基于甘蔗及其近缘属参考基因组开发SSR标记及数据库

doi:10.3724/SP.J.1006.2025.44056

Abstract

Abstract:

Sugarcane (Saccharum spp. hybrid) is an important crop for both sugar production and bioenergy. However, due to the complexity of the sugarcane genome, research in its population genetics has lagged behind other crops. Currently, the reference genome for sugarcane still requires significant improvements. The development of SSR (Simple Sequence Repeat) markers and databases based on the genomes of sugarcane and its relatives will be instrumental in advancing population genetics research. In this study, we identified SSRs from the genomes of three sugarcane species (Saccharum spontaneum, Saccharum officinarum, and Saccharum spp. hybrid) and two related species (Miscanthus sinensis and Sorghum bicolor). We quantified and categorized the SSRs for each genome, selecting those with high polymorphism for the genetic diversity analysis of 104 sugarcane-related materials. A total of 1,860,645 SSRs were identified across the five genomes, with mononucleotide, dinucleotide, and trinucleotide repeats being the most common. Synteny analysis of SSRs across the genomes revealed the evolutionary relationships among species, with the kinship order from closest to most distant being: R570, Saccharum officinarum, Saccharum spontaneum, Miscanthus sinensis, and Sorghum bicolor. Genetic diversity analysis using SSR and InDel markers showed that Banmao 92-105 was the first to diverge from other samples, with Saccharum spontaneum forming a distinct group, Saccharum robustum and Saccharum officinarum clustering together, and Saccharum spp. hybrid forming its own separate group. Additionally, we developed a web-based database for sugarcane SSRs, which includes the identified SSRs from the five genomes, along with corresponding primers and other related information. This study provides a valuable molecular tool for sugarcane research and breeding efforts.

Key words: sugarcane, SSR marker, database, whole genome re-sequencing

KUANG Bo-Wen, WEI Ni, LIU Jin-Dian, CHEN Mei-Yan, MAO Xing-Jie, DUAN Wei-Xing, YANG Xi-Ping. Development of SSR markers and database based on genomes of sugarcane and its relatives[J].Acta Agronomica Sinica, 2025, 51(1): 103-116.

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品种名称 Variety name	物种 Species	来源 Origin
51NG3	Saccharum robustum	中国广西Guangxi, China
福建大野Fujiandaye	Saccharum robustum	中国广西Guangxi, China
NG57-012	Saccharum robustum	美国USA
IN84-045	Saccharum robustum	美国USA
IS76-184	Saccharum robustum	美国USA
NG77-043	Saccharum officinarum	美国USA
IJ76-470	Saccharum officinarum	美国USA
Hawaiian Original	Saccharum officinarum	美国USA
NG77-042	Saccharum officinarum	美国USA
IJ76-324	Saccharum officinarum	美国USA
CP88-1762	Saccharum spp. hybrid	中国广西Guangxi, China
桂糖42 Guitang 42	Saccharum spp. hybrid	中国广西Guangxi, China
POJ2878	Saccharum spp. hybrid	中国广西Guangxi, China
Q158	Saccharum spp. hybrid	中国广西Guangxi, China
新台糖25 ROC25	Saccharum spp. hybrid	中国广西Guangxi, China
云蔗89-7 Yunzhe 89-7	Saccharum spp. hybrid	中国广西Guangxi, China
SP79-9	Saccharum spontaneum	中国云南Yunnan, China
IN84089	Saccharum spontaneum	美国国家生物技术信息中心National Center for Biotechnology Information, USA
IND81013	Saccharum spontaneum	美国国家生物技术信息中心National Center for Biotechnology Information, USA
SES4A	Saccharum spontaneum	美国国家生物技术信息中心National Center for Biotechnology Information, USA
SES517	Saccharum spontaneum	美国国家生物技术信息中心National Center for Biotechnology Information, USA
红高粱Honggaoliang	Sorghum bicolor	美国国家生物技术信息中心National Center for Biotechnology Information, USA
斑茅87-36 Banmao 87-36	Erianthus arundinaceum	中国广西Guangxi, China
HBW-1	Narenga porphyrocoma	中国广西Guangxi, China
NG77-022	Miscanthus floridulus	美国国家生物技术信息中心National Center for Biotechnology Information, USA

