9 Oct 2021
Cited by 5 | Viewed by 2692
Abstract
The American tropics are hotspots of wild and domesticated plant biodiversity, which is still underutilized by breeding programs despite being conserved at regional gene banks. The improvement of those programs depends on long-term public funds and the maintenance of specialized staff. Unfortunately, financial [...] Read more.
The American tropics are hotspots of wild and domesticated plant biodiversity, which is still underutilized by breeding programs despite being conserved at regional gene banks. The improvement of those programs depends on long-term public funds and the maintenance of specialized staff. Unfortunately, financial ups and downs complicate staff connectivity and their research impact. Between 2000 and 2010, Agrosavia (Corporación Colombiana de Investigación Agropecuaria) dramatically decreased its public financial support. In 2017, we surveyed all 52 researchers from Agrosavia involved in plant breeding and plant genetic resource programs to examine the effect of decimating funds in the last ten years. We hypothesized that the staff dedicated to plant breeding still suffer a strong fragmentation and low connectivity. As we expected, the social network among researchers is weak. The top ten central leaders are predominantly males with an M.Sc. degree but have significant experience in the area. The staff has experience in 31 tropical crops, and 17 are on the list of underutilized species. Moreover, although 26 of these crops are in the national germplasm bank, this has not been the primary source for their breeding programs. We proposed five principles to improve connectivity among teams and research impact: (1) The promotion of internal discussion about gender gaps and generation shifts to design indicators to monitor and decrease this disparity over time. (2) The construction of long-term initiatives and synergies with the Colombian government to support the local production of food security crops independent of market trends. (3) Better collaboration between the National Plant Germplasm Bank and plant breeding researchers. (4) A concerted priority list of species (especially those neglected or underutilized) and external institutions to better focus the collaborative efforts in research using public funds. (5) Better spaces for the design of projects among researchers and training programs in new technologies. These principles could also apply in other tropical countries with public plant breeding research programs facing similar challenges. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Plant Crop-Wild Complexes: From Fundamental to Applied Research)
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17 pages, 3284 KiB  
Article
Allelic Diversity at Abiotic Stress Responsive Genes in Relationship to Ecological Drought Indices for Cultivated Tepary Bean, Phaseolus acutifolius A. Gray, and Its Wild Relatives
by María A. Buitrago-Bitar, Andrés J. Cortés, Felipe López-Hernández, Jorge M. Londoño-Caicedo, Jaime E. Muñoz-Florez, L. Carmenza Muñoz and Matthew Wohlgemuth Blair
Genes 2021, 12(4), 556; https://doi.org/10.3390/genes12040556 - 12 Apr 2021
Cited by 38 | Viewed by 5127
Abstract
Some of the major impacts of climate change are expected in regions where drought stress is already an issue. Grain legumes are generally drought susceptible. However, tepary bean and its wild relatives within Phaseolus acutifolius or P. parvifolius are from arid areas between [...] Read more.
Some of the major impacts of climate change are expected in regions where drought stress is already an issue. Grain legumes are generally drought susceptible. However, tepary bean and its wild relatives within Phaseolus acutifolius or P. parvifolius are from arid areas between Mexico and the United States. Therefore, we hypothesize that these bean accessions have diversity signals indicative of adaptation to drought at key candidate genes such as: Asr2, Dreb2B, and ERECTA. By sequencing alleles of these genes and comparing to estimates of drought tolerance indices from climate data for the collection site of geo-referenced, tepary bean accessions, we determined the genotype x environmental association (GEA) of each gene. Diversity analysis found that cultivated and wild P. acutifolius were intermingled with var. tenuifolius and P. parvifolius, signifying that allele diversity was ample in the wild and cultivated clade over a broad sense (sensu lato) evaluation. Genes Dreb2B and ERECTA harbored signatures of directional selection, represented by six SNPs correlated with the environmental drought indices. This suggests that wild tepary bean is a reservoir of novel alleles at genes for drought tolerance, as expected for a species that originated in arid environments. Our study corroborated that candidate gene approach was effective for marker validation across a broad genetic base of wild tepary accessions. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Plant Crop-Wild Complexes: From Fundamental to Applied Research)
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19 pages, 2265 KiB  
Article
QTL Mapping for Domestication-Related Characteristics in Field Cress (Lepidium campestre)—A Novel Oil Crop for the Subarctic Region
by Cecilia Hammenhag, Ganapathi Varma Saripella, Rodomiro Ortiz and Mulatu Geleta
Genes 2020, 11(10), 1223; https://doi.org/10.3390/genes11101223 - 19 Oct 2020
Cited by 2 | Viewed by 3764
Abstract
Domestication of a new crop requires identification and improvement of desirable characteristics Field cress (Lepidium campestre) is being domesticated as a new oilseed crop, particularly for northern temperate regions.. In the present study, an F2 mapping population and its F3 progenies [...] Read more.
