Population genomics and morphometric assignment of western honey bees (Apis mellifera L.) in the Republic of South Africa

Eimanifar, Amin; Brooks, Samantha A.; Bustamante, Tomas; Ellis, James D.

doi:10.1186/s12864-018-4998-x

Table 4 List of 83 divergent SNPs with their functions obtained by outlier tests as putative markers and used for their association with environmental variables using Samβada package

From: Population genomics and morphometric assignment of western honey bees (Apis mellifera L.) in the Republic of South Africa

SNPID	SNP Position	Gene product	Gene ID (BEEBASE)	Gene ID (FLYBASE)
S1_4,550,788	4,550,788	LIM/homeobox protein Awh	GB53183	FBgn0013751
S1_6,686,923	6,686,923	Uncharacterized LOC725682, transcript variant X1	GB40830	FBgn0260997
S1_12,811,137	12,811,137	Protein prickle-like, transcript variant X1	GB44796	FBgn0003090
S1_15,039,694	15,039,694	Krueppel-like factor 6, transcript variant X1	GB52133	FBgn0040765
S1_17,699,574	17,699,574	Protein-serine O-palmitoleoyltransferase porcupine	GB47458	FBgn0004957
S1_18,694,215	18,694,215	Protein eva-1, transcript variant X1	GB51947	FBgn0259821
S1_33386163	3,492,655	Unknown	Unknown	Unknown
S1_50443612	5,000,737	Dumpy	GB55781	FBgn0053196
S1_52257404	6,814,529	Unknown	Unknown	Unknown
S1_52257424	6,814,549	Unknown	Unknown	Unknown
S1_62957554	4,280,238	Sestrin homolog, transcript variant X1	GB49567	FBgn0034897
S1_69083742	10,406,426	Protein 4.1 homolog	GB44175	FBgn0010434
S1_74943997	3,548,247	Hemicentin-2, transcript variant X1	GB51391	Unknown
S1_77638337	6,242,587	Solute carrier family 35 member F5, transcript variant X1	GB46790	FBgn0034032
S1_77638361	6,242,611	Solute carrier family 35 member F5, transcript variant X1	GB46790	FBgn0034032
S1_86109011	349,889	Eye-specific diacylglycerol kinase, transcript variant X1	GB51219	FBgn0261549
S1_86386875	627,753	Lateral signaling target protein 2 homolog	GB51210	FBgn0039492
S1_88925416	3,166,294	Charged multivesicular body protein 7	GB54484	FBgn0027565
S1_88925462	3,166,340	UDP-glucuronosyltransferase 1–3-like	GB54485	Unknown
S1_89224631	3,465,509	Jazigo, transcript variant X1	GB43054	FBgn0261259
S1_90545383	4,786,261	GRAM domain-containing protein 3-like, transcript variant X1	GB52157	Unknown
S1_96460901	10,701,779	Guanylate cyclase, soluble, beta 1	GB52953	FBgn0013973
S1_103184872	17,425,750	Potassium channel subfamily T member 2	GB45474	FBgn0261698
S1_104349915	117,756	Zinc finger protein GLI4-like, transcript variant X1	GB40273	FBgn0039039
S1_108444799	4,212,640	Protein tincar, transcript variant X1	GB49246	FBgn0261649
S1_108537914	4,305,755	Tachykinin	GB49248	Unknown
S1_108537929	4,305,770	Tachykinin	GB49248	Unknown
S1_108682550	4,450,391	Unknown	Unknown	Unknown
S1_108724951	4,492,792	Uncharacterized LOC725260	GB54634	FBgn0034808
S1_108786716	4,554,557	Uncharacterized LOC725260	GB54634	FBgn0034808
S1_110307882	6,075,723	Thyrotropin-releasing hormone-degrading ectoenzyme-like, transcript variant X1	GB43314	Unknown
S1_110854546	6,622,387	CCR4-NOT transcription complex subunit 6-like, transcript variant X1	GB48300	FBgn0011725
S1_110950229	6,718,070	CCR4-NOT transcription complex subunit 6-like, transcript variant X1	GB48300	FBgn0011725
S1_110951124	6,718,965	CCR4-NOT transcription complex subunit 6-like, transcript variant X1	GB48300	FBgn0011725
S1_110951168	6,719,009	CCR4-NOT transcription complex subunit 6-like, transcript variant X1	GB48300	FBgn0011725
S1_123838315	6,386,711	Plasma membrane calcium-transporting ATPase 2	GB43909	FBgn0259214
S1_125133095	7,681,491	Uncharacterized LOC411277, transcript variant X1	GB41894	FBgn0023531
