Rice Genetics IV - IRRI books - International Rice Research Institute

Chen et al (2000) transferred the bacterial blight resistance gene Xa21 into a widelyused parent for hybrid rice production in China, Minghui 63. They used one markerthat is part of the Xa21 gene to select for resistance. Markers flanking the gene at 0.8and 3.0 cM on both sides were used to select for recombinants containing only a smallfragment of the donor chromosome. Another 128 RFLP markers distributed throughoutthe genome were used to select for chromosomal fragments derived from Minghui63. BC 1 F 1 individuals containing Xa21 and recombinant for one of the flanking markerswere backcrossed to Minghui 63. BC 2 F 1 individuals were selected for recombinationwith the other flanking marker. Xa21-containing plants in the BC 3 F 1 generation werescreened with markers covering the genome, and those homozygous for Minghui 63alleles were selfed. The improved version of Minghui 63 was shown to be identicalwith the original except for its resistance to bacterial blight.Practical considerations in marker-assisted selectionMolecular marker technology is starting to be integrated more and more into plantbreeding programs. However, several factors should be taken into consideration whendetermining how suitable this approach will be.Choice of molecular markers. Application of markers in selection schemes dependson identifying a closely linked marker or flanking markers near the gene orgenes of interest. The suitability of any particular marker would depend on severalfactors:1. DNA quality and quantity required. Markers such as RFLP, RAPD, and AFLPrequire high-quality DNA, necessitating more laborious extraction protocols.Also, compared with PCR-based methods, RFLPs need a large quantity of DNA.2. Difficulty of assay. RFLP markers are the most laborious, requiring preparationof filters and Southern blots and development of film. AFLP markers donot require blotting, but the assay is relatively laborious, requires higher skills,and must be detected on polyacrylamide gels. Simple PCR-based markers suchas RAPD, microsatellite, and CAPS (cleaved amplified polymorphic sequence)or STS are the simplest to detect, although microsatellite markers often requirepolyacrylamide gels.3. Degree of polymorphism. Ideally, a marker should be useful within thegermplasm pool to be used by breeders. Thus, although RFLP and AFLP markersare generally suitable for indica-japonica crosses, they are not highly polymorphicwithin a subspecies. Microsatellite markers are by far the most polymorphicand can be used within subspecies.4. Reliability. RAPD markers have the reputation of being the most unreliable,although they are still used because of their simplicity. The other types of markerstend to be more reliable; however, none could be said to be error-free.Many new types of markers are becoming available. As the rice genome sequenceis completed, markers based on specific sequence differences, such as CAPS andSNPs (single nucleotide polymorphisms), will become the markers of choice. Now,microsatellite markers are certainly the best choice for most purposes. These markersare highly polymorphic, reliable, and abundantly available (see McCouch et al, this144 Mackill and Junjian Ni