园艺学报 ›› 2021, Vol. 48 ›› Issue (11): 2275-2285.doi: 10.16420/j.issn.0513-353x.2020-0933
唐海霞1, 高瑞1, 王中堂1,2,*(), 张琼1,2,*(
)
收稿日期:
2021-04-14
修回日期:
2021-09-09
发布日期:
2021-12-02
通讯作者:
王中堂,张琼
E-mail:sdgss213@163.com
基金资助:
TANG Haixia1, GAO Rui1, WANG Zhongtang1,2,*(), ZHANG Qiong1,2,*(
)
Received:
2021-04-14
Revised:
2021-09-09
Published:
2021-12-02
Contact:
WANG Zhongtang,ZHANG Qiong
E-mail:sdgss213@163.com
摘要:
依托‘冬枣’ב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%。
中图分类号:
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.
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 | — | — | — | — |
表1 测序数据量统计
Table 1 Quality evaluation sequencing data
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 | — | — | — |
表2 亲本和子代与‘冬枣’基因组比对结果
Table 2 Compare results of genome between parents and offspring and Ziziphus jujuba‘Dongzao’
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 |
表3 SNP在基因组上的分布
Table 3 Distribution of SNP in genome
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 |
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 | ||
---|---|---|---|---|
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 |
表4 标记类型和数量
Table 4 Type and number of exploited markers
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 | ||
---|---|---|---|---|
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 | ||||||
---|---|---|---|---|---|---|---|---|---|
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 |
表5 亲本和整合数字遗传连锁图谱
Table 5 Parental and integrated digital genetic linkage maps
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 | ||||||
---|---|---|---|---|---|---|---|---|---|
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 |
图2 母本DF-map、父本DM-map和整合图谱D-map连锁群标记分布图 颜色深浅代表各连锁群上标记密度。
Fig. 2 DF-map(female),DM-map(male)and D-map(integrated)linkage group tag distribution The color depth represents the marker density on each linkage group.
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 | ||||||
---|---|---|---|---|---|---|---|---|---|
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 |
表6 亲本和整合遗传图谱标记间距统计
Table 6 Gaps of parental and integrated maps
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 | ||||||
---|---|---|---|---|---|---|---|---|---|
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 | — |
表7 整合图谱SNP标记与参考基因组‘冬枣’锚定情况
Table 7 Anchored sequenced genome scaffolds of Ziziphus jujuba‘Dongzao’with SNP markers
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 | — |
图3 D-map遗传图谱与物理图谱共线性分析 LG1 ~ LG12为遗传图谱连锁群编号。chr1 ~ chr12为枣基因组染色体编号。
Fig. 3 Collinearity analysis of D-map genetic map and physical map LG1-LG12 are the linkage group numbers of the genetic map. chr1-chr12 are the chromosome numbers of jujube genome.
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