Table 2.
Evaluation of the amplification efficiency and polymorphic potential of 47 fluorescent dye labeled primers
| Polymorphic potential | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sl. No. | Unigene Accession IDs' | Class I UGMS primersA |
Repeat-motifs | Location | Forward primer sequences (5'-3') | Reverse primer sequences (5'-3') | Putative functions | Actual annealing temperature (°C) | No. of locus | Total no. of alleles amplified | Size (bp) of allele (s) amplified | Type of allele size distribution | No. of heterozygous loci | Among sugarcane species and genera | Among sugarcane varieties | |
| P/MB | PIC | |||||||||||||||
| 1 | CA297715 | UGSuM2a | (AT)43 | CDS | CTGTGTATATGTTCGTAGTTTG | CACTTAGTCACACTCTCACACAC | Sucrose phosphate synthase | 55 | 2 | 20 | 206-302 | Step-wise | 1 | P | P | 0.86 |
| UGSuM2b | 4 | 481-512 | Mixed | |||||||||||||
| 2 | CA278792 | UGSuM5 | (TA)28 | CDS | TCACATCCATCATCCACAGC | TCCAATGCAAGCAAACTCAC | Maize-Cyclin III | 55 | 1 | 23 | 80-170 | Step-wise | 0 | P | P | 0.84 |
| 3 | AY596609 | UGSuM11 | (TA)21 | 3'UTRs | TGGTAACCCTAGGCAGGTGA | GTGCACCAGATTTGGATGGT | Fructose-bisphosphate aldolase | 56 | 1 | 23 | 92-190 | Step-wise | 0 | P | P | 0.83 |
| 4 | CA279221 | UGSuM15a | (CCTCGC)6 | CDS | GTTTAAGACAAGATGGTGTAGATG | TACATATTTACATTGTTACTCCGC | Hypothetical protein | 56 | 2 | 17 | 170-247 | Mixed | 1 | P | P | 0.80 |
| UGSuM15b | 3 | 360-378 | Step-wise | |||||||||||||
| 5 | CA278282 | UGSuM16 | (AT)18 | CDS | GCGTCTTCATCATCTGCAAC | GCGTCTTCATCATCTGCAAC | Pathogenesis-related PRMS protein | 55 | 1 | 22 | 150-244 | Step-wise | 0 | P | P | 0.82 |
| 6 | CA253277 | UGSuM17 | (AG)18 | CDS | TTTCCATTCTTCCATTCAACTG | GGCAGGCTGAGAGACTGTTC | Abcisic acid-protein kinase | 55 | 1 | 10 | 90-188 | Step-wise | 1 | P | P | 0.78 |
| 7 | CA227482 | UGSuM18a | (GA)18 | CDS | GGCGAGAGAGAGAGAGAGAGAG | AGGTGGAGATCTTGAGGTAGGC | Glycine decarboxylase | 56 | 2 | 20 | 96-193 | Mixed | 1 | P | P | 0.81 |
| UGSuM18b | 2 | 326-348 | Step-wise | |||||||||||||
| 8 | CA126180 | UGSuM20a | (TCA)12 | CDS | ATCCCTTATGCTACAGAAATGT | TTAGCCTAGAGGTTTGATTGAT | Acetyl-CoA synthetase | 54 | 2 | 16 | 190-259 | Step-wise | 1 | P | P | 0.83 |
| UGSuM20b | 4 | 392-428 | Step-wise | |||||||||||||
| 9 | CA177414 | UGSuM21 | (AGGA)9 | CDS | CGCTCCCTCACCGTCATT | CTCCGCATCCTCGTCACC | Transcription regulator protein | 62 | 1 | 20 | 160-252 | Step-wise | 0 | P | P | 0.81 |
| 10 | CA223153 | UGSuM22a | (GCG)12 | 3'UTRs | CTCCCTCCTCCTCCCGTTG | CTCTTGGGTGTGAACCAG | Polyadenylate-binding protein | 64 | 2 | 19 | 96-187 | Mixed | 1 | P | P | 0.85 |
| UGSuM22b | 3 | 322-358 | Step-wise | |||||||||||||
