Genetic diversity in Chinese rapeseed (Brassica napus) cultivars based on EST-SSR markers

doi:10.3724/SP.J.1003.2009.09074

Abstract

Abstract:

In order to assess genetic variation in Chinese rapeseed (Brassica napus), the genetic diversity of 91 cultivars released in recent years was assessed using EST-SSR markers. In total, 100 amplified fragments were detected using 16 EST-SSR primer pairs; of these fragments 84 were polymorphic. The number of amplified and polymorphic fragments was 6.25 and 5.25 per primer pair, respectively. The PIC (polymorphism information content) value of these markers varied from 0.022 to 0.926, averaging 0.677. The genotypes revealed by each marker ranged from 2 to 24 with average of 12.44. Genetic distance (GD) varied widely, from 0.0530 to 0.7223, suggesting the presence of broad genetic variation in the accessions we used. Diversity was higher in hybrid varieties and varieties released after the year 2000 than in traditional open-pollinated varieties and varieties released before or during the year 2000, respectively. At GD = 0.313 the tested varieties could be classified into three groups clustered by UPGMA, in which the first group containing 87 cultivars could be further divided into 10 sub-groups at GD = 0.223. The cluster results generally agreed with pedigree analysis and reveal the true genetic variation in the materials tested.

Key words: Brassica napus, EST-SSR, polymorphism, genetic distance, cluster analysis

Lichuan Dai, Minglong Zhang, Jiye Liu, Xiaobai Li, Hairui Cui. Genetic diversity in Chinese rapeseed (Brassica napus) cultivars based on EST-SSR markers[J]. Biodiv Sci, 2009, 17(5): 482-489.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2009.09074

https://www.biodiversity-science.net/EN/Y2009/V17/I5/482

Figures/Tables 7

References 35

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编号 Code	EST-SSR 引物序列 Sequences	退火温度 Annealing temp. (℃)	重复基元 Repeat motif	目标片段 Target fragment(bp)		扩增条带数 Bands amplified	多态性条带数 Polymorphic bands
编号 Code	EST-SSR 引物序列 Sequences	退火温度 Annealing temp. (℃)	重复基元 Repeat motif	预期大小Expected size	实际大小 Actual size	扩增条带数 Bands amplified	多态性条带数 Polymorphic bands
P1	CTGGGAAAGGGAAAGTGGC	60	(TC)31	131	130-200	3	3
P1	TGGCTGAATCCTGCGGAC	60	(TC)31	131	130-200	3	3
P2	TTCTTCGTCTTCTCCACTCTTATTC	60	(CA)15	150	150-190	4	3
P2	TGATCTTCTGCTCGACATATCTTTA	60	(CA)15	150	150-190	4	3
P6	ACTCCGTCATCACCGTCCTT	50	(AG)11	212	210-230	3	3
P6	CCTATTCAACGCTGCGTCTTA	50	(AG)11	212	210-230	3	3
P7	TATCCATCGTCTGGTTTTGTTC	55	(TG)9(T)11	217	220-310	5	4
P7	TTTTCAGATTTACCGTTCACCT	55	(TG)9(T)11	217	220-310	5	4
P11	CTACTCGCATGGAAACGCC	60	(TG)10	302	308-580	8	7
P11	GCAGCAAGAAGCATTATCGC	60	(TG)10	302	308-580	8	7
P13	ACCCCAGATATTTTGTTAGCCG	50	(AG)17	341	700-1000	8	8
P13	CAGGTCTTGCCCATTTTGTCA	50	(AG)17	341	700-1000	8	8
P14	AGAACTAATCCGAAGGAGACCG	65	(GAT)14	343	505-800	8	6
P14	GGCTAAGCCGCAAACGAC	65	(GAT)14	343	505-800	8	6
P16	TCATATCCATCCATGTCTCAACG	65	(TCA)10	365	365-900	10	8
P16	CAACAGAAACTCGGTGCAAATC	65	(TCA)10	365	365-900	10	8
P17	CTGGAATACTTGTTTCAATGGGT	65	(GGTCTA)6	384	380-520	7	3
P17	GCTCACTTTCAGTCTGGGTGTC	65	(GGTCTA)6	384	380-520	7	3
P19	AGTGTTGGAAGCGGAAAAGG	60	(TCA)11	390	220-570	6	5
P19	GCGTAGGCAGGAAAATAGGG	60	(TCA)11	390	220-570	6	5
P20	TTATCTCAGAACGCTCCGACG	60	(GAT)10	412	405-750	8	8
P20	CCTCATCCTCCTCTTTCCTCAG	60	(GAT)10	412	405-750	8	8
P21	ATTACCCTGAACCACCACCC	55	(GCT)18	320	320, 680-980	6	4
P21	TGCTTGTCCAAATAGCTCTTGA	55	(GCT)18	320	320, 680-980	6	4
P22	TTCATTTTGCTTGATGTGATTCTC	50	(CT)21	267	260-340	5	5
P22	GCTTGGCGTAAAAGGATTCTACT	50	(CT)21	267	260-340	5	5
P23	GAAGTTGGGTTGAAGAGCAGTT	50	(TC)23	232	232-480	9	8
P23	TCTGTAAAGTGTCCAGGAGCAAC	50	(TC)23	232	232-480	9	8
P24	TGGTCTTGATTTTATTGCGAGC	60	(GAT)14	223	170-250	6	6
P24	TTTGGGCGTGATACCTTGAG	60	(GAT)14	223	170-250	6	6
P25	GCTCTAACCACTGACCACCGA	60	(TC)19	390	390-680	4	3
P25	ACATCCTGCTCTGGGAAACAT	60	(TC)19	390	390-680	4	3

