High-density Genetic Linkage Map Reconstruction in Jujube Using SNP Markers

doi:10.16420/j.issn.0513-353x.2020-0933

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (11): 2275-2285.doi: 10.16420/j.issn.0513-353x.2020-0933

• Original article • Previous Articles Next Articles

High-density Genetic Linkage Map Reconstruction in Jujube Using SNP Markers

TANG Haixia¹, GAO Rui¹, WANG Zhongtang¹^,²^,^*(), ZHANG Qiong¹^,²^,^*()

¹Shandong Institute of Pomology,Tai’an,Shandong 271000,China
²Dry Fruit Breeding Technology Center of Shandong Province,Tai’an,Shandong 271000,China

Received:2021-04-14 Revised:2021-09-09 Published:2021-12-02
Contact: WANG Zhongtang,ZHANG Qiong E-mail:sdgss213@163.com

Abstract

Abstract:

The genetic linkage map was reconstructed referred to the whole genome sequencing data of‘Dongzao’jujube,based on the 103 F₁ population of‘Dongzao’×‘Jinsi 4’that have been published and SNP（38.45 Gb） developed from the population by our team. The new linkage map consisted a total of 3 678 SNP markers,spanning 939.23 cM,with an average marker distance of 0.26 cM. The genetic map anchored 324 Mb（74.17%）of scaffolds to the sequenced‘Dongzao’genome.

Key words: jujube, SNP, genome, genetic linkage map

CLC Number:

S665.1

TANG Haixia, GAO Rui, WANG Zhongtang, ZHANG Qiong. High-density Genetic Linkage Map Reconstruction in Jujube Using SNP Markers[J]. Acta Horticulturae Sinica, 2021, 48(11): 2275-2285.

Figures/Tables 10

References 32

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材料 Material	有效数据/ Gb Clean base	碱基正确率/% Effective rate	Q20/%	Q30/%	GC含量/% GC Content
冬枣（♀）Dongzao	1.52	99.99	95.92	90.16	36.29
金丝4号（♂）Jinsi 4	1.40	99.99	94.88	87.57	36.28
F₁极大值Maximum	0.59	99.99	95.16	88.83	36.57
F₁极小值Minimum	0.19	99.99	93.82	85.00	34.94
F₁平均值Average	0.35	99.99	94.60	87.27	35.94
F₁	35.53	—	—	—	—
合计All	38.45	—	—	—	—

材料 Material	有效数据/ Gb Clean base	碱基正确率/% Effective rate	Q20/%	Q30/%	GC含量/% GC Content
冬枣（♀）Dongzao	1.52	99.99	95.92	90.16	36.29
金丝4号（♂）Jinsi 4	1.40	99.99	94.88	87.57	36.28
F₁极大值Maximum	0.59	99.99	95.16	88.83	36.57
F₁极小值Minimum	0.19	99.99	93.82	85.00	34.94
F₁平均值Average	0.35	99.99	94.60	87.27	35.94
F₁	35.53	—	—	—	—
合计All	38.45	—	—	—	—

样品 Sample	比对上的序列数/Mb Mapping reads	比对率/% Mapping rate	平均测序深度 Average depth	覆盖度/1× Coverage
冬枣（♀）Dongzao	9.56	86.41	15.42	20.17
金丝4号（♂）Jinsi 4	8.92	87.58	16.02	17.98
F₁极大值Maximum of F₁	3.74	84.33	8.95	14.51
F₁极小值Minimum of F₁	1.25	88.84	4.83	8.49
F₁合计Total of F₁	205.53	—	—	—
合计All	224.01	—	—	—

样品 Sample	比对上的序列数/Mb Mapping reads	比对率/% Mapping rate	平均测序深度 Average depth	覆盖度/1× Coverage
冬枣（♀）Dongzao	9.56	86.41	15.42	20.17
金丝4号（♂）Jinsi 4	8.92	87.58	16.02	17.98
F₁极大值Maximum of F₁	3.74	84.33	8.95	14.51
F₁极小值Minimum of F₁	1.25	88.84	4.83	8.49
F₁合计Total of F₁	205.53	—	—	—
合计All	224.01	—	—	—

连锁群 CHR	起始位置 Start	结束位置 End	SNP数量 SNP-count	SNP密度/（Variants · kb^-1） SNP density
NC_029679.1（LG1）	1	42 390 363	5 924	0.139
NC_029680.1（LG2）	1	27 986 743	3 376	0.121
NC_029681.1（LG3）	1	26 737 297	3 521	0.130
NC_029682.1（LG4）	1	30 445 767	3 506	0.115
NC_029683.1（LG5）	1	31 365 312	3 343	0.106
NC_029684.1（LG6）	1	25 259 912	3 204	0.126
NC_029685.1（LG7）	1	27 644 224	2 827	0.101
NC_029686.1（LG8）	1	23 350 829	2 544	0.108
NC_029687.1（LG9）	1	25 348 792	3 975	0.156
NC_029688.1（LG10）	1	20 983 256	2 635	0.126
NC_029689.1（LG11）	1	20 703 932	2 638	0.126
NC_029690.1（LG12）	1	19 346 091	2 456	0.126
平均Average	—	—	3 329	0.123