基因型 Genotype	物种 Species
AP85-441	割手密种Saccharum spontaneum
LA-purple	热带种Saccharum officinarum
R570	栽培种Saccharum spp. hybrid
DH1	芒Miscanthus sinensis
BTx623	高粱Sorghum bicolor

基因型 Genotype	物种 Species
福建大野Fujiandaye	大茎野生种Saccharum robustum
崖城一号Yacheng 1	割手密种Saccharum spontaneum
桂林竹蔗Guilinzhuzhe	热带种Saccharum officinarum
云蔗71-545 Yunzhe 71-545	栽培种Saccharum spp. hybrid
斑茅87-36 Banmao 87-36	斑茅Erianthus arundinaceum

物种 Species	割手密种 Saccharum spontaneum	热带种 Saccharum officinarum	栽培种 Saccharum spp. hybrid	芒 Miscanthus sinensis	高粱 Sorghum bicolor
基因组大小Genome size (Mb)	3141	6805	427	2079	709
SSR总数Total SSR number (K)	476	959	67	242	116
基因组中SSR密度 Density of SSR in genomes (No. Mb^-1)	152	141	157	117	164
基因区域SSR密度 Density of SSR in the genes (No. Mb^-1)	199	189	177	206	284
外显子区域SSR密度 Density of SSR in the exons (No. Mb^-1)	138	133	118	166	245

物种 Species	SSR数量 SSR number				多态性信息量 Polymorphism information content (PIC)	平均等位基因数 Average number of alleles	PIC大于0.5的SSR数量 SSR numbers (PIC > 0.5)
物种 Species	去重前 Before filtering	去重后 After filtering (%)	重测序数据可检测 Detected in resequencing data	具有多态性 Polymorphic SSR	多态性信息量 Polymorphism information content (PIC)	平均等位基因数 Average number of alleles	PIC大于0.5的SSR数量 SSR numbers (PIC > 0.5)
割手密种 Saccharum spontaneum	475,899	288,390 (61%)	103,493	76,457	0.034-0.970	4.14	64,812
热带种 Saccharum officinarum	959,080	441,994 (46%)	183,098	133,053	0.007-0.960	3.88	117,697
栽培种 Saccharum spp. hybrid	67,219	43,172 (64%)	17,326	11,092	0.013-0.960	6.53	9900
高粱 Sorghum bicolor	116,124	72,566 (62%)	9723	1382	0.011-0.940	3.45	955
芒 Miscanthus floridulus	242,323	162,686 (67%)	15,042	2499	0.012-0.880	3.77	1171

Development of SSR markers and database based on genomes of sugarcane and its relatives

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物种 Species	初始SSR数量 Raw SSRs number	保留SSR数量 Retained SSRs number	占比 Proportion (%)
栽培种Saccharum spp. hybrid	67,219	52,418	84
芒Miscanthus floridulus	242,323	175,647	79
高粱Sorghum bicolor	116,124	82,258	78
割手密种Saccharum spontaneum	475,899	252,458	57
热带种Saccharum officinarum	959,080	394,732	45

物种 Species	高粱 Sorghum bicolor	芒 Miscanthus sinensis	割手密种 Saccharum spontaneum	热带种 Saccharum officinarum	栽培种 Saccharum spp. hybrid
高粱Sorghum bicolor	—
芒Miscanthus sinensis	1962	—
割手密种Saccharum spontaneum	2323	10,993	—
热带种Saccharum officinarum	3521	15,382	80,127	—
栽培种Saccharum spp. hybrid	1280	3221	14,751	35,865	—

