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Background  Awns are bristle-like organs at the tips of the glumes. Wild rice has maintained long awns for successful seed propagation through seed dispersal. Seed awning is an interesting trait in rice domestication. Long awns might have been beneficial for seed gatherers in the initial phase of domestication; however, awnless phenotypes were preferably selected in a later phase with non-seed-shattering plants. Investigation of domestication loci associated with awnlessness in cultivated rice will be useful in clarifying the process and history of rice domestication.    Results  Quantitative trait locus (QTL) analysis for seed awning was carried out using a BC 3 F 2  population between  Oryza sativa  IR36 (a cultivated donor parent with awnless phenotype) and  O. rufipogon  W630 (a wild recurrent parent with awns). As a result, two QTLs on chromosome 4 (corresponding to  An-1  and  LABA1 ) and one on chromosome 2 (designated as  qAWNL2 ) were detected. Gene interaction among three seed-awning QTLs were further examined with the plants having eight different combinations of homozygous genotypes. Their awn length variation indicated that the IR36 alleles at these loci had the additive awnlessness effects in the genetic background of wild rice. The shortest awn length was observed for the plants having IR36 homozygous alleles at all loci, giving about 75% reduction in awn length. By the fine mapping, the candidate region of the novel  qAWNL2  locus was delimited in a 157.4-kb region containing 22 predicted genes in Nipponbare genome.    Conclusions  QTL analysis revealed that three loci,  An-1, LABA1  and  qAWNL2 , were mainly responsible for the awnlessness of  O. sativa  IR36. In the wild genetic background, loss-of-function alleles at three awning loci showed additive effects on length reduction. In rice domestication, awnless forms may be gradually generated through the accumulation of mutations at awning loci.

Evaluation of Domestication Loci Associated with Awnlessness in Cultivated Rice, Oryza sativa