Welcome to Acta Agronomica Sinica,

Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (4): 631-642.doi: 10.3724/SP.J.1006.2020.94135

• RESEARCH NOTES • Previous Articles    

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 Online:2020-04-12 Published:2020-01-15
  • Contact: You-Xiong QUE E-mail:queyouxiong@126.com
  • 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)

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

Table 1

Name and origin of sugarcane varieties"

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

Table 2

Distribution of various nucleotide repeat motifs in the genome of sugarcane cultivar R570"

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

Table 3

SSR number and relative abundance of 1-6 nucleotide repeat motif types in five Gramineae plants"

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

Table 4

The first three longest SSR motifs in the five Gramineae plants"

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

Fig. 1

Number and types of mono-, di-, and tri-nucleotide repeat motifs"

Table 5

Primers information of sugarcane SSR with polymorphic amplification"

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 -

Fig. 2

Electrophoretic patterns of seven pairs of SSR primers amplified in four Saccharum clones 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. The amplification products of four samples were 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), and R570 (4, 8, 12, 16, 20, 24, 28). M: 50 bp DNA ladder (3421A)."

Fig. 3

Electrophoretic patterns of SSR primers FAFUR-S22 in twenty four tested Saccharum clones 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: C73-219; 11: Guitang 11; 12: Huanan 56-12; 13: POJ2878; 14: Ke 5; 15: Yacheng 71-374; 16: Yuenong 73-204; 17: Yunzhe 65-225; 18: Huanan 56-21; 19: LCP85-384; 20: R570; 21: ROC16; 22: ROC22; 23: LA purple; 24: SES208; M: 50 bp DNA ladder (3421A)."

Fig. 4

UPGMA dendrogram of twenty four Saccharum clones based on SSR markers"

