Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates

López-Malvar, A.; Butrón, A.; Samayoa, L. F.; Figueroa-Garrido, D. J.; Malvar, R. A.; Santiago, R.

doi:10.1186/s12870-019-2135-x

BMC Plant Biology

Table 4 Complete list of candidate genes for hydroxycinnamates^a identified in a maize diversity panel. Genes in bold are the ones mentioned in the manuscript

From: Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates

Trait^a	Marker	Chr^b	Bin^c	Physical position^d	Gene ^e	Gene Function^f
PCA	S1_174637686	1	1.05	174,637,686	Zm00001d031086	Nced2 - nine-cis-epoxycarotenoid dioxygenase2
					Zm00001d031088	Putative kelch repeat-containing protein containing ser/thr protein kinase family protein
					Zm00001d031090	GTP binding protein
					Zm00001d031091	Hypothetical protein
PCA	S1_108071292	1	1.05	108,071,292	Zm00001d030173	Calmodulin-binding receptor-like cytoplasmic kinase 3
PCA	S1_108071293	1	1.05	108,071,293	Zm00001d030174	Lecithin-cholesterol acyltransferase-like 1
					Zm00001d030176	Hypothetical protein
					Zm00001d030177	Hypothetical protein
FA	S1_187590405	1	1.06	187,590,405	Zm00001d031426	Serine/threonine-protein kinase UCNL
					Zm00001d031427	Leucine-rich repeat receptor-like protein kinase PEPR1
					Zm00001d031428	Monogalactosyldiacylglycerol synthase 2 chloroplastic
					Zm00001d031429	pfkB-like carbohydrate kinase family protein
					Zm00001d031430	Hypothetical protein
FA DFA 8–O–4 DFA 5–5	S1_220067812	1	1.07	220,067,812	Zm00001d032339	Hypothetical protein
					Zm00001d032342	Leucine-rich repeat receptor protein kinase EMS1
					Zm00001d032343	sdg103 - SET domain group 103)
FA DFA 8–O–4 DFA 8–5 l DFA 5–5	S1_220067811	1	1.07	220,067,811	Zm00001d032344	Receptor-like protein kinase HSL1
					Zm00001d032345	Nudix hydrolase 15 mitochondrial
					Zm00001d032346	UDP-glucose 4-epimerase 4
					Zm00001d032347	DNAJ heat shock family protein
					Zm00001d032348	Zinc finger BED domain-containing protein RICESLEEPER 2
					Zm00001d032350	Hypothetical protein
PCA	S1_288696782	1	1.11	288,696,782	Zm00001d034469	PRA1 prenylated Rab receptor 2
					Zm00001d034471	Ketol-acid reductoisomerase chloroplastic
					Zm00001d034473	Metal transporter Nramp6-heavy metal uptake
					Zm00001d034475	WRKY12 -WRKY-transcription factor 12
					Zm00001d034476	Hypothetical protein
					Zm00001d034477	Hypothetical protein
					Zm00001d034479	hon110 histone one H1
					Zm00001d034480	Seed Specific protein Bn15D14A
					Zm00001d034482	Hypothetical protein
					Zm00001d034483	Hypothetical protein
					Zm00001d034484	Hypothetical protein
					Zm00001d034485	rtl4- reversion-to-ethylene sensitivity1 like4
					Zm00001d034486	GTP binding protein
FA	S1_295476576	1	1.11	295,476,576	Zm00001d034727	Polygalacturonase
					Zm00001d034728	Uncharacterized
					Zm00001d034729	Carbohydrate-binding X8 domain superfamily protein
					Zm00001d034730	sbp17 - SBP-transcription factor 17
FA	S1_295476338	1	1.11	295,476,338	Zm00001d034731	Short-chain dehydrogenase reductase 3b
					Zm00001d034732	gpat3 - glycerol-3-phosphate acyltransferase3
					Zm00001d034733	Galactokinase
					Zm00001d034734	Nucleic acid-binding proteins superfamily
					Zm00001d034735	Methyltransferase superfamily protein
					Zm00001d034736	cps1 - chloroplast protein synthesis1
					Zm00001d034737	Hypothetical protein
					Zm00001d034739	Fumarylacetoacetate FAA hydrolase family
					Zm00001d034740	Epoxide hydrolase 2
					Zm00001d034741	Hypothetical protein
					Zm00001d034742	Hypothetical protein
					Zm00001d034743	OsNAC protein-like
					Zm00001d034744	Pentatricopeptide repeat-containing protein
DFA 8–5 l DFA 8–5 DFA 5–5	S1_297490295	1	1.11	297,490,295	Zm00001d034817	Protein phosphatase 2A regulatory subunit B′
					Zm00001d034818	GDSL esterase/lipase
					Zm00001d034819	Putative replication protein
					Zm00001d034820	Defective in cullin neddylation protein
					Zm00001d034822	Hypothetical protein
					Zm00001d034823	ALBINO3-like protein 1 chloroplastic
					Zm00001d034824	aldose-1-epimerase