High-density Genetic Linkage Map Reconstruction in Jujube Using SNP Markers

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Figures/Tables 10

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父本基因型 P₁ genotype	母本基因型 P₂ genotype	标记类型和数量Type and number of exploited markers
父本基因型 P₁ genotype	母本基因型 P₂ genotype	基因型（P₁× P₂）Genotype	标记数量Marker numbers	占有效标记/% Percentage
lm	ll	lm × ll	6 001	36.07
hk	hk	hk × hk	3 038	18.26
nn	np	nn × np	4 453	26.76
aa	bb	aa × bb	1 670	10.04
缺失Missing			494	2.97
P1 = P2			983	5.91
总计Total			16 639	100.00

连锁群 Linkage group	标记数量 Number of markers			遗传距离/cM Genetic distance			标记间平均距离/cM Average distance between markers
连锁群 Linkage group	母本图谱 DF-map	父本图谱 DM-map	整合图谱 D-map	母本图谱DF-map	父本图谱 DM-map	整合图谱 D-map	母本图谱 DF-map	父本图谱 DM-map	整合图谱 D-map
LG1	265	131	376	75.07	85.86	84.58	0.28	0.66	0.22
LG2	193	199	334	70.94	80.12	92.87	0.37	0.40	0.28
LG3	108	234	309	74.34	70.26	80.68	0.69	0.30	0.26
LG4	243	257	369	71.33	43.75	76.73	0.29	0.17	0.21
LG5	217	202	288	52.26	67.54	75.91	0.24	0.33	0.26
LG6	198	153	290	77.21	73.88	82.73	0.39	0.48	0.29
LG7	169	173	299	70.13	65.66	81.38	0.41	0.38	0.27
LG8	152	194	256	86.56	71.40	83.33	0.57	0.37	0.33
LG9	83	160	209	71.81	60.70	71.92	0.87	0.38	0.34
LG10	238	110	330	73.31	39.62	78.23	0.31	0.36	0.24
LG11	168	154	306	56.80	55.93	56.97	0.34	0.36	0.19
LG12	202	133	312	69.79	67.06	73.90	0.35	0.50	0.24
合计Total	2 236	2 100	3 678	849.54	781.75	939.23	—	—	—
均值Average	—	—	—	—	—	—	0.38	0.37	0.26

连锁群 Linkage Group	小于5 cM间距数 Number of gaps < 5 cM			大于5 cM间距数 Number of gaps > 5 cM			最大间距 Distance of maximum gap
连锁群 Linkage Group	母本图谱 DF-map	父本图谱 DM-map	整合图谱 D-map	母本图谱 DF-map	父本图谱 DM-map	整合图谱 D-map	母本图谱 DF-map	父本图谱 DM-map	整合图谱 D-map
LG1	130	264	375	1	1	1	6.00	17.10	5.35
LG2	199	190	334	0	3	0	4.61	10.00	4.37
LG3	234	106	309	0	2	0	6.26	7.22	4.98
LG4	256	243	368	1	0	1	10.60	3.90	10.60
LG5	202	217	288	0	0	0	2.55	4.05	2.98
LG6	152	197	290	1	1	0	5.92	9.50	3.45
LG7	171	168	298	1	1	0	7.14	5.98	4.88
LG8	192	152	255	2	0	1	13.40	3.20	6.46
LG9	158	83	208	2	0	1	18.00	4.00	6.34
LG10	109	237	329	1	1	1	5.33	8.13	5.33
LG11	152	167	306	2	1	0	6.36	8.57	4.44
LG12	131	200	312	2	2	0	6.55	10.50	6.43

连锁群 Linkage group	锚定标记数量 Number of anchored markers	遗传距离/cM Genetic length	物理距离/kb Physical length	物理距离/遗传距离/（kb · cM^-1） Physical length/ genetic length
LG1	342	84.58	42 356.19	500.78
LG2	317	92.87	27 809.17	299.44
LG3	293	80.68	26 633.83	330.12
LG4	332	76.73	30 413.79	396.37
LG5	265	75.91	29 155.05	384.07
LG6	268	82.73	30 887.33	373.35
LG7	221	75.59	27 404.28	362.54
LG8	126	83.33	25 763.93	309.18
LG9	180	71.92	25 186.14	350.20
LG10	304	78.23	22 319.02	285.30
LG11	210	56.83	15 578.13	274.12
LG12	267	73.90	21 145.16	286.13
均值Average	260	77.78	27 054.33	345.97
合计Total	3 125.00	933.30	324 652.01	—

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