Table 1 Examples of domesticated crops with domestication origin, available reference genomes and sequencing strategies.
Crop | Botanical name | Lifecycle | Ploidy level | Time of domestication | Geographical origin | Reference genome | Genome size | Sequencing strategy |
|---|---|---|---|---|---|---|---|---|
African rice | Oryza glaberrima | Annual | Diploid | ~3 000 BP | Upper Niger River? | Wang et al. [200] | ~860 Mb | Sanger, Roche/454 |
Amaranth | Amaranthus spp. | Annual | Tetraploid | Aztecs? ~13th – 15th century | Mesoamerica | Clouse et al. [46] | ~456 Mb | Illumina, physical map |
Apple | Malus x domestica | Perennial | Diploid; polyploid karyotypes exist | Late Bronze Age? ~2 000 – 1 500 BC | West-Asia | Daccord et al. [157] | ~651 Mb | Illumina, PacBio, optical map |
Asian rice | Oryza sativa | Annual | Diploid | >6 200 BC | China | Kawahara et al. [201] | ~500 Mb | Sanger, Illumina, Roche/ 454, optical mapping |
Barley | Hordeum vulgare | Annual | Diploid | ~10 000 BC | Southwest Asia | Mascher et al. [52] | ~5 Gb | Illumina, optical mapping, genetic map, HiC |
Beet | Beta vulgaris | Biennial | Diploid | Before 800 BC | Middle East | Dohm et al. [202] | ~750 Mb | Roche/454, Illumina, Sanger |
Bread wheat | Triticum aestivum | Annual | Hexaploid | ~10 000 BC | Southwest Asia | Zimin et al. [65] | ~17 Gb | Illumina, PacBio |
Carrot | Daucus carota | Annual/bie-nnial | Diploid | Classical antiquity | Central Asia (south-west Asia) | Iorizzo et al. [49] | ~473 Mb | Illumina, Roche/454, linkage map |
Cassava | Manihot esculenta | Annual | Diploid | 10 000 – 5 000 BC in South America | Amazon basin | Wang et al. [203] | ~770 Mb | Illumina, Roche/454 |
Chickpea | Cicer arientinum | Annual | Diploid | ~10 000 BC | Fertile Crescent | Varshney et al. [204] | ~740 Mb | Illumina |
Cotton | Gossypium hirsutum | Perennial | Tetraploid | ~6 000 – 5 000BC | India/Mexico | Li et al. [205] | ~2.4 Gb | Illumina, genetic map |
Cowpea | Vigna unguiculata | Annual | Diploid | ~4 000 BC | West Africa | Muñoz-AmatriaÃn et al. [206] | ~620 Mb | Illumina, physical map, genetic map |
Emmer wheat | Triticum dicoccon | Annual | Tetraploid | ~10 000 BC | Southwest Asia | Avni et al. [58] | ~12 Gb | Illumina, genetic map, HiC |
Ginseng | Panax ginseng | Perennial | Tetraploid | Cultivated since ~3000 BC | China | Jayakodi et al. [207] | ~3.5 Gb | Illumina |
Intermediate wheatgrass | Thinopyrum intermedium | Perennial | Hexaploid | ~6 000 BC | Central and south-eastern Europe to Anatolia | No reference available | ~12.75 Gb | Genetic map [208] |
Maize | Zea mays | Annual | Diploid | ~6 700 BC | Mexico | Jiao et la. [63] | ~2.4 Gb | PacBio, optical mapping, Illumina |
Oat | Avena sativa | Annual | Hexaploid | European Bronze Age ~1 800 BC | Fertile Crescent | In progress: The Oat Genome Project [209] | ~12 Gb | Â |
Pepper | Capsicum spp. | Annual | Diploid | ~4 000 BC | South and Middle America | Qin et al. [99] | ~3.5 Gb | Illumina, 10X, genetic map |
Potato | Solanum tuberosum | Annual | Autotetraploid | ~ 7 000 – 6 000 BC | Andean region | The Potato Genome Sequencing Consortium 2011 [210] | ~844 Mb | Illumina, Roche/454, Sanger |
Pumpkin | Cucurbita maxima | Annual | Tetraploid | ~8 000 BC | South America | Sun et al. [47] | ~378 Mb | Illumina, genet map |
Quinoa | Chenopodium quinoa | Annual | Tetraploid | > 5 000 BC | Mesoamerica | Jarvis et al. [32] | ~ 1.5 Gb | PacBio, Illumina, optical mapping |
Rapeseed | Brassica napus | Annual | Tetraploid | ~400 – 500 BP | Europe | Yang et al. [211] | ~1.13 Gb | Illumina, PacBio, optical mapping |
Raspberry | Rubus idaeus | Perennial | Tetraploid | ~450 BP | Europe and northern Asia | Van Buren et al. [48] | ~293 Mb (black raspberry) | Illumina, genetic map |
Rye | Secale cereale | Annual | Diploid | European Bronze Age ~1 500 – 1 000 BC | Europe | Bauer et al. [212] | ~7.9 Gb | Illumina, genetic map |
Sorghum | Sorghum bicolor | Annual | Diploid | ~7 100 – 6 900 BC | Sahel | McCormick et al. [213] | ~730 Mb | Illumina, Roche/454, Sanger |
Sugar cane | Saccharum spp. | Perennial | Allopolyploid | ~8 000 BC | Southeast Asia | Riaño-Pachón et al. [214] | ~10 Gb | Illumina |
Sunflower | Helianthus annuus | Annual | Diploid | ~6 000 BC | Eastern North America | Badouin et al. [215] | ~3.6 Gb | PacBio, genetic map |
Tomato | Solanum lycopersicum | Annual | Diploid | Before 15th century | Andean region | The Tomato Genome Sequencing Consortium 2012 [216] | ~900 Mb | Roche/454, Illumina |