Literature DB >> 29768494

A new method based on SNP of nrDNA-ITS to identify Saccharum spontaneum and its progeny in the genus Saccharum.

Shan Yang1, Xueting Li1, Fei Huang1, Yongji Huang1, Xinlong Liu2, Jiayun Wu3, Qinnan Wang3, Zuhu Deng1,4, Rukai Chen1, Muqing Zhang4.   

Abstract

The identification of germplasm resources is an important aspect of sugarcane breeding. The aim of this study was to introduce a new method for identifying Saccharum spontaneum and its progeny. First, we cloned and sequenced nuclear ribosomal DNA internal transcribed spacer (nrDNA-ITS) sequences from 20 Saccharum germplasms. Analysis of these nrDNA-ITS sequences showed a stable mutation at base 89. Primers (FO13, RO13, FI16, and RI16) were then designed for tetra-primer amplification refractory mutation system (ARMS) PCR based on mutations at base 89 of the nrDNA-ITS sequence. An additional 71 Saccharum germplasms were identified using this tetra-primer ARMS PCR method, which confirmed that the method using the described primers successfully identified Saccharum spontaneum and progeny. These results may help improve the efficiency of modern molecular breeding of sugarcane and lay a foundation for identification of sugarcane germplasms and the relationships among them.

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Year:  2018        PMID: 29768494      PMCID: PMC5955562          DOI: 10.1371/journal.pone.0197458

Source DB:  PubMed          Journal:  PLoS One        ISSN: 1932-6203            Impact factor:   3.240


Introduction

Sugarcane is an important sugar and energy crop worldwide. Sugarcane plants belong to the grass family Gramineae, genus Saccharum, and related plants in this family include Miscanthus, Sclerostachya, Erianthus, and Narenga. The Saccharum genus consists of six species, including Saccharum officinarum (2n = 80), S. sinense (2n = 112–120), S. barberi (2n = 82–124), S. edule (2n = 60, 70, 80), and two wild species, S. robustum (2n = 60–120) and S. spontaneum (2n = 40–128) [1]. S. barberi and S. sinense are secondary species derived from hybridization of S. officinarum and S. spontaneum [2]. Moreover, S. sinense, S. barberi, S. robustum, S. spontaneum, and S. officinarum are important parental resources in sugarcane breeding [3]. Sugarcane cultivars are multiple interspecific hybrids and highly heterogeneous, and almost all contain some S. spontaneum genetic material at levels up to 10% of all chromosomes [4]. Internal transcribed spacers (ITS) of nuclear ribosomal DNA (nrDNA) contain ITS1, 5.8s rDNA, and ITS2 [5]. In recent years, several features of nrDNA-ITS have made a useful tool for evaluating and analyzing evolutionary relationships at the subspecies level, including rich variances and rapid evolutionary rate, as well as simple PCR amplification and sequencing [6-8]. In view of these features, Yang et al. analyzed the nrDNA-ITS sequence characteristics of 19 S. spontaneum germplasms and 11 local sugarcane varieties [9]. The results showed that 11 S. spontaneum germplasms could be divided into several branches, and that local sugarcane varieties were closely related to S. spontaneum. Moreover, the ITS1 sequence could be used as a DNA barcode to further study the genetic diversity of Saccharum and related genera. Liu et al. analyzed differences among nrDNA-ITS sequences from 62 different multiple S. spontaneum materials and showed that 4 species had high variation, especially the nonuploid and decaploid population [10]. As a third-generation molecular marker, single nucleotide polymorphisms (SNPs) are highly stable and widely used for studies of crop molecular genetics [11]. Due to the limited availability of sugarcane genomic maps, research on SNPs in sugarcane lags behind that of rice, rapeseed, and other crops [12]. SNPs for many crops have been discovered through analysis of nrDNA-ITS sequences and in turn have served as valuable molecular markers to identify interspecies germplasms [13] that can contribute to strategies for molecular breeding of crops [14]. Tetra-primer amplification refractory mutation system PCR (tetra-primer ARMS PCR) is a derivative technique based on common PCR that can be specifically used to detect SNPs [15]. Tetra-primer ARMS PCR is rapid, simple, and economical. According to the SNP site, the tetra-primer ARMS PCR technique has been used to identify various germplasm genotypes in rice, wheat, capsicum, and other crops [16-18]. Based on previous studies on nrDNA-ITS in sugarcane germplasms, the tetra-primer ARMS PCR technique can be used to analyze genetic diversity and phylogenetic relationships in interspecific and intergenus samples [9, 10, 19]. However, studies exploring the identification and use of SNPs as molecular markers in Saccharum breeding have not been performed. As such, we cloned, sequenced, and analyzed nrDNA-ITS sequences of 20 Saccharum germplasms to identify a stable SNP. Based on the SNP site, primers were designed according to the principles of tetra-primer ARMS PCR. PCR of 71 materials was performed to identify the presence of Saccharum spontaneum genetic material. This study provides a foundation for improving the efficiency of modern molecular breeding of sugarcane and a molecular basis for identifying sugarcane germplasms.

