甘蔗栽培种单倍体基因组SSR位点的发掘与应用

doi:10.3724/SP.J.1006.2020.94135

作物学报 ›› 2020, Vol. 46 ›› Issue (4): 631-642.doi: 10.3724/SP.J.1006.2020.94135

• 研究简报 • 上一篇

甘蔗栽培种单倍体基因组SSR位点的发掘与应用

王恒波,祁舒婷,陈姝琦,郭晋隆,阙友雄()

福建农林大学农业部福建甘蔗生物学与遗传育种重点实验室 / 国家甘蔗工程技术研究中心, 福建福州 350002

收稿日期:2019-09-11 接受日期:2019-12-26 出版日期:2020-04-12 网络出版日期:2020-01-15
通讯作者: 阙友雄
作者简介:E-mail: wanghengbo_0354@126.com, Tel: 0591-83789177
基金资助:
本研究由引进国际先进农业科学技术计划(948计划)项目(2014-S18);国家现代农业产业技术体系建设专项(CARS-17);福建农林大学校科技发展专项资助(KFA18025A)

Development and application of SSR loci in monoploid reference genome of sugarcane cultivar

WANG Heng-Bo,QI Shu-Ting,CHEN Shu-Qi,GUO Jin-Long,QUE You-Xiong()

Key Laboratory of Sugarcane Biology and Genetic Breeding (Fujian), Ministry of Agriculture, Fujian Agriculture and Forestry University / Sugarcane Research & Development Center, China Agricultural Technology System, Fuzhou 350002, Fujian, China

Received:2019-09-11 Accepted:2019-12-26 Published:2020-04-12 Published online:2020-01-15
Contact: You-Xiong QUE
Supported by:
This study was supported by the Program of Introducing International Super Agricultural Science and Technology(2014-S18);the Agricultural Research System(CARS-17);Fujian Agriculture and Forestry University Science and Technology Development Special Fund(KFA18025A)

摘要/Abstract

摘要：

甘蔗是世界上最重要的糖料作物之一, 由于尚未完全破译栽培种基因组, 导致SSR标记匮乏, 难以覆盖全基因组, 限制了甘蔗遗传研究的进展。本研究以栽培种R570的4660个BAC文库片段序列(累计总长为382 Mb, 预测到25,316个编码蛋白基因)组装成的一套甘蔗单倍体基因组的模板, 利用MISA (Microsatellite identification tool)软件, 发掘SSR位点; 并综合分析其与4种禾本科植物(高粱、玉米、水稻和二岁短柄草)SSR位点的分布特征; 选取50对以TG和AG重复基序的SSR引物, 分别利用4个甘蔗属材料(R570、ROC1、LA purple和SES208)和24个重要甘蔗亲本, 对SSR引物进行扩增效率验证和多态性分析。共发掘到27,241个SSR位点, 平均每个BAC片段有6.29个SSR位点, 平均密度为71.33个SSR Mb ^-1, 远低于高粱的平均密度(350.00个SSR Mb ^-1)。在重复基序中, 占比前2位的分别为单核苷酸基序(11,079个)和三核苷酸重复基序(6447个), 合计占总SSR位点数的64.33%。与甘蔗不同的是, 4种禾本科植物中的三核苷酸基序类型数量最多、占比最大。此外, 在单核苷酸重复基序中, A/T所占比例最高, 为84.8%, C/G所占比例最低, 为15.2%; 在三核苷酸重复基序中, TGT/ACA所占比例最高, 为16.04%。总之, 禾本科植物基因组富含A/T的基序。在50对SSR引物(TG基序41对和AG基序9对)的多态性验证中, 共有45对(90%)能够扩增出清晰的条带, 其中35对(70%)在4个甘蔗材料上呈现多态性。进一步利用20对多态性较高的SSR引物对24个甘蔗重要亲本材料进行分析, 共扩增到95个等位基因, 平均每对引物扩增4.75个, 验证了这些引物应用于甘蔗遗传多样性研究的可行性。本研究鉴定的甘蔗栽培种单倍体基因组SSR标记, 有效增加了甘蔗遗传研究中可用的分子标记数量, 可直接用于甘蔗群体遗传多样性分析和重要性状遗传机制的解析, 为甘蔗分子育种的深入研究奠定了基础。