Domestication of a new crop requires identification and improvement of desirable characteristics Field cress (Lepidium campestre) is being domesticated as a new oilseed crop, particularly for northern temperate regions.. In the present study, an F2 mapping population and its F3 progenies were used to identify quantitative trait loci (QTLs) for plant height (PH), number of stems per plant (NS), stem growth orientation (SO), flowering habit (FH), earliness (ER), seed yield per plant (SY), pod shattering resistance (SHR), and perenniality (PE). A highly significant correlation (p < 0.001) was observed between several pairs of characteristics, including SY and ER (negative) or ER and PE (positive). The inclusive composite interval mapping approach was used for QTL mapping using 2330 single nucleotide polymorphism (SNP) markers mapped across the eight field cress linkage groups. Nine QTLs were identified with NS, PH, SO, and PE having 3, 3, 2, and 1 QTLs, explaining 21.3%, 29.5%, 3.8%, and 7.2% of the phenotypic variation, respectively. Candidate genes behind three of the QTLs and favorable marker alleles for different classes of each characteristic were identified. Following their validation through further study, the identified QTLs and associated favorable marker alleles can be used in marker-aided breeding to speed up the domestication of field cress. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Plant Crop-Wild Complexes: From Fundamental to Applied Research)
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Review

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21 pages, 988 KiB  
Review
Harnessing Crop Wild Diversity for Climate Change Adaptation
by Andrés J. Cortés and Felipe López-Hernández
Genes 2021, 12(5), 783; https://doi.org/10.3390/genes12050783 - 20 May 2021
Cited by 79 | Viewed by 9145
Abstract
Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer concrete opportunities to increase yield and crop adaptability. However, the rate at which the [...] Read more.
Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer concrete opportunities to increase yield and crop adaptability. However, the rate at which the threat is happening requires powering new strategies in order to meet the global food demand. In this review, we highlight major recent ‘big data’ developments from both empirical and theoretical genomics that may speed up the identification, conservation, and breeding of exotic and elite crop varieties with the potential to feed humans. We first emphasize the major bottlenecks to capture and utilize novel sources of variation in abiotic stress (i.e., heat and drought) tolerance. We argue that adaptation of crop wild relatives to dry environments could be informative on how plant phenotypes may react to a drier climate because natural selection has already tested more options than humans ever will. Because isolated pockets of cryptic diversity may still persist in remote semi-arid regions, we encourage new habitat-based population-guided collections for genebanks. We continue discussing how to systematically study abiotic stress tolerance in these crop collections of wild and landraces using geo-referencing and extensive environmental data. By uncovering the genes that underlie the tolerance adaptive trait, natural variation has the potential to be introgressed into elite cultivars. However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated by many low-effect genes). Therefore, we finish prospecting modern analytical approaches that will serve to overcome this issue. Concretely, genomic prediction, machine learning, and multi-trait gene editing, all offer innovative alternatives to speed up more accurate pre- and breeding efforts toward the increase in crop adaptability and yield, while matching future global food demands in the face of increased heat and drought. In order for these ‘big data’ approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding. The recent developments and perspectives discussed throughout this review ultimately aim to contribute to increased crop adaptability and yield in the face of heat waves and drought events. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Plant Crop-Wild Complexes: From Fundamental to Applied Research)
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