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Genomics of Plant Domestication and Crop Evolution
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Genomics of Plant Domestication and Crop Evolution

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

Deadline for manuscript submissions: closed (3 September 2018) | Viewed by 94064

Special Issue Editors

Prof. Dr. Roberto Papa

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Guest Editor
D3A-Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
Interests: plant breeding; domestication; genomics; CWR; population genetics; evolution; biodiversity and genetic resources conservation; legumes; cereals
Dr. Domenico Rau

E-Mail
Guest Editor
Department of Agriculture, University of Sassari, Sassari, Italy
Interests: long-standing interest in understanding how organisms cope with the challenges of adapting to changing environments: crop evolutionary genetics, population genomics, adaptation genomics, conservation and exploitation of plant biodiversity and plant breeding
Dr. Tania Gioia

E-Mail
Guest Editor
School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
Interests: domestication; genetic and morphological diversity; adaptation; population genomics; crop evolution

Special Issue Information

Dear Colleagues,

As defined by Charles Darwin, the processes of crop domestication and breeding can be seen as a giant experiment to test the evolutionary hypothesis. During domestication, similar sets of traits were selected over a wide range of plant species, as the so-called domestication syndrome, which shows numerous examples of convergent phenotypic evolution associated with adaptation to novel agro-ecosystems, and to human needs. This evolutionary scenario makes crops excellent models to understand the process of adaptation to new ecological conditions, to test evolutionary hypotheses, and to identify the molecular basis of phenotypic diversity. At the same time the understanding of the domestication and crop evolution process along with the knowledge about the level and structure of the molecular and functional diversity present in wild and domesticated germplasm has a major potential to boost plant breeding and gene discovery.

Progress in our understanding of genetic diversity and molecular evolution phenomena has accelerated dramatically over the last decade, driven by advances in genomic technologies. New genomic technologies have provided unprecedented knowledge about plants domestication and crop evolution representing a fundamental support for researchers and breeders involved in crop improvement and will eventually lead to improvements in crop yield and human health.

In this Special Issue, we would like to invite submissions of high-quality original research or review articles on topics related to the genomics of plant domestication and crop evolution.

Sincerely,

Prof. Roberto Papa
Dr. Domenico Rau
Dr. Tania Gioia
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 evolution
  • crop wild relatives
  • domestication syndrome
  • gene flow
  • genetic diversity
  • adaptation
  • population genomics
  • population bottleneck
  • natural selection
  • convergent evolution
  • selection signatures
  • molecular evolution
  • genome evolution, selection and adaptation

Published Papers (17 papers)

