Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

Yamamoto, Naoki; Garcia, Richard; Suzuki, Tomohiro; Solis, Celymar Angela; Tada, Yuichi; Venuprasad, Ramaiah; Kohli, Ajay

doi:10.1186/s12284-018-0224-3

Rice

Table 6 Occurrence of WAB 56–104 specific genes in NU varieties and CG 14

From: Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

Category	Gene identifier	Functional annotation		Gene occurrence
Category	Gene identifier	Gene of BLAST hit in Swiss prot	Species of BLAST hit in Swiss-prot	NU3	NU4	NU5	NU7	CG14	Remarks
Disease	g13.t1	Putative disease resistance protein RGA4	Solanum bulbocastanum	No	No	No	Yes	No	WAB 56–104 allele
	g51.t1	Putative disease resistance RPP13-like protein 3	Arabidopsis thaliana	Yes	Yes	Yes	No	No	WAB 56–104 allele
	g98.t1	Disease resistance protein RPP13	Arabidopsis thaliana	Yes	Yes	No	Yes	Yes	WAB 56–104 allele
	g108.t1	Putative disease resistance RPP13-like protein 1	Arabidopsis thaliana	No	No	No	No	Yes	Polymorphic in parents
	g342.t1	Chitin elicitor-binding protein	Oryza sativa	Yes	Yes	No	No	No	WAB 56–104 allele
	g632.t1	Putative disease resistance RPP13-like protein 2	Arabidopsis thaliana	Yes	Yes	No	Yes	No	WAB 56–104 allele
Receptor	g85.t1	Wall-associated receptor kinase-like 18	Arabidopsis thaliana	Yes	Yes	Yes	No	Yes	Both parental allele
	g115.t1	Wall-associated receptor kinase-like 18	Arabidopsis thaliana	Yes	Yes	Yes	No	Yes	Both parental allele
	g227.t1	Wall-associated receptor kinase 2	Arabidopsis thaliana	Yes	Yes	No	Yes	No	WAB 56–104 allele
	g162.t1	Receptor-like protein 12	Arabidopsis thaliana	Yes	Yes	Yes	No	Yes	WAB 56–104 allele in NU3 and NU4.CG 14 allele in NU5.
	g418.t1	G-type lectin S-receptor-like serine/threonine-protein kinase LECRK3	Oryza sativa	Yes	Yes	No	No	No	WAB 56–104 allele
Others	g173.t1	11-oxo-beta-amyrin 30-oxidase	Glycyrrhiza uralensis	No	No	Yes	No	Yes	Unspecified
	g268.t1	Uncharacterized protein	Arabidopsis thaliana	Yes	Yes	No	Yes	No	WAB 56–104 allele in NU3 and NU4. Unspecified in NU7.
	g338.t1	F-box/FBD/LRR-repeat protein	Arabidopsis thaliana	No	No	No	No	Yes	Polymorphic in parents
	g361.t1	Cytochrome P450 87A3	Oryza sativa	Yes	Yes	No	Yes	No	Both parental allele
	g427.t1	UPF0481 protein	Arabidopsis thaliana	Yes	Yes	No	No	No	WAB 56–104 allele
	g453.t1	Tetraspanin-8	Arabidopsis thaliana	Yes	Yes	No	No	No	WAB 56–104 allele
	g500.t1	Protein Brevis radix-like 2	Arabidopsis thaliana	Yes	Yes	Yes	No	Yes	WAB 56–104 allele
	g517.t1	UDP-glycosyltransferase 76E11	Arabidopsis thaliana	Yes	Yes	Yes	No	Yes	WAB 56–104 allele
	g597.t1	Basic blue protein	Cucumis sativus	Yes	Yes	Yes	No	Yes	WAB 56–104 allele
	g643.t1	Autonomous transposable element EN-1 mosaic protein	Zea mays	No	No	Yes	No	No	WAB 56–104 allele

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