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Recent Advances in Orphan Crop Genetics and Genomics
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Recent Advances in Orphan Crop Genetics and Genomics

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

Deadline for manuscript submissions: closed (21 January 2020) | Viewed by 42539

Special Issue Editor

Dr. Allen Van Deynze

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Guest Editor
Department of Plant Sciences, University of California, Davis, CA 95616, USA

Special Issue Information

Dear Colleagues,

The definition of orphan crops varies, but generally refers to crop plants important in agriculture that are not well studied, and thus they have limited genetic or genomic resources. These crops are often the backyard crops that feed rural populations, especially in developing countries. Unlike the few staple crops that contribute to food security, the diversity of annual and perennial grain, fruit, nut and vegetable orphan crops can deliver the much-needed vitamins, macro and micronutrients essential for nutritional security in developing countries. Furthermore, because of the way these crops are maintained, they can often be climate resilient and can be locally adapted, representing genetic diversity for a species. Despite this, they are usually low yielding and the best quality genotypes are not productive or selected. The advent of technologies in genomics, objective high throughput phenotyping, and sensor and computing technologies have allowed disruptive improvements in breeding strategies that can be rapidly applied to orphan crops, bringing them to mainstream breeding and production programs. This special issue will focus on the development and application of such technologies to orphan crops.

Prof. Allen Van Deynze
Guest Editor

Manuscript Submission Information

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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

  • Orphan crops
  • Genomics
  • Breeding
  • Objective Phenotyping
  • Nutritional Security

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Published Papers (4 papers)

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Research

11 pages, 522 KiB  
Article
High Contiguity de novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing
by Christian Siadjeu, Boas Pucker, Prisca Viehöver, Dirk C. Albach and Bernd Weisshaar
Genes 2020, 11(3), 274; https://doi.org/10.3390/genes11030274 - 4 Mar 2020
Cited by 38 | Viewed by 22953
Abstract
Trifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to [...] Read more.
Trifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We sequenced the D. dumetorum genome and generated the corresponding annotation. The two haplophases of this highly heterozygous genome were separated to a large extent. The assembly represents 485 Mbp of the genome with an N50 of over 3.2 Mbp. A total of 35,269 protein-encoding gene models as well as 9941 non-coding RNA genes were predicted, and functional annotations were assigned. Full article
(This article belongs to the Special Issue Recent Advances in Orphan Crop Genetics and Genomics)
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17 pages, 1881 KiB  
Article
Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)
by Sunil Kumar Sahu, Min Liu, Anna Yssel, Robert Kariba, Samuel Muthemba, Sanjie Jiang, Bo Song, Prasad S. Hendre, Alice Muchugi, Ramni Jamnadass, Shu-Min Kao, Jonathan Featherston, Nyree J. C. Zerega, Xun Xu, Huanming Yang, Allen Van Deynze, Yves Van de Peer, Xin Liu and Huan Liu
Genes 2020, 11(1), 27; https://doi.org/10.3390/genes11010027 - 24 Dec 2019
Cited by 27 | Viewed by 11129
Abstract
Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they [...] Read more.
Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism. Full article
(This article belongs to the Special Issue Recent Advances in Orphan Crop Genetics and Genomics)
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7 pages, 13235 KiB  
Communication
ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes
by Anna E. J. Yssel, Shu-Min Kao, Yves Van de Peer and Lieven Sterck
Genes 2019, 10(12), 950; https://doi.org/10.3390/genes10120950 - 20 Nov 2019
Cited by 10 | Viewed by 3723
Abstract
ORCAE (Online Resource for Community Annotation of Eukaryotes) is a public genome annotation curation resource. ORCAE-AOCC is a branch that is dedicated to the genomes published as part of the African Orphan Crops Consortium (AOCC). The motivation behind the development of the ORCAE [...] Read more.
ORCAE (Online Resource for Community Annotation of Eukaryotes) is a public genome annotation curation resource. ORCAE-AOCC is a branch that is dedicated to the genomes published as part of the African Orphan Crops Consortium (AOCC). The motivation behind the development of the ORCAE platform was to create a knowledge-based website where the research-community can make contributions to improve genome annotations. All changes to any given gene-model or gene description are stored, and the entire annotation history can be retrieved. Genomes can either be set to “public” or “restricted” mode; anonymous users can browse public genomes but cannot make any changes. Aside from providing a user- friendly interface to view genome annotations, the platform also includes tools and information (such as gene expression evidence) that enables authorized users to edit and validate genome annotations. The ORCAE-AOCC platform will enable various stakeholders from around the world to coordinate their efforts to annotate and study underutilized crops. Full article
(This article belongs to the Special Issue Recent Advances in Orphan Crop Genetics and Genomics)
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18 pages, 4401 KiB  
Article
Genomic Variance and Transcriptional Comparisons Reveal the Mechanisms of Leaf Color Affecting Palatability and Stressed Defense in Tea Plant
by Xuewen Wang, Ben-ying Liu, Qingshi Zhao, Xuemei Sun, Youyong Li, Zhifen Duan, Xinli Miao, Shan Luo and Jianbin Li
Genes 2019, 10(11), 929; https://doi.org/10.3390/genes10110929 - 14 Nov 2019
Cited by 18 | Viewed by 3897
Abstract
Leaves are one of the most important organs of plants, and yet, the association between leaf color and consumable traits remains largely unclear. Tea leaves are an ideal study system with which to investigate the mechanism of how leaf coloration affects palatability, since [...] Read more.
Leaves are one of the most important organs of plants, and yet, the association between leaf color and consumable traits remains largely unclear. Tea leaves are an ideal study system with which to investigate the mechanism of how leaf coloration affects palatability, since tea is made from the leaves of the crop Camellia sinensis. Our genomic resequencing analysis of a tea cultivar ZiJuan (ZJ) with purple leaves and altered flavor revealed genetic variants when compared with the green-leaf, wild type cultivar YunKang(YK). RNA-Seq based transcriptomic comparisons of the bud and two youngest leaves in ZJ and YK identified 93%, 9% and 5% expressed genes that were shared in YK- and ZJ-specific cultivars, respectively. A comparison of both transcript abundance and particular metabolites revealed that the high expression of gene UFGT for anthocyanin biosynthesis is responsible for purple coloration, which competes with the intermediates for catechin-like flavanol biosynthesis. Genes with differential expression are enriched in response to stress, heat and defense, and are casually correlated with the environmental stress of ZJ plant origin in the Himalayas. In addition, the highly expressed C4H and LDOX genes for synthesizing flavanol precursors, ZJ-specific CLH1 for degrading chlorophyll, alternatively spliced C4H and FDR and low photosynthesis also contributed to the altered color and flavor of ZJ. Thus, our study provides a better molecular understanding of the effect of purple coloration on leaf flavor, and helps to guide future engineering improvement of palatability. Full article
(This article belongs to the Special Issue Recent Advances in Orphan Crop Genetics and Genomics)
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