Table 1.
Examples of published plant multi-parent populations.
| Population type | Species | Founders | Details | Genotype data | References |
|---|---|---|---|---|---|
| NAM | Barley (Hordeum vulgare) | 26 | 25 wild barleys crossed to elite spring barley cultivar, 1420 RILs | 5.709 genotyping array SNPs in 1420 RILs | (Maurer et al. 2015) |
| 26 | 25 wild barleys crossed to six-rowed spring malting barley cultivar (related to reference cultivar) and then backcrossed twice before RIL development, 769 RILs | 384 SNPs assayed in 769 RILs; 4022 genotyping array SNPs and 263,531 variants from founder exome capture imputed into the population | (Nice et al. 2016) | ||
| 5 | 4 wild barleys crossed to reference cultivar, 916 RILs | 384 SNPs assayed in 916 RILs | (Liller et al. 2017) | ||
| 89 | 88 six-row barley cultivars crossed to a six-rowed spring malting barley cultivar (related to reference cultivar), 6160 RILs | 7773 genotyping array SNPs in 6160 RILs | (Hemshrot et al. 2019) | ||
| NAM | Bread wheat (Triticum aestivum) | 11 | 9 Kenyan and 1 US spring wheats with stem rust resistance crossed against a Canadian spring wheat, 852 RILs | 13.413 GBS SNPs in 852 RILs | (Bajgain et al. 2016) |
| 61 | 60 landraces crossed to elite spring wheat, reference line, 6240 RILs | 2373 KASP SNPs and 33 SSRs on 2498 loci in 6240 RILs | (Wingen et al. 2017) | ||
| 29 | 25 global spring wheat landraces and 3 cultivars crossed to a broadly adapted cultivar, 2100 RILs | 57,657 genotyping array SNPs, 71,312 GBS SNPs and 136,071 indels in 2100 RILs; founder exome sequences with 638,045 SNPs and 63,022 insertions/deletions | (Jordan et al. 2018) | ||
| NAM | Durum wheat (Triticum durum) | 37 | 50 Ethiopian farmer varieties crossed with an elite international variety, 6280 RILs | 13,000 genotyping array SNPs for 100 RILs from each of 12 families | (Kidane et al. 2019) |
| NAM | Maize (Zea mays) | 26 | 25 US inbred lines crossed to reference line, 6825 RILs | 1536 genotyping array SNPs in 6825 RILs; up to 26 million SNPs imputed from ~4.3x founder WGS; 294,962 GBS SNPs in 4623 RILs; founder whole-genome assemblies available | (McMullen et al. 2009; Tian et al. 2011; Chia et al. 2012; Peiffer et al. 2014; Li et al. 2015) http://nam-genomes.org |
| 23 | 10 Dent founders crossed against a common Dent line and 11 Flint founders crossed against a common Flint line. Dent and Flint are major European maize germplasm pools. 2233 double haploid lines | 39,439 genotyping array SNPs in 2233 double haploid lines | (Bauer et al. 2013) | ||
| 12 | 11 Chinese inbred lines crossed to a common reference line, 2000 RILs | 238,945 GBS SNPs in 1696 RILs | (Li et al. 2015) | ||
| 6 | 4 parviglumis inbred teosinte lines and 1 mexicana teosinte inbred line crossed and backcrossed to a maize inbred line, 1257 RILs | 51,544 GBS SNPs in 1257 RILs | (Chen et al. 2019) | ||
| NAM | Oilseed rape/Canola (Brassica napus) | 16 | 15 semi-winter and spring inbred lines crossed to elite inbred variety, 2425 RILs | 141,687 GBS SNPs in 2425 RILs; 3,885,328 SNPs and 558,981 indels from founder WGS (10–18x) imputed in the population | (Schmutzer et al. 2015; Hu et al. 2018) |
| NAM | Peanut (Arachis hypogaea) | 9 | 8 diverse lines crossed to 2 runner cultivars to create two NAM panels, ~6400 RILs | 3874 genotyping array SNPs in 581 RILs in one NAM; 2680 genotyping array SNPs in 496 RILs in the other NAM | (Holbrook et al. 2013; Gangurde et al. 2019) |
