Genetic diversity in Fusarium solani f. sp. pisi based on SSR markers

doi:10.3724/SP.J.1003.2012.10062

Abstract

Abstract:

Pea root rot, caused by Fusarium solani f. sp. pisi (Fsp), is one of the most important diseases on pea (Pisum sativum). Assessing the genetic diversity of the pathogen isolates from different geographical regions is crucially important for understanding of the genetic background of this pathogen and intelligently deploying host resistance. We screened SSRs in complete genome sequence of Nectria haematococca MPVI, and 107 SSR loci were selected for designing markers, from which 24 polymorphic primer pairs were developed. The 24 primer pairs were used to assess genetic diversity of 96 Fsp isolates from different geographical regions. Among 24 SSR markers, a total of 132 alleles were detected among the 96 Fsp isolates, the number of alleles for each of the loci ranged from 3 to 15 with an average of 5.5. The genetic diversity was estimated to range from 0.4855 to 0.8264 with the average value of 0.738. Using these markers, 93 genotypes were detected. When the genetic similarity coefficient was 0.8, 96 Fsp isolates were clustered into 10 groups by phylogenetic analysis. There was no correlation between SSR profile and either geographic origin or pathogenicity. Analysis of AMOVA revealed that variation mainly presented within Fsp populations (86.14%), and genetic differentiation of Fsp was significantly affected by geographical conditions and ecological environment.

Key words: pea root rot, Pisum sativum, Fusarium solani f. sp. pisi, SSR marker, genetic variation

Ni Xiang, Yannong Xiao, Canxing Duan, Xiaoming Wang, Zhendong Zhu. Genetic diversity in Fusarium solani f. sp. pisi based on SSR markers[J]. Biodiv Sci, 2012, 20(6): 693-702.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2012.10062

https://www.biodiversity-science.net/EN/Y2012/V20/I6/693

Figures/Tables 7

References 41

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来源 Location	数量 Amount	分离物 Isolates
安徽 Anhui	17	AH-1^a、AH-2、AH-3、AH-4、AH-5、AH-6、AH-7、AH-8、AH-9、AH-10、AH-11、AH-12、AH-13、AH-14^b、AH-15^a、AH-16、AH-17
北京 Beijing	13	BJ-1、BJ-2、BJ-3、BJ-4、BJ-5、BJ-6、BJ-7、BJ-8、BJ-9、BJ-10、BJ-11、BJ-12、BJ-13
福建 Fujian	4	FJ-1^b、FJ-2^a、FJ-3^b、FJ-4^a
甘肃 Gansu	20	LZ-1、LZ-2、LZ-3^b、LZ-4、LZ-5、LZ-6、DX-1、DX-2、DX-3、DX-4^a、DX-5、DX-6、DX-7、DX-8、DX-9、DX-10、DX-11、DX-12、DX-13、DX-14
河北 Hebei	10	ZB-1、ZB-2、ZB-3、ZB-4、ZB-5、ZB-6、ZB-7、ZB-8、ZB-9、ZB-10
内蒙古 Inner Mongolia	7	NM-1、NM-2、NM-3、NM-4^b、NM-5、NM-6^b、NM-7
吉林 Jilin	1	BC-1^a
宁夏 Ningxia	12	SB-1、SB-2、SB-3、SB-4、SB-5、SB-6、SB-7、SB-8、XB-1、XB-2、PC-1、PC-2
青海 Qinghai	5	QH-1、QH-2、QH-3^b、QH-4^b、QH-5^b
四川 Sichuan	3	SC-1、SC-2、SC-3
云南 Yunnan	4	YN-1^a、YN-2^a、YN-3、YN-4