Materials and methods

Plant materials

In this study, 20 clones were selected for nrDNA-ITS sequencing, including 5 S. officinarum, 5 S. robustum, and 15 different multiple S. spontaneum samples that contained octoploid, nonuploid, decaploid, dodecaploid, and tridecaploid S. spontaneum (Table 1). A total of 71 clones were selected for testing and analysis of the specificity of tetra-primer ARMS PCR primers that we developed and designed, including 5 S. officinarum and 3 F1 (S. officinarum×S. spontaneum), which all have similar morphology to S. officinarum, 6 S. robustum, 43 S. spontaneum, 3 S. sinense, 3 S. barberi, 3 sugarcane cultivars and 5 F1 (S. officinarum×S. robustum) materials (Table 2).
Table 1

Plant materials for cloning and sequencing of nrDNA-ITS sequences.

No.Clone nameSpecies namePloidyNumber of chromosomes
1BadilaSaccharum officinarumoctoploid80
2VN cattle caneSaccharum officinarumoctoploid80
3LoethersSaccharum officinarumoctoploid80
4CrystalinaSaccharum officinarumoctoploid80
5S. CheribonSaccharum officinarumoctoploid80
657NG208Saccharum robustumoctoploid80
751NG63Saccharum robustumoctoploid80
8NG77-004Saccharum robustumoctoploid80
928NG21Saccharum robustumoctoploid80
10DayeSaccharum robustumoctoploid80
11YN75-2-11Saccharum spontaneumoctoploid64
12YN82-110Saccharum spontaneumoctoploid64
13YN83-160Saccharum spontaneumoctoploid64
14FJ89-1-1Saccharum spontaneumnonuploid72
15YN83-201Saccharum spontaneumnonuploid72
16YN82-44Saccharum spontaneumdecaploid80
17YN83-171Saccharum spontaneumdecaploid80
18GZ78-2-28Saccharum spontaneumdodecaploid96
19FJ88-1-13Saccharum spontaneumdodecaploid96
20FJ89-1-19Saccharum spontaneumtridecaploid104
Table 2

Plant materials used for identifying genetic material from Saccharum spontaneum with tetra-primer ARMS PCR.

