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. 2019 Jan 23;9:395. doi: 10.1038/s41598-018-36630-7

Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers

Ahmad Ali 1,#, Yong-Bao Pan 2,#, Qin-Nan Wang 3,#, Jin-Da Wang 1, Jun-Lü Chen 3, San-Ji Gao 1,✉
PMCID: PMC6344583  PMID: 30674931

Abstract

In order to understand the genetic diversity and structure within and between the genera of Saccharum and Erianthus, 79 accessions from five species (S. officinarum, S. spontaneum, S. robustum, S. barberi, S. sinense), six accessions of E. arundinaceus, and 30 Saccharum spp. hybrids were analyzed using 21 pairs of fluorescence-labeled highly poloymorphic SSR primers and a capillary electrophoresis (CE) detection system. A total of 167 polymorphic SSR alleles were identified by CE with a mean value of polymorphic information content (PIC) of 0.92. Genetic diversity parameters among these 115 accessions revealed that Saccharum spp. hybrids were more diverse than those of Saccharum and Erianthus species. Based on the SSR data, the 115 accessions were classified into seven main phylogenetic groups, which corresponded to the Saccharum and Erianthus genera through phylogenetic analysis and principle component analysis (PCA). We propose that seven core SSR primer pairs, namely, SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, SMC24DUQ, mSSCIR3, and mSSCIR43, may have a wide appicability in genotype identification of Saccharum species and Saccharum spp. hybrids. Thus, the information from this study contibites to manage sugarcane genetic resources.

Introduction

Sugarcane (Saccharum spp.) plays a vital role as a primary sugar-producing crop (sugar 80%) and has major potential as a renewable bioenergy crop (ethanol 50%) in world agriculture1. The Saccharum complex contains six main species: the two wild species are S. spontaneum and S. robustum, and the four cultivated species are S. officinarum, S. sinense, S. barberi and S. edule2. In addition, Erianthus arundinaceus is a species of Erianthus genus with strong abiotic stress tolerance and could be widely used for modern sugarcane breeding and a potential bioenergy plant3. Currently, sugarcane commercial breeding populations in the world share a narrow genetic base due to their common origins from a number of popular cultivars, such as POJ2878, Co419 and NCo310 which were achieved in the early 1900s2. Furthermore, these exotic varieties were developed from complex interspecific hybridization through Noblization Breeding process among wild clones of S. spontaneum and S. officinarum4. There is still a great attention among sugarcane breeders in broadening the genetic base of the crop and also in taping into the gene pool of the wild relatives to enhance stress-resistance and sucrose content5.

Since the late 1980s, sugarcane breeders and geneticists have discovered and use several DNA molecular markers including amplified fragment length polymorphisms (AFLP), restriction fragment length polymorphisms (RFLP), random amplification of polymorphic DNAs (RAPD), single nucleotide polymorphism (SNP), simple sequence repeats (SSRs), inter simple sequence repeat (ISSRs), and expressed sequence tag- simple sequence repeat (EST-SSRs) to improve Saccharum breeding6. Among these molecular markers, SSR (microsatellite) markers have been widely used to study sugarcane genetic diversity7, genetic mapping8, cross-transferability9, paternity analysis10, segregation analysis11, and marker-assisted selection12. SSR primer pairs are considered the most capable marker for plant genetics and breeding programs, because of co-dominant, multi-allelic nature, and relatively abundant with an excellent genome coverage13.

Early molecular marker research focused on the origin of wild Saccharum species. Lu et al.14 proposed a hybrid origin for S. barberi and S. sinense from natural hybridization between S. spontaneum and S. officinarum, based on a factorial correspondence analysis of RFLP markers. Subsequently, these results were supported by Irvine15 and Selvi et al.16 using SSR markers and by D’Hont et al.17 utilizing genomic in situ hybridization (GISH). Based on analysis of agronomic traits and mitochondrial profiles, S. barberi and S. sinense were placed in adjacent clusters, but apart from S. robustum18–20. Later on a number of reports focused on the analysis of genetic diversity and population structure among commercial Saccharum spp. hybrids varieties7,21–25 and among S. spontaneum populations with different ploidy levels in China26. Therefore, there has been an increasing interest among sugarcane breeders to investigate the genetic diversity of parental resources and to broaden the genetic base by tapping into the gene pools of the wild relatives27–29.