					Zm00001d034826	Elongation factor G-1 mitochondrial
PCA	S3_20426421	3	3.04	20,426,421	Zm00001d039926	WAK1 - OsWAK receptor-like cytoplasmic kinase OsWAK-RLCK
					Zm00001d039927	Hypothetical protein
					Zm00001d039928	Hypothetical protein
					Zm00001d039929	Hypothetical protein
					Zm00001d039930	Hypothetical protein
					Zm00001d039931	Leaf rust 10 disease-resistance locus receptor-like protein kinase-like 1.1
					Zm00001d039932	Hypothetical protein
					Zm00001d039933	16.9 kDa class I heat shock protein 1
					Zm00001d039935	hsp17.2 - heat shock protein17.2
					Zm00001d039936	hsp12 - heat shock protein12
					Zm00001d039937	TIM-barrel signal transduction protein isoform 2
					Zm00001d039938	Calmodulin-binding transcription activator 1
DFAT DFA 5–5	S3_184608458	3	3.06	184,608,458	Zm00001d043050	RING-H2 finger protein ATL74
					Zm00001d043052	Unknown Endoplasmic reticulum vesicle transporter protein
					Zm00001d043056	Serine/threonine-protein kinase NAK
					Zm00001d043057	Unknown Protein kinase
					Zm00001d043058	Leucine-rich repeat receptor-like serine/threonine-protein kinase IRK
DFA 5–5	ss3_60941077	3	3.04	60,941,077	Zm00001d040735	invan10 - invertase alkaline neutral10
					Zm00001d040737	ga2ox5 - gibberellin 2-oxidase5
FA	ss4_10220935	4	4.01	10,220,935	Zm00001d048968	Leucine-rich repeat receptor-like serine/threonine-protein kinase BAM1
					Zm00001d048969	phd28 - PHD-transcription factor 28
					Zm00001d048970	Glycerophosphodiester phosphodiesterase GDPD4
					Zm00001d048972	Hypothetical protein
					Zm00001d048973	Hypothetical protein
					Zm00001d048974	Glycine cleavage system H protein 2 mitochondrial
					Zm00001d048975	Hypothetical protein
					Zm00001d048977	Hypothetical protein
					Zm00001d048978	F-box domain containing protein
					Zm00001d048979	Probable sucrose-phosphate synthase 5
FA	ss5_169927760	5	5.04	169,927,760	Zm00001d016731	Digalactosyldiacylglycerol synthase 1
					Zm00001d016732	bzip103 - bZIP-transcription factor 103
					Zm00001d016733	NDR1/HIN1-like 1
					Zm00001d016734	Hypothetical protein
					Zm00001d016735	Protein SMAX1-LIKE 3
					Zm00001d016736	2-cys peroxiredoxin BAS1
					Zm00001d016737	e2f4 - E2F-DP-transcription factor 24)
					Zm00001d016738	Pectinesterase inhibitor domain containing protein
					Zm00001d016740	Hypothetical protein
					Zm00001d016741	Pectinesterase inhibitor domain containing protein
					Zm00001d016742	Hypothetical protein
					Zm00001d016743	Hypothetical protein
					Zm00001d016744	Hypothetical protein
FA	S8_138322127	8	8.05	138,322,127	Zm00001d011187	bhlh92 - bHLH-transcription factor 92
					Zm00001d011188	3′-5′ exonuclease domain-containing protein / K homology domain-containing protein / KH domain-containing protein
					Zm00001d011189	DUF3511 domain protein
					Zm00001d011190	Hypothetical protein
					Zm00001d011192	Carbamoyl-phosphate synthase large chain, chloroplastic
					Zm00001d011193	Integral membrane protein
					Zm00001d011195	Putative protein phosphatase 2C 74
DFAT DFA 8–O–4, DFA 5–5	S10_22521088	10	10.03	22,521,088	Zm00001d023813	Polygalacturonase, pectin
					Zm00001d023815	Triacylglycerol lipase

a: a: PCA: p-coumaric acid; FA: ferulic acid; DFA 8–5 l: 8–5 linear diferulic acid; DFA 5–5: 5–5 diferulic acid; DFA 8–O–4: 8–O–4 diferulic acid; DFA 8–5b: 8–5 benzofuran diferulic acid; DFA 8–5: sum (DFA 8–5 l + DFA 8–5b); DFAT: total diferulates sum (DFA 5–5 + DFA 8–O–4 + DFA 8–5b + DFA 8–5 l)
b: Chr: Chromosome
c: A bin is the interval that includes all loci from the leftmost or top Core Marker to the next Core Marker. The genetic maps are divided into 100 segments of approximately 20 centiMorgans designated with the chromosome number followed by a two-digit decimal [26]
d: Physical position of the marker in the B73 Reference Genome version 2
e: Name of the gene in B73 Reference Genome version 4
f: Gene function according to Zm-B73 reference form Gramene

Back to article page

ISSN: 1471-2229

Contact us

General enquiries: journalsubmissions@springernature.com