S1_126922494	9,470,890	Probable G-protein coupled receptor 158	GB52840	FBgn0085401
S1_127479850	10,028,246	Ecdysone receptor, transcript variant A	GB48059	FBgn0000546
S1_130971599	13,519,995	Uncharacterized LOC725485	GB51646	FBgn0259927
S1_132727867	1,729,619	Prefoldin subunit 5	GB43750	FBgn0038976
S1_134667854	3,669,606	Fasciclin-1	Unknown	Unknown
S1_141112580	10,114,332	Sortilin-related receptor	GB53341	Unknown
S1_143133972	1,015,171	Uncharacterized LOC102654435	Unknown	Unknown
S1_143743719	1,624,918	Unknown	Unknown	Unknown
S1_150101379	7,982,578	Beta-1-syntrophin, transcript variant X1	GB54295	FBgn0037130
S1_153385191	11,266,390	Uncharacterized protein CG43867	GB51041	FBgn0259100
S1_153549815	11,431,014	Brachyury protein, transcript variant X1	GB51013	FBgn0011723
S1_153549857	11,431,056	Brachyury protein, transcript variant X1	GB51013	FBgn0011723
S1_155093443	8589	Unknown	Unknown	Unknown
S1_155468419	383,565	Uncharacterized protein C1orf112 homolog	GB46620	FBgn0050424
S1_162084123	6,999,269	Protein FAM49B, transcript variant X1	GB53506	FBgn0052066
S1_162216249	7,131,395	tRNA dimethylallyltransferase, mitochondrial-like	GB53505	Unknown
S1_164267544	9,182,690	Carbonic anhydrase-related protein 10, transcript variant X1	GB45092	FBgn0029962
S1_167336698	12,251,844	Tyrosine-protein kinase transmembrane receptor Ror2, transcript variant X1	GB45194	FBgn0020391
S1_168107630	13,022,776	Fringe glycosyltransferase	GB44913	FBgn0011591
S1_176503904	6,692,394	Disks large 1 tumor suppressor protein	GB40648	FBgn0001624
S1_182557882	843,618	Unknown	Unknown	Unknown
S1_192304686	301,823	Inactive rhomboid protein 1	GB49046	FBgn0041723
S1_193370056	1,367,193	Unknown	GB53054	Unknown
S1_197495828	5,492,965	Negative elongation factor E-like, transcript variant X1	Unknown	Unknown
S1_200092025	8,089,162	Chromatin assembly factor 1 subunit A-B, transcript variant X1	GB52767	FBgn0025833
S1_202452286	195,668	MAX dimerization protein	Unknown	Unknown
S1_209285909	7,029,291	Uncharacterized LOC100576529	GB50066	Unknown
S1_212445471	21,524	Scavenger receptor class B member 1-like, transcript variant X1	Unknown	Unknown
S1_217211608	4,787,661	Unknown	Unknown	Unknown
S1_218446595	6,022,648	Ankyrin repeat domain-containing protein 39-like, transcript variant X1	GB45961	FBgn0031674
S1_220569872	317,721	Histone-lysine N-methyltransferase SETMAR-like	Unknown	Unknown
S1_226482382	27,314	Histone-lysine N-methyltransferase SETMAR-like	Unknown	Unknown
S1_226482388	27,320	Histone-lysine N-methyltransferase SETMAR-like	Unknown	Unknown
S1_227605662	117,306	Unknown	Unknown	Unknown
S1_228624508	85,274	Unknown	Unknown	Unknown
S1_228990350	24,441	Unknown	Unknown	Unknown
S1_229285085	47,268	Cytohesin-1-like	GB55123	FBgn0086779
S1_229285093	47,276	Cytohesin-1-like	GB55123	FBgn0086779
S1_229818309	42,135	Unknown	Unknown	Unknown
S1_231880268	35,546	Lactosylceramide 4-alpha-galactosyltransferase, transcript variant X1	GB46832	FBgn0039378
S1_231894656	49,934	Unknown	Unknown	Unknown
S1_231918135	9237	Putative phosphatidate phosphatase, transcript variant X1	GB49207	FBgn0016078
S1_233321962	34,497	Homogentisate 1,2-dioxygenase	GB53288	FBgn0040211
S1_233858922	67,499	Zinc finger and BTB domain-containing protein 24-like	GB51241	Unknown
S1_234352063	52,465	Unknown	Unknown	Unknown
S1_241871073	419	Unknown	Unknown	Unknown

The Gene IDs mapped with Apis mellifera and Drosophila melanogaster genomes are listed for each SNP

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ISSN: 1471-2164

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