To better understand the genetic background of these euploid sugarcane clones, this study aimed to characterize the genetic diversity and population structure of 115 accessions belonging to S. officinarum, S. spontaneum, S. robustum, S. barberi, S. sinense, E. arundinaceus, and Saccharum spp. hybrids. The results may provide invaluable information for the better utilization of Saccharum and Erianthus wild germplasms at different ploidy levels in sugarcane breeding.

Results

Total alleles amplification of 21 SSR markers

A total of 167 SSR alleles were amplified from the DNA of 115 accessions including five Saccharum species, E. arundinaceus, and 30 clones of Saccharum spp. hybrids with the 21 fluorescence-labeled SSR primer pairs and capillary electrophoresis (CE) detection system. We could not find in our CE data the 16 SSR alleles reported earlier by Pan30, but instead, we have found 38 new SSR alleles that were never reported before (Table 1). Furthermore, the numbers of new and absent SSR alleles detected in this study were greater than the 20 new and 13 absent SSR alleles reported previously by Ali et al.7.

Table 1.

The general utility and amplification profile of 21 SSR primer pairs based on a capillary electrophoresis (CE) detection platform.

No. Markersa Size range (bp) Number of original bands Number of detected bands Absent alleles (bp)b New alleles (bp)b PIC
1 SMC119CG 104–135 5 6 ND 104 0.92
2 SMC1604SA 105–130 6 7 109,124 105,107,110 0.93
3 SMC1751CL 132–160 5 7 ND 132,138 0.94
4 SMC18SA 135–150 5 6 ND 135 0.93
5 SMC22DUQ 125–165 7 8 125 142146 0.94
6 SMC24DUQ* 124–150 6 10 ND 124,133,139,150 0.95
7 SMC278CS 138–182 9 9 140,153,176 138,164,172 0.94
8 SMC31CUQ* 135–180 11 12 138 135,169 0.95
9 SMC334BS 143–165 6 7 ND 143 0.94
10 SMC336BS* 140–185 11 10 154 0 0.95
11 SMC36BUQ 100–125 3 4 ND 102 0.80
12 SMC486CG 220–245 5 5 227 235 0.91
13 SMC569CS 165–225 5 5 167,170,222 165,202 0.82
14 SMC597CS* 140–180 11 13 ND 150,152 0.95
15 SMC703BS* 200–225 9 11 ND 204,218 0.95
16 SMC7CUQ 140–170 6 7 158 143,160 0.90
17 SMC851MS 125–145 6 7 ND 138 0.94
18 mSSCIR3* 140–190 10 10 141,145 149,169 0.95
19 mSSCIR43* 200–255 9 10 209 203,229 0.95
20 mSSCIR66 120–145 4 7 ND 125,136,142 0.94
21 mSSCIR74 210–232 5 6 ND 214 0.94
Total 144 167
Average 7.95 0.92
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aCore primer was marked with asterisk (*).

bAbsent and new alleles detected in this study comparing with the 144 alleles Pan30; ND, no data.

The number of alleles detected by the CE system varied from as few as four (SMC36BUQ) to as many as 13 (SMC597CS), with an average of 7.95 per SSR primer pair. Seven SSR primer pairs, namely SMC24DUQ, SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, mSSCIR3 and mSSCIR43, were highly polymorphic, each producing 10 to 13 alleles. Other eleven SSR primer pairs, namely, SMC119CG, SMC1604SA, SMC1751CL, SMC18SA, SMC22DU, SMC278CS, SMC334BS, SMC7CUQ, SMC851MS, mSSCIR66 and mSSCIR74, were moderately polymorphic, each producing six to nine alleles. The remaining three SSR primer pairs, namely, SMC36BUQ, SMC486CG and SMC569CS, were less polymorphic by producing less than six alleles each (Table 1). The PIC values of these primer pairs ranged from 0.80 (SMC36BUQ) to 0.95 (SMC24DUQ, SMC31CUQ, SMC336BUQ, SMC597CS, SMC703BS, mSSCIR3, mSSCIR43) with an average of 0.92 (Table 1).

The PIC values of each Saccharum and E. arundinaceus species were also calculated in our study. The maximum PIC value was 0.95 for mSSCIR3 on S. spontaneum and the minmum PIC value was 0.28 for SMC119CG on E. arundinaceus. Generally, higher PIC values were found in Saccharum spp. hybrids with an average value of 0.87, followed by an average PIC value of 0.86 in S. spontaneum (Table 2).