关键词: 甘蔗栽培种, BAC 文库, SSR, 标记开发, 多态性

Abstract:

Sugarcane is one of the most important sugar crops in the world. However, it is difficult to develop SSR on a large scale since the genome of cultivar has not been sequenced, which limits the genetic improvement of sugarcane. In this study, a template of monoploid sugarcane genome was assembled using a set of 4660 BAC library sequences (with a cumulative length of 382 Mb, predicting 25,316 genes) from cultivar ‘R570’. SSR loci were identified by using MISA (Microsatellite identification tool) software. The distribution characteristics of the monoploid genome ‘R570’ was comprehensively analyzed by comparing with the SSR loci of four Gramineae plants (Sorghum bicolor, Zea mays, Oyrza sativa, and Brachypodium distachyon). Fifty pairs of primers with TG and AG repeat motifs were designed to verify the amplification efficiency and polymorphism by PCR amplification in four Saccharum clones (R570, ROC1, LA purple, and SES208) and twenty four core parents of sugarcane. A total of 27,241 SSR loci were identified, with an average of 6.29 SSR loci per BAC clone and an average density of 71.33 SSR Mb ^-1 which was much lower than that of sorghum (350.00 SSR Mb ^-1). The mono-nucleotide (11,079) and tri-nucleotide repeat motifs (6447) accounted for 64.33% of the total SSR loci. The number and proportion of tri-nucleotide repeat motifs were the largest in the four Gramineae plants. In addition, A/T (accounting for 84.8%) motif had the highest proportion and C/G (accounting for 15.2%) motif the lowest proportion in the mono-nucleotide repeat motifs and TGT/ACA (accounting for 16.04%) motif had the highest proportion in the trinucleotide repeat motifs. In general, the genomes in Gramineae plants are rich in A/T repeat motifs. In the polymorphism validation of 50 pairs of primers (41 pairs of TG motif and 9 pairs of AG motif), 45 pairs of primers (90%) were found to be able to amplify successfully, of which 35 (70%) were polymorphic in 4 sugarcane clones. Furthermore, 20 pairs of polymorphic SSR primers were used to detect 24 core parents of sugarcane, a total of 95 alleles were amplified with an average of 4.75 alleles per primer, verifying the application feasibility of these primers for the genetic diversity analysis in sugarcane. The development of SSR markers from the monoploid genome of cultivars ‘R570’ not only enriches the number of SSR markers available in sugarcane genetic analysis, but also facilitates the genetic diversity analysis of sugarcane population and the genetic mechanism dissection of important agronomic traits, which provides a foundation for the in-depth research of molecular breeding in sugarcane.

Key words: sugarcane cultivars, bacterial artificial chromosome library, SSR, development, polymorphism

王恒波,祁舒婷,陈姝琦,郭晋隆,阙友雄. 甘蔗栽培种单倍体基因组SSR位点的发掘与应用[J]. 作物学报, 2020, 46(4): 631-642.

WANG Heng-Bo,QI Shu-Ting,CHEN Shu-Qi,GUO Jin-Long,QUE You-Xiong. Development and application of SSR loci in monoploid reference genome of sugarcane cultivar[J]. Acta Agronomica Sinica, 2020, 46(4): 631-642.

图/表 9

表1

表2

表3

表4

图1

表5

具有扩增多态性的甘蔗SSR引物信息表"

