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 BC3F2 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.
Fine mapping of qAWNL2. a Molecular markers between RM5707 and RM6380 on chromosome 2 were used to detect recombinants near the qAWNL2 locus. b Graphical genotypes of BC3F5 lines derived from five critical recombinant BC3F4 plants (nos. 146–82, − 211, − 228, − 137 and − 17) in the candidate region of qAWNL2. C, W and R: Homozygous IR36, W630 and recombinant chromosomes, respectively. Awn lengths (means ± SD, n = 5) of the 5th spikelets of the BC3F5 lines are shown on right. ** and n.s.: significant at P < 0.01 and not significant, respectively. The qAWNL2 locus was estimated in the 157.4-kb region between RM13335 and RM13349