Table 2. Estimated genomic diversity in the breeding populations of select field and vegetable crops.
Not all forms of genomic variation were assessed for all species listed. In addition, because of the short-read sequencing technologies used, the number of PAV/CNV structural variants, representing large deletions, inversions, and duplications, is likely underestimated. ND, Not determined.
| Plant Species | Evaluated Sample Size and Description | Estimated Genome Sizea | Estimated SNPs Present | Average Pairwise Diversityb | Estimated Indels | Structural Variants (CNVs and PAVs) | References |
|---|---|---|---|---|---|---|---|
| Mbp | Millions | Millions | |||||
| Bean (Phaseolus vulgaris) | 37 | 521 | 45.0 | ∼5.0 × 10−3 Mesoamerican | 2.1 | 18.5 k | Schmutz et al., 2014; Lobaton et al., 2018 |
| ∼1.7 × 10−3 Andean | |||||||
| Wild Cabbage (Brassica oleracea) | 10 (1 wild species) | 489 | 4.8 | ND | ND | 11.5 k | Golicz et al., 2016 |
| Chickpea (Cicer arietinum) | 35 | 738 | 2.0 | ND | 0.3 | 9.9 k | Thudi et al., 2016 |
| Cucumber (Cucumis sativus) | 115 | 194 | 3.3 | ND | 0.03 | 0.8 k | Zhang et al., 2015b |
| Qi et al., 2013a | |||||||
| Maize (Z. mays) | 2,815 accessions | 2,400 | 0.7 | ∼6.0 × 10−3 | ND | 1.1 M | Gore et al., 2009; Romay et al., 2013; Wang et al., 2017 |
| 13 lines | 2.91 | 0.4 | |||||
| Rice (O. sativa ssp. Japonica) | 3010 | 375 | 29.0 | ∼1.0 × 10−3 | 2.4 | 94 k | Liu et al., 2017b; Wang et al., 2018 |
| Soybean (Glycine max) | 106 (Landraces, US cultivars and wild) | 978 | 10.4 | 1.8 × 10−3 | 0.7 | 7.9 k | Valliyodan et al., 2016 |
| Tomato (S. lycopersicum) | 69 (incl 12 wild species) | 950 | 17.0 | ∼2 × 10−4 | 3.6 | 1.7 k | Causse et al., 2013; Sauvage et al., 2017 |
| Pepper (Capsicum annuum) | 20 (3 wild species) | 3,500 | 9.8 | ∼2.6 × 10−3 | 0.24 | ND | Aguilar-Meléndez et al., 2009; Qin et al., 2014 |
a
Estimated genome sizes are from references or the EnsemblPlants database (https://plants.ensemble.org April 2019).
b
Pairwise diversity (also referred to as nucleotide diversity) is the average number of nucleotide differences per site between any two DNA sequences in all possible pairs in the sample population (Tajima, 1983). It is a measure that allows for diversity/variation to be compared across organisms that vary widely in genome size.