[1] 刘燕群, 李玉萍, 梁伟红, 宋启道, 秦小立, 叶露 . 国外甘蔗产业发展现状. 世界农业, 2015, ( 8):147-152.
Liu Y Q, Li Y P, Liang W H, Song Q D, Qin X L, Ye L . Current situation of sugarcane industr in the world, World Agric, 2015, ( 8):147-152 (in Chinese with English abstract).
[2] FAOSTAT: .
[3] 彭绍光 . 甘蔗育种学. 北京. 农业出版社, 1990. pp 4-5.
Peng S G . Sugarcane Genetic Breeding. Beijing: Agricultural Press, 1990. pp 4-5(in Chinese).
[4] Hermann S R, Aitken K S, Jackson P A, George A W, Piperidis N, Wei X, Kilian A, Detering F . Evidence for second division restitution as the basis for 2 n +n maternal chromosome transmission in a sugarcane cross. Euphytica, 2012,187:359-368.
[5] Piperidis G, Piperidis N, D’Hont A . Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane. Mol Genet Genomics, 2010,284:65-73.
[6] Wang H B, Chen P H, Yang Y Q, D'Hont A, Lu Y H . Molecular insights into the origin of the brown rust resistance gene Bru1 among Saccharum species. Theor Appl Genet, 2017,130:2431-2443.
[7] Smith D, Devey M E . Occurrence and inheritance of microsatellites in Pinus radiata. Genome, 1994,37:977-983.
[8] Morgante M, Hanafey M, Powell W . Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet, 2002,30:194-200.
[9] Levinson G, Gutman G A . Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol, 1987,4:203-221.
[10] Michael K, Eva-Maria D, Ugo R, Nicoletta C, Uta-Dorothee I, Manfred K, Wolfgang R M . Haplotype studies support slippage as the mechanism of germline mutations in short tandem repeats. Electrophoresis, 2004,25:3344-3348.
[11] Liu X L, Ma L, Chen X K, Ying X M, Cai Q, Liu J Y, Wu C W . Establishment of DNA fingerprint identity for sugarcane cultivars in Yunnan, China. Acta Agron Sin, 2010, 36:202-210.
[12] Pan Y B . Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Technol, 2006,8:246-256.
[13] Ram K S, Satya N J, Suhail K, Sonia Y, Nandita B, Saurabh R, Vasudha B, Sanjay K D, Raman K, Sushil S . Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane. Gene, 2013,524:309-329.
[14] Oliveira K M, Pinto L R, Marconi T G, Mollinari M, Ulian E C, Chabregas S M, Falco M C, Burnquist W, Garcia A A, Souza A P . Characterization of new polymorphic functional markers for sugarcane. Genome, 2009,52:191-209.
[15] 关玲, 章镇, 王新卫, 薛华柏, 刘艳红, 王三红, 乔玉山 . 苹果基因组SSR位点分析与应用. 中国农业科学, 2011,44:4415-4428.
Guan L, Zhang Z, Wang X W, Xue H B, Liu Y H, Wang S H, Qiao Y S . Evaluation and application of the SSR loci in apple genome. Sci Agric Sin, 2011,44:4415-4428 (in Chinese with English abstract).
[16] 刘新龙, 毛钧, 陆鑫, 马丽, Karen S A, Jackson P A, 蔡青, 范源洪 . 甘蔗SSR和AFLP分子遗传连锁图谱构建. 作物学报, 2010,36:177-183.
Liu X L, Mao J, Lu X, Ma L, Karen S A, Jackson P A, Cai Q, Fan Y H . Construction of molecular genetic linkage map of sugarcane based on SSR and AFLP markers. Acta Agron Sin, 2010,36:177-183 (in Chinese with English abstract).
[17] Andru S, Pan Y B, Thongthawee S, Burner D M, Kimbeng C A . Genetic analysis of the sugarcane ( Saccharum spp.) cultivar ‘LCP 85-384’: I. linkage mapping using AFLP, SSR, and TRAP markers. Theor Appl Genet, 2011,123:77-93.
[18] Yang X, Islam M S, Sood S, Maya S, Hanson E A, Comstock J, Wang J . Identifying quantitative trait loci (QTLs) and developing diagnostic markers linked to orange rust resistance in sugarcane ( Saccharum spp.). Front Plant Sci, 2018,9:350.
[19] Shamshad U H, Kumar P, Singh R K, Verma K S, Bhatt R, Sharma M, Kachhwaha S, Kothari S L . Assessment of functional EST-SSR markers (Sugarcane) in cross-species transferability, genetic diversity among Poaceae plants, and bulk segregation analysis. Genet Res Int, 2016,2016:7052323.
[20] Jianping W, Bruce R, Simone M, Qingyi Y, Jan E M, Haibao T, Cuixia C, Fares N, Graham W, John B . Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics, 2010,11:261.
[21] Laurent G, Paulo A . Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr Opin Plant Biol, 2002,5:122-127.
[22] Jannoo N, Grivet L, Chantret N, Garsmeur O, Glaszmann J C, Arruda P , D’Hont A. Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. Plant J, 2007,50:574-585.
[23] Paterson A H, Bowers J E, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A . The Sorghum bicolor genome and the diversification of grasses. Nature, 2009,457:551-556.
