Table 1.
Applications of high-throughput phenotyping integrated with GWAS in plant.
| Crop | Population size | Technique | Environment | Traits | Number of associated loci/SNP/QTL/candidate genes | Reference |
|---|---|---|---|---|---|---|
| rice | 533 accessions | x-ray CT, color-imaging | Greenhouse | 15 morphological traits (e.g. plant height, tiller number, green leaf area) | 141 loci | [79] |
| rice | 242 accessions | visible light imaging | Field | 49 panicle traits (e.g. panicle length, rachis length, primary branch number) | 10 candidate genes | [80] |
| rice | 225 accessions | RGB imaging | Laboratory | number of spikelets per panicle (NSP), the number of primary (PBN) and secondary branches (SBN), the length of primary (PBL) and secondary (SBL) branches | 17 GWAS sites for NSP, 10 for PBN, 11 for SBN, 7 for PBL, 11 for SBL | [3] |
| rice | 533 accessions | RGB imaging | Laboratory | 29 leaf traits (6 size–related traits, 7 color–related traits, 16 shape–related traits) | 73 loci for size-related traits, 123 for color-related traits, 177 for shape related traits | [81] |
| rice | 360 accessions | visible light/RGB imaging | Greenhouse | projected shoot area | 7 QTLs | [51] |
| rice | 357 accessions | RGB imaging | Greenhouse | projected shoot area | 442 SNPs | [52] |
| rice | 165 lines | unmanned aerial vehicle, RGB imaging | Field | vegetation fraction | 4 QTLs | [82] |
| rice | 234 accessions | micro-CT, RGB imaging | Laboratory | 739 traits during tillering process (e.g. tiller number, convex hull area, total tiller area, height/width ratio) | 402 loci | [83] |
| rice | 80 accessions | visible/near-infrared spectroscopy | Laboratory | 5 hyperspectral traits (reflectance at wavelength 1177 nm and 1227 nm, normalized difference spectral index (NDSI), differential spectral index, simple ratio index) | NDSI: 65 genes | [84] |
| rice | 529 accessions | hyperspectral imaging | Laboratory | 1540 hyperspectral indices | 989 loci | [13] |
| rice | 221 accessions | visible and near-infrared hyperspectral imaging | Laboratory | the first principal component for spectral values in the range 702–922 nm | 44 chromosomal candidate regions | [85] |
| rice | 553 genotypes | visible light/RGB imaging | Greenhouse | relative growth rate, transpiration rate, transpiration use efficiency (TUE) | previously undetected loci affecting TUE on chromosome 11 | [86] |
| rice | 378 genotypes | visible light/RGB imaging, fluorescence imaging | Greenhouse | 97 digital traits (7 morphology and growth traits, 90 fluorescence responses traits) | visible light/RGB imaging: a genomic region on chromosome 3; fluorescence imaging: 4 genomic regions | [87] |
| rice | 507 accessions | RGB imaging | Greenhouse | 51 image-based traits (e.g. total projected area, plant compactness, height/width ratio) | 443 loci | [88] |
| rice | 378 accessions | visible light/RGB imaging, | Greenhouse | projected shoot area | \ | [89] |
| maize | 942 inbred accessions, three 200 biparental lines | visible light /RGB imaging | Field | 15 tassel morphological traits (e.g. branch number, tassel length, tortuosity) | 242 SNPs | [90] |
| maize | 942 inbred lines | visible light/RGB imaging | Field | tassel weight, tassel length, spike length, branch number | \ | [91] |
| maize | 384 inbred lines | visible light /RGB imaging | Laboratory | total root length, total surface area | \ | [92] |
| maize, sorghum | maize: 369 inbred lines; sorghum: 294 accessions | visible light/RGB imaging | Field | root area, convex hull area, median width, maximum width, width-profile angle, adjusted depth | maize: 139 genes, sorghum: 115 SNPs | [93] |
| maize | 252 inbred lines | aerial visible light/RGB imaging | Field | plant height at 4 different growth stages, the growth rate of plant height | 68 QTLs | [94] |
| maize | 252 inbred lines | near-infrared, visible light/RGB and fluorescence imaging | Laboratory | plant fresh weight, plant dry weight, biovolume estimation at 11 different developmental time points | 12 MTAs, 6 pairs of epistatic interactions | [10] |
| maize | 255 hybrids lines | RGB imaging | Laboratory | biomass, radiation interception efficiency, radiation use efficiency | \ | [11] |
| maize | 468 inbred lines | Microscope, RGB imaging | Laboratory | bulliform cell column number and width | 5 candidate genes | [95] |
| maize | 480 inbred lines | micro-CT imaging | Laboratory | 48 stem vascular bundles traits | 1562 SNPs | [96] |
| bread wheat | 231 synthetic hexaploids | visible light /RGB imaging | Field | grain size and shape traits (e.g. length, width, volume of seed) | 197 loci using general linear model, 79 loci using mixed linear model | [97] |
| bread wheat | 211 bread wheat cultivars | visible/near-infrared reflectance spectroscopy | Field | the modified canopy adjusted ratio index 2 (MCARI2), the MERIS terrestrial chlorophyll index (MTCI), the normalized difference vegetation index (NDVI) | 105 QTLs for MTCI, 97 QTLs for NDVI, 159 QTLs for MCARI2 | [12] |
