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Feeding a growing world population and adapting to climate change requires a sustainable and diversified food supply system. Orphan crops are usually well-adapted for low-input agricultural conditions. These crops are typically grown in Africa, Asia, and South America and they not only play vital roles in local areas but also contribute to food and nutritional needs worldwide. However, orphan crops have often been neglected by the scientific community with little to none investment into research and genetic improvements. Rapid advancement in, and development of, genomic tools provides opportunities to generate genomic resources to facilitate breeding of orphan crops. This Orphan Crop Genomics and Improvement Collection welcomes submissions to Nature Communications, Scientific Reports, and npj Sustainable Agriculture on orphan crops genomics, genetics, and breeding. Topics of interest include genome assembly, population genetics, mark-trait association study, gene cloning, and breeding technique development and implementation.
All participating journals invite submissions of original research, with Nature Communications and npj Sustainable Agriculture also considering Reviews, Perspectives and Comments which fall within the scope of the collection. All submissions will be subject to the same peer review process and editorial standards as other articles submitted to the participating journals.
Orphan crops hold the potential to diversify our food systems. Considering their unique characteristics, our deep understanding of major crops, and the availability of modern genomic tools, taking a different research path from what major crops have gone through could accelerate the genetic improvement of orphan crops.
Underutilised crops or orphan crops are important for diversifying our food systems towards food and nutrition security. Here, the authors discuss how the development of underutilised crop genomic resource should align with their breeding and capacity building strategies, and leverage advances made in major crops.
While greater yam provides food and income security for millions of people around the world, there are limited genomic resources available. Here, the authors report a chromosome-scale assembly of the greater yam genome as well as quantitative trait loci associated with anthracnose resistance and tuber traits.
Lima bean is an important crop for improving food security in Latin America and elsewhere. Here, the authors assemble its genome, conduct population genomics analysis using genotyping-by-sequencing data, and identify differentially expressed genes between two pod developmental stages.
In contrast to common bean, tepary bean is highly adapted to heat and drought. Here, the authors assemble the genomes of tepary bean landrace and wild accession, discuss the possible mechanism for resilience to heat stress, and reveal a reduced disease resistance gene repertoire.
Macadamia is a recently domesticated nut crop. Here, the authors report the genome assembly of Hawaiian cultivar ‘Kau’ and conduct population genomic analyses to reveal the origin of Hawaiian cultivars and the genomic basis for one-step operation for the clonal crop domestication.
Echinochloa is an important genus in the grass family as many of them are either problematic weeds or domesticated millets. Here, the authors assemble three polyploidy genomes in this genus using the diploid-assisted scaffolding method DipHic and provide genomic insights into the dual roles of some species as weeds and orphan crops.
Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits.
Lablab is a legume native to Africa and cultivated throughout the tropics for food and forage; however, as an orphan crop, limited genomic resources hampers its genetic improvement. Here, an African-led South-North plant genome collaboration produces an improved genome assembly and population genomic resource to accelerate its breeding.
Activating the expression of host susceptibility (S) genes is one of the strategies plant pathogens employed to promote infection of their host. Here, the authors show that targeted methylation at the TAL20 effector binding element of the cassava SWEET10a gene lead to resistance to Xanthomonas phaseoli.