Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution

Botanical Studies

Table 4 The 11 TN1 genes that underwent positive selection

Gene	Description	FDR	# of PS sites
OsTN5g000040	Hypothetical protein	6.23E−11	5
OsTN5g002486	–	1.93E−05	3
OsTN2g002903	PLATZ transcription factor family protein	3.73E−05	1
OsTN5g001087	GA 3β-hydroxylase	4.12E−05	2
OsTN1g003572	Armadillo/beta-catenin repeat protein-like	4.12E−05	2
OsTN1g003413	Transmembrane protein 56 isoform X1	5.07E−05	2
OsTN8g001161	Probable TPP C	5.07E−04	4
OsTN12g002058	L-type lectin-domain containing receptor kinase IX.1-like	1.55E−03	2
OsTN12g001576	–	1.88E−03	1
OsTN1g000744	KARI, chloroplastic	3.50E−02	1
OsTN4g000152	Probable LRR receptor-like serine/threonine-protein kinase At3g47570	4.90E−02	2

The criterion for positive selection was FDR < 0.05
The PS sites are indicated in the CDS alignments created by PosiGene in Additional file 1: Fig. S10