[24] Garsmeur O, Charron C, Bocs S, Jouffe V, Samain S, Couloux A, Droc G, Zini C, Glaszmann J, Van Sluys M . High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane. New Phytol, 2011,189:629-642.
[25] Garsmeur O, Droc G, Antonise R, Grimwood J, Potier B, Aitken K, Jenkins J, Martin G, Charron C, Hervouet C . A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nat Commun, 2018,9:2638-2638.
[26] 郑燕, 张耿, 吴为人 . 禾本科植物微卫星序列的特征分析和比较. 基因组学与应用生物学, 2011,30:513-520.
Zheng Y, Zhang Z, Wu W R . Characterization and comparison of microsatellites in Gramineae. Genom Appl Biol, 2011,30:513-520 (in Chinese with English abstract).
[27] Martins W, de Sousa D, Proite K, Guimarães P, Moretzsohn M, Bertioli D . New softwares for automated microsatellite marker development. Nucleic Acids Res, 2006,34:e31.
[28] Smith J S, Chin E C, Shu H, Smith O S, Wall S J, Senior M L, Mitchell S E, Kresovich S, Ziegle J . An evaluation of the utility of SSR loci as molecular markers in maize ( Zea mays L.): comparisons with data from RFLPS and pedigree. Theor Appl Genet, 1997,95:163-173.
[29] 张琼, 齐永文, 张垂明, 陈勇生, 邓海华 . 我国大陆甘蔗骨干亲本亲缘关系分析. 广东农业科学, 2009, ( 10):44-48.
Zhang Q, Qi Y W, Zhang T M, Chen Y S, Deng H H . Pedigree analysis of genetic relationship among core parents of sugarcane in mainland China. Guangdong Agric Sci, 2009, ( 10):44-48 (in Chinese with English abstract).
[30] Lawson M J, Zhang L . Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol, 2006,7:R14.
[31] Kantety R V, La Rota M, Matthews D E, Sorrells M E . Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol, 2002,48:501-510.
[32] Tang J, Baldwin S J, Jacobs J M, Linden C G, Voorrips R E, Leunissen J A, van Eck H, Vosman B . Large-scale identification of polymorphic microsatellites using an in silico approach. BMC Bioinformatics, 2008,9:374.
[33] 蔡斌, 李成慧, 姚泉洪, 周军, 陶建敏, 章镇 . 葡萄全基因组SSR分析和数据库构建. 南京农业大学学报, 2009,32(4):28-32.
Cai B, Li C H, Yao Q H, Zhou J, Tao J M, Zhang Z . Analysis of SSRs in grape genome and development of SSR database. J Nanjing Agric Univ, 2009,32(4):28-32 (in Chinese with English abstract).
[34] 陆景标, 李杰勤, 卢杰, 詹秋文 . 高梁非编码区SSR引物设计以及e-PCR的验证. 种子, 2010,29(9):1-6.
Lu J B, Li J Q, Lu J, Zhan Q W . Design of SSR primers and verification of e-PCR in non-coding regions of sorghum genome. Seed, 2010,29(9):1-6 (in Chinese with English abstract).
[35] 高亚梅, 韩毅强, 汤辉, 孙东梅, 王彦杰, 王伟东 . 根瘤菌基因组内简单重复序列的分析. 中国农业科学 2008,41:2992-2998.
Gao Y M, Han Y Q, Tang H, Sun D M, Wang Y J, Wang W D . Analysis of simple sequence repeats in Rhizobium genomes. Sci Agric Sin, 2008,41:2992-2998 (in Chinese with English abstract).
[36] Toth G, Gaspari Z, Jurka J . Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res, 2000,10:967-981.
[37] Harr B, Schlotterer C . Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide under representation. Genetics, 2000,155:1213-1220.
[38] 童治军, 焦芳婵, 肖炳光 . 普通烟草及其祖先种基因组SSR位点分析. 中国农业科学, 2015,48:2108-2117.
Tong Z J, Jiao F C, Xiao B G . Analysis of SSR loci in Nicotina tabacum genome and its two ancestral species genome . Sci Agric Sin, 2015,48:2108-2117 (in Chinese with English abstract).
[39] Yu J K, La Rota M, Kantety R V, Sorrells M E . EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics, 2004,271:742-751.
[40] Schorderet D F, Gartler S M . Analysis of CpG suppression in methylated and nonmethylated species. Proc Natl Acad Sci USA, 1992,89:957-961.
[41] Cordeiro G M, Casu R, McIntyre C L, Manners J M, Henry R J . Microsatellite markers from sugarcane ( Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci, 2001,160:1115-1123.
[42] Bushman B S, Larson S R, Mott I W, Cliften P F, Wang R R, Chatterton N J, Hernandez A G, Ali S, Kim R W, Thimmapuram J . Development and annotation of perennial Triticeae ESTs and SSR markers. Genome, 2008,51:779-788.
[43] Fernandez I, Eduardo I, Blanca J, Esteras C, Pico B, Nuez F, Arus P, Garcia J, Monforte A J . Bin mapping of genomic and EST-derived SSRs in melon ( Cucumis melo L.). Theor Appl Genet, 2008,118:139-150.
[44] Hwang J Y, Ahn S G, Youl Oh J, Choi Y W, Kang J S, Park Y H . Functional characterization of watermelon ( Citrullus lanatus L.) EST-SSR by gel electrophoresis and high resolution melting analysis. Sci Hortic, 2011,130:715-724.
[45] Pinto L R, Oliveira K M, Ulian E C, Garcia A, de Souza A P . Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats. Genome, 2004,47:795-804.
