基于SNP标记的枣高密度遗传连锁图谱重新构建

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

摘要/Abstract

摘要：

依托‘冬枣’×‘金丝4号’的F₁代103株群体,以采用GBS简化基因组测序技术开发的SNP（38.45 Gb）为材料,参考‘冬枣’全基因组测序数据,重新构建了1张包含12条连锁群,遗传标记数量3 678个,总遗传距离939.23 cM,平均遗传距离为0.26 cM的枣高密度遗传连锁图谱。与‘冬枣’基因组共线性分析,锚定数据量为324 Mb,占‘冬枣’基因组的74.17%。

关键词: 枣, 单核苷酸多态性, 基因组, 遗传图谱

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

中图分类号:

S665.1

唐海霞, 高瑞, 王中堂, 张琼. 基于SNP标记的枣高密度遗传连锁图谱重新构建[J]. 园艺学报, 2021, 48(11): 2275-2285.

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.

图/表 10

参考文献 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