Table 2.

Polymorphism information content (PIC) of 21 SSR primer pairs analysed using 115 accessions from Saccharum, Erianthus, and Saccharum spp. hybrids.

No. SSR markers S. spontaneum S. officinarum S. barberi S. robustum S. sinense Saccharum spp. hybrids E. arundinaceus
1 SMC119CG 0.82 0.91 0.79 0.73 0.76 0.86 0.28
2 SMC7CUQ 0.88 0.84 0.67 0.85 0.62 0.84 0.38
3 SMC18SA 0.86 0.82 0.80 0.81 0.70 0.91 0.50
4 SMC22DUQ 0.88 0.89 0.83 0.73 0.61 0.88 0.59
5 SMC24DUQ 0.85 0.88 0.83 0.73 0.67 0.88 0.55
6 SMC31CUQ 0.90 0.88 0.64 0.83 0.81 0.91 0.76
7 SMC36BUQ 0.79 0.68 0.59 0.61 0.63 0.82 0.72
8 SMC278CS 0.93 0.77 0.65 0.81 0.81 0.86 0.78
9 SMC334BS 0.91 0.72 0.84 0.71 0.67 0.84 0.38
10 SMC336BS 0.92 0.88 0.84 0.71 0.71 0.88 0.73
11 SMC486CG 0.77 0.72 0.80 0.68 0.72 0.86 0.45
12 SMC569CS 0.61 0.77 0.49 0.73 0.61 0.83 0.55
13 SMC597CS 0.83 0.86 0.82 0.72 0.35 0.93 0.78
14 SMC703BS 0.82 0.60 0.56 0.77 0.64 0.92 0.88
15 SMC851MS 0.89 0.91 0.83 0.72 0.83 0.88 0.79
16 SMC1604SA 0.89 0.83 0.66 0.82 0.62 0.86 0.74
17 SMC1751CL 0.88 0.84 0.79 0.80 0.72 0.82 0.78
18 mSSCIR3 0.95 0.91 0.78 0.86 0.85 0.89 0.89
19 mSSCIR43 0.92 0.90 0.82 0.85 0.58 0.91 0.88
20 mSSCIR66 0.86 0.86 0.82 0.82 0.80 0.82 0.76
21 mSSCIR74 0.92 0.92 0.81 0.81 0.78 0.83 0.79
Average 0.86 0.83 0.75 0.77 0.69 0.87 0.66
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Genetic variability

Using the CE detection system, an average of 138 polymorphic SSR bands was observed in each Saccharum or E. arundinaceus species. Among the five species of Saccharum, one species of Erianthus, and Saccharum spp. hybrids, both the highest number of polymorphic loci (NPL) and the highest percentage of polymorphic loci (PPL) were observed in Saccharum spp. hybrids population (NPL = 165, PPL = 98.8%), followed by S. spontaneum (NPL = 159, PPL = 95.21%), while the lowest number and percentage of polymorphic loci were found in E. arundinaceus (NPL = 93, PPL = 55.69%) (Fig. 1a). The highest number of observed alleles (Na = 1.98) was found in Saccharum spp. hybrids, while the lowest number of observed alleles (Na = 1.55) was found in E. arundinaceus (Fig. 1b). Morever, the highest number of effective alleles (Ne = 1.70) was found in the Saccharum spp. hybrids, followed by S. spontaneum (Ne = 1.64). The lowest number of effective alleles (Ne = 1.30) was observed in E. arundinaceus (Fig. 1c). Shannon’s index information of different populations ranged from 0. 28 (E. arundinaceus) to 0.57 (Saccharum. spp. hybrids). Analysis of Shannon’s index (I) showed that Saccharum spp. hybrids and S. spontaneum were different from the rest of other Sccharum species by sharing the highest shannon’s index value of 0.57. The lowest shannon’s diversity index value of 0.28 was observed in S. sinense (Fig. 1d). The Nei’s gene diversity (h) of the seven populations ranged from 0.21 to 0.39. The higher genetic diversity values of 0.39, 0.36 and 0.34 were observed in Saccharum spp. hybrids, S. spontaneum and S. officinarum populations, respectivaly; while the E. arundinaceus and S. barberi populations had the lower genetic diversity values of 0.21 and 0.26 (Fig. 1e).