| NAM | Rice (Oryza sativa) | 11 | 10 tropical japonica lines crossed to elite indica reference line, 1879 RILs | 70–85k GBS SNPs per family, most missing data imputed | (Fragoso et al. 2017) |
| NAM | Sorghum (Sorghum bicolor) | 57 | 56 diverse lines backcrossed to a male-sterile version of an elite line, 4000 RILs | 932 DArT markers in 1389 RILs in 24 families | (Jordan et al. 2011; Mace et al. 2013) |
| 6 | 1 short, early elite line crossed and backcrossed to 5 tall, late, exotic lines, 724 lines | 9139 GBS SNPs in 724 lines | (Higgins et al. 2014) | ||
| 11 | 10 diverse global lines to elite line, 2214 RILs | 90,000 GBS SNPs in 2214 RILs | (Bouchet et al. 2017) | ||
| NAM | Soybean (Glycene max) | 41 | 40 elite or diverse accessions to high yielding cultivar, 5600 RILs | 4312 genotyping array SNPs in 5176 RILs | (Song et al. 2017; Xavier et al. 2018) |
| MAGIC | Arabidopsis thaliana | 19 | 19 accessions crossed in 342 pairs, then randomly inter-crossed for four generations, 1026 RILs | 1260 genotyping array SNPs in 527 RILs; annotated reference genomes and transcriptomes for founders; 0.3x WGS on 488 RILs | (Scarcelli et al. 2007; Kover et al. 2009; Gan et al. 2011; Imprialou et al. 2017) |
| 8 | 8 accessions crossed in 6 four-founder funnels, 532 RILs | 91 SSRs and 230 SNPs in 532 RILs | (Huang et al. 2011) | ||
| MAGIC | Barley (Hordeum vulgare) | 8 | 7 German landraces and 1 modern variety, crossed in 2 funnels, 533 doubled haploid lines | 4.550 genotyping array SNPs in 533 doubled haploid lines | (Sannemann et al. 2015) |
| MAGIC | Bread wheat (Triticum aestivum) | 4 | 4 elite Australian cultivars, crossed in 3 funnels, 1,579 RILs | 826 DArT markers, 283 SNPs, and 53 microsatellites in 871 RILs | (Huang et al. 2012) |
| 60 | 1 male-sterile line crossed and backcrossed with 59 European and worldwide lines before 12 generations of random intermating, 1000 RILs | 8,632 genotyping array SNPs in 380 RILs and 56 founders | (Thépot et al. 2014) | ||
| 8 | 8 winter wheat varieties selected by UK wheat breeders, crossed in 180 funnels, 1091 RILs | 18,601 genotyping array SNPs in 643 RILs | (Mackay et al. 2014; Gardner et al. 2016) | ||
| 8 | 1 Danish and 7 German elite winter wheat lines, crossed in 2 funnels with one further round of inter-crossing, 516 RILs | 5436 genotyping array SNPs in 394 RILs | (Stadlmeier et al. 2018) | ||
| 8 | 8 elite winter wheats with high German market share, crossed in 2 funnels, 910 RILs | 7849 SNPs in 910 RILs | (Sannemann et al. 2018) | ||
| 8 | 3 Australian elite spring wheat cultivars, 4 worldwide spring wheat cultivars, and 1 Chinese winter wheat, crossed in 313 funnels followed by 0, 2 or 3 generations of inter-crossing, 3412 RILs | 27,687 genotyping array SNPs | (Shah et al. 2019) | ||
| MAGIC | Chinese mustard (Brassica juncea) | 8 | 8 founders chosen for agronomic traits, crossed in 1 funnel, 408 RILs | 346 intron length polymorphism (ILP) markers in 113 RILs | (Yan et al. 2020) |
| MAGIC | Cotton (Gossypium hirsutum) | 11 | 10 cultivars and one landrace crossed in 50 pairs, then randomly mated for 5 generations, 550 RILs in 55 families | 6071 GBS SNPs and 223 microsatellite markers for 547 RILs; 473,517 SNPs from WGS founders at 20x and 550 RILs at 3x | (Islam et al. 2016; Naoumkina et al. 2019; Thyssen et al. 2019) |
