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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()   

  1. 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()   

  1. 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:

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

表1

甘蔗品种资源名称和来源"

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

表2

甘蔗栽培种R570基因组上各类核苷酸重复基序分布特征信息"

重复次数
Repeat number
核苷酸重复基序 Nucleotide repeat motif 合计
Total
Mono- Di- Tri- Tetra- Penta- Hexa-
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

表3

5种禾本科植物中1~6核苷酸重复基序类型的SSR数量和相对丰度"

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

表4

5种禾本科植物中前3种最长SSR基序类型"

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

图1

1~3核苷酸重复基序类型及数量"

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
Tm (℃)
右引物序列
Right-primer (5°-3°)
退火温度
Tm (℃)
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
Tm (℃)
右引物序列
Right-primer (5°-3°)
退火温度
Tm (℃)
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 -

图2

7对不同SSR引物在4个甘蔗属材料上扩增的电泳图 1~4: FAFUR-S44; 5~8: FAFUR-S45; 9~12: FAFUR-S46; 13~16: FAFUR-S47; 17~20: FAFUR-S48; 21~24: FAFUR-S49; 25~28: FAFUR-S50。4个扩增产物为SES208 (1, 5, 9, 13, 17, 21, 25)、LA purple (2, 6, 10, 14, 18, 22, 26)、ROC16 (3, 7, 11, 15, 19, 23, 27)和R570 (4, 8, 12, 16, 20, 24, 28); M: 50 bp DNA ladder (3421A)。"

图3

SSR引物(FAFUR-S22)在24个甘蔗材料上扩增的电泳图 1: Co 1001; 2: Co 419; 3: CP28-11; 4: CP49-50; 5: CP67-412; 6: CP72-1210; 7: F108; 8: NCo310; 9: ROC1; 10: 川73-219; 11: 桂糖11号; 12: 华南56-12; 13: POJ2878; 14: 科5; 15: 崖城71-374; 16: 粤农73-204; 17: 云蔗65-225; 18: 华南56-21; 19: LCP85-384; 20: R570; 21: ROC16; 22: ROC22; 23: LA purple; 24: SES208; M: 50 bp DNA ladder (3421A)。"

图4

基于SSR分子标记的24份甘蔗属材料的UPGMA聚类分析"

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