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Research

Jump to: Review

15 pages, 2615 KiB  
Article
Development and Validation of a Gene-Targeted dCAPS Marker for Marker-Assisted Selection of Low-Alkaloid Content in Seeds of Narrow-Leafed Lupin (Lupinus angustifolius L.)
by Magdalena Kroc, Katarzyna Czepiel, Paulina Wilczura, Monika Mokrzycka and Wojciech Święcicki
Genes 2019, 10(6), 428; https://doi.org/10.3390/genes10060428 - 04 Jun 2019
Cited by 17 | Viewed by 3511
Abstract
Low-alkaloid content is an important breeding target to improve the quality of lupin seeds. An APETALA2/ethylene response transcription factor, RAP2-7, is likely a candidate gene for the major alkaloid locus iucundus, and plays a crucial role in regulation of seed alkaloid [...] Read more.
Low-alkaloid content is an important breeding target to improve the quality of lupin seeds. An APETALA2/ethylene response transcription factor, RAP2-7, is likely a candidate gene for the major alkaloid locus iucundus, and plays a crucial role in regulation of seed alkaloid content in narrow-leafed lupin (NLL; Lupinus angustifolius L.). Here, we exploited a single-nucleotide polymorphism within RAP2-7 credibly associated with seed alkaloid content, to develop the co-dominant derived cleaved amplified polymorphic sequence (dCAPS) marker iuc_RAP2-7. Marker validation in 202 NLL accessions demonstrated that seed alkaloid content ≥0.9% of the seed dry weight was associated with the high-alkaloid marker band (Iucundus genotypes), whereas alkaloid content up to 0.5% of the seed dry weight was associated with the low-alkaloid marker band (iucundus genotypes). Within a given detection limit, iuc_RAP2-7 unambiguously identified all but three low-alkaloid accessions. The latter accessions apparently have a different regulatory mechanism for seed alkaloid content because the RAP2-7 gene/putative promoter sequence and expression of alkaloid-associated genes in the leaves of the three ambiguous accessions were similar to those of bitter Iucundus lines. We consider the iuc_RAP2-7 marker is a powerful tool that will facilitate NLL marker-assisted selection by rapid rejection of bitter Iucundus genotypes and thus accelerate development of new low-alkaloid cultivars. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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25 pages, 5093 KiB  
Article
Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution
by Karolina Susek, Wojciech Bielski, Katarzyna B. Czyż, Robert Hasterok, Scott A. Jackson, Bogdan Wolko and Barbara Naganowska
Genes 2019, 10(4), 259; https://doi.org/10.3390/genes10040259 - 01 Apr 2019
Cited by 6 | Viewed by 3918
Abstract
Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other [...] Read more.
Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other legumes approximately 60 mya. In contrast to New World lupins, Old World lupins show high variability not only for chromosome numbers (2n = 32–52), but also for the basic chromosome number (x = 5–9, 13) and genome size. The evolutionary basis that underlies the karyotype evolution in lupins remains unknown, as it has so far been impossible to identify individual chromosomes. To shed light on chromosome changes and evolution, we used comparative chromosome mapping among 11 Old World lupins, with Lupinus angustifolius as the reference species. We applied set of L. angustifolius-derived bacterial artificial chromosome clones for fluorescence in situ hybridization. We demonstrate that chromosome variations in the species analyzed might have arisen from multiple changes in chromosome structure and number. We hypothesize about lupin karyotype evolution through polyploidy and subsequent aneuploidy. Additionally, we have established a cytogenomic map of L. angustifolius along with chromosome markers that can be used for related species to further improve comparative studies of crops and wild lupins. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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13 pages, 1793 KiB  
Article
Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains
by Raz Avni, Leah Oren, Gai Shabtay, Siwar Assili, Curtis Pozniak, Iago Hale, Roi Ben-David, Zvi Peleg and Assaf Distelfeld
Genes 2018, 9(12), 636; https://doi.org/10.3390/genes9120636 - 17 Dec 2018
Cited by 34 | Viewed by 5235
Abstract
The domestication and subsequent genetic improvement of wheat led to the development of large-seeded cultivated wheat species relative to their smaller-seeded wild progenitors. While increased grain weight (GW) continues to be an important goal of many wheat breeding programs, few genes underlying this [...] Read more.
