Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations

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]