| 11 | CA122659A | UGSuM24a | (TTTTC)7 | 5'UTRs | CTGTACAACAGCAATTATGAATCT | CTCGACTACGAGAGGATATGAT | Hypothetical protein | 55 | 3 | 12 | 240-294 | Mixed | 1 | P | P | 0.86 |
| UGSuM24b | 4 | 398-428 | Step-wise | |||||||||||||
| UGSuM24c | 5 | 531-571 | Step-wise | |||||||||||||
| 12 | BU103692A | UGSuM26 | (CT)17 | 5'UTRs | CTCGATCCCAGAGAGCTCCACAG | AGTACCGAATTCATTAAACTCCT | Beta-amylase | 55 | 1 | 21 | 250-346 | Step-wise | 0 | P | P | 0.85 |
| 13 | CA073284 | UGSuM27a | (GGC)11 | CDS | CTGCAGTACGGTCCGGAATC | GTACCACCATGGCTCTAGCTTC | 30 S ribosomal protein S16 | 60 | 2 | 2 | 50-54 | Mixed | 1 | P | P | 0.84 |
| UGSuM27b | 22 | 154-288 | Mixed | |||||||||||||
| 14 | AY596606 | UGSuM33a | (AGC)10 | CDS | CGAGGCACTGAACCCATATC | TGTTTGAACTGGATGGCGTA | Hypothetical protein | 58 | 3 | 17 | 92-189 | Mixed | 1 | P | P | 0.84 |
| UGSuM33b | 2 | 293-305 | Step-wise | |||||||||||||
| UGSuM33c | 2 | 431-491 | Step-wise | |||||||||||||
| 15 | CA268640 | UGSuM34a | (AAG)10 | CDS | TTACAAATGTAGCCTTGCCTTG | ATCTTTCCTTGCTTGCCTCTC | Soluble acid invertase | 61 | 2 | 19 | 99-178 | Mixed | 1 | P | P | 0.83 |
| UGSuM34b | 4 | 333-351 | Step-wise | |||||||||||||
| 16 | CA131350 | UGSuM41 | (CCG)10 | CDS | ATCATTCTCCATCATTTCTCA | AGGCTCTTCAACCGTGCT | Unknown protein | 54 | 1 | 20 | 120-210 | Step-wise | 0 | P | P | 0.80 |
| 17 | CA133924 | UGSuM42a | (CTCTCC)5 | 5'UTRs | TTCATACAGAAGAACCTCCAC | TCCATCAGAGACAAGCAGA | Auxin-independent growth promoter | 54 | 3 | 12 | 130-212 | Mixed | 1 | P | P | 0.83 |
| UGSuM42b | 8 | 325-367 | Step-wise | |||||||||||||
| UGSuM42c | 2 | 475-487 | Step-wise | |||||||||||||
| 18 | CA136599 | UGSuM43a | (CCG)10 | 3'UTRs | CAAAGTGCTGTAGGGCTG | TTCAATGGGTGATAAGTGTGT | Ribose-phosphate pyrophosphokinase 1 | 55 | 2 | 17 | 90-187 | Mixed | 1 | P | P | 0.85 |
| UGSuM43b | 2 | 332-368 | Step-wise | |||||||||||||
| 19 | CA139800 | UGSuM44a | (CT)15 | 5'UTRs | TCCATCAAGCCGTTCCTC | GCCAAGCAGATAAAGAAGTG | Rudimentary enhancer | 55 | 2 | 16 | 220-308 | Step-wise | 1 | P | P | 0.84 |
| UGSuM44b | 1 | 419 | - | |||||||||||||
| 20 | CA171090 | UGSuM45a | (AAAAG)6 | CDS | ATCTCCTCTTATTCGTTCTGG | AGCAGCGTCTTATCTGGG | PAP fibrillin | 56 | 3 | 5 | 91-141 | Step-wise | 1 | P | P | 0.79 |
| UGSuM45b | 2 | 267-287 | Step-wise | |||||||||||||
| UGSuM45c | 2 | 368-393 | Step-wise | |||||||||||||
| 21 | CA196477 | UGSuM46a | (GAC)10 | CDS | ACTCCTCCCGCCTCCACTAC | CTCACCGAAGCAATCAAG | Hypothetical protein | 60 | 2 | 15 | 101-188 | Mixed | 1 | P | P | 0.81 |
| UGSuM46b | 3 | 341-377 | Step-wise | |||||||||||||
| 22 | CA228772 | UGSuM47a | (GCC)10 | CDS | ATTTATGGAGGAAGAAACGG | ATTACAAACAAGAAGAGCGG | Transport protein particle component | 55 | 2 | 3 | 82-97 | Step-wise | 1 | P | P | 0.80 |
