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

Abstract

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 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.

Identification and characterization of An-4, a potential quantitative trait locus for awn development in rice

“…To isolate An-4 , a map-based cloning strategy was employed and An-4 was finally narrowed down within a 56-kb region on the long arm of chromosome 2. Around An-4 locus, qAWNL2 had been reported to be associated with awn development [ 30 ]. However, the physical distance between An-4 and qAWNL2 was about 3.8-Mb.…”

The role of wild rice (Oryza rufipogon) awns in seed dispersal

“…Similarly, seeds with half awns showed better contribution for seed dispersal. In wild rice, seed awning is dominantly controlled by wild functional alleles at several loci, and the plants with the drastic reduction of awn length are hardly produced (Luo et al, 2013;Hua et al, 2015;Bessho-Uehara et al, 2016;Ikemoto et al, 2017;Amarasinghe et al, 2020). In other wild grass species, long awns were also reported to assist seed dispersal and burial (Garnier and Dajoz, 2001;Li et al, 2015;Ntakirutimana et al, 2019).…”

“…At each locus, the wild functional allele induces awn formation. In addition, wild rice has some other minor genes for seed awning, and an awnless phenotype is not produced by a single mutation in wild rice (Ikemoto et al, 2017;Amarasinghe et al, 2020). This suggests that wild rice has a mechanism to prevent awn length reduction by the multiple genetic controls.…”

Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species

“…WK56-IL2 carried a segment of the long arm of the chromosome 1 region covering the An10 locus, which suggests that WK56 (O. nivara) may carry functional An10. Recently, a locus responsible for awn length was detected on chromosome 2 and designated as qAWL2 [39]. This locus was narrowed down between a pair of simple sequence repeat (SSR) markers, RM13335 and RM13349, within a 157.4-kb region.…”