Sweeney et al.

Page 1 Supplemental Figure 1.

1-600

Sequence alignments used in phylogenetic analysis.

Sweeney et al.

Page 2 Supplemental Figure 1.

600-1200

Sequence alignments used in phylogenetic analysis.

Sweeney et al.

Page 3

Supplemental Figure 1.

1200-1449

Sequence alignments used in phylogenetic analysis.

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Supplemental Figure 2.

Ks and two times standard error bars for pairwise rice-maize

comparisons for the following loci: NAM (left), Rc rice - In1

maize (middle) and Cellulose Synthase (right). The solid line

indicates c. 0.65 Ks, which is the expected value for orthologous loci for these species.

Supplemental Table 1. Primers Developed for Fine Mapping

Locus

name Forward primer Reverse primer Bp position

on TIGR assembly, v3 Allele size Nipponbare RID6 cgtcgaaaacgacatgtatga

gttggggatggaagaattga 6,060,924 - 6,061,098 175RID7 tcaacgtttgaccgttcatc

cacatgtgtcgacaaaggaaa 6,060,277 - 6,060,976 700RID8 aactcttagtggggtcttagtcct

caaagggagtgatacctacacatt 6,108,072 - 6,107,956 117RID9 atcatatctggggtcggatagaa

gtacatgcagtaccgcgaca 6,747,632 - 6,747,880 249RID10 aggggcagttttcagtcaga ctattgccccctgtggtcta

6,411,490 - 6,412,048 559RID11 ggagtggttcttcgacagtaaaa

ggagacgcagttgaagatcc 6,133,359 - 6,133,934 576RID12 tacaggggagcagaaacacc

aaaggtaccaaagatcgcagaa 6,066,321 - 6,066,473 153RID13 acctacgacacgatgcacag

atgccatgcgatcacaacta 6,061,299 - 6,061,598 300RID14 tgcatgcttaattacgtggtc tgggacggagggagtagtag

6,068,728 - 6,068,850 123RID15 acgcaaggcttagctgtgat aaatgaaagcgatgcgagtc 6,083,097 - 110