Table 1.
Modern genomics platforms for wheat genetic resources with different breeding and genetics objectives
| Method | Species | Genomics technology/strategy | Reference |
|---|---|---|---|
| Draft or whole-genome sequencing | Aegilops tauschii | Illumina HiSeq2000, Roche 454 | Jia et al. (2013) |
| Triticum turgidum (subsp. dicoccoides) | Whole genome sequencing | Avni et al. (2017) | |
| T. urartu | Illumina HiSeq2000, Roche 454 | Ling et al. (2013) | |
| T. monococcum, T urartu, Ae. sharonensis, Ae. speltoides, Ae. tauschii | Illumina HiSeq2000 | Marcussen et al. (2014) | |
| Transcriptome sequencing | Ae. tauschii | Roche 454 | Iehisa et al. (2014) |
| T. urartu | Roche 454 | Ling et al. (2013) | |
| Ae. sharonensis | Roche 454 | Bouyioukos et al. (2013) | |
| T. urartu | Illumina HiSeq2000 | Krasileva et al. (2013) | |
| T. monococcum | Illumina HiSeq2000 | Fox et al. (2014) | |
| Ae. variabilis | Illumina HiSeq2000 | Xu et al. (2012) | |
| T. turgidum subsp. dicoccoides | Illumina HiSeq2000 | Akpinar et al. (2015) | |
| Genotyping platforms for diversity studies | Ae. tauschii | 10K SNP infinium | Wang et al. (2014) |
| 10 wild species | 820K Affymetrix | Winfield et al. (2016) | |
| Ambylopyrum muticum but applicable to many species | 35K wheat relative array from Affymetrix | King et al. (2016) | |
| Landraces | 35K wheat breeder’s array | Allen et al. (2017) | |
| Thinopyrum elongatum | SLAF-seq | Chen et al. (2013) | |
| Agropyron cristatum | SLAF-seq | Zhang et al. (2015) | |
| Creole landraces | DArTseq | Vikram et al. (2016) | |
| CIMMYT landraces collection | Genotyping-by-sequencing | Sehgal et al. (2015) | |
| Watkins landrace collection | Illumina 90K SNP | Jordan et al. (2015) | |
| Vavilov landrace collection | DArTseq | Riaz et al. (2016) | |
| Watkins landrace collection | Exome capture | Shi et al. (2017) | |
| Wild emmer | Illumina GoldenGate | Ren et al. (2013a, b) | |
| Wheat/Aegilops geniculata | Chromosome-specific SNP discovery | Tiwari et al. (2014) | |
| Gene/allele discovery | Ae. tauschii | Sr33 | Periyannan et al. (2013) |
| T. urartu | Sr22 | ||
| Secale cereale | Sr50 | Mago et al. (2015) | |
| T. dicoccoides | Gpc-B1 | Trick et al. (2012) | |
| Watkins landrace collection | Pin-D1 | Qamar et al. (2014) | |
| Sumai 3 landrace | Fhb1 | Rawat et al. (2016) | |
| Genome-wide association studies | Synthetic hexaploids | Illumina 9K for stripe rust response | Zegeye et al. (2014) |
| Synthetic hexaploids | Illumina 9K for tolerance to boron toxicity | Emebiri and Ogbonnaya (2015) | |
| Watkins landrace collection | Illumina 90K SNP array for rust resistance | Jordan et al. (2015) | |
| Ae. tauschii | 10K Infinium array/agronomic traits | Liu et al. (2015b) | |
| Ae. tauschii | 10K Infinium array/drought tolerance | Qin et al. (2016) | |
| Ae. tauschii | 10K Infinium array/phosphorus deficiency traits | Liu et al. (2015a ) | |
| T. spelta | 15K SNP array/agronomic traits | Würschum et al. (2017) | |
| Ae. sharonensis | Stem rust resistance | Yu et al. (2017) | |
| Wild emmer | Illumina SNP GoldenGate/agronomic traits | Hu et al. (2015) | |
| Genomic predictions | Mexican and Iranian landraces | DArTseq genotyping/agronomic traits | Crossa et al. (2016) |
| Th. intermedium | Genotyping-by-sequencing | Zhang et al. (2016) | |
| Synthetically derived wheats | GBS/heat and drought adaptability | Jafarzadeh et al. (2016) | |
| Landraces | Minerals/GBS | Manickavelu et al. (2017) | |
| Landraces | Rust resistance | Pasam et al. (2017), Daetwyler et al. (2014) |