Figure 1.

Figure 1

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Statistical analysis of genetic variability among Saccharum, Erianthus and Saccharum spp. hybrids populations based on SSR data. Polymorphism index (PI) (a), Number of observed alleles (Na) (b), Number of effective alleles (Ne) (c), Shannon’s index (I) (d), and Nei’s genetic diversity (h) (e).

Principal Component Analysis (PCA)

Principal component analysis (PCA) data for all 115 accessions are shown in Fig. 2. The analysis classified these accessions into evelen groups involving different Saccharum and Erianthus species to some extent, i.e., Group I-A and I-B (Saccharum spp. hybrids), Group II-A and II-B (S. spontaneum), Group III (S. barberi), Group IV-A and IV-B (S. robustum), Group V-A and V-B (S. sinense), Group VI (S. officinarum), and Group VII (E. arundinaues) (Fig. 2). The amount of variance accounted for by the globle three-dimensional plot is 13.4% of Dim1, 7.12% of Dim2, and 6.51% of Dim3, with a total of 27.03% for three dimensions. This is an acceptale fit, given the small amount of variability from the large number of accessions and SSR alleles used in the analysis.

Figure 2.

Figure 2

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Three-dimensional principal component analysis (PCA) plot of Saccharum, Erianthus, and Saccharum spp. hybrids based on SSR data.

Phyolgenetic analysis

A phylogenetic tree is shown in Fig. 3. Based on phylogenetic analysis, the 115 accessions were clearly clustered at Saccharum and Erianthus genera level into seven major clades, also involving different Saccharum and Erianthus species to some extent. Clade-I contained 27 accessions from S. officinarum, S. robustum, S. barberi and S. sinense. Clade-II included 16 accessions from S. spontaneum. Clade-III comprised of three accessions of S. officinarum, three accessions of S. robustum, and three accessions of S. barberi. Clade-IV and Clade-V held 22 accessions of Saccharum spp. Hybrids. Clade-VI clustered 13 accessions of S. robustum and S. spontaneum and five accessions of E. arundinaceus. However, one E. arundinaceus accession, Guizhou 78-I-24 (Earu05), was clustered with six S. spontaneum accessions. Finally, Clade-VII contained eight accessions of Saccharum spp. hybrids, four accessions of S. officinarum, five accessions of S. barberi, and six accessions of S. sinense.

Figure 3.

Figure 3

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Phylogenetic trees of Saccharum, Erianthus, and Saccharum spp. hybrids based on SSR data. A distance tree was constructed in MEGA 6 using the UPGMA method. Robustness of the node of the phylogenetic tree was assessed from 1000 bootstrap replicates and bootstrap values of >60% are shown.

To verify some core SSR primer pairs out of the 21 primer pairs, we compared two phylogenetic trees constructed based on CE-data of 21 SSR primer pairs vs 7 SSR primer pairs and of 21 SSR primer pairs vs 6 SSR primer pairs with the Robinson-Foulds distance. Further analysis with Dendextend showed a higher cophenetic correlation coefficient value (0.93) between 21 SSR primer pairs and 7 SSR primer pairs than the 0.91 cophenetic correlation coefficient value between 21 SSR primer pairs and 6 SSR primer pairs. The plots of two phylogenetic trees based on the CE-data of 21 SSR primer pairs vs 7 SSR primer pairs are shown in Fig. 4 with tanglegrams.

Figure 4.

Figure 4

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Two phylogenetic trees constrcuted using SSR data derived from 21 SSR primer pairs vs 7 SSR primer pairs with tanglegrams.

Genetic identity analysis

Percent of genetic identity was estimated between and within the seven phylogenetic groups. Percent genetic identity between phylogenetic groups ranged from 26.9% (Saccharum spp. hybrids and S. spontaneum) to 96.4% (E. arundinaceus and S. spontaneum). Percent genetic identity within phylogenetic groups ranged from 38.9% (within S. barberi or Saccharum spp. hybrids) to 100% (within S. robustum) (Table 3).

Table 3.

Genetic identity (%) among five Saccharum species, one Erianthus species, and Saccharum spp. hybrids based on SSR data.