引物名称 Primer name	重复基序 Motif	左引物序列 Left-primer (5°-3°)	退火温度 T_m(℃)	右引物序列 Right-primer (5°-3°)	退火温度 T_m (℃)	产物大小 Product size (bp)	PIC
FAFUR-S1	(TG)69	TCATACCCATTGGAAGAAGC	60.5	GTTATGTTGCCGTGCCAAGT	59.8	278	0.85
FAFUR-S3	(TG)39	TAGCCTTTGGTCGTTCTTGG	58.2	AATGCTTCATCCATAGGGGA	59.3	259	0.84
FAFUR-S7	(TG)32	GCCTGGGGAACTATGCTGTA	59.1	CAAGCATTGAAGTTGCCAAA	59.0	254	0.61
FAFUR-S12	(TG)24	CGTCAGTTGCTCAGCTCTTG	58.0	CCCTGGGAAGAAGAGGTAGG	58.6	223	0.69
FAFUR-S17	(TG)19	AATGATGTTTCGCCTGATCC	60.2	ACCAACACAACTCGCTACCC	60.1	166	0.77
FAFUR-S18	(TG)19	CCACATTCTTCGACCCTGTT	59.8	CCATCCTGCGAACTAACCAT	59.7	183	0.71
FAFUR-S22	(TG)18	AGGGCACGAGGTATTGCTTA	58.9	AACCGGTCAAATCACACACA	59.2	179	0.68
FAFUR-S24	(TG)17	ATCTTTCGGCATCAACTTGG	60.1	GCTTCAAGCCATCTGTCTCC	60.3	274	0.73
FAFUR-S32	(TG)13	CAACGAATTCCACTTGCACA	60.0	TCATGGCTATTGTGGTCTGG	60.4	207	0.61
FAFUR-S33	(TG)13	CTCCTCTGTCACCCAGCACT	58.8	GATCACCCCAGATCCAGAGA	59.6	179	0.75
FAFUR-S34	(TG)13	TGCTGATTATGTGCTGCCTC	58.5	CACGCCTAGGGCATAAGAGA	58.4	222	0.67
FAFUR-S36	(TG)12	AGGCATGGGAATTTCTCTCC	60.1	GGCCTCTCTTTAGTGCAGGA	59.8	265	0.77
FAFUR-S38	(TG)12	GACACCCACCACAGGACTTT	60.3	CCCTCCCCAATCCTATCAGT	60.1	198	0.66
FAFUR-S40	(TG)11	GCTGATGTTTGGTCATGTGG	61.0	TGCAGACTCAGAAGTAGCCG	60.5	246	0.86
FAFUR-S41	(TG)11	TGTTTCAGGCACTGTTTTGG	60.9	AGCAATGTGTTCTCCATCCA	60.5	261	0.73
FAFUR-S42	(AG)38	CGGCACAAGTAAATGCAAGA	59.7	AGTACTGCCAACAAGGCAGG	58.3	230	0.85
FAFUR-S43	(AG)34	CTTGAGCTCGTAGCCTCCTC	60.3	GCCTCTGCTGTCTGCTCTCT	59.6	267	0.92
FAFUR-S44	(AG)31	AGTGCAGGTTGGCTTTCTGT	60.2	GGGGATTCCAAGTCTCAACA	59.8	206	0.82
FAFUR-S47	(AG)25	GTACCAGCCCAAAAACTGGA	59.8	TTGTCACTGGGAACACGGTA	60.1	280	0.73
FAFUR-S49	(AG)23	TTCTCCGTCAACTGTCATGC	59.6	TCCTACGGAGGGAAATCAAA	60.2	273	0.81
FAFUR-S4^#	(TG)33	CGACTGGAAGAAGATCGAGG	58.2	GAGGTACTGCATGCCCAAAT	60.1	185	-
FAFUR-S5^#	(TG)33	CTTCCTCCCAGTAGCCGAGT	59.3	TCTCGAATTCGCAAGGAACT	57.9	257	-
FAFUR-S6^#	(TG)32	GGAAGGAGGAGATGGAAAGG	59.4	CGCAACACGTACACACACAC	59.6	245	-
FAFUR-S9^#	(TG)26	GTTTTCTTCTCGGAGGGGAG	57.9	AATGCTGGGATCGAAGTTTG	60.2	213	-
FAFUR-S15^#	(TG)20	TGCTATCTCCTGCTTGGACA	60.2	GCCTCACACACACACACACA	59.4	268	-
FAFUR-S16^#	(TG)19	TGCTTGCTAGCTTGGCACTA	60.4	ACAACTAGGCCATCAGTGGG	59.7	268	-
FAFUR-S19^#	(TG)19	AGCCCAACAGAAATACGCAC	60.6	GGGCTCACTCAAAAACCAAA	58.8	269	-
引物名称 Primer name	重复基序 Motif	左引物序列 Left-primer (5°-3°)	退火温度 T_m(℃)	右引物序列 Right-primer (5°-3°)	退火温度 T_m (℃)	产物大小 Product size (bp)	PIC
FAFUR-S20^#	(TG)18	TCGATTGGAGTCTTCAGCAA	59.9	CCCATGAGATTGTATTCGGC	60.3	269	-
FAFUR-S21^#	(TG)18	TGCACTGTTTAAATTCCCCC	60.3	AAATCTCCCTTCATGATGCC	58.8	229	-
FAFUR-S25^#	(TG)17	TCGTAGAAGCACTTCAGGGAG	58.8	CCAAAATAAGGCCATCGAAA	60.1	162	-
FAFUR-S26^#	(TG)17	CTTTGTCCCCTTCTCCATCC	57.9	TCTCGAAGTCGCAAGGAACT	60.5	185	-
FAFUR-S28^#	(TG)16	TGGCTCACTGAAAATCTCCC	61.1	TGTGTGGCAAGATAAGAAGGG	60.3	250	-
FAFUR-S29^#	(TG)15	TGCTGATTATGTGCTGCGTC	59.6	ATCGATCACACACCTAGGGC	59.5	234	-
FAFUR-S46^#	(AG)25	ATCGATCCTGGGGTAGCTTT	58.4	TTTCCTCTGCAAGACTGCAA	58.7	262	-
FAFUR-S48^#	(AG)23	TTCCAGATTCTTTTCCACGG	60.3	GTCACCTGGGAACTACCCCT	59.6	257	-