来源 Location	数量 Amount	分离物 Isolates
安徽 Anhui	17	AH-1^a、AH-2、AH-3、AH-4、AH-5、AH-6、AH-7、AH-8、AH-9、AH-10、AH-11、AH-12、AH-13、AH-14^b、AH-15^a、AH-16、AH-17
北京 Beijing	13	BJ-1、BJ-2、BJ-3、BJ-4、BJ-5、BJ-6、BJ-7、BJ-8、BJ-9、BJ-10、BJ-11、BJ-12、BJ-13
福建 Fujian	4	FJ-1^b、FJ-2^a、FJ-3^b、FJ-4^a
甘肃 Gansu	20	LZ-1、LZ-2、LZ-3^b、LZ-4、LZ-5、LZ-6、DX-1、DX-2、DX-3、DX-4^a、DX-5、DX-6、DX-7、DX-8、DX-9、DX-10、DX-11、DX-12、DX-13、DX-14
河北 Hebei	10	ZB-1、ZB-2、ZB-3、ZB-4、ZB-5、ZB-6、ZB-7、ZB-8、ZB-9、ZB-10
内蒙古 Inner Mongolia	7	NM-1、NM-2、NM-3、NM-4^b、NM-5、NM-6^b、NM-7
吉林 Jilin	1	BC-1^a
宁夏 Ningxia	12	SB-1、SB-2、SB-3、SB-4、SB-5、SB-6、SB-7、SB-8、XB-1、XB-2、PC-1、PC-2
青海 Qinghai	5	QH-1、QH-2、QH-3^b、QH-4^b、QH-5^b
四川 Sichuan	3	SC-1、SC-2、SC-3
云南 Yunnan	4	YN-1^a、YN-2^a、YN-3、YN-4

位点^a Locus^a	引物序列 Primer sequence(5'-3')	重复基元 Repeat motif	基因组位置^b Location in the genome ^b	期望大小 Expected size (bp)	片段大小 Allele size range (bp)	退火温度 Annealing tem- perature (℃)
Fsp1.7	F: TGTTCCCATAGTCCGATTCCG	(AC)₁₇	Contig 1: 3457867-3458072	206	180-220	54
	R: GCCGCTTGACTTGCTAACCA
Fsp1.10	F: CGATTCGTTCTTCCCAACACC	(TCT)₁₄	Contig 1/: 709046-709225	180	147-242	54
	R: AAACCTGCCTCAAGCCCTGA
Fsp1.17	F: AATCCCATTGTTTCGGTGCG	(GT)₂₁	Contig 1/: 245108-245324	217	165-217	54
	R: CCGTTGAGGAATAGAGAGGCA
Fsp2.2	F: GCTTTGGGTCCAGGTATTACG	(AC)₁₁	Contig 15/: 2408632-2409004	373	600-622	54
	R: TTCTCTCTCTCCCGTCACCA
Fsp2.3	F: TGCTCCTACACCTCCGTCTC	(TG)₁₂	Contig 15: 1878221-1878425	205	160-209	54
	R: CACGTTTTATCTGCCTTGCTG
Fsp2.4	F: GATGATTGTGCTGGTAGCCTG	(TTTC)₈	Contig 15: 802092-802323	232	195-238	54
	R: CGCTTGACGCCATAATTGAG
Fsp3.1	F: AACAAGGAGGGTGACGGGAT	(AC)₁₃	Contig 2/: 1062296-1062559	264	210-290	54
	R: AGTGACAAATAGGGAGGTGGG
Fsp3.6	F: CTTGCCCAAACGCATTGAAG	(TG)₁₆	Contig 2/: 2066491-2066782	292	260-320	54
	R: ACTAACACACACCCAGCCTC
Fsp3.7	F: CCATTTCCATTCCACCTCACC	(AGC)₉	Contig 2/: 1170545-1170752	208	180-217	52
	R: CAGTCTGCTGTTATGAAGGGC
Fsp4.2	F: TTGACCTCTGCACACCATCAG	(AC)₁₅	Contig 3/: 2330520-2330703	184	160-200	54
	R: CTCACTCTCGGCTCTCGTTAT
Fsp4.4	F: CGGTCACAGGCAAAGCAAT	(TG)₁₅	Contig 3/: 2288923-2289149	227	190-250	54
	R: GGGATAGAGCAAGCAGCGTT
Fsp4.7	F: ACACACACACAGGCACAAG	(AC)₁₀	Contig 4/: 1510008-1510245	238	201-260	54
	R: TGAGTAAGGTAGGCTGGGTCT
Fsp5.3	F: TACACTCCCGTTCCTGGCTA	(TC)₁₅	Contig 4/: 161679-161833	155	90-147	54
	R: CCAAATCTCAACCGTCGTGG
Fsp5.4	F: TGAATCTGACTGTGGCTGGAG	(TG)11	Contig 4/: 330399-330579	181	160-210	54
	R: ATGGTTCGCCTTGGCTCTGA
Fsp5.8	F: CAGTTAGGTTCCACTCCAGGT	(ACT)₁₄	Contig 4/: 216245-216574	330	260-375	54
	R: TGGGCGGTCATTGTGTAGGT
Fsp6.3	F: AGCACGAGGAACGAGTCTA	(AC)₁₅	Contig 18/: 1864740-1864874	135	110-150	52
	R: CGCTACTTGTTTGTGTCCG
Fsp6.7	F: TGACCGAGAACTGAAGCCA	(TTC)₉	Contig 18/: 2280272-2280530	259	250-350	52
	R: GACGACGAAACCTTTGAAGAG
Fsp7.3	F: CTCTCATTATGTAGCGACGAC	(TCG)₁₀	Contig 7/: 808299-808470	173	150-250	52
	R: TCGATACCCCTGAGTTCTGTG
Fsp9.6	F: GCATCCAATGTCTTTCCCAAT	(TG)₁₇	Contig 5/: 189772--190021	250	230-275	52
	R: GACTCGATATTCATCAACACCA
Fsp9.8	F: TTGGTTTCCCTGCCTTGT	(TG)₂₀	Contig 5/: 1802083-1802348	266	240-300	52
	R: TGTTGGGTCATCTTGGTTTC
Fsp9.9	F: ACGCCACTCTTCCATACTCAG	(AAC)₁₅	Contig 5/: 764399-764632	234	200-280	54
	R: GTTGACGGTCTTGTGGCATAC
Fsp9.10	F: TCAACAACACCAACCACCTG	(AGC)₉	Contig 5/: 509965-510211	247	200-300	54
	R: TTCGTCCGAGTCGCCTTCTA
Fsp9.15	F: GCTTGTGCTGGAGTTGACCT	(GAAT)₈	Contig 5/: 168328-168492	165	123-155	52
	R: CAGGAGCATAGGAGGAATAC
Fsp10.2	F: CGAGAAAGGTGAGGAAGGGA	(GGA)₈	Contig 11/: 258852-259033	182	175-200	52
	R: TATCTGTGAGGTGTGGCGA

