Table 1.
Examples of marker-assisted selection in rice. na = not applicable.
| Application | Traits or germplasm | Gene/QTLs | Markers used | Reference |
|---|---|---|---|---|
| Early generation selection | Bacterial blight | Xa21 | STS | [78] |
| Gene surveys in parental material | Blast disease, predom. Korean germplasm | Pi5(t) | PCR/DNA gel blot | [79] |
| Gene surveys in parental material | Blast disease | Pi-z | SSR | [42] |
| Gene surveys in parental material | Blast disease | Pi-ta | Gene-specific marker | [80] |
| Genetic diversity assessment | Japonica varieties for hybrid combinations | na | SSR and RAPD | [77] |
| Genetic diversity assessment | Indian aromatic and quality rice | na | SSR | [74] |
| Genetic diversity assessment | U.S. varieties | na | SSR | [76] |
| Genetic diversity assessment | Nepalese landraces | na | SSRs | [81] |
| Genetic diversity assessment | Representative wild rice in China, Oryza rufipogon Griff. | na | SSR | [82] |
| Genetic diversity assessment | Indonesian varieties and landraces | na | SSR | [83] |
| Genotype identity testing | Hybrid rice | na | STS and SSR | [70, 72] |
| MABC | Bacterial blight | Xa21 | STS and RFLP | [84] |
| MABC | Bacterial blight | Xa21 | STS and AFLP | [85] |
| MABC | Bacterial blight | xa5 | STS | [86] |
| MABC | Deep roots | QTLs on chromosomes 1, 2, 7, and 9 | RFLP and SSR | [87] |
| MABC | Bacterial blight | xa5, xa13, Xa21 | STS | [88, 89] |
| MABC | Blast | Pi1 | SSR and ISSR | [90] |
| MABC | Quality | Waxy | RFLP and AFLP | [91] |
| MABC | Bacterial blight + quality | xa13, Xa21 | STS, SSR, and AFLP | [92] |
| MABC | Submergence tolerance, disease resistance, quality | Subchr9 QTL, Xa21, Bph and blast QTLs, and quality loci | SSR and STS | [93] |
| MABC | Blast disease | na | SSR | [94] |
| MABC | Root traits and aroma | QTLs on chromosomes 2, 7, 8, 9, and 11 | RFLP and SSR | [95, 96] |
| MABC | Heading date | QTLs for heading date (Hd1, Hd4, Hd5, or Hd6) | RFLP, STS, SSR, CAPS, dCAPs | [97] |
| MABC | Submergence tolerance | Sub1 QTL | SSR | [98] |
| MES | Indirect selection for adaptation | na | SSRs | [99] |
| Pyramiding | Bacterial blight | Xa4, xa5, Xa10 | RFLP and RAPD | [100] |
| Pyramiding | Bacterial blight | xa5, xa13, Xa4, Xa21 | RFLP, STS | [17] |
| Pyramiding | Blast disease | Pi1, Piz-5, Pi2, Pita | RFLP, STS | [101] |
| Pyramiding | Bacterial blight | xa5, xa13, Xa21 | STS and CAPS | [102] |
| Pyramiding | Bacterial blight | xa5, xa13, Xa21 | SSR and STS | [103] |
| Pyramiding | Bacterial blight and waxy genes | xa5, xa13, Xa21, Wx | SSR, STS, and CAPS | [104] |
| Pyramiding | Insect resistance and bacterial blight | Xa21 and Bt | STS | [59] |
| Pyramiding | Brown plant-hopper | Bph1 and Bph2 | STS | [105] |
| Pyramiding | Thermosensitive genetic male sterility (TGMS) genes | tms2, tgms, tms5 | SSR | [106] |
| Pyramiding | Bacterial blight | Xa7 and Xa21 | STS | [107] |
| Pyramiding | Bacterial blight | Xa4, xa5, and Xa21 | STS | [108] |
| Pyramiding | Bacterial blight | Xa4, Xa7, and Xa21 | STS | [109, 110] |
| Pyramiding/transgene selection | Blast and bacterial blight | Pi-z and Xa21 | STS | [111] |
| Pyramiding/transgene selection | Bacterial blight | xa5, xa13, Xa21 | STS (check) | [112] |
| Pyramiding/transgene selection | Bacterial blight, yellow stem borer, sheath blight | Xa21, Bt RC7 chitinase gene, Bt | STS | [113] |