The domestication and subsequent genetic improvement of wheat led to the development of large-seeded cultivated wheat species relative to their smaller-seeded wild progenitors. While increased grain weight (GW) continues to be an important goal of many wheat breeding programs, few genes underlying this trait have been identified despite an abundance of studies reporting quantitative trait loci (QTL) for GW. Here we perform a QTL analysis for GW using a population of recombinant inbred lines (RILs) derived from the cross between wild emmer wheat accession ‘Zavitan’ and durum wheat variety ‘Svevo’. Identified QTLs in this population were anchored to the recent Zavitan reference genome, along with previously published QTLs for GW in tetraploid wheat. This genome-based, meta-QTL analysis enabled the identification of a locus on chromosome 6A whose introgression from wild wheat positively affects GW. The locus was validated using an introgression line carrying the 6A GW QTL region from Zavitan in a Svevo background, resulting in >8% increase in GW compared to Svevo. Using the reference sequence for the 6A QTL region, we identified a wheat ortholog to OsGRF4, a rice gene previously associated with GW. The coding sequence of this gene (TtGRF4-A) contains four single nucleotide polymorphisms (SNPs) between Zavitan and Svevo, one of which reveals the Zavitan allele to be rare in a core collection of wild emmer and completely absent from the domesticated emmer genepool. Similarly, another wild emmer accession (G18-16) was found to carry a rare allele of TtGRF4-A that also positively affects GW and is characterized by a unique SNP absent from the entire core collection. These results exemplify the rich genetic diversity of wild wheat, posit TtGRF4-A as a candidate gene underlying the 6A GW QTL, and suggest that the natural Zavitan and G18-16 alleles of TtGRF4-A have potential to increase wheat yields in breeding programs. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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21 pages, 3308 KiB  
Article
Genetic Diversity within Snap Beans and Their Relation to Dry Beans
by Lyle Wallace, Haidar Arkwazee, Kelly Vining and James R. Myers
Genes 2018, 9(12), 587; https://doi.org/10.3390/genes9120587 - 28 Nov 2018
Cited by 25 | Viewed by 4803
Abstract
Two hundred forty-six snap bean genotypes and 49 dry beans representing both centers of domestication and six bean races with materials from Europe, Asia, and the Americas were genotyped using a single nucleotide polymorphism (SNP) array. The data was analyzed for expected heterozygosity, [...] Read more.
Two hundred forty-six snap bean genotypes and 49 dry beans representing both centers of domestication and six bean races with materials from Europe, Asia, and the Americas were genotyped using a single nucleotide polymorphism (SNP) array. The data was analyzed for expected heterozygosity, K-means clustering, principal components, phylogenetic relationships, and population substructure. When all gene pools of snap bean were assembled, the expected heterozygosity was roughly equivalent to a carefully chosen panel of dry beans representing all bean races and centers of domestication demonstrating the genetic richness of snap materials in total. K-means clustering and K = 2 structure analysis showed significant mixing of gene pools in the European and American commercial snap materials and the dominance of the Andean center of domestication among commercial contemporary snap beans. Conversely, the same analysis showed that Chinese, Iberian, and heirloom materials were underrepresented in contemporary materials. Further, Structure analysis revealed eight distinct groups within snap beans. Two showed strong kinship to the Middle American center of domestication, three to the Andean center of domestication, and three showed admixture between the two centers. Snap beans may have been independently derived from dry beans more than once and from both centers. Overall, we identified eight potential germplasm pools for snap bean. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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20 pages, 5777 KiB  
Article
Molecular Evidence for Two Domestication Events in the Pea Crop
by Oldřich Trněný, Jan Brus, Iveta Hradilová, Abhishek Rathore, Roma R. Das, Pavel Kopecký, Clarice J. Coyne, Patrick Reeves, Christopher Richards and Petr Smýkal
Genes 2018, 9(11), 535; https://doi.org/10.3390/genes9110535 - 06 Nov 2018
Cited by 38 | Viewed by 6534
Abstract
Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide [...] Read more.
Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide analysis of 11,343 polymorphic single nucleotide polymorphisms (SNPs) on a set of wild P. elatius (134) and P. fulvum (20) and 74 domesticated accessions (64 P. sativum landraces and 10 P. abyssinicum), we demonstrated that domesticated P. sativum and the Ethiopian pea (P. abyssinicum) were derived from different P. elatius genepools. Therefore, pea has at least two domestication events. The analysis does not support a hybrid origin of P. abyssinicum, which was likely introduced into Ethiopia and Yemen followed by eco-geographic adaptation. Both P. sativum and P. abyssinicum share traits that are typical of domestication, such as non-dormant seeds. Non-dormant seeds were also found in several wild P. elatius accessions which could be the result of crop to wild introgression or natural variation that may have been present during pea domestication. A sub-group of P. elatius overlaps with P. sativum landraces. This may be a consequence of bidirectional gene-flow or may suggest that this group of P. elatius is the closest extant wild relative of P. sativum. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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15 pages, 2096 KiB  