位点^a Locus^a	引物序列 Primer sequence(5'-3')	重复基元 Repeat motif	基因组位置^b Location in the genome ^b	期望大小 Expected size (bp)	片段大小 Allele size range (bp)	退火温度 Annealing tem- perature (℃)
Fsp1.7	F: TGTTCCCATAGTCCGATTCCG	(AC)₁₇	Contig 1: 3457867-3458072	206	180-220	54
	R: GCCGCTTGACTTGCTAACCA
Fsp1.10	F: CGATTCGTTCTTCCCAACACC	(TCT)₁₄	Contig 1/: 709046-709225	180	147-242	54
	R: AAACCTGCCTCAAGCCCTGA
Fsp1.17	F: AATCCCATTGTTTCGGTGCG	(GT)₂₁	Contig 1/: 245108-245324	217	165-217	54
	R: CCGTTGAGGAATAGAGAGGCA
Fsp2.2	F: GCTTTGGGTCCAGGTATTACG	(AC)₁₁	Contig 15/: 2408632-2409004	373	600-622	54
	R: TTCTCTCTCTCCCGTCACCA
Fsp2.3	F: TGCTCCTACACCTCCGTCTC	(TG)₁₂	Contig 15: 1878221-1878425	205	160-209	54
	R: CACGTTTTATCTGCCTTGCTG
Fsp2.4	F: GATGATTGTGCTGGTAGCCTG	(TTTC)₈	Contig 15: 802092-802323	232	195-238	54
	R: CGCTTGACGCCATAATTGAG
Fsp3.1	F: AACAAGGAGGGTGACGGGAT	(AC)₁₃	Contig 2/: 1062296-1062559	264	210-290	54
	R: AGTGACAAATAGGGAGGTGGG
Fsp3.6	F: CTTGCCCAAACGCATTGAAG	(TG)₁₆	Contig 2/: 2066491-2066782	292	260-320	54
	R: ACTAACACACACCCAGCCTC
Fsp3.7	F: CCATTTCCATTCCACCTCACC	(AGC)₉	Contig 2/: 1170545-1170752	208	180-217	52
	R: CAGTCTGCTGTTATGAAGGGC
Fsp4.2	F: TTGACCTCTGCACACCATCAG	(AC)₁₅	Contig 3/: 2330520-2330703	184	160-200	54
	R: CTCACTCTCGGCTCTCGTTAT
Fsp4.4	F: CGGTCACAGGCAAAGCAAT	(TG)₁₅	Contig 3/: 2288923-2289149	227	190-250	54
	R: GGGATAGAGCAAGCAGCGTT
Fsp4.7	F: ACACACACACAGGCACAAG	(AC)₁₀	Contig 4/: 1510008-1510245	238	201-260	54
	R: TGAGTAAGGTAGGCTGGGTCT
Fsp5.3	F: TACACTCCCGTTCCTGGCTA	(TC)₁₅	Contig 4/: 161679-161833	155	90-147	54
	R: CCAAATCTCAACCGTCGTGG
Fsp5.4	F: TGAATCTGACTGTGGCTGGAG	(TG)11	Contig 4/: 330399-330579	181	160-210	54
	R: ATGGTTCGCCTTGGCTCTGA
Fsp5.8	F: CAGTTAGGTTCCACTCCAGGT	(ACT)₁₄	Contig 4/: 216245-216574	330	260-375	54
	R: TGGGCGGTCATTGTGTAGGT
Fsp6.3	F: AGCACGAGGAACGAGTCTA	(AC)₁₅	Contig 18/: 1864740-1864874	135	110-150	52
	R: CGCTACTTGTTTGTGTCCG
Fsp6.7	F: TGACCGAGAACTGAAGCCA	(TTC)₉	Contig 18/: 2280272-2280530	259	250-350	52
	R: GACGACGAAACCTTTGAAGAG
Fsp7.3	F: CTCTCATTATGTAGCGACGAC	(TCG)₁₀	Contig 7/: 808299-808470	173	150-250	52
	R: TCGATACCCCTGAGTTCTGTG
Fsp9.6	F: GCATCCAATGTCTTTCCCAAT	(TG)₁₇	Contig 5/: 189772--190021	250	230-275	52
	R: GACTCGATATTCATCAACACCA
Fsp9.8	F: TTGGTTTCCCTGCCTTGT	(TG)₂₀	Contig 5/: 1802083-1802348	266	240-300	52
	R: TGTTGGGTCATCTTGGTTTC
Fsp9.9	F: ACGCCACTCTTCCATACTCAG	(AAC)₁₅	Contig 5/: 764399-764632	234	200-280	54
	R: GTTGACGGTCTTGTGGCATAC
Fsp9.10	F: TCAACAACACCAACCACCTG	(AGC)₉	Contig 5/: 509965-510211	247	200-300	54
	R: TTCGTCCGAGTCGCCTTCTA
Fsp9.15	F: GCTTGTGCTGGAGTTGACCT	(GAAT)₈	Contig 5/: 168328-168492	165	123-155	52
	R: CAGGAGCATAGGAGGAATAC
Fsp10.2	F: CGAGAAAGGTGAGGAAGGGA	(GGA)₈	Contig 11/: 258852-259033	182	175-200	52
	R: TATCTGTGAGGTGTGGCGA