No.Clone nameSpecies namePloidyNumber of chromosomes
1BadilaSaccharum officinarumoctoploid80
2VN cattle caneSaccharum officinarumoctoploid80
3LoethersSaccharum officinarumoctoploid80
4CrystalinaSaccharum officinarumoctoploid80
5S. CheribonSaccharum officinarumoctoploid80
6MuckcheF1(S. officinarum×S. spontaneum)octoploid141–143
7BaimeizheF1(S. officinarum×S. spontaneum)octoploid104–106
8Cana BlancaF1(S. officinarum×S. spontaneum)octoploid113–115
928NG21Saccharum robustumoctoploid80
1051NG63Saccharum robustumoctoploid80
1151NG3Saccharum robustumoctoploid80
12DayeSaccharum robustumoctoploid80
1357NG208Saccharum robustumoctoploid80
14NG77-004Saccharum robustumoctoploid80
15YN75-2-11Saccharum spontaneumoctoploid64
16YN83-160Saccharum spontaneumoctoploid64
17YN83-225Saccharum spontaneumoctoploid64
18YN82-58Saccharum spontaneumoctoploid64
19YN4Saccharum spontaneumoctoploid64
20YN83-238Saccharum spontaneumoctoploid64
21Vietnam-3Saccharum spontaneumoctoploid64
22YN82-9Saccharum spontaneumoctoploid64
23YN-mengziSaccharum spontaneumoctoploid64
24YN84-268Saccharum spontaneumoctoploid64
25YN82-110Saccharum spontaneumoctoploid64
26GZ78-1-11Saccharum spontaneumnonuploid72
27YN76-1-16Saccharum spontaneumnonuploid72
28FJ89-1-11Saccharum spontaneumnonuploid72
29YN82-50Saccharum spontaneumnonuploid72
30SC92-42Saccharum spontaneumnonuploid72
31FJ89-1-1Saccharum spontaneumnonuploid72
32YN83-201Saccharum spontaneumnonuploid72
33SC88-49Saccharum spontaneumdecaploid80
34FJ89-1-21Saccharum spontaneumdecaploid80
35YN76-1-24Saccharum spontaneumdecaploid80
36YN75-2-35Saccharum spontaneumdecaploid80
37SC79-2-16Saccharum spontaneumdecaploid80
38SC79-1-26Saccharum spontaneumdecaploid80
39YN83-171Saccharum spontaneumdecaploid80
40Wenshan caneSaccharum sinenseUnknownUnknown
41UbaSaccharum sinenseUnknown116–118
42GD-sinenseSaccharum sinenseUnknownUnknown
43NagansSaccharum barberiUnknownUnknown
44PansahiSaccharum barberiUnknownUnknown
45SarethaSaccharum barberiUnknown91–92
46ROC10CultivarsUnknownUnknown
47ROC22CultivarsUnknownUnknown
48CP84-1198CultivarsUnknownUnknown
49FJ92-1-11Saccharum spontaneumdecaploid80
50HeqingSaccharum spontaneumdecaploid80
51YN75-2-35Saccharum spontaneumdecaploid80
52GD-16Saccharum spontaneumdecaploid80
53GD-60Saccharum spontaneumdecaploid80
54GD-71Saccharum spontaneumdecaploid80
55YN82-44Saccharum spontaneumdecaploid80
56Ledong-1Saccharum spontaneumdecaploid80
57XundianSaccharum spontaneumdecaploid80
58GZ78-1-5Saccharum spontaneumdecaploid80
59GZ79-1-4Saccharum spontaneumdecaploid80
60FJ88-1-13Saccharum spontaneumdodecaploid96
61GZ78-2-28Saccharum spontaneumdodecaploid96
62FJ-HuiAnSaccharum spontaneumdodecaploid96
63FJ89-1-16Saccharum spontaneumdodecaploid96
64GD-30Saccharum spontaneumdodecaploid96
65FJ89-1-18Saccharum spontaneumdodecaploid96
66FJ89-1-19Saccharum spontaneumtridecaploid104
67RL12-38-1F1(S. officinarum×S. robustum)UnknownUnknown
68RL12-38-5F1(S. officinarum×S. robustum)UnknownUnknown
69RL12-38-76F1(S. officinarum×S. robustum)UnknownUnknown
70RL12-38-81F1(S. officinarum×S. robustum)UnknownUnknown
71RL12-38-84F1(S. officinarum×S. robustum)UnknownUnknown

Reagents and materials

Takala Ex Taq® polymerase, Takala LA Taq® polymerase, PMD19-T vector, and E. coli DH5α competent cells were obtained from Takara Biotechnology Co., Ltd. (Dalian of China). Primers were synthesized by the Beijing Genomics Institute (Beijing, China).