Populations S. spontaneum S. officinarum S. barberi S. robustum S. sinense Saccharum spp. hybrids E. arundinaceus
S. spontaneum 98.8–39.5
S. officinarum 74.8–34.7 97.6-39.5
S. barberi 73.0–37.7 83.2–36.5 99.4–38.9
S. robustum 79.0–36.5 83.2–37.1 79.0–37.1 100–431
S. sinense 73.6–42.5 74.2–46.7 78.4–41.3 74.2–44.3 99.4–43.7
Saccharum spp. hybrids 73.6–26.9 79.6–29.9 72.4–33.5 70.0–28.1 69.4–35.9 98.8–38.9
E. arundinaceus 96.4–40.1 56.2–38.3 53.8–39.5 59.2–40.7 57.4–37.1 57.4–39.5 96.4–50.8
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Discussion

Since 1950s, wild accessions of Saccharum and Erianthus have been continuously collected on mainland China and maintained in the Sugarcane Germplasm Nurseries in Yacheng, Hainan province or Kaiyuan, Yunnan Province, China. However, the genetic relationship and molecular identification between these two germplasm collections have never been entirely examined. Molecular markers are considered to be most effective in analyzing the genetic diversity, population structure, and phylogenetic relationship within sugarcane germplasm31. In recent years, SSR markers are proven to be very useful for a variety of applications in plants, including linkage maps analysis, segregation analysis, population structure analysis, marker-assisted selection, assessment of genetic relationships between individuals, mapping genes of interest, and marker-assisted backcrosses, population genetics and phylogenetic studies32,33.

In this study, we investigated the genetic diversity and population structure for 115 accessions of Saccharum and Erianthus genera that originated from two collections on mainland China and a local collection in the USA by 21 SSR primer pairs. The 21 primer pairs primed the amplification of 167 polymorphic SSR alleles detectable by the CE platform, of which 38 alleles have never been reported before. Every primer pair was able to amplify varying numbers of SSR alleles from all accessions tested, regardless of their geographical origins. Seven core SSR primer pairs, namely, SMC24DUQ, SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, mSSCIR3, and mSSCIR43, produced more than ten alleles among the 115 accessions, while four of the seven core primer pairs, namely, SMC31CUQ, SMC336BS, SMC597CS, and mSSCIR3, also primed the amplification of more than 10 alleles among 92 Chinese commercial sugarcane varieties7. Therefore, these seven core SSR primer pairs would have a priority of choice in identifying clones either from Saccharum species or Saccharum spp. hybrids.

The number of polymorphic SSR alleles detected in this study was higher than the 144 alleles reported by Pan30 or the 151 alleles reported by Ahmad et al.7, but lower than the 205 polymorphic alleles reported by You et al.25. We considered that the differences were due to different Saccharum clones being used in previous studies or to different scoring criteria. The differences may also be due to the complex genomes of Saccharum and Erianthus on one hand and relatively narrow genetic base of commercial sugarcane varieties on the other hand.

In this study, we observed different levels of genetic variations among accessions of Saccharum and Erianthus tested. In general, Saccharum spp. hybrids and S. spontaneum accessions had a higher genetic diversity than S. sinense and E. arundinaceus accessions. However, the highest number of observed alleles, number of effective alleles and polymorphism index were observed in accessions of Saccharum spp. hybrids, which are polyploidy with genome contributions from several Saccharum species. Historically, the modern Saccharum spp. hybrids were developed from crosses between the “Noble” cane S. officinarum and its relatives, namely, S. spontaneum, S. sinense, or S. barberi in the early 20th century34,35. The overall genetic variation values from this study were higher than those reported by You et al.24,25. We hypothesize that this phenomenon was due to the utilization of a larger number of SSR primer pairs and the large number of accessions from diverse Saccharum and Erianthus species in our study.

