PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes

BMC Genomics

Table 2 Chromosome locations and putative annotations of the PLUG markers

		Wheat chromosome
Marker no.	Type	undigested, 1% agarose	Hae III-digest, 4% agarose	Taq I-digest, 4% agarose	Annotation of orthologous rice gene (Pseudomolecules ver. 4)
1	III			3A, 3B, 3D	Phospholipase/Carboxylesterase family protein
2	III		3A, 3B	3A, 3B	Elicitor-responsive protein 1, putative
3	II	6B	6B	6A, 6B, 6D	GTP-binding protein, putative
4	III			6B, 6D	expressed protein
5	III		5A, 4D	5A, 4D	CIPK-like protein 1, putative
6	III				magnesium transporter CorA-like family protein, putative
7	III				Cysteine synthase, chloroplast precursor, putative
8	III		2A, 2B, 2D	2B	RNA recognition motif family protein
9	III			1A, 1B, 1D	AML6, putative
10	I	1A, 1B, 1D	1A, 1B, 1D	1A	chlorophyll synthase, ChlG family protein
11	III		7A, 7D		senescence-associated protein, putative
12	I	7A, 7B, 7D	7A, 7B, 7D	7A, 7B, 7D	Polyprenyl synthetase family protein
13	III			3A, 5A, 5D	Phosphatidylinositol N-acetylglucosaminyltransferase subunit A, putative
14	III				COP9 signalosome complex subunit 7, putative
15	III		7A	7B, 7D	MSP domain containing protein
16	II	7B		7B	expressed protein
17	III			7A	BadF/BadG/BcrA/BcrD ATPase family protein
18	II	5A	5A, 5B	5A, 5B, 5D	Triosephosphate isomerase, chloroplast precursor, putative
19	II	1A	1B, 1D	1A, 1B, 1D	ATP synthase gamma chain, mitochondrial precursor, putative
20	III		1A	1A	PRP19/PSO4 homolog, putative
21	III				Ubiquinol-cytochrome c reductase complex 7.8 kDa protein, putative
22	III				Small GTP-binding protein domain containing protein
23	III		5A	5B	Aspartyl aminopeptidase, putative
24	II	5B	5A, 5B, 5D	5A, 5B	expressed protein

Types I, II and III indicate that 1% agarose gel electrophoresis of PCR products resulted in the separation of three, two, or single bands, respectively. PLUG markers were assigned to chromosomes by electrophoresis on 1% agarose gels, or by electrophoresis of Hae III- or Taq I-digested fragments on 4% agarose gels. The table also shows the annotations of TaEST-LUGs that were used for marker development.

ISSN: 1471-2164