物种 Species	割手密种 Saccharum spontaneum	栽培种 Saccharum spp. hybrid	热带种 Saccharum officinarum	高粱 Sorghum bicolor	芒 Miscanthus sinensis
单核苷酸Mono	66.22	75.48	60.35	69.18	51.18
二核苷酸Di	34.30	34.60	34.93	40.65	30.76
三核苷酸Tri	36.78	31.12	31.30	32.33	23.73
四核苷酸Tetra	2.73	3.03	2.46	5.69	1.27
五核苷酸Penta	1.02	1.52	1.22	1.10	0.43
六核苷酸Hexa	0.86	0.97	0.91	0.82	0.60

引物名称 Primer name	基序类型 Motif type	引物序列 Primer sequence (5°-3°)
1D15	(GT)6	F: ACTTCGTAGCATCCCTGTTC R: TCACCATACGTAATAGTGGC
2A43	(TC)11	F: AGTCGTGCTAAACATAAGCC R: ATGTCGACAGTCAGCCATTA
2A63	(AGAA)12	F: CATTTGTATTCAACGAGCAC R: CGTGCAGGAATGAAGAACCT
2B56	(AGAA)5	F: CATTTGTATTCAACGAGCAC R: CGTGCAGGAATGAAGAACCT
2C63	(AGAA)12	F: CATTTGTATTCAACGAGCAC R: CGTGCAGGAATGAAGAACCT
2D38	(TCT)11	F: CAGGTTTCCAGTGCCTTACG R: ATTGAGTCCACAACCAGCTG
2D94	(AGC)7	F: CTGTAAAGCCCGAGTCACTG R: TCGATGGCGTACAATCACTA
3B87	(CT)7	F: GTCCTCGATTGGCCTGTCAA R: GTGTACGGGGTTCAGATCTT
4A61	(A)14	F: CGGGATTCCTTACAAACTCA R: GACGGACGTCCTGAGCATTA
4B15	(CT)9	F: AGGTATACATGCTCAAGTGC R: GGCACGAAGAATAGCACTTC
5A15	(AAC)6	F: TAGCCGGTGGTTTCGAACAC R: GTGCCTGAACCGTGATTAGG
5A39	(TG)38	F: ATTTCCTCAGTTGGCAACTC R: CACGGCCATTGCTAATTTTC
5B17	(AC)20	F: CACGGCCATTGCTAATTTTC R: ATTTCCTCAGTTGGCAACTC
5D17	(AAC)6	F: TAGCCGGTGGTTTCGAACAC R: CGTGCCTGAACCGTGATTAG
5D36	(GTTG)7	F: ACTCGGAATTTCGATGTGGC R: CGAATCCACTCGTACATGCA
IRG2	A/AACACAAACCTATGTCCATGAACATAAA	F: TTGCTTACAGTTTAGTTTCGTGGC R: ACCCAAGTGAGTACATGTTTAGGC
IRG4	A/AGAGGGTGGTTCT	F: TTGCATGTCTAAGGATTTGGCAAG R: GCAAAGAGAGCAAAAGAGTCATCA
IRG5	T/TCTGGCTACGAGCAAGCTGCTCTCCAGGCTATATCCTTCCTGCA	F: GGGATTGAAATTGAAGTTCCCTGT R: TGCACTGAACTACACCCTCAAAAT
ID_1	A/AAGTTCATCTGGAATAGTCATGCTCCTCCAA	F: AAACTTGATTCCGGCAGCCTTTA R: CAAAGACTATGTGTGTGCTTGTCT
ID_4	T/TTACTATAAGAGTCA	F: AGGCTTGTAGCCTCCCAAAAGATG R: GGTTAACTGCACAACTGAGACCAA
ID_6	C/CCTACAATCCTCCGGGAGAGCTGTGGCATCATCCTCA	F: ATATCCAAAGTCCTCATCCGATCC R: TGATGGGTTCTTCACACTACCAAT

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