Article
Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing
by Ana Campa, Ester Murube and Juan José Ferreira
Genes 2018, 9(11), 518; https://doi.org/10.3390/genes9110518 - 23 Oct 2018
Cited by 33 | Viewed by 4597
Abstract
A common bean (Phaseolus vulgaris) diversity panel of 308 lines was established from local Spanish germplasm, as well as old and elite cultivars mainly used for snap consumption. Most of the landraces included derived from the Spanish common bean core collection, [...] Read more.
A common bean (Phaseolus vulgaris) diversity panel of 308 lines was established from local Spanish germplasm, as well as old and elite cultivars mainly used for snap consumption. Most of the landraces included derived from the Spanish common bean core collection, so this panel can be considered to be representative of the Spanish diversity for this species. The panel was characterized by 3099 single-nucleotide polymorphism markers obtained through genotyping-by-sequencing, which revealed a wide genetic diversity and a low level of redundant material within the panel. Structure, cluster, and principal component analyses revealed the presence of two main subpopulations corresponding to the two main gene pools identified in common bean, the Andean and Mesoamerican pools, although most lines (70%) were associated with the Andean gene pool. Lines showing recombination between the two gene pools were also observed, most of them showing useful for snap bean consumption, which suggests that both gene pools were probably used in the breeding of snap bean cultivars. The usefulness of this panel for genome-wide association studies was tested by conducting association mapping for determinacy. Significant marker–trait associations were found on chromosome Pv01, involving the gene Phvul.001G189200, which was identified as a candidate gene for determinacy in the common bean. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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19 pages, 8123 KiB  
Article
The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution
by Nunzio D’Agostino, Rachele Tamburino, Concita Cantarella, Valentina De Carluccio, Lorenza Sannino, Salvatore Cozzolino, Teodoro Cardi and Nunzia Scotti
Genes 2018, 9(10), 503; https://doi.org/10.3390/genes9100503 - 17 Oct 2018
Cited by 27 | Viewed by 5185
Abstract
Members of the genus Capsicum are of great economic importance, including both wild forms and cultivars of peppers and chilies. The high number of potentially informative characteristics that can be identified through next-generation sequencing technologies gave a huge boost to evolutionary and comparative [...] Read more.
Members of the genus Capsicum are of great economic importance, including both wild forms and cultivars of peppers and chilies. The high number of potentially informative characteristics that can be identified through next-generation sequencing technologies gave a huge boost to evolutionary and comparative genomic research in higher plants. Here, we determined the complete nucleotide sequences of the plastomes of eight Capsicum species (eleven genotypes), representing the three main taxonomic groups in the genus and estimated molecular diversity. Comparative analyses highlighted a wide spectrum of variation, ranging from point mutations to small/medium size insertions/deletions (InDels), with accD, ndhB, rpl20, ycf1, and ycf2 being the most variable genes. The global pattern of sequence variation is consistent with the phylogenetic signal. Maximum-likelihood tree estimation revealed that Capsicum chacoense is sister to the baccatum complex. Divergence and positive selection analyses unveiled that protein-coding genes were generally well conserved, but we identified 25 positive signatures distributed in six genes involved in different essential plastid functions, suggesting positive selection during evolution of Capsicum plastomes. Finally, the identified sequence variation allowed us to develop simple PCR-based markers useful in future work to discriminate species belonging to different Capsicum complexes. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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22 pages, 11767 KiB  
Article
Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume
by Xiaokang Zhuo, Tangchun Zheng, Zhiyong Zhang, Yichi Zhang, Liangbao Jiang, Sagheer Ahmad, Lidan Sun, Jia Wang, Tangren Cheng and Qixiang Zhang
Genes 2018, 9(10), 494; https://doi.org/10.3390/genes9100494 - 12 Oct 2018
