Development, Characterization and Speciality of Microsatellite Markers in AP85-441 and R570 Genomic Reference Sequences

doi:10.3969/j.issn.1000-2561.2020.04.013

Abstract

Abstract:

Lacking of molecular markers is an important factor restricting the development of marker-based genetic and breeding research. In this study, 512 835 and 97 839 microsatellite sequence, which accounted for 0.32% and 0.35% of the genome, were identified based AP85-441 and R570 genomic reference sequences respectively, using the MISA software. In the genomes, the dominant repeat units were single nucleotide, dinucleotide and trinucleotide, and each repeat unit was dominated by AT-enriched elements. 472 117 and 89 748 loci of the genomes could be used to develop SSR markers. 16 691 and 13 271 homologous genes corresponding to sorghum chromosome 1-10 were identified by homology analysis on the genes of Saccharum spontaneum, sugarcane and sorghum, and 13 224 and 7624 pairs of SSR primers were developed by the gene sequence. In silico PCR analysis of these SSR markers revealed that the markers were mostly multilocus amplified in Saccharum spontaneum genome, and the effective markers in the two genomes were 79.35% and 36.13%, 79.01% and 93.36%, respectively. Part of the SSR markers showed specific amplification in the genomes. 1368 and 1420 SSR were specific single-locus amplification in AP85-441 and R570, respectively. 752 SSR were single-locus amplification in the two genomes, and the amplification sites and source genes of these SSR were distributed on all chromosomes in the genome. In this study, the SSR loci identified would be conducive to enriching the molecular markers of sugarcane, and the 3540 pairs of SSR primers developed will provide support for the determination of homologous linkage groups and group genetic origin in the construction of sugarcane genetic map.

Key words: sugarcane, microsatellite sequence, homologous gene, SSR marker, specific amplification

CLC Number:

XU Zhijun,ZHAO Sheng,HU Xiaowen,KONG Ran,SU Junbo,LIU Yang. Development, Characterization and Speciality of Microsatellite Markers in AP85-441 and R570 Genomic Reference Sequences[J]. Chinese Journal of Tropical Crops, 2020, 41(4): 722-729.

Figures/Tables 9

References 30

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重复单元类型 Repeat unit type	基序种类 Motif	SSR位点数量 SSR number	比例 Ratio/%	优势基序Dominating motif
重复单元类型 Repeat unit type	基序种类 Motif	SSR位点数量 SSR number	比例 Ratio/%	基序类型Motif type	数量Number	比例Ratio/%
单核苷酸	4	230 315	44.91	A/T	124 986	54.27
二核苷酸	12	137 466	26.81	AT/AT	20 228	14.71
三核苷酸	60	128 309	25.02	AAG/CTT	18 276	14.24
四核苷酸	231	9 889	1.93	AAAT/ATTT	1 034	10.46
五核苷酸	662	3 565	0.70	AAAAG/CTTTT	309	8.67
六核苷酸	980	3 291	0.64	AGATAT/ATATCT	217	6.59
总计	1 949	512 835

重复单元类型 Repeat unit type	基序种类 Motif	SSR位点数量 SSR number	比例 Ratio/%	优势基序Dominating motif
重复单元类型 Repeat unit type	基序种类 Motif	SSR位点数量 SSR number	比例 Ratio/%	基序类型Motif type	数量Number	比例Ratio/%
单核苷酸	4	230 315	44.91	A/T	124 986	54.27
二核苷酸	12	137 466	26.81	AT/AT	20 228	14.71
三核苷酸	60	128 309	25.02	AAG/CTT	18 276	14.24
四核苷酸	231	9 889	1.93	AAAT/ATTT	1 034	10.46
五核苷酸	662	3 565	0.70	AAAAG/CTTTT	309	8.67
六核苷酸	980	3 291	0.64	AGATAT/ATATCT	217	6.59
总计	1 949	512 835

重复单元类型 Repeat unit type	基序种类 Motif	SSR位点数量 SSR number	比例 Ratio/%	优势基序Dominating motif
重复单元类型 Repeat unit type	基序种类 Motif	SSR位点数量 SSR number	比例 Ratio/%	基序类型Motif type	数量Number	比例Ratio/%
单核苷酸	4	47 243	48.29	A/T	39 923	84.51
二核苷酸	12	26 295	26.88	AT/AT	11 844	45.04
三核苷酸	60	20 562	21.02	CCG/CGG	4 356	21.18
四核苷酸	210	2 081	2.13	AAAT/ATTT	482	23.16
五核苷酸	368	975	1.00	AAAAG/CTTTT	128	13.13
六核苷酸	408	683	0.70	AGATAT/ATATCT	110	16.11
总计	1 062	97 839

重复单元类型 Repeat unit type	基序种类 Motif	SSR位点数量 SSR number	比例 Ratio/%	优势基序Dominating motif
重复单元类型 Repeat unit type	基序种类 Motif	SSR位点数量 SSR number	比例 Ratio/%	基序类型Motif type	数量Number	比例Ratio/%
单核苷酸	4	47 243	48.29	A/T	39 923	84.51
二核苷酸	12	26 295	26.88	AT/AT	11 844	45.04
三核苷酸	60	20 562	21.02	CCG/CGG	4 356	21.18
四核苷酸	210	2 081	2.13	AAAT/ATTT	482	23.16
五核苷酸	368	975	1.00	AAAAG/CTTTT	128	13.13
六核苷酸	408	683	0.70	AGATAT/ATATCT	110	16.11
总计	1 062	97 839

高粱染色体Sorghum bicolor	栽培种甘蔗单倍体序列 Saccharum spp. mosaic haploid reference sequence			栽培种甘蔗-割手密同源基因 Homologous genes between the three genomes	割手密单倍体基因组 Saccharum spontaneum genome
高粱染色体Sorghum bicolor	同源基因数 Number of homologous genes	包含SSR位点基因数 Number of genes contain SSR	SSR位点数 Number of SSR	栽培种甘蔗-割手密同源基因 Homologous genes between the three genomes	同源基因数 Number of homologous genes	包含SSR位点基因数 Number of genes contain SSR	SSR位点数 Number of SSR
Sb01	2 774	609	1 771	1 512	2 964	1 430	2 482
Sb02	1 732	635	976	1 167	2 249	988	1 714
Sb03	2 201	912	1 356	1 462	2 548	1 218	2 078
Sb04	1 961	802	1 198	1 324	2 270	1 109	1 938
Sb05	607	218	350	433	975	461	873
Sb06	969	383	559	654	1 294	607	1 010
Sb07	793	316	456	627	1 123	528	911
Sb08	529	203	307	369	777	365	644
Sb09	823	308	457	632	1 168	560	939
Sb10	882	380	628	674	1 323	621	1 119
合计	13 271	4 766	8 059	8 854	16 691	7 887	13 708