[46] Marconi T G, Costa E A, Miranda H R, Mancini M C, Cardoso C B, Oliveira K M, Pinto L R, Mollinari M, Garcia A A, Souza A P . Functional markers for gene mapping and genetic diversity studies in sugarcane. BMC Res Notes, 2011,4:264.
[1] YUAN Da-Shuang, DENG Wan-Yu, WANG Zhen, PENG Qian, ZHANG Xiao-Li, YAO Meng-Nan, MIAO Wen-Jie, ZHU Dong-Ming, LI Jia-Na, LIANG Ying. Cloning and functional analysis of BnMAPK2 gene in Brassica napus [J]. Acta Agronomica Sinica, 2022, 48(4): 840-850.
[2] CHEN Xiao-Hong, LIN Yuan-Xiang, WANG Qian, DING Min, WANG Hai-Gang, CHEN Ling, GAO Zhi-Jun, WANG Rui-Yun, QIAO Zhi-Jun. Development of DNA molecular ID card in hog millet germplasm based on high motif SSR [J]. Acta Agronomica Sinica, 2022, 48(4): 908-919.
[3] ZHANG Xia, YU Zhuo, JIN Xing-Hong, YU Xiao-Xia, LI Jing-Wei, LI Jia-Qi. Development and characterization analysis of potato SSR primers and the amplification research in colored potato materials [J]. Acta Agronomica Sinica, 2022, 48(4): 920-929.
[4] YANG Jin, BAI Ai-Ning, BAI Xue, CHEN Juan, GUO Lin, LIU Chun-Ming. Phenotypic and genetic analyses of a rice mutant eed1 with defected embryo and endosperm development [J]. Acta Agronomica Sinica, 2022, 48(2): 292-303.
[5] ZHANG Ming-Cong, HE Song-Yu, QIN Bin, WANG Meng-Xue, JIN Xi-Jun, REN Chun-Yuan, WU Yao-Kun, ZHANG Yu-Xian. Effects of exogenous melatonin on morphology, photosynthetic physiology, and yield of spring soybean variety Suinong 26 under drought stress [J]. Acta Agronomica Sinica, 2021, 47(9): 1791-1805.
[6] HE Jun-Yu, ZHONG Wei, CHEN Yun-Qiong, WANG Wei-Bin, XIONG Jing-Lei, JIANG Ya-Li, SHI Hui-Meng, CHEN Sheng-Wei. Analysis on the accumulation characteristics of seven flavonoids at grain development stage in barley [J]. Acta Agronomica Sinica, 2021, 47(8): 1624-1630.
[7] WANG Yan-Yan, WANG Jun, LIU Guo-Xiang, ZHONG Qiu, ZHANG Hua-Shu, LUO Zheng-Zhen, CHEN Zhi-Hua, DAI Pei-Gang, TONG Ying, LI Yuan, JIANG Xun, ZHANG Xing-Wei, YANG Ai-Guo. Construction of SSR fingerprint database and genetic diversity analysis of cigar germplasm resources [J]. Acta Agronomica Sinica, 2021, 47(7): 1259-1274.
[8] LI Fu, WANG Yan-Zhou, YAN Li, ZHU Si-Yuan, LIU Tou-Ming. Characterization of the expression profiling of circRNAs in the barks of stems in ramie [J]. Acta Agronomica Sinica, 2021, 47(6): 1020-1030.
[9] WU Ran-Ran, LIN Yun, CHEN Jing-Bin, XUE Chen-Chen, YUAN Xing-Xing, YAN Qiang, GAO Ying, LI Ling-Hui, ZHANG Qin-Xue, CHEN Xin. Genetic and cytological analysis of male sterile mutant msm2015-1 in mungbean [J]. Acta Agronomica Sinica, 2021, 47(5): 860-868.
[10] MA Huan-Huan, FANG Qi-Di, DING Yuan-Hao, CHI Hua-Bin, ZHANG Xian-Long, MIN Ling. GhMADS7 positively regulates petal development in cotton [J]. Acta Agronomica Sinica, 2021, 47(5): 814-826.
[11] HU Dong-Xiu, LIU Hao, HONG Yan-Bin, LIANG Xuan-Qiang, CHEN Xiao-Ping. Identification and expression analysis of microRNA during peanut (Arachis hypogaea L.) pod development [J]. Acta Agronomica Sinica, 2021, 47(4): 613-625.
[12] HAN Bei, WANG Xu-Wen, LI Bao-Qi, YU Yu, TIAN Qin, YANG Xi-Yan. Association analysis of drought tolerance traits of upland cotton accessions (Gossypium hirsutum L.) [J]. Acta Agronomica Sinica, 2021, 47(3): 438-450.
[13] LU Hai, LI Zeng-Qiang, TANG Mei-Qiong, LUO Deng-Jie, CAO Shan, YUE Jiao, HU Ya-Li, HUANG Zhen, CHEN Tao, CHEN Peng. DNA methylation in response to cadmium stress and expression of different methylated genes in kenaf [J]. Acta Agronomica Sinica, 2021, 47(12): 2324-2334.
[14] LIU Shao-Rong, YANG Yang, TIAN Hong-Li, YI Hong-Mei, WANG Lu, KANG Ding-Ming, FANG Ya-Ming, REN Jie, JIANG Bin, GE Jian-Rong, CHENG Guang-Lei, WANG Feng-Ge. Genetic diversity analysis of silage corn varieties based on agronomic and quality traits and SSR markers [J]. Acta Agronomica Sinica, 2021, 47(12): 2362-2370.
[15] LU He-Quan, TANG Wei, LUO Zhen, KONG Xiang-Qiang, LI Zhen-Huai, XU Shi-Zhen, XIN Cheng-Song. Effects of commercial organic fertilizer substituting chemical fertilizer partially on soil nutrients, plant development, and yield in cotton [J]. Acta Agronomica Sinica, 2021, 47(12): 2511-2521.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!