Genomic DNA extraction

Young leaves from different sugarcane species were collected and powdered after freezing in liquid nitrogen. Genomic DNA was extracted from the leaves using a traditional CTAB method that was performed according to Porebski et al. [20].

Cloning and sequencing

The nrDNA-ITS sequences from 20 clones (Table 1) were amplified using the universal primers ITS1 and ITS4 (ITS1: TCCGTAGGTGAACCTGCGG; ITS4: TCCTCCGCTTATTGATATGC) [21]. The PCR reaction mixtures were prepared on ice (Table 3) and carried out in a thermal cycler (ABI, 9902, USA). The reaction sequences were as follows: pre-denaturation at 95°C for 5 min followed by 35 cycles of 95°C for 15 s, 54°C for 15 s, and 72°C for 10 s. A final extension was conducted at 72°C for 5 min. The PCR products were tested by 1.5% agarose gel electrophoresis and purified using an Omega EZNA gel extraction kit. The purified products were then cloned into a PMD19-T vector and transformed into E. coli DH5α competent cells. Recombinant clones were grown in LB medium supplemented with ampicillin (100 μg/mL). Five clones per sample were selected for sequencing by Sangon Biotech Co., Ltd. (Shanghai, China).
Table 3

nrDNA-ITS PCR reaction mixture.

ComponentsVolume (μL)
ddH2O13.9
10× LA buffer (Mg2+ plus)2.0
dNTP (2.5 mM each)1.6
ITS1 (10 μM)0.8
ITS4 (10 μM)0.8
Template (gDNA; 50 ng/μL)0.8
LA Taq (5 U/μL)0.1
Total volume20.0

Sequence analysis

DNA sequence homology was estimated using a nucleotide BLAST tool in the NCBI database. All DNA sequences were analyzed by DNAMAN 6.0 and BioEdit 7.0.9.0 to obtain variable site information.

Primer design

Optimized primers for PCR were designed according to the design principle of tetra-primer ARMS PCR primers. Specific reference to the design method for tetra-primer ARMS PCR primers is made in Medrano and de Oliveira [22].

Tetra-primer ARMS PCR procedure

Tetra-primer ARMS PCR of 71 samples (Table 2) was performed using the primers FO13, RO13, FI16, and RI16 (FO13: GTTTTTGAACGCAAG TTGCGCCCGAGGC; RO13: AATTCGGGCGACGAAGCCACCCGATTCT; FI16: GCCGGCGCATCGGC CCTAAGGACCTAT; RI16: GAGCGGCTATGCGCTGCGGTGCTTCT). Tetra-primer ARMS PCR reaction mixtures were prepared on ice (Table 4) and carried out in a thermal cycler (ABI, 9902, USA). The reaction conditions were as follows: pre-denaturation at 95°C for 5 min, followed by 6 cycles of 95°C for 30 s, 78°C for 20 s for one cycle and descending by 1°C for each subsequent 20 s cycle, 72°C for 20 s; the reaction ended with 24 cycles of 95°C for 30 s, 71°C for 10 s, 72°C for 10 s, and a final extension at 72°C for 5 min. The PCR products were tested by 1.5% agarose gel electrophoresis.
Table 4

Tetra-primer ARMS PCR mixtures.