编号 Code	EST-SSR 引物序列 Sequences	退火温度 Annealing temp. (℃)	重复基元 Repeat motif	目标片段 Target fragment(bp)		扩增条带数 Bands amplified	多态性条带数 Polymorphic bands
编号 Code	EST-SSR 引物序列 Sequences	退火温度 Annealing temp. (℃)	重复基元 Repeat motif	预期大小Expected size	实际大小 Actual size	扩增条带数 Bands amplified	多态性条带数 Polymorphic bands
P1	CTGGGAAAGGGAAAGTGGC	60	(TC)31	131	130-200	3	3
P1	TGGCTGAATCCTGCGGAC	60	(TC)31	131	130-200	3	3
P2	TTCTTCGTCTTCTCCACTCTTATTC	60	(CA)15	150	150-190	4	3
P2	TGATCTTCTGCTCGACATATCTTTA	60	(CA)15	150	150-190	4	3
P6	ACTCCGTCATCACCGTCCTT	50	(AG)11	212	210-230	3	3
P6	CCTATTCAACGCTGCGTCTTA	50	(AG)11	212	210-230	3	3
P7	TATCCATCGTCTGGTTTTGTTC	55	(TG)9(T)11	217	220-310	5	4
P7	TTTTCAGATTTACCGTTCACCT	55	(TG)9(T)11	217	220-310	5	4
P11	CTACTCGCATGGAAACGCC	60	(TG)10	302	308-580	8	7
P11	GCAGCAAGAAGCATTATCGC	60	(TG)10	302	308-580	8	7
P13	ACCCCAGATATTTTGTTAGCCG	50	(AG)17	341	700-1000	8	8
P13	CAGGTCTTGCCCATTTTGTCA	50	(AG)17	341	700-1000	8	8
P14	AGAACTAATCCGAAGGAGACCG	65	(GAT)14	343	505-800	8	6
P14	GGCTAAGCCGCAAACGAC	65	(GAT)14	343	505-800	8	6
P16	TCATATCCATCCATGTCTCAACG	65	(TCA)10	365	365-900	10	8
P16	CAACAGAAACTCGGTGCAAATC	65	(TCA)10	365	365-900	10	8
P17	CTGGAATACTTGTTTCAATGGGT	65	(GGTCTA)6	384	380-520	7	3
P17	GCTCACTTTCAGTCTGGGTGTC	65	(GGTCTA)6	384	380-520	7	3
P19	AGTGTTGGAAGCGGAAAAGG	60	(TCA)11	390	220-570	6	5
P19	GCGTAGGCAGGAAAATAGGG	60	(TCA)11	390	220-570	6	5
P20	TTATCTCAGAACGCTCCGACG	60	(GAT)10	412	405-750	8	8
P20	CCTCATCCTCCTCTTTCCTCAG	60	(GAT)10	412	405-750	8	8
P21	ATTACCCTGAACCACCACCC	55	(GCT)18	320	320, 680-980	6	4
P21	TGCTTGTCCAAATAGCTCTTGA	55	(GCT)18	320	320, 680-980	6	4
P22	TTCATTTTGCTTGATGTGATTCTC	50	(CT)21	267	260-340	5	5
P22	GCTTGGCGTAAAAGGATTCTACT	50	(CT)21	267	260-340	5	5
P23	GAAGTTGGGTTGAAGAGCAGTT	50	(TC)23	232	232-480	9	8
P23	TCTGTAAAGTGTCCAGGAGCAAC	50	(TC)23	232	232-480	9	8
P24	TGGTCTTGATTTTATTGCGAGC	60	(GAT)14	223	170-250	6	6
P24	TTTGGGCGTGATACCTTGAG	60	(GAT)14	223	170-250	6	6
P25	GCTCTAACCACTGACCACCGA	60	(TC)19	390	390-680	4	3
P25	ACATCCTGCTCTGGGAAACAT	60	(TC)19	390	390-680	4	3

标记编号 Marker code	多态性信息含量 PIC	基因型数 No. of genotypes
P1	0.468	3
P2	0.296	7
P6	0.728	6
P7	0.514	8
P11	0.851	24
P13	0.842	23
P14	0.886	15
P16	0.891	24
P17	0.022	2
P19	0.552	10
P20	0.926	15
P21	0.788	12
P22	0.639	7
P23	0.829	13
P24	0.910	24
P25	0.696	6

标记编号 Marker code	多态性信息含量 PIC	基因型数 No. of genotypes
P1	0.468	3
P2	0.296	7
P6	0.728	6
P7	0.514	8
P11	0.851	24
P13	0.842	23
P14	0.886	15
P16	0.891	24
P17	0.022	2
P19	0.552	10
P20	0.926	15
P21	0.788	12
P22	0.639	7
P23	0.829	13
P24	0.910	24
P25	0.696	6

材料 Accession	数目 Number	遗传距离 Genetic distance
材料 Accession	数目 Number	变化范围 Range	变异系数 CV (%)	标准差 SD	平均 Average
常规品种 Open-pollinated variety	28	0.0921-0.4208	24.83	0.0563	0.2383^a
杂交品种 Hybrid variety	63	0.0530-0.6336	31.59	0.0808	0.2474^b