Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species
Abstract
:1. Introduction
2. Under-Utilised Species
2.1. Cereal Grains
2.2. Vegetable/Pulse Crops
2.3. Tuberous Crops
2.4. Industrial Crops
2.5. Fruits
3. Developments in Pangenome Resources to Aid in the Breeding of Under-Utilised Crops
4. The Breeding Potential of Under-Utilised Crop Species
5. The Future of Pangenomics in Breeding Under-Utilised Crops
Species Name | # of Individual Genomes | Assembly Method | References |
---|---|---|---|
Amborella trichopoda | 10 | Iterative mapping and assembly | [76,77] |
Arabidopsis thaliana | 7 | De novo assembly | [157] |
Brachypodium distachyon | 54 | De novo assembly | [33,158] |
Brachypodium hybridum | 4 | De novo assembly | [158] |
Brassica napus | 53 | Iterative mapping and assembly | [34] |
Brassica napus | 8 | De novo assembly | [11] |
Brassica oleracea | 10 | Iterative mapping and assembly | [32] |
Cajanus cajan | 89 | Iterative mapping and assembly | [37] |
Capsicum | 5 | Iterative mapping and assembly | [156] |
Glycine max | 29 | Graph-based de novo assembly | [9] |
Glycine max | 1110 | Iterative mapping and assembly | [10] |
Gossypium | 1961 | De novo assembly | [38] |
Hordeum vulgare | 20 | De novo assembly | [8] |
Helianthus annuus | 287 | De novo assembly | [159] |
Malus domestica | 91 | De novo assembly | [160] |
Manihot esculenta | 57 | Practical haplotype graphs | [161] |
Medicago truncatula | 15 | De novo assembly | [162] |
Oryza sativa | 3 | De novo assembly | [31] |
Oryza | 31 | De novo assembly | [6] |
Poplar | 10 | De novo assembly | [163] |
Sesamum indicum | 5 | De novo assembly | [35] |
Solanum lycopersicum | 725 | De novo assembly | [36] |
Sorghum bicolor | 398 | Practical haplotype graphs | [92] |
Sorghum bicolor | 176 | Iterative mapping and assembly | [12] |
Triticum aestivum | 18 | Iterative mapping and assembly | [20] |
Zea mays | 4705 | Practical haplotype graphs | [96] |
Scientific Names | Common Names | Type of Resource | References |
---|---|---|---|
Basella alba | Malabar spinach | Reports of viruses infecting Malbar spinach | [164,165] |
Chromosome counts/Nuclear DNA quantification | [166] | ||
Calathea allouia | Guinea arrowroot | Future prospects for underutilised medicinally valuable plants | [167] |
Couma utilis | Milk tree | Identifying pollinators in edible Amazon fruit plants | [168] |
Crambe cordifolia | Greater sea-kale | Ancestral chromosomal blocks in Brassiceae species | [169] |
Leopoldia comosa | Tassel grape hyacinth | Identifying physiological responses | [170] |
Mineral content and chemical analysis | [171] | ||
Schinziophyton rautanenii | Mongongo tree | Sustainability review | [172] |
Chemical composition of oil | [173] | ||
Ullucus tuberosus | Ulluco | Viruses detected in ulluco | [174] |
High throughput sequencing to detect novel viruses in ulluco | [175] |
Scientific Names | Common Names | Type of Genomic Resources | References |
---|---|---|---|
Cereal grains | |||
Canna edulis | African arrowroot | Chloroplast genome sequence | [68] |
Digitaria exilis | White fonio | Genome assembly and annotation | [17,47] |
Genotype-by-sequencing and SNP data | [48] | ||
Panicum sumatrense | Little Millet | Chloroplast genome sequences | [43] |
De novo transcriptome assembly | [44] | ||
Vegetable/Pulse crops | |||
Lablab purpureus | Hyacinth bean/Lablab bean | Chloroplast genome assembly | [61] |
Draft genome assembly | [60] | ||
Upregulation of drought tolerant genes | [58] | ||
RFLP markers | [176] | ||
Solanum nigrum | Black nightshade plant | Transcriptome sequence | [177,178] |
Chloroplast genome sequence | [179,180] | ||
Vigna aconitifolia | Moth bean | Genetic linkage map | [54] |
Novel Vigna genetic resources | [53] | ||
Tuberous crops | |||
Pachyrhizus erosus | Yam bean | Draft genome assembly | [15] |
Vigna vexillata | Zombi pea or Wild cowpea | Anti-inflammatory bioactivity | [181] |
QTL analysis | [182] | ||
Molecular linkage analysis | [183] | ||
Hybridisation accession analysis | [184] | ||
Industrial Crops | |||
Carthamus tinctorius | Safflowers | Transcriptome sequencing | [185,186] |
Chromosome-scale reference genome | [73] | ||
Chloroplast genome sequence | [187] | ||
Genetic mapping of SNPs | [71] | ||
Hibiscus cannabinus | Kenaf | Mitochondrial genome assembly | [70] |
Genome assembly and annotation | [16] | ||
De novo transcriptome assembly | [69] | ||
Fruit/Nuts | |||
Bactris gasipaes | Peach palm | Chloroplast DNA for phylogenetic study | [188] |
Macaúba palm transcriptome sequencing | [189] | ||
RNA-seq of tropical palms | [190] | ||
Plastome sequence | [191] | ||
Citrullus colocynthis | Desert Watermelon or Wild watermelon | Gene markers | [192] |
Transcriptome assembly | [193] | ||
Genome Resequencing | [194] | ||
Elaeagnus angustifolia | Russian olive or wild olive | Geographic study using machine learning | [195] |
Hi-C assembly | [196] | ||
Transciptome profiling | [197] | ||
Plant signalling regarding salt | [198] | ||
Ensete ventricosum | Ethiopian Banana | Genome assembly | [199,200] |
Pangenome assembly | [80] | ||
Markers/Microsatellites | [201] | ||
Metabolite data | [202] | ||
Euterpe oleracea | Açaí | Chemical genomic profiling | [203] |
Karyotype and genome size | [204] | ||
Psidium guajava | Guava | Genome assembly | [76,77] |
Genome Markers | [76] | ||
RNA-seq/transcriptome assembly | [78] | ||
Vaccinium meridionale | Agraz or Colombian Berry | Phylogenetic relationships within the Vaccinieae tribe | [205] |
Chemical, antimicrobial and molecular characterisation | [206] | ||
Characterisation of phenotypic plasticity | [207] | ||
Antiproliferative potential of Agraz juice | [208] |
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Tay Fernandez, C.G.; Nestor, B.J.; Danilevicz, M.F.; Gill, M.; Petereit, J.; Bayer, P.E.; Finnegan, P.M.; Batley, J.; Edwards, D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. Int. J. Mol. Sci. 2022, 23, 2671. https://doi.org/10.3390/ijms23052671
Tay Fernandez CG, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. International Journal of Molecular Sciences. 2022; 23(5):2671. https://doi.org/10.3390/ijms23052671
Chicago/Turabian StyleTay Fernandez, Cassandria Geraldine, Benjamin John Nestor, Monica Furaste Danilevicz, Mitchell Gill, Jakob Petereit, Philipp Emanuel Bayer, Patrick Michael Finnegan, Jacqueline Batley, and David Edwards. 2022. "Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species" International Journal of Molecular Sciences 23, no. 5: 2671. https://doi.org/10.3390/ijms23052671