. 2023 Apr 29;14(5):1010. doi: 10.3390/genes14051010

Table 2.

Single-nucleotide polymorphism (SNP) chromosomal positions and candidate genes significantly associated with chlorophyll content and AUCCC identified by genome-wide association study.

Trait	SNP	Chr	Position (bp)	p Value	Gene	Gene Interval (bp)	Annotation	Pathway
17BLUP chlorophyll content	Marker.247949	2	2.20 × 10⁸	9.10 × 10⁻⁶	Zm00001d007009	Chr2:220125041-220148355	DNAJ heat shock N-terminal domain-containing protein	Chloroplast targeting, photosystem II repair
					Zm00001d007011	Chr2:220152033-220155206	ATP synthase	Energy metabolism
					Zm00001d007012	Chr2:220170458-220175539	CHLOROPLAST RNA-BINDING PROTEIN	Chloroplast morphogenesis
					Zm00001d007016	Chr2:220204271-220219191	disease resistance protein RGA2	Disease-resistant
					Zm00001d007017	Chr2:220217348-220221222	thioredoxin-like protein AAED1 chloroplastic	Electronic circulation and daylighting
17FS chlorophyll content	2376873-7-G	10	1.48 × 10⁸	7.08 × 10⁻⁶	Zm00001d026563	Chr10:148153479-148157015	AP2/EREBP transcription factor 40	Plant growth and development
					Zm00001d026569	Chr10:148185247-148190302	chloroplastic palmitoyl-acyl carrier protein thioesterase	De novo synthesis of fatty acids
					Zm00001d026568	Chr10:148184610-148195615	pentatricopeptide repeat-containing protein	Chloroplast development
					Zm00001d026573	Chr10:148201459-148207853	5-methylthioribose kinase	Methylthioadenosine (MTA) cycle
					Zm00001d026574	Chr10:148208912-148217798	UDP-D-galacturonate	Homogalacturonan biosynthesis
17LD chlorophyll content	Marker.190636	2	43,281,907	6.97 × 10⁻⁶	Zm00001d003403	Chr2:43279990-43285413	aaap10—amino acid/auxin permease10	Amino acid transportation
					Zm00001d003404	Chr2:43284025.43288746	transmembrane protein	Transmembrane
					Zm00001d003405	Chr2:43285551-43289511	protease inhibitor/seed storage/LTP family protein	Signal transduction
					Zm00001d003406	Chr2:43298285-43304459	actin binding protein	Plant growth and development
	Marker.346487	4	8,724,268	8.32 × 10⁻⁶	Zm00001d027598	Chr1:8676135-8681000	cct101—CO CO-LIKE TIMING OF CAB1 protein domain101)	Transcription factors, floral completion
					Zm00001d027599	Chr1:8699800-8704356	alkane hydroxylase MAH1	Cuticular wax biosynthesis
					Zm00001d027601	Chr1:8772748-8777355	behenate ω-hydroxylase	Suberin monomers biosynthesis
	2504165-22-G	5	2,775,822	9.93 × 10⁻⁶	Zm00001d012982	Chr5:2770681-2776100	NAD(P)-binding domain containing protein	Energy metabolism
17LD AUCCC	Marker.571424	6	1.73 × 10⁸	7.40 × 10⁻⁶	Zm00001d039222	Chr6:173160699-173165510	cct40—CO CO-LIKE TIMING OF CAB1 protein domain40)	Transcription factors, floral completion
17LD AUCCC	Marker.571424	6	1.73 × 10⁸	7.40 × 10⁻⁶	Zm00001d039221	Chr6:173158717-173163744	nucleoside diphosphate kinase 4	Signal transduction
17FS AUCCC	2376873-7-G	10	1.48 × 10⁸	5.82 × 10⁻⁶	Zm00001d026563	Chr10:148153479-148157015	ereb40—AP2-EREBP-transcription factor 40	Plant growth and development
					Zm00001d026568	Chr10:148184610-148195615	pentatricopeptide repeat-containing protein, mitochondrial-like	Chloroplast development
					Zm00001d026569	Chr10:148185247-148190302	palmitoyl-acyl carrier protein thioesterase, chloroplastic	De novo synthesis of fatty acids
					Zm00001d026573	Chr10:148201459-148207853	5-methylthioribose kinase	Methylthioadenosine (MTA) cycle
					Zm00001d026574	Chr10:148208912-148217798	UDP-D-galacturonate	Homogalacturonan biosynthesis