SSR位点 SSR locus	观测等位基因数 Observed number of alleles (Na)	有效等位基因数 Effective number of alleles (Ne)	基因多样性指数 Gene diversity index (H)	Shannon指数 Shannon index (I)
Fsp1.7	5	2.8447	0.6485	1.2162
Fsp1.10	15	4.0502	0.7531	1.9836
Fsp1.17	5	3.6560	0.7265	1.4019
Fsp2.2	6	4.8578	0.7941	1.6700
Fsp2.3	5	3.3457	0.7011	1.3637
Fsp2.4	5	2.1525	0.5354	0.9979
Fsp3.1	4	2.3027	0.5657	1.0762
Fsp3.6	3	2.7466	0.6359	1.0521
Fsp3.7	5	4.4211	0.7738	1.5415
Fsp4.2	4	1.9438	0.4855	0.8826
Fsp4.4	4	3.5333	0.7170	1.3187
Fsp4.7	4	2.5645	0.6101	1.0413
Fsp5.3	6	4.3986	0.7727	1.5779
Fsp5.4	5	4.2793	0.7663	1.5211
Fsp5.8	6	5.1658	0.8064	1.7170
Fsp6.3	4	2.5908	0.6140	1.1040
Fsp6.7	7	5.2721	0.8103	1.7429
Fsp7.3	5	2.7909	0.6417	1.2545
Fsp9.6	5	4.0180	0.7511	1.4874
Fsp9.8	4	3.1232	0.6798	1.2192
Fsp9.9	8	5.7601	0.8264	1.8905
Fsp9.10	7	5.3629	0.8135	1.7745
Fsp9.15	4	3.1419	0.6817	1.2351
Fsp10.2	6	4.5338	0.7794	1.6062
平均 Mean	5.5	3.7023	0.7038	1.4031