Table 1. Gene expression near the im locus in 28-DPA fiber cells by RNAseq.

Gene/Marker	Position Chr. A03	TM-1 RPKM	im RPKM	log2 (im/TM-1)	P-value	TAIR Ortholog	Description
CFB5887	10,257,310						Flanking SNP marker
Gh_A03G0468	10,292,732	6.4	1.5	−2.1	0.024	None	Protoheme IX farnesyltransferase
Gh_A03G0469	10,294,222	1.2	1.4	0.2	0.052	AT5G50580	SUMO-activating enzyme 1B
Gh_A03G0473	10,352,804	1.5	1.3	−0.2	0.752	AT3G26890	None
Gh_A03G0475	10,381,659	3.1	2.9	−0.1	0.685	AT4G00650	FRIGIDA-like protein
Gh_A03G0480	10,491,490	1.4	1.2	−0.2	0.840	AT5G51050	Mitochondrial substrate carrier family protein
Gh_A03G0483	10,599,666	3.0	2.3	−0.4	0.193	AT5G51020	CRUMPLED LEAF
Gh_A03G0484	10,616,903	16.8	15.9	−0.1	0.660	AT1G01630	Sec14p-like phosphatidylinositol transfer protein
CFB5888	10,999,373						Flanking SNP marker
Gh_A03G0489	11,022,670	2.4	1.0	−1.3	0.164	AT1G64580	Pentatricopeptide repeat (PPR) protein, mitochondrial
CFBid0001	11,025,170						im-Linked 22-bp deletion in exon of PPR
Gh_A03G0491	11,449,872	12.7	9.6	−0.4	0.192	AT5G50920	Chaperone protein ClpC, chloroplastic
Gh_A03G0492	11,458,109	4.0	4.3	0.1	0.139	AT2G42490	Copper methylamine oxidase
Gh_A03G0493	11,495,867	29.6	26.1	−0.2	0.933	AT4G24690	NBR1, a selective autophagy substrate
Gh_A03G0495	11,523,884	2.9	1.8	−0.7	0.676	None	None
Gh_A03G0496	11,525,162	1.1	0.3	−1.9	0.126	AT4G24700	None
Gh_A03G0498	11,626,203	14.3	13.5	−0.1	0.457	AT4G20360	RAB GTPase homolog E1B
Gh_A03G0500	11,796,370	1.7	1.9	0.2	0.529	AT5G62350	Pectin methylesterase inhibitor superfamily protein
CFBid0002	12,155,364						Flanking deletion marker
Gh_A03G0506	12,155,624	0.0	0.0	1.6	0.559	AT1G12260	NAC 007

Only annotated proteins with >1 RPKM and a select cell wall gene are presented. Nearby marker locations are indicated