| spring wheat | 1185 lines | unmanned aerial system integrate RGB and RedEdge multispectral imaging | Field | lodging traits: 3 visual scores of lodging namely intensity, severity and lodging index per plot and additional supporting agronomic measurements per plot, 2 digital lodging scores obtained by taking overall summary mean per plot or combined lodging index of normal mixture parameters | a key genomic region on chromosome 2A | [98] |
| Durum wheat | 248 accessions | unmanned aerial vehicles integrated with multi-spectral imaging, tractor-based system integrated with GreenSeeker spectral sensors | Field | normalized difference vegetation index (NDVI) | 46 QTLs | [99] |
| winter wheat | 335–352 genotypes | light detection and ranging (LIDAR) | Field | canopy height, average daily stem elongation rates | 10 MTAs for final height, 3 MTAs for temperature response, 4 MTAs for vigour | [100] |
| winter wheat | 335 cultivars | RGB imaging | Field | septoria tritici blotch infected traits (e.g. the percentage of leaf area covered by lesions, average pycnidia density within lesions, pycnidia size, pycnidia gray value) | 26 chromosome segments | [101] |
| winter wheat | 215 lines | visible light/RGB scan | Laboratory | total seminal root (TSR) length, root diameter (RD), the length of seminal axis roots (SAR), branched root (BR) length; root dry matter (RDM) | 63 MTAs with 7 for SAR, 24 for BR, 4 for TSR, 8 for RDM, and 20 for RD | [102] |
| spring barley | 100 genotypes | visible light imaging | Greenhouse | biomass and related traits (tiller number, tipping time, the calculated inflection point, fresh weight) | 21 loci | [104] |
| barley | 1420 lines | RGB imaging | Greenhouse | 14 growth traits (e.g. absolute growth rate, relative growth rate, shoot area smoothed, convex hull area integral, caliper length integral) | \ | [105] |
| barley | 109 accessions | chlorophyll fluorescence | Laboratory | 23 traits, including 19 chlorophyll fluorescence induction parameters | 205 markers | [106] |
| soybean | 373 genotypes | visible/near-infrared spectroscopy | Field | photochemical reflectance index (PRI), canopy spectral reflectance | 31 SNPs | [110] |
| soybean | 332 genotypes | visible/near-infrared spectroscopy | Field | chlorophyll a (eChl_A), chlorophyll b (eChl_B), total chlorophyll (eChl_T) content, chlorophyll a/b ratio (eChl_R) | 14 loci for eChl_A, 7 loci for eChl_B, 10 loci for eChl_R, 27 putative loci for total chlorophyll content | [111] |
| soybean | 189 genotypes | chlorophyll fluorescence | Field | 21 fluorescence phenotypes | 288 SNPs | [112] |
| soybean | 5555 lines | ground-based and unmanned aerial system-based RGB imaging | Field | canopy coverage | a large QTL on chromosome 19 | [113] |
| soybean | 200 accessions | unmanned aircraft system, digital imaging | Field | dark green color index (DGCI) | 45 SNPs | [114] |
| soybean | 341 accessions | Photosynthetic System II imaging, visible and near-infrared hyperspectral imaging | Greenhouse | NDVI, chlorophyll index (CHL) | 38 QTLs for NDVI, 32 QTLs for CHL | [115] |
| spinach | 284 accessions | unmanned aircraft system, RGB imaging | Field | 9 plant growth traits: canopy cover, canopy volume, excess greenness index; days after sowing to maximum seasonal values of canopy cover, canopy volume and excess greenness index; days after sowing for manually collected plant bolting stages: early bolting. pollination, and kernel filling | 99 SNPs | [9] |
| cotton | 200 accessions | RGB imaging | Greenhouse | 119 image-based digital traits (56 morphological traits and 63 texture traits) | 390 loci | [116] |
| sorghum | 381 accessions | near-infrared spectroscopy | Laboratory | total phenol, proanthocyanidin, and 3-deoxyanthocyanidin concentrations | \ | [14] |
| arabidopsis | 382 accessions | visible light imaging, fluorescent imaging | Laboratory | seed width, seed length, seed area, projected leaf area, relative growth rates | 238 MTAs | [118] |
| arabidopsis | 96 accessions | visible light/RGB imaging | Laboratory | 75 lesion traits for each infected leaf (e.g. the number of pixels for specific hues within the lesion, lesion perimeter, proportion of the leaf the lesion occupied) | 7940 genes | [119] |
| arabidopsis | 110 and 70 ecotypes | visible light/RGB imaging | Laboratory | disease symptoms (e.g. the percent of tissue that is chlorotic yellow) | \ | [120] |
| rapeseed | 477 genotypes | visible light imaging, fluorescence imaging | Greenhouse | estimated biovolume, projected leaf area, early plant height, colour uniformity | 787 MTAs | [117] |
| rapeseed | 248 accessions | visible light/RGB imaging | Laboratory | 9 seed germination and vigor traits | 18 candidate genes | [121] |
| rapeseed | 238 inbred lines | near-infrared reflectance spectroscopy, nuclear magnetic resonance | Laboratory | seed traits: erucic acid content (EAC), glucosinolate content (GSC), oil content (SOC) | 6 loci for EAC, 49 loci for GSC, 17 loci for SOC | [122] |
MTA: marker-trait association