Development and Analysis of Polymorphism of SSR Markers in the Whole Genome of Loquat

doi:10.16420/j.issn.0513-353x.2020-0497

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (5): 1013-1022.doi: 10.16420/j.issn.0513-353x.2020-0497

• Research Notes • Previous Articles Next Articles

Development and Analysis of Polymorphism of SSR Markers in the Whole Genome of Loquat

JIANG Shuang^*(), ZHANG Xueying, AN Haishan, XU Fangjie, ZHANG Jiaying

Shanghai Key Laboratory of Protected Horticultural Technology,Forestry and Fruit Tree Research Institute,Shanghai Academy of Agricultural Sciences,Shanghai 201403,China

Received:2020-12-15 Revised:2021-02-08 Online:2021-05-25 Published:2021-06-07

Abstract

Abstract:

In this study,we searched the SSR loci in the whole loquat genome and analyzed its distribution characteristics. The resequencing data of 10 cultivars were used to analyze the genotypes of these loci. The results showed that 103 509 SSR sites were obtained,of which 73 604 SSRs were dinucleotide repeat,accounting for 71.1% of total discovered SSRs. The main dinucleotide repeat motif was AT/TA. The trinucleotide repeat type of SSRs accounts for 15.0%,with AAG/CTT as the main type. Ten cultivars of loquat were resequenced,and 32-206 Mb reads were obtained with a depth of 12.9×-81.3×. Two new scripts(Flank and SSRtype)were developed to analyze the length of SSR sites embedded in the resequencing data reads. The sequencing depth of Zaozhong 6 loquat was 12.9×,covering 80% of SSR sites,indicating that a sequencing depth of more than 12 times was enough to the analysis of the SSR loci. A large number of SSR loci in loquat are multiple copies(accounting for 78.4%),producing more than three bands in a locus in a cultivar. There are 12 962 SSR loci with two copies in all cultivars(accounting for 12.5%). The polymorphic bands generated by these loci range from two to 10. The median of the polymorphism information content(PIC)is 0.269. The PIC value of 526 SSR sites was more than 0.5. Twenty pairs of primers were screened to perform fluorescent PCR. The results of polymorphism of these primers were consistent with the resequencing analysis.

Key words: loquat, SSR marker, whole genome, polymorphism, re-sequencing data

CLC Number:

S667.3

JIANG Shuang, ZHANG Xueying, AN Haishan, XU Fangjie, ZHANG Jiaying. Development and Analysis of Polymorphism of SSR Markers in the Whole Genome of Loquat[J]. Acta Horticulturae Sinica, 2021, 48(5): 1013-1022.