Cited by 47 | Viewed by 6861
Abstract
NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity. Prunus mume, an excellent horticultural crop, is widely cultivated in [...] Read more.
NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity. Prunus mume, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence PmNAC genes and characterized them by bioinformatics tools and expression profiles. These PmNACs were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of PmNACs were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (PmNAC59/66/73) and three miRNA-targeted genes (PmNAC40/41/83) were identified. Most PmNAC genes presented tissue-specific and time-specific expression patterns. Sixteen PmNACs (PmNAC11/19/20/23/41/48/58/74/75/76/78/79/85/86/103/111) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (PmNAC11/12/17/21/29/42/30/48/59/66/73/75/85/86/93/99/111) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative PmNACs was observed under 4 °C at different treatment times. The expression of 10 genes (PmNAC11/20/23/40/42/48/57/60/66/86) was upregulated, while 5 genes (PmNAC59/61/82/85/107) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the NAC gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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20 pages, 3901 KiB  
Article
Molecular Genotyping (SSR) and Agronomic Phenotyping for Utilization of Durum Wheat (Triticum durum Desf.) Ex Situ Collection from Southern Italy: A Combined Approach Including Pedigreed Varieties
by Stefania Marzario, Giuseppina Logozzo, Jacques L. David, Pierluigi Spagnoletti Zeuli and Tania Gioia
Genes 2018, 9(10), 465; https://doi.org/10.3390/genes9100465 - 20 Sep 2018
Cited by 31 | Viewed by 3786
Abstract
In South Italy durum wheat (Triticum durum Desf.) has a long-time tradition of growing and breeding. Accessions collected and now preserved ex situ are a valuable genetic resource, but their effective use in agriculture and breeding programs remains very low. In this [...] Read more.
In South Italy durum wheat (Triticum durum Desf.) has a long-time tradition of growing and breeding. Accessions collected and now preserved ex situ are a valuable genetic resource, but their effective use in agriculture and breeding programs remains very low. In this study, a small number (44) of simple sequence repeats (SSR) molecular markers were used to detect pattern of diversity for 136 accessions collected in South Italy over time, to identify the genepool of origin, and establish similarities with 28 Italian varieties with known pedigree grown in Italy over the same time-period. Phenotyping was conducted for 12 morphophysiological characters of agronomic interest. Based on discriminant analysis of principal components (DAPC) and STRUCTURE analysis six groups were identified, the assignment of varieties reflected the genetic basis and breeding strategies involved in their development. Some “old” varieties grown today are the result of evolution through natural hybridization and conservative pure line selection. A small number of molecular markers and little phenotyping coupled with powerful statistical analysis and comparison to pedigreed varieties can provide enough information on the genetic structure of durum wheat germplasm for a quick screening of the germplasm collection able to identify accessions for breeding or introduction in low input agriculture. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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16 pages, 1098 KiB  
Article
Specific LTR-Retrotransposons Show Copy Number Variations between Wild and Cultivated Sunflowers
by Flavia Mascagni, Alberto Vangelisti, Tommaso Giordani, Andrea Cavallini and Lucia Natali
Genes 2018, 9(9), 433; https://doi.org/10.3390/genes9090433 - 29 Aug 2018
Cited by 19 | Viewed by 3806
Abstract
The relationship between variation of the repetitive component of the genome and domestication in plant species is not fully understood. In previous work, variations in the abundance and proximity to genes of long terminal repeats (LTR)-retrotransposons of sunflower (Helianthus annuus L.) were [...] Read more.
The relationship between variation of the repetitive component of the genome and domestication in plant species is not fully understood. In previous work, variations in the abundance and proximity to genes of long terminal repeats (LTR)-retrotransposons of sunflower (Helianthus annuus L.) were investigated by Illumina DNA sequencingtocompare cultivars and wild accessions. In this study, we annotated and characterized 22 specific retrotransposon families whose abundance varies between domesticated and wild genotypes. These families mostly belonged to the Chromovirus lineage of the Gypsy superfamily and were distributed overall chromosomes. They were also analyzed in respect to their proximity to genes. Genes close to retrotransposon were classified according to biochemical pathways, and differences between domesticated and wild genotypes are shown. These data suggest that structural variations related to retrotransposons might have occurred to produce phenotypic variation between wild and domesticated genotypes, possibly by affecting the expression of genes that lie close to inserted or deleted retrotransposons and belong to specific biochemical pathways as those involved in plant stress responses. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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20 pages, 5998 KiB  