ComponentsVolume (μL)
ddH2O1.4
2×GC buffer10.0
dNTP (2.5 mM each)2.4
Dimethylsulphoxide0.8
FO13 (5 μM)1.6
RO13 (5 μM)1.2
FI16 (5 μM)0.4
RI16 (5 μM)1.6
Template (gDNA; 50 ng/μL)0.4
Ex Taq (5 U/μL)0.2
Total volume20.0

Results

nrDNA-ITS PCR

The nrDNA-ITS sequences of different samples were obtained by PCR with ITS1 and ITS4 primers. The nrDNA-ITS PCR product from each material tested appeared in the electrophoresis map as a single, intense 678 bp band (Fig 1).
Fig 1

Electrophoretogram of nrDNA-ITS PCR products.

M: 100 bp DNA ladder marker. Lanes 1–5: Badila, VN cattle cane, Loethers, Crystalina, Cheribon, respectively, belong to S. officinarum. Lanes 6–10: 57NG208, 51NG63, NG77-004, 28NG21, Daye, respectively, belong to S. robustum. Lanes 11–20: YN75-2-11, YN82-110, YN83-160, FJ89-1-1, YN83-201, YN82-44, YN83-171, GZ78-2-28, FJ88-1-13, FJ89-1-19, respectively, belong to S. spontaneum.

Electrophoretogram of nrDNA-ITS PCR products.

M: 100 bp DNA ladder marker. Lanes 1–5: Badila, VN cattle cane, Loethers, Crystalina, Cheribon, respectively, belong to S. officinarum. Lanes 6–10: 57NG208, 51NG63, NG77-004, 28NG21, Daye, respectively, belong to S. robustum. Lanes 11–20: YN75-2-11, YN82-110, YN83-160, FJ89-1-1, YN83-201, YN82-44, YN83-171, GZ78-2-28, FJ88-1-13, FJ89-1-19, respectively, belong to S. spontaneum. All of the clone sequences were analyzed using the BLAST tool in the NCBI database. The homology of all cloned sequences with other germplasm nrDNA-ITS sequences of sugarcane was >98%, which indicated that the clone sequences contained nrDNA-ITS sequences and were highly conserved. All clone sequences were analyzed using DNAMAN 6.0 and BioEdit 7.0.9.0 to obtain variable site information. At least five samples had mutations at bases 73, 79, 89, 125, 308, 445, 471, 484, 506, 562, 589, 615, and 621 (Fig 2). Among all mutations, those at base 73 and 89 were in a regular form because the mutation occurred only in S. spontaneum clones (Fig 2). However, only the mutation at base 89 was conserved for 10 S. spontaneum clones, which could be a good target region of tetra-primer ARMS PCR.
Fig 2

Analysis of nrDNA-ITS sequences.

“······” represents sequences that are identical to that of Badila. Only base mutations are shown.

Analysis of nrDNA-ITS sequences.

“······” represents sequences that are identical to that of Badila. Only base mutations are shown.

Tetra-primer ARMS PCR

A total of 71 Saccharum genus germplasm materials were amplified around base 89 using tetra-primer ARMS PCR. Tetra-primer ARMS PCR results showed a 428 bp common electrophoretic band in all materials tested, of which S. spontaneum had a 203 bp-specific electrophoretic band, whereas S. officinarum and S. robustum had a 278 bp-specific electrophoretic band (Fig 3). Considering the bands for ROC10, ROC22, and CP84-1196, we successfully identified the presence of S. spontaneum genetic material. RL12-38-1, RL12-38-5, RL12-38-76, RL12-38-81, and RL12-38-84 yielded two bands (428 bp and 278 bp), which indicated the absence of S. spontaneum genetic material. Moreover, analysis of electrophoretic bands allowed for the determination that Muckche, Baimeizhe, and Canablanca were F1 (S. officinarum × S. spontaneum) (Fig 3).
Fig 3

Electrophoretogram of tetra-primer ARMS PCR products.