Figures/Tables 7

References 26

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标记 Marker	位置 Position	上游引物(5′-3′) F-primer	下游引物(5′-3′) R-primer
EjSSR1	LG06_22780531_22780756	GTGGCGGATACAAGATTTCA	CACCATTTGCCATTCTACCG
EjSSR2	LG07_28161826_28162057	GGCAAGTTTGTCACGCTATT	AAGAAAAGAAAGCGGTAATCGT
EjSSR3	LG02_12437057_12437286	TATGCAGCCATACTAATGTA	TTAGCGTAGACTCCAGGTGA
EjSSR4	LG15_2449146_2449395	ACAAGATTATGCAGCTACCTTAC	CCGCTAACGATGGAATGAAC
EjSSR5	LG17_10249126_10249370	GAGGGTCTGTTGGCTTGGAT	GAAATGTGGGCATCTTCTTC
EjSSR6	LG02_13068397_13068630	AATATGAGACGTACAAGCTG	TCTTTACTCGCACTGAATGT
EjSSR7	LG09_33605598_33605838	AAATGATCCCTCAACTATAACC	CATTGCTCTATACTCGCATC
EjSSR8	LG05_8474062_8474283	ATAAATAGCAGCAAGGGCTCCAT	GAAACCCCTACCTCAAATCCAA
EjSSR9	LG16_306060_306291	TTCGTACTCATTGAGTTTGGTAT	TGTTGATTAGAATACTGCCTCCC
EjSSR10	LG05_7308571_7308855	CCCATAATCCATCTAAGTACCAAA	GACCTTGAAGGACCTCCATACAC
EjSSR11	LG04_14003826_14004069	CTCGGAGGATGATAAATCAATTC	CCTATTCGACAAGGACGACAAT
EjSSR12	LG11_26083798_26084019	GCCTAAACTTGCCTAGATTCTGAC	ACGGAGCCTAAGCGGACTAA
EjSSR13	LG07_37064315_37064546	TTGGACGGGTTGAGGAACTTAG	CCCACGACTTTGTCTCGCTTCT
EjSSR14	LG17_32809624_32809843	TGCAGTGCCGAACTAAGCTACATA	ACCTGCTGTACCGCAACTTCTG
EjSSR15	LG06_27714710_27714930	ATTGGGAAGCCGTAGTTGGTGA	TCGCAGCTCTTTCTTCTCACTT
EjSSR16	LG01_38250590_38250807	AGTTGAGGCTTAGAAGGCAAGG	GAAAGAACTTTGAAAATTCCATCA
EjSSR17	LG12_5320901_5321127	GAGTGGGACTTCGCATTTGATA	GGAATAACTAACGCCCGCAAC
EjSSR18	LG03_45350948_45351163	CTCGTTATTGCGTTCAAGCATATT	TTTCTGTTTGGAGCTGGGATTT
EjSSR19	LG16_264901_265127	CCTTGCCCTGTAGTATTATGTGAT	ATCTGCGGATAAGGAGCACAAG
EjSSR20	LG14_23903168_23903387	TTTGCGTGATGATCGTTGTCCT	ACACTAAACGGGAGGATGTGGG

标记 Marker	位置 Position	上游引物(5′-3′) F-primer	下游引物(5′-3′) R-primer
EjSSR1	LG06_22780531_22780756	GTGGCGGATACAAGATTTCA	CACCATTTGCCATTCTACCG
EjSSR2	LG07_28161826_28162057	GGCAAGTTTGTCACGCTATT	AAGAAAAGAAAGCGGTAATCGT
EjSSR3	LG02_12437057_12437286	TATGCAGCCATACTAATGTA	TTAGCGTAGACTCCAGGTGA
EjSSR4	LG15_2449146_2449395	ACAAGATTATGCAGCTACCTTAC	CCGCTAACGATGGAATGAAC
EjSSR5	LG17_10249126_10249370	GAGGGTCTGTTGGCTTGGAT	GAAATGTGGGCATCTTCTTC
EjSSR6	LG02_13068397_13068630	AATATGAGACGTACAAGCTG	TCTTTACTCGCACTGAATGT
EjSSR7	LG09_33605598_33605838	AAATGATCCCTCAACTATAACC	CATTGCTCTATACTCGCATC
EjSSR8	LG05_8474062_8474283	ATAAATAGCAGCAAGGGCTCCAT	GAAACCCCTACCTCAAATCCAA
EjSSR9	LG16_306060_306291	TTCGTACTCATTGAGTTTGGTAT	TGTTGATTAGAATACTGCCTCCC
EjSSR10	LG05_7308571_7308855	CCCATAATCCATCTAAGTACCAAA	GACCTTGAAGGACCTCCATACAC
EjSSR11	LG04_14003826_14004069	CTCGGAGGATGATAAATCAATTC	CCTATTCGACAAGGACGACAAT
EjSSR12	LG11_26083798_26084019	GCCTAAACTTGCCTAGATTCTGAC	ACGGAGCCTAAGCGGACTAA
EjSSR13	LG07_37064315_37064546	TTGGACGGGTTGAGGAACTTAG	CCCACGACTTTGTCTCGCTTCT
EjSSR14	LG17_32809624_32809843	TGCAGTGCCGAACTAAGCTACATA	ACCTGCTGTACCGCAACTTCTG
EjSSR15	LG06_27714710_27714930	ATTGGGAAGCCGTAGTTGGTGA	TCGCAGCTCTTTCTTCTCACTT
EjSSR16	LG01_38250590_38250807	AGTTGAGGCTTAGAAGGCAAGG	GAAAGAACTTTGAAAATTCCATCA
EjSSR17	LG12_5320901_5321127	GAGTGGGACTTCGCATTTGATA	GGAATAACTAACGCCCGCAAC
EjSSR18	LG03_45350948_45351163	CTCGTTATTGCGTTCAAGCATATT	TTTCTGTTTGGAGCTGGGATTT
EjSSR19	LG16_264901_265127	CCTTGCCCTGTAGTATTATGTGAT	ATCTGCGGATAAGGAGCACAAG
EjSSR20	LG14_23903168_23903387	TTTGCGTGATGATCGTTGTCCT	ACACTAAACGGGAGGATGTGGG