Article
Comparative Transcriptomics of Root Development in Wild and Cultivated Carrots
by Gabriela Machaj, Hamed Bostan, Alicja Macko-Podgórni, Massimo Iorizzo and Dariusz Grzebelus
Genes 2018, 9(9), 431; https://doi.org/10.3390/genes9090431 - 24 Aug 2018
Cited by 15 | Viewed by 4897
Abstract
The carrot is the most popular root vegetable worldwide. The genetic makeup underlying the development of the edible storage root are fragmentary. Here, we report the first comparative transcriptome analysis between wild and cultivated carrot roots at multiple developmental stages. Overall, 3285, 4637, [...] Read more.
The carrot is the most popular root vegetable worldwide. The genetic makeup underlying the development of the edible storage root are fragmentary. Here, we report the first comparative transcriptome analysis between wild and cultivated carrot roots at multiple developmental stages. Overall, 3285, 4637, and 570 genes were differentially expressed in the cultivated carrot in comparisons made for young plants versus developing roots, young plants versus mature roots, and developing roots versus mature roots, respectively. Of those, 1916, 2645, and 475, respectively, were retained after filtering out genes showing similar profiles of expression in the wild carrot. They were assumed to be of special interest with respect to the development of the storage root. Among them, transcription factors and genes encoding proteins involved in post-translational modifications (signal transduction and ubiquitination) were mostly upregulated, while those involved in redox signaling were mostly downregulated. Also, genes encoding proteins regulating cell cycle, involved in cell divisions, development of vascular tissue, water transport, and sugar metabolism were enriched in the upregulated clusters. Genes encoding components of photosystem I and II, together with genes involved in carotenoid biosynthesis, were upregulated in the cultivated roots, as opposed to the wild roots; however, they were largely downregulated in the mature storage root, as compared with the young and developing root. The experiment produced robust resources for future investigations on the regulation of storage root formation in carrot and Apiaceae. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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13 pages, 2427 KiB  
Article
Neo-Domestication of an Interspecific Tetraploid Helianthus annuus × Helianthus tuberous Population That Segregates for Perennial Habit
by Michael B. Kantar, Sariel Hüber, Adam Herman, Dan G. Bock, Greg Baute, Kevin Betts, Matthew Ott, Yaniv Brandvain, Donald Wyse, Robert M. Stupar and Loren H. Rieseberg
Genes 2018, 9(9), 422; https://doi.org/10.3390/genes9090422 - 21 Aug 2018
Cited by 10 | Viewed by 4143
Abstract
Perennial agriculture has been proposed as an option to improve the sustainability of cropping systems, by increasing the efficiency of resource use, while also providing ecosystem services. Neo-domestication, the contemporary domestication of plants that have not previously been used in agriculture, can be [...] Read more.
Perennial agriculture has been proposed as an option to improve the sustainability of cropping systems, by increasing the efficiency of resource use, while also providing ecosystem services. Neo-domestication, the contemporary domestication of plants that have not previously been used in agriculture, can be used to generate new crops for these systems. Here we explore the potential of a tetraploid (2n = 4x = 68) interspecific hybrid sunflower as a perennial oilseed for use in multifunctional agricultural systems. A population of this novel tetraploid was obtained from crosses between the annual diploid oilseed crop Helianthus annuus (2n = 2x = 34) and the perennial hexaploid tuber crop Helianthus tuberosus (2n = 6x = 102). We selected for classic domestication syndrome traits for three generations. Substantial phenotypic gains were made, in some cases approaching 320%. We also analyzed the genetic basis of tuber production (i.e., perenniality), with the goal of obtaining molecular markers that could be used to facilitate future breeding in this system. Results from quantitative trait locus (QTL) mapping suggest that tuber production has an oligogenic genetic basis. Overall, this study indicates that substantial gains towards domestication goals can be achieved over contemporary time scales. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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Review