M: 100 bp DNA ladder marker. Lanes 1–5: Badila, VN cattle cane, Loethers, Crystalina, and S. Cheribon, respectively, are S. officinarum. Lanes 6–8: Muckche, Baimeizhe, and Canablanca, respectively, are F1 generations produced between S. officinarum and S. spontaneum. Lanes 9–14: 28NG21, 51NG63, 51NG3, Daye, 57NG208, and NG77-004, respectively, are S. robustum. Lanes 15–39: YN75-2-11, YN83-160, YN83-225, YN82-58, YN4, YN83-238, Vietnam-3, YN82-9, YN-mengzi, YN84-268, YN82-110, GZ78-1-11, YN76-1-16, FJ89-1-11, YN82-50, SC92-42, FJ89-1-1, YN83-201, SC88-49, FJ89-1-21, YN76-1-24, YN75-2-35, SC79-2-16, SC79-1-26, and YN83-171, respectively, are S. spontaneum. Lanes 40–42: Wenshan cane, Uba, and GD-sinense, respectively, are S. sinense. Lanes 43–45: Nagans, Pansahi, and Saretha, respectively, are S. barberi. 46–48: ROC10, ROC22, and CP84-1196, respectively, are cultivars. Lanes 49–66: FJ92-1-11, Heqing, YN75-2-35, GD-16, GD-60, GD-71, YN82-44, Ledong-1, Xundian, GZ78-1-5, GZ79-1-4, FJ88-1-13, GZ78-2-28, FJ-HuiAn, FJ89-1-16, GD-30, FJ89-1-18, and FJ89-1-19, respectively, are S. spontaneum. Lanes 67–71: RL12-38-1, RL12-38-5, RL12-38-76, RL12-38-81, and RL12-38-84, respectively, are F1 generations produced between S. officinarum and S. robustum. Lane 72: H2O.

Electrophoretogram of tetra-primer ARMS PCR products.

M: 100 bp DNA ladder marker. Lanes 1–5: Badila, VN cattle cane, Loethers, Crystalina, and S. Cheribon, respectively, are S. officinarum. Lanes 6–8: Muckche, Baimeizhe, and Canablanca, respectively, are F1 generations produced between S. officinarum and S. spontaneum. Lanes 9–14: 28NG21, 51NG63, 51NG3, Daye, 57NG208, and NG77-004, respectively, are S. robustum. Lanes 15–39: YN75-2-11, YN83-160, YN83-225, YN82-58, YN4, YN83-238, Vietnam-3, YN82-9, YN-mengzi, YN84-268, YN82-110, GZ78-1-11, YN76-1-16, FJ89-1-11, YN82-50, SC92-42, FJ89-1-1, YN83-201, SC88-49, FJ89-1-21, YN76-1-24, YN75-2-35, SC79-2-16, SC79-1-26, and YN83-171, respectively, are S. spontaneum. Lanes 40–42: Wenshan cane, Uba, and GD-sinense, respectively, are S. sinense. Lanes 43–45: Nagans, Pansahi, and Saretha, respectively, are S. barberi. 46–48: ROC10, ROC22, and CP84-1196, respectively, are cultivars. Lanes 49–66: FJ92-1-11, Heqing, YN75-2-35, GD-16, GD-60, GD-71, YN82-44, Ledong-1, Xundian, GZ78-1-5, GZ79-1-4, FJ88-1-13, GZ78-2-28, FJ-HuiAn, FJ89-1-16, GD-30, FJ89-1-18, and FJ89-1-19, respectively, are S. spontaneum. Lanes 67–71: RL12-38-1, RL12-38-5, RL12-38-76, RL12-38-81, and RL12-38-84, respectively, are F1 generations produced between S. officinarum and S. robustum. Lane 72: H2O.