表5

图2

图3

图4

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序号 No.	名称 Name	育成品种数 Number of released varieties	类型 Type	来源 Origin
1	CP49-50	38	Saccharun hybrid	美国USA
2	Co 419	25	Saccharun hybrid	印度India
3	CP72-1210	17	Saccharun hybrid	美国USA
4	NCo 310	13	Saccharun hybrid	印度India
5	F108	12	Saccharun hybrid	中国台湾Taiwan, China
6	华南56-12 Huanan 56-12	10	Saccharun hybrid	中国China
7	崖城71-374 Yacheng 71-374	9	Saccharun hybrid	中国China
8	粤农73-204 Yuenong 73-204	9	Saccharun hybrid	中国China
9	CP28-11	8	Saccharun hybrid	美国USA
10	Co 1001	6	Saccharun hybrid	印度India
11	桂糖11号 Guitang 11	6	Saccharun hybrid	中国China
12	云蔗65-225 Yunzhe 65-225	6	Saccharun hybrid	中国China
13	川73-219 Chuan 73-219	-	Saccharun hybrid	中国China
14	ROC 1	6	Saccharun hybrid	中国台湾Taiwan, China
15	科5 Ke 5	4	Saccharun hybrid	菲律宾Philippines
16	CP67-412	3	Saccharun hybrid	美国USA
17	POJ2878	3	Saccharun hybrid	印度尼西亚爪哇岛Java, Indonesia
18	华南56-21 Huanan 56-21	3	Saccharun hybrid	中国China
19	R570	-	Saccharun hybrid	法国France
20	LA purple	-	Saccharun officinarum	美国USA
21	SES208	-	Saccharun spontaneum	美国USA
22	LCP85-384		Saccharun hybrid	美国USA
23	ROC16	-	Saccharun hybrid	中国台湾Taiwan, China
24	ROC22	-	Saccharun hybrid	中国台湾Taiwan, China

重复次数 Repeat number	核苷酸重复基序 Nucleotide repeat motif						合计 Total
重复次数 Repeat number	Mono-	Di-	Tri-	Tetra-	Penta-	Hexa-	合计 Total
3					2044	2104	4148
4				941	313	355	1609
5			3718	225	112	72	4127
6		1210	1342	78	26	18	2674
7		527	636	29	9	6	1207
8		305	281	10	7	5	608
9		199	168	9	4	3	383
10	6297	128	77	8	4	0	6514
11	1997	84	71	5	2	4	2163
12	891	57	38	8	3	2	999
13	496	45	17	6	3	2	569
14	262	49	11	2	3	0	327
15	182	39	17	2	0	0	240
>15	954	619	71	18	8	3	1673
合计Total	11079	3262	6447	1341	2538	2574	27241
优势重复次数 Dominant repeat number (%)	56.84	37.09	57.67	70.17	80.54	81.74	78.08
比例 Proportion (%)	40.67	11.97	23.67	4.92	9.32	9.45	100
平均重复次数 Mean repeat number	11.68	11.23	6.1	4.78	3.38	3.3
设计引物的位点数 Number of loci primer designed	11079	3262	6447	1122	1995	1815
比例 Proportion (%)	100	100	100	83.67	78.61	70.51