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16 pages, 5905 KiB  
Review
Convergent Evolution of the Seed Shattering Trait
by Valerio Di Vittori, Tania Gioia, Monica Rodriguez, Elisa Bellucci, Elena Bitocchi, Laura Nanni, Giovanna Attene, Domenico Rau and Roberto Papa
Genes 2019, 10(1), 68; https://doi.org/10.3390/genes10010068 - 19 Jan 2019
Cited by 34 | Viewed by 7041
Abstract
Loss of seed shattering is a key trait in crop domestication, particularly for grain crops. For wild plants, seed shattering is a crucial mechanism to achieve greater fitness, although in the agricultural context, this mechanism reduces harvesting efficiency, especially under dry conditions. Loss [...] Read more.
Loss of seed shattering is a key trait in crop domestication, particularly for grain crops. For wild plants, seed shattering is a crucial mechanism to achieve greater fitness, although in the agricultural context, this mechanism reduces harvesting efficiency, especially under dry conditions. Loss of seed shattering was acquired independently in different monocotyledon and dicotyledon crop species by ‘convergent phenotypic evolution’, leading to similar low dehiscent and indehiscent phenotypes. Here, the main aim is to review the current knowledge about seed shattering in crops, in order to highlight the tissue modifications that underlie the convergent phenotypic evolution of reduced shattering in different types of fruit, from the silique of Brassicaceae species, to the pods of legumes and spikes of cereals. Emphasis is given to legumes, with consideration of recent data obtained for the common bean. The current review also discusses to what extent convergent phenotypes arose from parallel changes at the histological and/or molecular levels. For this reason, an overview is included of the main findings relating to the genetic control of seed shattering in the model species Arabidopsis thaliana and in other important crops. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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19 pages, 777 KiB  
Review
Sunflower Genetics from Ancestors to Modern Hybrids—A Review
by Aleksandra Radanović, Dragana Miladinović, Sandra Cvejić, Milan Jocković and Siniša Jocić
Genes 2018, 9(11), 528; https://doi.org/10.3390/genes9110528 - 30 Oct 2018
Cited by 32 | Viewed by 6908
Abstract
Domestication and the first steps of sunflower breeding date back more than 4000 years. As an interesting crop to humans, sunflower underwent significant changes in the past to finally find its place as one of the most significant oil crops today. Substantial progress [...] Read more.
Domestication and the first steps of sunflower breeding date back more than 4000 years. As an interesting crop to humans, sunflower underwent significant changes in the past to finally find its place as one of the most significant oil crops today. Substantial progress has already been made in understanding how sunflower was domesticated. Recent advances in molecular techniques with improved experimental designs contributed to further understanding of the genetic and molecular basis underlying the architectural and phenotypic changes that occurred during domestication and improvements in sunflower breeding. Understanding the domestication process and assessing the current situation concerning available genotypic variations are essential in order for breeders to face future challenges. A review of the tools that are used for exploring the genetic and genome changes associated with sunflower domestication is given in the paper, along with a discussion of their possible implications on classical sunflower breeding techniques and goals. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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14 pages, 1148 KiB  
Review
Genomic Insights into Date Palm Origins
by Muriel Gros-Balthazard, Khaled Michel Hazzouri and Jonathan Mark Flowers
Genes 2018, 9(10), 502; https://doi.org/10.3390/genes9100502 - 17 Oct 2018
Cited by 21 | Viewed by 5892
Abstract
With the development of next-generation sequencing technology, the amount of date palm (Phoenix dactylifera L.) genomic data has grown rapidly and yielded new insights into this species and its origins. Here, we review advances in understanding of the evolutionary history of the [...] Read more.