Discussion

In this study, we found for the first time that base 89 was a stable base mutation in the nrDNA-ITS sequence of the Saccharum genus and was present in S. spontaneum genetic material. We thus designed primers for tetra-primer ARMS PCR based on this nrDNA-ITS sequence SNP. After optimization and identification, the primers FO13, RO13, FI16, and RI16 were found to be suitable for identification of S. spontaneum genetic material and its progeny. To the best of our knowledge, this is the first instance of the use of tetra-primer ARMS PCR to identify S. spontaneum genetic signatures in the Saccharum genus. These findings will be valuable for classifying sugarcane germplasms and will improve sugarcane hybridization breeding efficiency. In angiosperms, this entire ITS region (ITS1+5.8S+ITS2) can be easily amplified using universal primers that recognize conserved coding regions to produce a 700 bp amplicon [23]. Here, a 678 bp fragment was amplified using the general primers ITS1 and ITS4 that cover the entire ITS sequence. This ITS sequence is not only widely used for germplasm classification and phylogeny analysis, but also for identification of germplasm resources in sample plants. Previous studies have suggested that this ITS sequence has higher conservation than the medium-height repetitive sequence and non-coded sequences, and that the mutation rate is relatively rapid compared with the coded gene sequence [24]. In allopolyploid plants, ITS sequence evolution is complex, such that ancestral ITS sequences can coexist in some offspring, but in other offspring may evolve in another direction [25, 26]. For example, in the polyploid plants of wheat, ancestral nrDNA-ITS sequences coexist in the offspring [27]. In this study, tetra-primer ARMS PCR results showed that the hybrid generation generated between S. officinarum and S. spontaneum yielded three bands (428 bp, 278 bp, 203 bp), the offspring generated between S. officinarum and S. robustum yielded two bands (428 bp, 278 bp), which respectively revealed parents’ traits. Therefore, we found that the ancestral nrDNA-ITS sequences could coexist in the offspring in the hybrid process of sugarcane. Our sequence analysis in this study indicated that the nrDNA-ITS sequence in sugarcane is relatively conserved. Moreover, the SNPs we identified were highly stable genetic markers. Therefore, the primers we developed for tetra-primer ARMS PCR could be used for accurate and reliable identification of S. spontaneum genetic material and progeny in the Saccharum genus. The identification of Saccharum germplasm collections is mainly based on morphological observation, which can result in misclassification. In recent years, several molecular markers, such as SSR, AFLP, ISSR, and RAPD, have been applied for identification of Saccharum germplasms and progeny identification [28-31]. Many specific bands can be obtained from the progeny of hybrid offspring using these molecular markers, which contribute significantly to the separation and identification of sugarcane hybrids and germplasms. However, these molecular markers cannot intuitively identify sugarcane germplasms, as they produce multiple amplification bands that complicate interpretation and quantification. Of course, single-copy gene marker had been applied in phylogenetics in many plants with the development of sequencing technology [32, 33]. Compare with nrDNA-ITS sequence, the use of a single-copy gene mostly demands development of PCR primers specific for the taxonomic group of interest [34]. Moreover, this can result in the inclusion of paralogous copies in phylogenetic studies in the polyploid plans, resulting in wrong taxon relationships. To avoid this problem, the single-copy nuclear genes that occured mostly only with a single copy in the haploid genome might be preferable in phylogenetic analyses and identification of different species [35]. Therefore, selection of single-copy gene marker is an issue at present, especially in the polyploid plant. Because the sugarcane is an allopolyploids plant, its genome research is not yet complete and it is very difficult to obtain the haploid of sugarcane at present. Thus, selection of a single-copy gene as molecular marker is very difficult in sugarcane. In a more visual identification of sugarcane germplasm materials, Piperidis et al. used genomic in situ hybridization (GISH) to show that Kokea, Muntok Java, and Bourbonriet suriname were not S. officinarum, but instead were hybridized progeny of S. officinarum and S. spontaneum [36]. Moreover, many breeders believed that Muckche, Canablanca, and Baimeizhe were S. officinarum based on similar morphology. However, in 2016 Wang et al. identified 10 S. officinarum types using GISH technology and found that Muckche, Canablanca, and Baimeizhe were in fact hybridized progeny of S. officinarum and S. spontaneum [37]. These results are consistent with our study, which supports the reliability of the molecular markers we identified. Based on tetra-primer ARMS PCR results, we easily distinguished S. spontaneum and other Saccharum germplasm materials in this study. Moreover, tetra-primer ARMS PCR using the primers FO13, RO13, FI16, and RI16 to identify S. spontaneum and progeny is simpler and less time-consuming than GISH. The breeding of a sugarcane variety typically requires approximately 10 years. Historically, the breeding process could not be accelerated because plants could not be selected early in the seedling stage due to a lack of molecular markers. The tetra-primer ARMS PCR technology developed in this study could have broad applications for sugarcane breeding in the future. This approach could address the problem of early selection and identify whether seedlings incorporate S. spontaneum genetic material. Germplasms from plants thought to include S. spontaneum as a predecessor could be identified using tetra-primer ARMS PCR technology to determine whether such plants are indeed hybridized progeny of S. officinarum and S. spontaneum.
  16 in total

