Table 2.

Summary of amplicon sequences used to identify genomic polymorphism at ms5 on A12 and ms6 on D12 and their in silico comparative map positions on D5 genome of Gossypium raimondii

Chromosome	Sequence annotation	Position on chromosome 08 of D5 genome syntenic to A12/D12 (base pairs)a	Polymorphism
A12	Cytochrome p450	36601681—36601890	C/T
A12	Cytochrome p450	36601598—36601781	A/G
A12	Cytochrome p450	36600316—36600453	A/G
A12	SINA protein family (zinc finger)	36517055—36517264	A/G
A12	Ubiquitin family	36513917—36513713	A/G
A12	Eukaryotic translation initiation factor 3 subunit	36487438—36486837	C/T
A12	PHD-zinc-finger-like domain	36448804—36448648	A/G
A12	PHD-zinc-finger-like domain	36448539—36448899	C/T
A12	PHD-zinc-finger-like domain	36444422—36444671	C/T
A12	Telomere stability and silencing	36437252—36437058	C/T
A12	Telomere stability and silencing	36436860—36436639	C/T
A12	Kinetochore centromere component	36404821—36405030	C/G
A12	Mitochondrial carrier-like protein	36180644—36180843	G/T
D12	Homeobox-associated leucine zipper	36829091—36829251	C/T
D12	ORDML family protein	36823054—36823710	C/G
D12	AP2(ERF domain)	36670553—36670417	C/G
D12	Cytochrome P450	36600741—36600580	A/G
D12	Cytochrome P450	36600741—36600580	A/G
D12	Aspartic proteinase	36590566—36590776	A/G
D12	PHD-zinc-finger-like domain	36443655—36443785	G/C
D12	Cyclic nucleotide-gated ion channel	36432550—36432377	C/T
D12	Cyclic nucleotide-gated ion channel	36432269—36432083	C/G
D12	Cyclic nucleotide-gated ion channel	36429252—36429459	C/G

^aPhysical position of amplicon sequences on whole genome of Gossypium raimondii (JGI assembly v2.0, www.cottongen.org)