Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

Liu, Shengrui; An, Yanlin; Tong, Wei; Qin, Xiuju; Samarina, Lidia; Guo, Rui; Xia, Xiaobo; Wei, Chaoling

doi:10.1186/s12864-019-6347-0

Table 1 Characteristics of 48 newly developed InDel markers

From: Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

Marker ID	Scaffold location	Fragment size (bp)	Na	MAF	Ho	He	PIC
CsInDel01	Scaffold 5: 236696	139–156	3	0.787	0.383	0.361	0.327
CsInDel02	Scaffold 5: 1208833	186–205	4	0.489	1.000	0.633	0.555
CsInDel03	Scaffold 12: 195263	332–354	3	0.500	0.489	0.577	0.478
CsInDel04	Scaffold 30: 3820588	214–242	5	0.532	0.532	0.636	0.576
CsInDel05	Scaffold 39: 128636	236–264	4	0.479	0.979	0.556	0.448
CsInDel06	Scaffold 41: 2074123	280–295	3	0.808	0.180	0.319	0.273
CsInDel07	Scaffold 46: 249178	176–189	3	0.734	0.362	0.405	0.336
CsInDel08	Scaffold 51: 314982	206–215	6	0.394	0.638	0.691	0.627
CsInDel09	Scaffold 51: 760768	201–248	7	0.532	0.660	0.679	0.645
CsInDel10	Scaffold 52: 469482	288–306	3	0.745	0.255	0.394	0.329
CsInDel11	Scaffold 60: 843530	292–332	6	0.383	0.213	0.748	0.701
CsInDel12	Scaffold 60: 843632	240–275	5	0.426	0.660	0.704	0.645
CsInDel13	Scaffold 64: 151635	270–289	3	0.404	0.617	0.643	0.559
CsInDel14	Scaffold 66: 500052	203–232	4	0.436	0.064	0.621	0.535
CsInDel15	Scaffold 77: 505984	185–207	2	0.500	1.000	0.505	0.375
CsInDel16	Scaffold 89: 1202911	231–248	2	0.819	0.149	0.300	0.252
CsInDel17	Scaffold 98: 664107	306–354	6	0.395	0.256	0.731	0.677
CsInDel18	Scaffold 114: 416691	283–326	6	0.489	0.809	0.703	0.661
CsInDel19	Scaffold 129: 540746	180–214	6	0.422	1.000	0.652	0.579
CsInDel20	Scaffold 154: 767901	285–297	5	0.266	0.979	0.763	0.709
CsInDel21	Scaffold 225: 80286	191–204	2	0.649	0.362	0.461	0.352
CsInDel22	Scaffold 1000: 52494	216–288	3	0.532	0.404	0.612	0.537
CsInDel23	Scaffold 1001: 123324	236–326	6	0.628	0.489	0.568	0.526
CsInDel24	Scaffold 1001: 149678	190–199	2	0.798	0.021	0.326	0.271
CsInDel25	Scaffold 1001: 155681	195–218	2	0.649	0.319	0.461	0.352
CsInDel26	Scaffold 1001: 1251845	341–363	3	0.583	0.833	0.511	0.399
CsInDel27	Scaffold 1001: 1261469	273–290	3	0.777	0.064	0.359	0.306
CsInDel28	Scaffold 1001: 1400899	213–253	6	0.660	0.383	0.537	0.501
CsInDel29	Scaffold 1001: 1491192	182–226	4	0.457	1.000	0.586	0.489
CsInDel30	Scaffold 1001: 1691928	238–258	4	0.745	0.362	0.411	0.363
CsInDel31	Scaffold 1001: 1982826	284–316	4	0.489	0.915	0.619	0.539
CsInDel32	Scaffold 1452: 285463	272–299	3	0.596	0.426	0.511	0.406
CsInDel33	Scaffold 1539: 196438	271–280	2	0.798	0.404	0.326	0.271
CsInDel34	Scaffold 1541: 138532	265–286	3	0.564	0.851	0.523	0.413
CsInDel35	Scaffold 1543: 253456	172–207	2	0.915	0.128	0.157	0.144
CsInDel36	Scaffold 1551: 196819	157–237	3	0.606	0.745	0.499	0.391
CsInDel37	Scaffold 1553: 529121	211–237	4	0.564	0.511	0.547	0.451
CsInDel38	Scaffold 1555: 5209	109–340	14	0.298	0.489	0.869	0.849
CsInDel39	Scaffold 1579: 1466247	261–272	2	0.606	0.787	0.483	0.363
CsInDel40	Scaffold 1592: 672899	276–329	7	0.596	0.979	0.666	0.489
CsInDel41	Scaffold 1593: 1022219	172–187	2	0.957	0.085	0.082	0.078
CsInDel42	Scaffold 1594: 195199	184–206	3	0.691	0.426	0.454	0.380
CsInDel43	Scaffold 1611: 1270988	226–254	5	0.426	0.319	0.684	0.619
CsInDel44	Scaffold 2220: 166816	292–328	3	0.543	0.575	0.521	0.402
CsInDel45	Scaffold 15,285: 211487	281–321	5	0.333	0.952	0.752	0.699
CsInDel46	Scaffold 15,433: 302840	190–253	2	0.638	0.468	0.467	0.355
CsInDel47	Scaffold 15,579: 267174	176–186	2	0.957	0.043	0.082	0.078
CsInDel48	Scaffold 15,650: 137667	228–266	6	0.489	0.596	0.671	0.614
Average	–	–	4.02	0.585	0.524	0.528	0.457

Na number of alleles, MAF major allele frequency, Ho observed heterozygosity, He expected heterozygosity, PIC polymorphism information content

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ISSN: 1471-2164

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