品种 Cultivar	过滤后 reads数 Clean_reads No.	Q30/%	重测序数据登录号 Accession number in NGDC	测序深度 Sequencing depth	SSR序列匹配reads数 Mapped reads of SSR sequences	SSR序列平均匹配reads数 Average number of mapped reads for each SSR sequence	检测到的位点数 Detected loci
早钟6号 Zaozhong 6	32 739 024	92.35	CRR144065	12.9×	3 979 224	38.4	82 844
长崎早生 Changqizaosheng	35 296 384	92.02	CRR144066	13.9×	4 311 146	41.6	84 013
茂木 Maomu	37 259 455	92.30	CRR144067	14.7×	4 439 618	42.9	84 265
大五星 Dawuxing	53 101 602	90.54	CRR144068	20.9×	6 407 584	61.9	86 560
月光 Yueguang	53 088 745	91.36	CRR144069	20.9×	6 406 910	61.9	86 712
宁海白 Ninghaibai	34 771 714	91.50	CRR144070	13.7×	4 207 108	40.6	86 373
白玉 Baiyu	49 199 883	90.30	CRR144071	19.4×	5 915 743	57.2	86 267
二八东 Erbadong	37 032 139	92.03	CRR144072	14.6×	4 016 303	38.8	84 313
七星^* Sevenstar^*	158 575 610	93.41	CRR078405	62.6×	18 755 558	181.2	93 943
火炬^* Huoju^*	206 173 911	93.16	CRR056810	81.3×	25 660 354	247.9	90 345

品种 Cultivar	过滤后 reads数 Clean_reads No.	Q30/%	重测序数据登录号 Accession number in NGDC	测序深度 Sequencing depth	SSR序列匹配reads数 Mapped reads of SSR sequences	SSR序列平均匹配reads数 Average number of mapped reads for each SSR sequence	检测到的位点数 Detected loci
早钟6号 Zaozhong 6	32 739 024	92.35	CRR144065	12.9×	3 979 224	38.4	82 844
长崎早生 Changqizaosheng	35 296 384	92.02	CRR144066	13.9×	4 311 146	41.6	84 013
茂木 Maomu	37 259 455	92.30	CRR144067	14.7×	4 439 618	42.9	84 265
大五星 Dawuxing	53 101 602	90.54	CRR144068	20.9×	6 407 584	61.9	86 560
月光 Yueguang	53 088 745	91.36	CRR144069	20.9×	6 406 910	61.9	86 712
宁海白 Ninghaibai	34 771 714	91.50	CRR144070	13.7×	4 207 108	40.6	86 373
白玉 Baiyu	49 199 883	90.30	CRR144071	19.4×	5 915 743	57.2	86 267
二八东 Erbadong	37 032 139	92.03	CRR144072	14.6×	4 016 303	38.8	84 313
七星^* Sevenstar^*	158 575 610	93.41	CRR078405	62.6×	18 755 558	181.2	93 943
火炬^* Huoju^*	206 173 911	93.16	CRR056810	81.3×	25 660 354	247.9	90 345

Development and Analysis of Polymorphism of SSR Markers in the Whole Genome of Loquat

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