It is worthnoting that the 21 SSR primer pairs worked well in clustering Saccharum, Erianthus, and Saccharum spp. hybrids clones during phylogenetic analysis process. Two Saccharum spp. hybrids clones [(R570 (Sspp17)] from France and [(Q124 (Sspp18)] from Australia were clustered into a sub-clade in Clade-VII with four accessions of S. officinarum. The reason could be that R570 and Q124 varieties may have a closer affiliation with S. officinarum. In addition, the six accessions of E. arundinaceus were clustered with accessions of S. robustum and S. spontaneum in Clade-VI rather than forming a separate clade. This was because all the 21 SSR primer pairs were designed from the genomic DNA sequences of two cultivars, either Q124 or R-57030. Unlike some consensus primers that are able to prime the PCR amplification of plant genomic sequences36, these SSR primer pairs may not be able to amplify Erianthus genomic DNA at equivalent efficiency as they do to the Saccharum genomes. Another reason is that it is now generally accepted that Noble cultivars might directly emerge from S. robustum. It also has hypothesized that S. robustum be evolved from complex introgressions between S. spontaneum and other genera, particularly Erianthus and Miscanthus sharing close genetic affiliation37,38. The genetic diversity results from our study were in general conformity with the evolutionary course of the sugarcane cultivars in that the order of contributing species in today’s accessions is S. officinarum, S. spontaneum, S. robustum, S. barberi, S. sinense, E. arundinaceus and Saccharum spp. hybrids. PCA analysis also revealed a similar pattern of phylogeny to some extent.

Today, China holds more than 2,000 accessions of Saccharum and Erianthus, among which some are wild types. These accessions are either China-born or through foreign introductions. As the size of sugarcane germplasm grows, the genetic information among accessions becomes more critical for maintaining and utilization strategies designed to establish cross parentages in China’s breeding programs. We conclude that the estimation of genetic diversity and population structure of 115 accessions of Saccharum and Erianthus genera using SSR primer pairs may provide more accurate information to sugarcane breeders than the classical pedigree method. The 21 SSR primer pairs used in our study may also be of potential value for further research on genetic mapping, segregation analysis, marker-assisted selections, QTL mapping and gene tagging in sugarcane. In addition, further study with consensus PCR primers may be needed to assess the phylogenetic status of the Erianthus genus within the “Saccharum Complex”38.

Materials and Methods

Plant materials

One hundred and fifteen asseccions were used in this study, including 12 accessions from S. officinarum, 22 from S. spontaneum, 14 from S. robustum, 17 from S. barberi, 14 from S. sinense, 30 from Saccharum spp. hybrids, and six from E. arundinaceus. The leaf samples of all the clones were collected either from the Sugarcane Germplasm Nursery in Yacheng, Hainan, China or a local collection at the USDA-ARS, Sugarcane Research Unit, Houma, Louisiana, USA (Table 4). The leaf samples were collected, wiped off with 75% ethanol, and kept at −80 °C until DNA extraction.

Table 4.

A list of 115 accessions from Saccharum, Erianthus, and Saccharum spp. hybrids.

