Molecular Analysis in an Aromatic Breeding Program

Rice breeding at the U of A Rice Research and Extension Center is using DNA marker analysis to enhance the development of rice (Oryza sativa L.) cultivars for market.  To determine the genotype, seed purity, and value as a parent in aromatic breeding, analysis was conducted in 2010 using markers linked to the traits of aroma, kernel elongation, amylose content, plant height, and rice blast disease resistance.  Twenty-five advanced breeding lines and seven F₂ generation populations were included in the parental screening.  Initial analysis on pooled samples of each entry showed that 20 of the 25 advanced breeding lines were homozygous for the predicted alleles and were ready to use as parents.  Four of the F₂ populations were segregating for the desired alleles.  The initial analysis also revealed that six of the 32 entries, or 19%, had either seed purity issues or amplified non-aromatic alleles, and a second screening of individual samples from these “problem lines” was conducted.  It was determined from the second screening that three of the lines had seed of unknown germplasm mixed with the cultivar comprising up to 20% of the seed total.  In 2011, two F₅ populations of 1,573 progeny were processed through marker-assisted selection for aroma and amylose.  Selecting only the families with homozygous aromatic genotype eliminated 63% of the progeny from further development, saving resources for material with greater commercial potential.