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) |