Table 1.
Some orphan crops, their potential trait for crop improvement, research gaps and genome sequence status.
| Crop [Common name) | Scientific name | Potential | Genomic Markers | Genome Sequence Status | Chromosome Number | Genome Size | Breeding Effort | Available Genomic Tools | Availability Transformation system |
Research Gap | References |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Hyacinth bean | Lablab purpureus L. | Drought and salinity tolerance, nutritious, nutraceutical properties | EST-SSRs, RAPD, EST-SNP, InDel. | No | 2 n = 2x = 24 | 367Mb | Improved photoperiod insensitive and development of determinate pureline varieties | Linkage map, QTL mapping | Nil | No superior cultivars and resistant varieties to pest and weeds | 44,45 |
| Zombi pea | Vigna vexillata [L.] A. Rich | Nutritious, biotic and abiotic stresses resistance | RAD-seq, SSR, SNP | No | 2 n = 2x = 22 | 803Mb | Identification of candidate gene, VvTaXI for Bruchid resistance | QTL mapping | Nil | No improved zombi pea for abiotic stress resistance | 24,46,47 |
| African Yam Bean | [Sphenostylis stenocarpa [Hochst ex. A. Rich.] Harms] | Nutritious, versatile | AFLP, ISSR, SSR, SNP | 77–81% | 2 n = 2x = 22 | > 649Mb | Identification of various agronomic traits | Association mapping | Nil | There is need to improve crop yield, shorten the cooking and maturity periods, and increase the crop’s resilience to pests and diseases. | 48,39 |
| Winged bean | Psophocarpus tetragonolobus (L.) DC. | Nutritious, versatile, adaptable to diverse soil types | AFLP, RAPD, SSR, SNP, | 98.9% | 2 n = 2x = 18 | 1.22Gb | Identification of quantitative trait loci [QTLs) for traits such as pod and seed characteristics | Cloning, transcriptomics, Genetic linkage maps | Nil | Little or no information on how to improve the long maturation period, indeterminate growth habit, low seed yield, and the need for a stake to support the vigorously growing vines | 19,49 |
| Bambara groundnut | Vigna subterranea [L.] Verdc | Nutritious, climate-resilient, versatile, adaptable to diverse environment | ISSR, SSR, SNP | No | 2 n 2x = 22 | 550Mb | Identification of QTL for some agronomic traits | Whole Genome Sequencing, Transcriptome sequencing | Nil | No improved line for yield and adaptation to moisture stress | 44,50,51 |
| Finger millet | Eleusine coracana | Resilience to adverse climatic conditions, high nutritional content, versatile | EST-SSR, ISSR, SSR, SNP | 100% | 2 n = 4x = 36 | 1.45Gb | Development of lines with improved agronomic traits | Linkage mapping, QTL mapping, Whole Genome sequencing, Reference genome, Transcriptomic, Proteomics, RNA-Seq | Agrobacterium-mediated transformation and particle bombardment [biolistics] | Identification of novel genes for abiotic stress tolerance and nutritional traits | 52,53 |
| Chickpea | Cicer arietinum | Nutritious, adaptability to diverse climates | AFLP, ISSR, InDel, ISM, ILP, SSR, SNP | 73.8% | 2 n = 2x = 16 | 738Mb | Identified loci associated with yield, drought tolerance, and resistance to diseases | Linkage mapping, QTL mapping, GWAS, Whole Genome sequencing, Reference genome, Proteomics, RNA-Seq, DGE, CRISPR/Cas9 | Agrobacterium-mediated transformation and particle bombardment [biolistics] | Selection of accessions that can be used as parental material in breeding programs. Lack of drought-tolerant cultivars. |
54,55 |
| Foxtail millet | Setaria italica | High nutritional content, environmental resilience, and potential health benefits | KASP, AFLP, RAPD, InDel, SSR, SNP | 100% | 2 n = 2x = 18 | 490Mb | Identification of genetic loci associated with drought resistance, plant height, flowering time, grain yield, and nutritional quality | Linkage mapping, QTL mapping, GWAS, Whole genome Sequencing, Comparative Genomics, CRISPR Cas9, DGE, TILLING, MAS, GS | Agrobacterium-mediated transformation and particle bombardment [biolistics] | Lack of high yielding varieties | 56,57 |