Review 1.  The essence of SNPs.

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2.  Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane.

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Review 3.  Applications of next-generation sequencing to phylogeography and phylogenetics.

Authors:  John E McCormack; Sarah M Hird; Amanda J Zellmer; Bryan C Carstens; Robb T Brumfield
Journal:  Mol Phylogenet Evol       Date:  2011-12-14       Impact factor: 4.286

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5.  Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants.

Authors:  Riet De Smet; Keith L Adams; Klaas Vandepoele; Marc C E Van Montagu; Steven Maere; Yves Van de Peer
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6.  Nuclear ribosomal RNA genes: ITS region.

Authors:  Pascale Besse
Journal:  Methods Mol Biol       Date:  2014

7.  Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane.

Authors:  Amaresh Chandra; Michael P Grisham; Yong-Bao Pan
Journal:  Genome       Date:  2014-08-26       Impact factor: 2.166

8.  Genetic segregation of microsatellite markers in Saccharum officinarum and S. spontaneum.

Authors:  S J Edmé; N G Glynn; J C Comstock
Journal:  Heredity (Edinb)       Date:  2006-08-16       Impact factor: 3.821

9.  An efficient procedure for genotyping single nucleotide polymorphisms.

Authors:  S Ye; S Dhillon; X Ke; A R Collins; I N Day
Journal:  Nucleic Acids Res       Date:  2001-09-01       Impact factor: 16.971

10.  Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus.

Authors:  Shunmou Huang; Linbin Deng; Mei Guan; Jiana Li; Kun Lu; Hanzhong Wang; Donghui Fu; Annaliese S Mason; Shengyi Liu; Wei Hua
Journal:  BMC Genomics       Date:  2013-10-20       Impact factor: 3.969

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1.  An improved suppression subtractive hybridization technique to develop species-specific repetitive sequences from Erianthus arundinaceus (Saccharum complex).

Authors:  Fan Yu; Yongji Huang; Ling Luo; Xueting Li; Jiayun Wu; Rukai Chen; Muqing Zhang; Zuhu Deng
Journal:  BMC Plant Biol       Date:  2018-11-06       Impact factor: 4.215

2.  Efficient Anchoring of Erianthus arundinaceus Chromatin Introgressed into Sugarcane by Specific Molecular Markers.

Authors:  Jiayun Wu; Mingxiao Zhang; Jiarui Liu; Yongji Huang; Liangnian Xu; Zuhu Deng; Xinwang Zhao
Journal:  Int J Mol Sci       Date:  2022-08-21       Impact factor: 6.208

3.  Enhanced sugar accumulation and regulated plant hormone signalling genes contribute to cold tolerance in hypoploid Saccharum spontaneum.

Authors:  Hongli Yang; Tianju Wang; Xinghua Yu; Yang Yang; Chunfang Wang; Qinghui Yang; Xianhong Wang
Journal:  BMC Genomics       Date:  2020-07-22       Impact factor: 3.969

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