Identification of genetic factors controlling domestication-related traitsof rice using an F-2 population of a cross between Oryza sativa and O-rufipogon

Domesticated rice differs from the wild progenitor in large arrays of morph ological and physiological traits. The present study was conducted to ident ify the genetic factors controlling the differences between cultivated rice and its wild progenitor, with the intention to assess the genetic basis of the changes associated with the processes of rice domestication. A total o f 19 traits, including seven qualitative and 12 quantitative traits, that a re related to domestication were scored in an F-2 population from a cross b etween a variety of the Asian cultivated rice (Oryza sativa) and an accessi on of the common wild rice (O. rufipogon). Loci controlling the inheritance of these traits were determined by making use of a molecular linkage map c onsisting of 348 molecular-marker loci (313 RFLPs, 12 SSRs and 23 AFLPs) ba sed on this F-2 population. All seven qualitative traits were each controll ed by a single Mendelian locus. Analysis of the 12 quantitative traits reso lved a total of 44 putative QTLs with an average of 3.7 QTLs per trait. The amount of variation explained by individual QTLs ranged from a low of 6.9% to a high of 59.8%, and many of the QTLs accounted for more than 20% of th e variation. Thus, genes of both major and minor effect were involved in th e differences between wild and cultivated rice. The results also showed tha t most of the genetic factors (qualitative or QTLs) controlling the domesti cation-related traits were concentrated in a few chromosomal blocks. Such a clustered distribution of the genes may provide explanations for the genet ic basis of the "domestication syndrome" observed in evolutionary studies a nd also for the "linkage drag" that occurs in many breeding programs. The i nformation on the genetic basis of some desirable traits possessed by the w ild parent may also be useful for facilitating the utilization of these tra its in rice-breeding programs.