Supplementary Fig. 1 Tassel Development in Fea*-9LB090 Mutants

Supplementary Fig. 1 Tassel development in fea*-9LB090 mutants. The tassel normally contains a central rachis and a few lateral branches. In mutant plants, the central rachis is thicker than normal but not fasciated (Supplementary Fig. 1 a), and becomes more obvious when male spikelets are removed with pedicels left (Supplementary Fig. 1 b). The arrangement of male spikelets is sparse at the base and gets tighter in the middle part, and becomes almost undistinguishable at the top (Supplementary Fig. 1 b, c). In addition, the male spikelet-pair normally has two spikelets, each of which has 2 florets with three stamens. fea*-9LB030 mutants have irregular numbers of spikelets, florets and stamens (Supplementary Fig. 1 d, e, f , g, h). The spikelet-pairs sometimes have 3 spikelets (Supplementary Fig. 1 d). A range of floret numbers in one male spikelet is from 2 to 4 (Supplementary Fig. 1 e, f). Anther numbers of each floret range between 3 and 5 (Supplementary Fig. 1 g, h).

a, b Thick central rachises in mutant tassels. Male spikelets are removed with pedicels left for an easier observation. c Amplification of the box section in b. The arrangement of the spikelet-pairs is undistinguishable. d A spikelet-pair with 3 an abnormal number of spikelets. e A male spikelet with an abnormal number of 4 florets, each of which has 3 stamens (arrowed). There are totally 12 stamens in one spikelet, which seems like combining two spikelets. f A male spikelet with 3 florets (arrowed). g A spikelet with 2 florets, each of which has 5 abnormal anthers (arrowed). h A spikelet with 2 florets, one has 4 anthers(yellow arrows) and the other has 3 anthers (blue arrows).

Supplementary Fig. 2 SLAF tag distribution on each chromosome According to the results of SLAF positioning on the genome, we calculated the SLAF tag numbers on each chromosome, and drew distribution diagram of SLAF tags on each chromosome (Supplementary Fig. 2). The SLAF tags were distributed equally on each chromosome and the maize genome has been successfully simplified. Abscissa: Position of SLAF tags on the chromosomes. Ordinate: Chromosome ID. The darker the color was, the more SLAF tags it meant.

Supplementary Fig. 3 Markers distribution on each chromosome Marker numbers on each chromosome according to the positioning result were calculated and distribution diagram of Markers on each chromosome was shown in Supplementary Fig. 3. The SLAF tags were distributed equally on each chromosome. Abscissa: Position of Markers on the chromosomes. Ordinate: Chromosome ID. The darker the color was, the more Markers it meant.

Fig. 4 Distribution of population percentage on Chromosomes The ratio of genotype f in aa and ab was shown in Supplementary Fig. 4. We can see that ab had a higher ratio than aa in chr3 and chr10.

Abscissa: Position of Markers on the chromosomes. Red line divides different chromosome regions. Ordinate: The percent of f in the aa and ab population. M_aa and M_ab mean the ratios of f in aa and ab population, respectively.