With the development of next-generation sequencing technology, the amount of date palm (Phoenix dactylifera L.) genomic data has grown rapidly and yielded new insights into this species and its origins. Here, we review advances in understanding of the evolutionary history of the date palm, with a particular emphasis on what has been learned from the analysis of genomic data. We first record current genomic resources available for date palm including genome assemblies and resequencing data. We discuss new insights into its domestication and diversification history based on these improved genomic resources. We further report recent discoveries such as the existence of wild ancestral populations in remote locations of Oman and high differentiation between African and Middle Eastern populations. While genomic data are consistent with the view that domestication took place in the Gulf region, they suggest that the process was more complex involving multiple gene pools and possibly a secondary domestication. Many questions remain unanswered, especially regarding the genetic architecture of domestication and diversification. We provide a road map to future studies that will further clarify the domestication history of this iconic crop. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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18 pages, 840 KiB  
Review
Genes Contributing to Domestication of Rice Seed Traits and Its Global Expansion
by Haiyang Liu, Qiuping Li and Yongzhong Xing
Genes 2018, 9(10), 489; https://doi.org/10.3390/genes9100489 - 10 Oct 2018
Cited by 17 | Viewed by 9398
Abstract
Asian rice (Oryza sativa) and African rice (Oryza glaberrima) are separately domesticated from their wild ancestors Oryza rufipogon and Oryza barthii, which are very sensitive to daylength. In the process of domestication, some traits that are favorable for [...] Read more.
Asian rice (Oryza sativa) and African rice (Oryza glaberrima) are separately domesticated from their wild ancestors Oryza rufipogon and Oryza barthii, which are very sensitive to daylength. In the process of domestication, some traits that are favorable for the natural survival of wild rice such as seed dormancy and shattering have become favorable ones for human consumption due to the loss-of-function mutations in the genes that are underlying these traits. As a consequence, many genes that are related to these kinds of traits have been fixed with favorable alleles in modern cultivars by artificial selection. After domestication, Oryza sativa cultivars gradually spread to temperate and cool regions from the tropics and subtropics due to the loss of their photoperiod sensitivity. In this paper, we review the characteristics of domestication-related seed traits and heading dates in rice, including the key genes controlling these traits, the differences in allelic diversity between wild rice and cultivars, the geographic distribution of alleles, and the regulatory pathways of these traits. A comprehensive comparison shows that these genes contributed to rice domestication and its global expansion. In addition, these traits have also experienced parallel evolution by artificial selection on the homologues of key genes in other cereals. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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21 pages, 2002 KiB  
Review
Unraveling the Roles of Regulatory Genes during Domestication of Cultivated Camellia: Evidence and Insights from Comparative and Evolutionary Genomics
by Chao Yan, Ping Lin, Tao Lyu, Zhikang Hu, Zhengqi Fan, Xinlei Li, Xiaohua Yao, Jiyuan Li and Hengfu Yin
Genes 2018, 9(10), 488; https://doi.org/10.3390/genes9100488 - 10 Oct 2018
Cited by 11 | Viewed by 5201
Abstract
With the increasing power of DNA sequencing, the genomics-based approach is becoming a promising resolution to dissect the molecular mechanism of domestication of complex traits in trees. Genus Camellia possesses rich resources with a substantial value for producing beverage, ornaments, edible oil and [...] Read more.
With the increasing power of DNA sequencing, the genomics-based approach is becoming a promising resolution to dissect the molecular mechanism of domestication of complex traits in trees. Genus Camellia possesses rich resources with a substantial value for producing beverage, ornaments, edible oil and more. Currently, a vast number of genetic and genomic research studies in Camellia plants have emerged and provided an unprecedented opportunity to expedite the molecular breeding program. In this paper, we summarize the recent advances of gene expression and genomic resources in Camellia species and focus on identifying genes related to key economic traits such as flower and fruit development and stress tolerances. We investigate the genetic alterations and genomic impacts under different selection programs in closely related species. We discuss future directions of integrating large-scale population and quantitative genetics and multiple omics to identify key candidates to accelerate the breeding process. We propose that future work of exploiting the genomic data can provide insights related to the targets of domestication during breeding and the evolution of natural trait adaptations in genus Camellia. Full article
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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