No. Accessions name Sample no. Species No. Accessions name Sample no. Species
1 48Mouna Soff01 S. officinarum 59 Djatiroto Sspo02 S. spontaneum
2 Badila Soff02 S. officinarum 60 Fujian 79-I-1 Sspo03 S. spontaneum
3 Bandjermasin Hitam Soff03 S. officinarum 61 Guangdong 29 Sspo04 S. spontaneum
4 Barwhspt Soff04 S. officinarum 62 Guangdong 51 Sspo05 S. spontaneum
5 EK02 Soff05 S. officinarum 63 IMP9068 Sspo06 S. spontaneum
6 Fiji1 Soff06 S. officinarum 64 IMP9089 Sspo07 S. spontaneum
7 IN84-068B Soff07 S. officinarum 65 IND81-080 Sspo08 S. spontaneum
8 LA Purple Soff08 S. officinarum 66 Mol1032A Sspo09 S. spontaneum
9 Muntok Java Soff09 S. officinarum 67 Mpth97-107 Sspo10 S. spontaneum
10 NG21-003 Soff10 S. officinarum 68 Mpth97-233 Sspo11 S. spontaneum
11 NG57-223 Soff11 S. officinarum 69 PCANOR84-2A Sspo12 S. spontaneum
12 Striped Cheribon Soff12 S. officinarum 70 PCAV84-12A Sspo13 S. spontaneum
13 51NG208 Srob01 S. robustum 71 PQ84-3 Sspo14 S. spontaneum
14 51NG63 Srob02 S. robustum 72 S66-084A Sspo15 S. spontaneum
15 IJ76-339 Srob03 S. robustum 73 S66-121A Sspo16 S. spontaneum
16 IN84-045 Srob04 S. robustum 74 SES323A Sspo17 S. spontaneum
17 IN84-076 Srob05 S. robustum 75 SPONT24 Sspo18 S. spontaneum
18 M3035-66 Srob06 S. robustum 76 SPONT37 Sspo19 S. spontaneum
19 NG28-289 Srob07 S. robustum 77 Yacheng 11 Sspo20 S. spontaneum
20 NG57-055 Srob08 S. robustum 78 Yacheng 12 Sspo21 S. spontaneum
21 NG77-004 Srob09 S. robustum 79 Yunnan 82-114 Sspo22 S. spontaneum
22 NG77-1 Srob10 S. robustum 80 Fijian 87-II-5 Earu01 E. arundinaceus
23 NG77-159 Srob11 S. robustum 81 Guangxi 83-27 Earu02 E. arundinaceus
24 NG77-235 Srob12 S. robustum 82 Hainan 92-79 Earu03 E. arundinaceus
25 NG77-75 Srob13 S. robustum 83 Hainan 92-105 Earu04 E. arundinaceus
26 Teboe Salak Toewa Srob14 S. robustum 84 Guizhou 78-I-24 Earu05 E. arundinaceus
27 Agoule Sbar01 S. barberi 85 Sichuan 79-I-13 Earu06 E. arundinaceus
28 Chunnee Sbar02 S. barberi 86 HoCP01-517 Sspp01 S. spp. hybrids
29 Dhaula Sbar03 S. barberi 87 HoCP85-845 Sspp02 S. spp. hybrids
30 Hatuni Sbar04 S. barberi 88 HoCP91-555 Sspp03 S. spp. hybrids
31 HulluKabbu Sbar05 S. barberi 89 HoCP96-540 Sspp04 S. spp. hybrids
32 Kacai Sbar06 S. barberi 90 L01-283 Sspp05 S. spp. hybrids
33 Keari Sbar07 S. barberi 91 L01-299 Sspp06 S. spp. hybrids
34 Khagzi Sbar08 S. barberi 92 L97-128 Sspp07 S. spp. hybrids
35 Mungo Sbar09 S. barberi 93 L99-233 Sspp08 S. spp. hybrids
36 Nagans Sbar10 S. barberi 94 LCP85-384 Sspp09 S. spp. hybrids
37 NEWRA Sbar11 S. barberi 95 MEX85-6196 Sspp10 S. spp. hybrids
38 Pansahi Sbar12 S. barberi 96 TCP93-4245 Sspp11 S. spp. hybrids
39 Pathri Sbar13 S. barberi 97 TCP97-4442 Sspp12 S. spp. hybrids
40 Rounda Sbar14 S. barberi 98 TCP98-4445 Sspp13 S. spp. hybrids
41 Ruckri Sbar15 S. barberi 99 TCP98-4447 Sspp14 S. spp. hybrids
42 Sewari Sbar16 S. barberi 100 US01-40 Sspp15 S. spp. hybrids
43 Sunnabile Sbar17 S. barberi 101 US02-99 Sspp16 S. spp. hybrids
44 Binchuanxiaozhe Ssin01 S. sinense 102 Q124 Sspp17 S. spp. hybrids
45 ChukChe Ssin02 S. sinense 103 R570 Sspp18 S. spp. hybrids
46 Guangdongzhuzhe Ssin03 S. sinense 104 ROC10 Sspp19 S. spp. hybrids
47 Guangxizhuzhe Ssin04 S. sinense 105 ROC16 Sspp20 S. spp. hybrids
48 Merehi Ssin05 S. sinense 106 ROC20 Sspp21 S. spp. hybrids
49 MiaLan Ssin06 S. sinense 107 ROC22 Sspp22 S. spp. hybrids
50 Nepal3 Ssin07 S. sinense 108 ROC25 Sspp23 S. spp. hybrids
51 TanzhonBamboo Ssin08 S. sinense 109 ROC27 Sspp24 S. spp. hybrids
52 Tanzhouzhuzhe Ssin09 S. sinense 110 FN41 Sspp25 S. spp. hybrids
53 TekchaOkinawa Ssin10 S. sinense 111 GT40 Sspp26 S. spp. hybrids
54 UbaDelNatal Ssin11 S. sinense 112 MT01-77 Sspp27 S. spp. hybrids
55 UbaIndia Ssin12 S. sinense 113 LC05-136 Sspp28 S. spp. hybrids
56 UbaNaquin Ssin13 S. sinense 114 YT00-236 Sspp29 S. spp. hybrids
57 Wenshanzhuzhe Ssin14 S. sinense 115 YZ05-51 Sspp30 S. spp. hybrids
58 Coimbatore Sspo01 S. spontaneum
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DNA extraction

Genomic DNA was extracted from leaf tissues using a modified cetyl tri-methyl ammonium bromide (CTAB) method39 as previously described by Ahmad et al.7. The quality and concentration of DNA were measured using UV absorbance assay with a Synergy™ H1 Multi-Mode Reader (BioTek, Winooski, VT, USA) and 0.8% agarose gel electrophoresis with ethidium bromide staining.