| UGSuM47b | 14 | 215-270 | Mixed | |||||||||||||
| 23 | CA161416 | UGSuM50 | (TC)14 | CDS | CTACTGCCGAGGAAAGATCG | GGAAAAGTTTGTGGCAAGGA | Hypothetical protein | 58 | 1 | 16 | 94-188 | Step-wise | 0 | P | P | 0.80 |
| 24 | CA228375 | UGSuM73a | (CGC)8 | 5'UTRs | CTTTCAACCTCTACACCTCCAC | ACTAGAAGACTGAGAAGAACCAGT | 40 S ribosomal protein S11 | 55 | 2 | 13 | 101-186 | Mixed | 1 | P | P | 0.82 |
| UGSuM73b | 5 | 354-375 | Step-wise | |||||||||||||
| 25 | CA261182 | UGSuM74 | (ACA)8 | CDS | TCAGCAGCTGTGAAGTTTCATT | CGTCTCTTTTGGGTTTCATCTC | Transcription regulator protein | 55 | 1 | 18 | 190-271 | Step-wise | 0 | P | P | 0.81 |
| 26 | CA219230 | UGSuM75a | (TA)12 | CDS | TTGTGCTGATGTTTCCTGCT | CAAGAGAAGATGCCATTAGCC | Patatin-like protein | 55 | 2 | 13 | 94-176 | Step-wise | 1 | P | P | 0.83 |
| UGSuM75b | 4 | 333-351 | Step-wise | |||||||||||||
| 27 | CA093071 | UGSuM96a | (AT)11 | CDS | TCAAACCAGGATCTAAGCTCAC | GGTAGTGCCATTGAGGTTGC | Putative apyrase | 57 | 2 | 11 | 205-290 | Mixed | 1 | P | P | 0.81 |
| UGSuM96b | 5 | 408-458 | Step-wise | |||||||||||||
| 28 | CA229840 | UGSuM97a | (GA)11 | 5'UTRs | GCGAGAGAGATAGAGGGAGAGA | AGGTGCCGTTCATGAGGTAGT | Glycine decarboxylase | 56 | 2 | 19 | 240-334 | Step-wise | 1 | P | P | 0.85 |
| UGSuM97b | 2 | 453-469 | Step-wise | |||||||||||||
| 29 | CA112979 | UGSuM149a | (AGC)7 | CDS | GTTCAATCAAATCCCTCTCCTC | AGCTTGGTCAGCTCCTCATCGTT | Ubiquitin-specific protease 4 (UBP4) | 60 | 2 | 4 | 104-141 | Mixed | 0 | P | P | 0.78 |
| UGSuM149b | 3 | 276-297 | Step-wise | |||||||||||||
| 30 | CA116368 | UGSuM150a | (GGC)7 | CDS | ACACTGACCGATGGATCCTCTT | ATCAACGTGGACCAGATCTTCTT | hAT family dimerisation domain protein | 60 | 2 | 12 | 90-167 | Mixed | 1 | P | P | 0.76 |
| UGSuM150b | 2 | 279-291 | Step-wise | |||||||||||||
| 31 | CA280782 | UGSuM177a | (TGC)7 | CDS | GGTGCTGTCCCTATCACTAC | GCCCTTGTTTCTTTGTCTACT | Hypothetical protein | 55 | 2 | 3 | 150-167 | Mixed | 0 | P | P | 0.79 |
| UGSuM177b | 3 | 287-314 | Step-wise | |||||||||||||
| 32 | CA291445 | UGSuM178 | (GAC)7 | 5'UTRs | GGACTACTACGACTACTGCGA | ACCTTGCTTACATCTTCCTCT | O-diphenol-O-methyl transferase | 54 | 1 | 15 | 100-196 | Step-wise | 0 | P | P | 0.80 |
| 33 | CA244023 | UGSuM186 | (AG)10 | CDS | AACATTTCGGCATTTGAAGC | GGTCTTTCTTGGGGATCTCTC | Ubiquitin C-terminal hydrolase | 56 | 1 | 4 | 190-232 | Step-wise | 0 | P | M | 0.73 |
| 34 | CA231668 | UGSuM187a | (CT)10 | CDS | CAACAATTGTCGAAGCCTCTC | TTTGCTTACCCCCTGTTGAC | ATP synthase | 58 | 2 | 10 | 200-264 | Step-wise | 0 | P | M | 0.83 |
| UGSuM187b | 6 | 376-418 | Step-wise | |||||||||||||
