| 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] |
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