SSR markers and SSR reactions

The 21 polymorphic SSR primer pairs from Pan30 were used in this study based on their high PIC values of greater than 0.787,40,41. All forward primers were labeled with the fluorescence dye, 6-carboxy-fluorescein (FAM). Serials of PCR-cycling conditions were performed to detect the SSR DNA fingerprints7,30. The PCR products for the capillary electrophoresis (CE) were conducted on ABI 3730XL DNA Analyzer (Applied Biosystems Inc., Foster City, CA, USA) following the manufacturer’s instructions to generate GeneScan files.

Marker scoring

The GeneScan files were analyzed with the GeneMarker™ software (version 1.80) (SoftGenetics LLC®, State College, PA, USA, www.softgenetics.com) to reveal capillary electrophoregrams of PCR amplified SSR-DNA fragments. Fragment sizes were computed automatically against the GS500 DNA size standards (Applied Biosystems, Inc., Foster City, CA, USA). SSR alleles were manually assigned to unique, true “Plus-adenine” DNA fingerprints that gave quantifiable fluorescence values. Irregular peaks and stutters peaks were not scored according to Pan et al.41. Data were scored manually in a binary format into a data matrix file, with the presence of a band scored as “1” or “A” and its absence scored as “0” or “C”. The polymorphism information content (PIC) values were calculated using the formula of Liu et al.23.

PIC=1−∑J=1nPij2

Where Pij is the frequency of jth allele for ith locus and summation extends over n alleles.

Data analysis

The allelic data matrix of “1” or “0” was used to calculate the population genetic analysis using POPGENE version 1.3242, including number of observed alleles (Na), and number of effective alleles (Ne). Nei’s genetic diversity (h), polymorphism index (PI) and Shannon’s index (I) were computed for each Saccharum and Erianthus populations based on the obtained allele frequencies. The allelic data matrix of “A” or “C” was used to perform phylogenetic analysis. Phylogenetic tree was constructed with MEGA 6 using UPGMA statistical method with substitution model of Maximum Composite Likelihood43. Robustness of the node of the phylogenetic tree was assessed from 1000 bootstrap replicates. To find out the core-primer pairs of 21 SSR primer pairs, two other phylogenetic trees were constructed using SSR data from six or seven highly polymorphic SSR primer pairs. Then, the three phylogenetic tree files were calculated and Robinson-Foulds distances of 21 SSR vs 7 SSR and 21 SSR vs 6 SSR determined with Phangorn Package44 and cophenetic correlation coefficients of the topological distance were analyzed with Dendextend45. To better view the comparison between trees, Dendextend were used to plot two trees with tanglegrams. Genetic identity matrix was calculated using BioEdit Sequence Alignment Editor Version 7.1.946. Genetic similarity coefficients among Saccharum and Erianthus populations were estimated with the SIMQUAL subprogram using the Jaccard’s coefficient, followed by principal component analysis (PCA) with the DICE subprogram as implemented in NTSYS-pc version 2.10e47.

Acknowledgements

This work was supported by Sugar Crop Research System, CARS (No. CARS-170302) and the Major Science and Technology Project of Fujian Province, China (No. 2015NZ0002-2).

Author Contributions

San-Ji Gao conceived the project and designed the experiments. Ali Ahmad performed the experiments, analyzed the data, and drafted the manuscript. Yong-Bao Pan collected the leaf samples, extracted the DNA in Louisiana, USA, interpreted SSR data, and critically revised the manuscript. Qin-Nan Wang collected the leaf samples from the Sugarcane Germplasm Nursery in Hainan, China and drafted the manuscript. Jin-Da Wang and Jun-Lü Chen participated in processing of SSR data and revision of the manuscript. All authors read and approved the final manuscript.

Competing Interests

The authors declare no competing interests.

Footnotes

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Ahmad Ali, Yong-Bao Pan and Qin-Nan Wang contributed equally.

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