| 35 | AY596560 | UGSuM188 | (GA)10 | 3'UTRs | CCCAAGCGAGCTAGAGAGAG | TCTTCTTTCCTTCGCACAGC | Hypothetical protein | 55 | 1 | 19 | 95-186 | Mixed | 0 | P | P | 0.81 |
| 36 | CA241232 | UGSuM189a | (CT)10 | CDS | CCGCGACTCTCCTCTCTCT | GTTCTTCTCGGCGTTCCTC | Auxin-regulated protein | 55 | 2 | 15 | 106-200 | Step-wise | 1 | P | P | 0.80 |
| UGSuM189b | 3 | 345-377 | Step-wise | |||||||||||||
| 37 | CA133642 | UGSuM196a | (AAAG)5 | 5'UTRs | GCTACTATGGACAACAGGG | ATGAAGAGACGAGACGAAGA | Cinnamoyl CoA reductase | 54 | 2 | 18 | 90-181 | Mixed | 1 | P | P | 0.81 |
| UGSuM196b | 2 | 373-393 | Step-wise | |||||||||||||
| 38 | CA134472 | UGSuM197 | (GA)10 | 3'UTRs | GAAGGAGCAGCAGCGCCAGT | GATTTGCCGTCCTAGGGTTT | Epsin N-terminal homology domain | 56 | 1 | 22 | 200-290 | Step-wise | 0 | P | P | 0.84 |
| 39 | CA297648 | UGSuM343a | (CAG)6 | 5'UTRs | ACTCCTCCTCCTCGCCGT | TCTTGTTGTAGTAGCCCTTGT | SOUL heme-binding family protein | 62 | 2 | 17 | 250-320 | Mixed | 1 | P | M | 0.87 |
| UGSuM343b | 3 | 438-450 | Step-wise | |||||||||||||
| 40 | CA300679 | UGSuM344 | (CTC)6 | CDS | CTATCCTCTTGTTGGGTCCT | TCCGCACCTCCGTTCACC | Nucleoside diphosphate kinase protein | 55 | 1 | 1 | 260 | Step-wise | 0 | M | M | 0.0 |
| 41 | CA084691 | UGSuM345 | (TC)8 | CDS | TATACAAGAATGAAAGGTGAGAGA | AAGCATACTCCCTCTATCTCTATG | DC1 domain-containing protein | 55 | 1 | 2 | 210-220 | Step-wise | 0 | M | P | 0.70 |
| 42 | CA093455 | UGSuM346 | (AG)8 | CDS | TATACGTAGTAGTGATGATGACCG | CTCCTTCGTCCAGTACCAGTAG | DNA-binding protein DF1 | 60 | 1 | 4 | 150-180 | Step-wise | 1 | P | M | 0.71 |
| 43 | CA110745 | UGSuM347a | (CT)8 | 5'UTRs | TCTGGCTTTATCGTAACTTGTAT | GAGCCTCGTTTGGGTGGCTTTC | Expressed protein | 55 | 2 | 5 | 230-254 | Step-wise | 1 | P | M | 0.74 |
| UGSuM347b | 1 | 365 | - | |||||||||||||
| 44 | CA112979 | UGSuM348 | (CG)8 | CDS | CTACCTCCTCGTCTCCTCCCTCTT | AACAAGGAATATGGTCCCTGAG | Unknown protein | 61 | 1 | 2 | 240-261 | Mixed | 0 | M | M | 0.0 |
| 45 | CA116458 | UGSuM349a | (TC)8 | CDS | CAAGATGTACCCGGACATGGCT | TGCTATACTAGCTATCTCCTTCCT | Unknown protein | 55 | 2 | 3 | 220-236 | Step-wise | 0 | P | M | 0.73 |
| UGSuM349b | 2 | 385-395 | Step-wise | |||||||||||||
| 46 | CA123971 | UGSuM464 | (ACA)5 | 5'UTRs | GGCTACTTCAGACACGCA | TCTACGCATCAACCTCTCA | SNF2-domain-containing protein | 55 | 1 | 1 | 220-232 | Step-wise | 0 | M | M | 0.0 |
| 47 | CA125310 | UGSuM465 | (GCA)5 | CDS | GCTAACCAACATCAGCAGT | AGGAGATTGACGAAGAAGAAG | Transducin family protein | 53 | 1 | 2 | 260-279 | Mixed | 0 | M | M | 0.0 |
AUGSuM stands for unigene derived sugarcane microsatellite primers as indicated in the Additional file 3
BPolymorphic (P) and Monomorphic (M)