物种 Species	项目 Item	甘蔗 S. spp.	高粱 S. bicolor	玉米 Z. mays	水稻 O. sativa	二穗短柄草 B. distachyon
单核苷酸	数量 Number	11079.00	14294.00	30700.00	15311.00	7991.00
Mono-nucleotide	相对丰度 Relative abundance	29.00	19.34	14.90	41.16	29.38
二核苷酸	数量 Number	3262.00	38090.00	64663.00	35315.00	9175.00
Di-nucleotide	相对丰度 Relative abundance	8.54	51.54	31.37	94.93	33.73
三核苷酸	数量 Number	6447.00	80299.00	185973.00	77566.00	37005.00
Tri-nucleotide	相对丰度 Relative abundance	16.88	108.66	90.23	208.51	136.05
四核苷酸	数量 Number	1341.00	47062.00	58806.00	26411.00	17428.00
Tetra-nucleotide	相对丰度 Relative abundance	3.51	63.68	28.53	71.00	64.07
五核苷酸	数量 Number	2538.00	16630.00	38408.00	17080.00	7972.00
Penta-nucleotide	相对丰度 Relative abundance	6.64	22.50	18.64	45.91	29.31
六核苷酸	数量 Number	2574.00	62227.00	119813.00	38940.00	18629.00
Hexa-nucleotide	相对丰度 Relative abundance	6.74	84.20	58.13	104.68	68.49
SSR 数量(丰度) SSR number (abundance)		27241.00	258602.00	498363.00	210623.00	98200.00
基因组大小 Genome size (Mb)		382.00	739.00	2061.00	372.00	272.00
总的相对丰度 Relative abundance		71.33	350.00	152.54	566.45	361.15
SSR频率SSR frequency (1 kb^-1)		14.02	2.86	6.56	1.77	2.77

项目 Item	甘蔗 S. spp	高粱 S. bicolor	玉米 Z. mays	水稻 O. sativa	二穗短柄草 B. distachyon
单核苷酸	(T)75	(A)71	(A)88	(C)51	(A)49
Mono-nucleotide	(T)63	(A)59	(A)85	(A)49	(C)45
	(G)49	(A)53	(A)83	(A)48	(A)43
二核苷酸	(TA)71	(AT)280	(AC)1366	(AC)170	(AT)312
Di-nucleotide	(TG)69	(AT)276	(AC)910	(AT)104	(AT)182
	(TA)55	(AT)270	(AT)178	(AT)100	(AT)158
三核苷酸	(TGT)123	(ACT)366	(ACC)291	(AAT)165	(AAT)225
Tri-nucleotide	(ATT)59	(AAT)327	(AAT)207	(AAT)147	(AAT)171
	(TTA)56	(AAT)318	(ACT)132	(AAT)126	(AAT)138
四核苷酸	(TTAT)23	(ACAT)524	(ACAT)196	(ACAT)132	(ACAT)196
Tetra-nucleotide	(ACAT)25	(AGAT)388	(ACAT)144	(ACAT)96	(ACAT)180
	(ATGT)26	(ACAT)260	(AAAG)100	(ACAT)96	(ACAT)180
五核苷酸	(CTTTT)29	(AATAT)740	(AATAT)115	(AATAT)55	(AGATC)100
Penta-nucleotide	(TTTTG)25	(AATAT)430	(ACTAT)115	(AATAT)55	(ACGCC)75
	(AATAT)24	(AATAT)315	(AATAT)85	(AATAT)55	(AGATG)65
六核苷酸	(ATTGTC)43	(AAATAT)390	(AATAGT)198	(ACCTAT)90	(AACAGC)90
Hexa-nucleotide	(TTTTTG)32	(AGATAT)366	(AATAGT)72	(ACATAT)78	(ACTGAT)78
	(TTATAT)16	(AAATAT)294	(AACCAT)66	(ACATAT)78	(AGAGAT)66

甘蔗栽培种单倍体基因组SSR位点的发掘与应用

Development and application of SSR loci in monoploid reference genome of sugarcane cultivar

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