After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers’ preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated.

The eating and cooking qualities of rice are heavily emphasized in breeding programs because they determine market values and they are the appealing attributes sought by consumers. Conventional breeding has developed traditional varieties with improved eating and cooking qualities. Recently, intensive genetic studies have pinpointed the genes that control eating and cooking quality traits. Advances in genetic studies have developed molecular techniques, thereby allowing marker-assisted breeding (MAB) for improved eating and cooking qualities in rice. MAB has gained the attention of rice breeders for the advantages it can offer that conventional breeding cannot. There have been successful cases of using MAB to improve the eating and cooking qualities in rice over the years. Nevertheless, MAB should be applied cautiously given the intensive effort needed for genotyping. Perspectives from conventional breeding to marker-assisted breeding will be discussed in this review for the advancement of the eating and cooking qualities of fragrance, amylose content (AC), gel consistency (GC) and gelatinization temperature (GT) in rice. These four parameters are associated with eating and cooking qualities in rice. The genetic basis of these four parameters is also included in this review. MAB is another approach to rice variety improvement and development in addition to being an alternative to genetic engineering. The MAB approach shortens the varietal development time, and is therefore able to deliver improved rice varieties to farmers within a shorter period of time.

Fragrance in rice is an appealing attribute to consumers. The increasing demand for fragrant rice highlights the need to develop fragrant rice variety that suit the preference of local consumers in addition to reduce fragrant rice imports. Marker-assisted backcrossing (MABC) was employed to develop advanced fragrant rice lines from the cross between MR269 and Basmati 370. MR269 is a Malaysian high-yielding rice variety but non-fragrant and was used as recurrent parent whereas Basmati 370 is a well-known fragrant traditional rice variety and was used as donor parent for the fragrance gene. Two generations of backcrosses and a generation of selfing were conducted to introgress the fragrance gene and restore the recurrent parent genome in the backcross progenies. As a result, 14 advanced fragrant rice lines were developed. These advanced fragrant rice lines carried homozygous alleles for the fragrance gene, similar to Basmati 370. The average recovery of recurrent parent genome was 88.4%. Besides being fragrant, the advanced fragrant rice lines also had most of the morphological and agronomical traits similar to MR269. Grain quality of the advanced fragrant rice lines in terms of gelatinization temperature, amylose content and gel consistency are also similar to both parents. Besides, the advanced fragrant rice lines had 2-acetyl-1pyrroline content similar to Basmati 370. MABC approach applied in this study has successfully introgressed the fragrance gene and accelerated the recovery of recurrent parent genome in advanced fragrant rice lines, therefore these lines can be delivered to the farmers and consumers for use in due time.

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