| MAGIC | Cowpea (Vigna unguiculata) | 8 | 1 US cultivar and 7 cultivars from sub-Saharan Africa chosen for agronomic traits, crossed in 6 funnels, 305 RILs | 32 130 genotyping array SNPs in 305 RILs | (Huynh et al. 2018) |
| MAGIC | Durum wheat (Triticum durum) | 4 | 4 founders selected for diversity in origin and traits, crossed in 1 funnel, 338 RILs | 7594 genotyping array SNPs in 338 RILs | (Milner et al. 2016) |
| MAGIC | Faba bean (Vicia faba) | 11 | 11 European inbred lines, outcrossed for 9 generations, 189 RILs | 156 SNPs assayed in 188 RILs | (Sallam and Martsch, 2015) |
| 4 | 4 inbred lines selected for geographic, genetic, and phenotypic diversity, crossed in one funnel, ~1200 RILs | To be genotyped using a genotyping array | (Khazaei et al. 2018) | ||
| MAGIC | Maize (Zea mays) | 8 | 8 diverse inbred lines (+1 used to replace an incompatible two-way cross), crossed in 35 funnels, 1636 RILs | 54,234k SNPs from WGS of founders (21–30x) imputed in 529 RILs; transcriptomes for 7 founders | (Dell’Acqua et al. 2015) |
| 4 | 4 inbred lines, crossed in 1 funnel, then 0, 1 or 2 rounds of inter-crossing before RIL development, 1005 RILs | 118,509 GBS SNPs and indels in 948 RILs | (Anderson et al. 2018; Mahan et al. 2018) | ||
| MAGIC | Rice (Oryza sativa) | 8 | 8 elite indica varieties, crossed in 35 funnels, 2000 RILs | 17,387 GBS SNPs for 200 RILs; 88,083 GBS SNPs for 1316 RILs | (Bandillo et al. 2013; Raghavan et al. 2017) |
| 8 | Funnels from indica population above with two further rounds of inter-crossing before RIL development | 14,242 GBS SNPs for 144 RILs | (Bandillo et al. 2013; Descalsota et al. 2018) | ||
| 8 | 8 elite japonica varieties, crossed in 35 funnels, 500 RILs | (Bandillo et al. 2013) | |||
| 16 | 150 inter-crosses made between funnels from the indica and japonica populations above, 1027 RILs | 66,309 GBS SNPs in 1027 RILs | (Bandillo et al. 2013; Zaw et al. 2019) | ||
| 12 | 12 breeder relevant lines, crossed in 2 funnels that share four founders between them, 206 RILs | 86 SSR markers in 206 RILs | (Li et al. 2014) | ||
| 8 | 4 indica and four japonica elite cultivars from Japan, crossed in 2 funnels, 981 RILs | 16,345 GBS SNPs in 981 RILs | (Ogawa et al. 2018) | ||
| 8 | 8 diverse indica lines from breeding programmes, crossed in 1 funnel, 1000 RILs with extra RILs developed from 4-way crosses | 1329 genotyping array SNPs in 532 RILs (and 271 and 268 RILs derived from 4-way crosses) | (Meng et al. 2016) | ||
| 4 | 4 lines crossed in one funnel, 247 RILs | 843,505 SNPs from 30x WGS of the founders and 2x WGS of 247 RILs | (Han et al. 2020) | ||
| MAGIC | Sorghum (Sorghum bicolor) | 29 | 10 male-sterile lines crossed with 19 lines chosen for agronomic traits, 9 rounds of random inter-crossing, 1000 RILs | 79,728 GBS SNPs for 200 RILs | (Ongom and Ejeta 2018) |
| MAGIC | Strawberry (Fragaria × ananassa) | 6 | 6 founders selected for genetic diversity crossed in 3 pairs then inter-crossed for 2 generations, 338 individuals | 336 expressed sequence tag – simple sequence repeat (EST-SSR) in 338 lines | (Wada et al. 2017) |
| MAGIC | Tomato (Solanum lycopersicum) | 8 | 4 S. lycopersicum and 4 S. lycopersicum var. cerasiforme diverse lines, crossed in 1 funnel, 397 RILs | 4 million SNPs from WGS of founders (6.7–16.6x); 1536 KASP SNPs genotyped in 397 RILs | (Causse et al. 2013; Pascual et al. 2015) |