| Grass pea | Lathyrus sativus | Ability to thrive in adverse conditions, high nutritional value | AFLP, RAPD, EST-SSR, KASP, SSR, SNP | 100% | 2 n = 2x = 14 | 6.3Gbp | Identification of stress-responsive genes | Draft Genome Assemblies, Transcriptome sequencing [RNA-Seq], Comparative Genomics, Gene Knockout, TILLING | Nil | Lack of genetic improvement through GWAS and MAS | 58,59 |
| Horsegram | Macrotyloma uniforum | Nutritional and therapeutic properties, resilience to harsh environmental conditions | RAPD, ISSR, SSR, SNP, ILP, COS | 83.53% | 2 n = 2x = 20 or 22 | 400Mb | Identification of genes involved in metabolic process, Identification of candidate gene involved in environmental adaptation | Linkage mapping, QTL mapping, Whole Genome Sequence, Transcriptome sequencing, Comparative Genomics, GWAS, DEG | Nil | Candidate genes underlying functional traits has not been identified | 60,61 |
| Pigeon pea | Cajanus cajan | Nutritious, versatile, nutraceutical properties, adaptability to marginal environments, drought resistance | SSAP, REMAP, SCAO, SSR, SNP | 100% | 2 n 2x = 22 | 833Mb | Identification of regions associated with Fusarium wilt resistance, sterility mosaic disease resistance, drought tolerance, and pod yield | Whole Genome sequence, GWAS, MAS, Transcriptomics, Comparative Genomics, CRISPR | Agrobacterium-mediated transformation | Lack of breeding for high yielding pure line and hybrid | 62,63 |
| Moth bean | Vigna aconitifolia | Nutritious, adaptability to harsh climates, nutraceutical properties | AFLP, RAPD, ISSR, SSR, SNP | 50% | 2 n 2x = 22 | 409Mb | Identification of stress-responsive genes | Linkage mapping, Proteomics, Comparative Genomics, | Nil | Lack of reference genome, little integration of modern genomics tools, Lack of common features of nutritional, anti-nutritional compounds, processing characteristics, and health benefits | 64,65 |
| Black gram | Vigna mungo | High protein content, adaptability to various cropping systems | AFLP, RAPD, ISSR , SSR, SNP |
79.2% | 2 n = 2x = 22 | 574Mb | Identification of SNPs associated with seed size, flowering time, and biotic stress resistance | Draft Genome Assembly, Linkage mapping, GWAS, QTL mapping, DEGs | Agrobacterium-mediated transformation | Incomplete reference genome, lack of high yielding and MYMV resistant varieties | 66,67 |
| Adzuki bean | Vigna angularis | Nutritious, functional food and medicinal applications | AFLP, ISSR, EST-SSR, SSR, SNP | 97.8% | 2 n = 2x = 22 | 542Mb | Identification of SNPs associated with seed size, flowering time, and disease resistance | Draft Genome Assembly, Linkage mapping, GWAS, QTL mapping, DEGs, Comparative Genomics, MAS | Agrobacterium-mediated transformation | Little knowledge on utilization. Little understanding of the anti-obesity mechanism and the specific bioactive components involved has not been identified. |
68–70 |
| Mung bean | Vigna radiata | Nutritious, nutraceutical properties, drought tolerance, disease resistance, climate-resilient | AFLP, RAPD, ISSR, SSR, SNP | 96.9% | 2 n = 2x = 22 | 543Mb | Identification of SNPs associated with seed size, flowering time, and disease resistance | Draft Genome Assembly, Linkage mapping, GWAS, QTL mapping, DEGs, Comparative Genomics, MAS | Agrobacterium-mediated transformation | Little knowledge on the unraveling of the main functional components relevant to health benefits | 71,72 |
| Fonio Millet | Digitaria exilis | Fast maturing, climate-resilient, nutritious, nutraceutical properties, highly adaptable to poor soils and drought conditions | AFLP, RAPD, SSR, SNP | 99% | 2 n = 4x = 36 | 761Mb | Identification of drought resistance traits | GWAS, DEGs, Comparative Genomics | Nil | Improvement and domestication is lacking | 73 |