Skip to main content
Have a personal or library account? Click to login
Diversity analysis and cross-species amplification of custard apple (Annona squamosa) using simple sequence repeats developed via next-generation sequencing technology Cover

Diversity analysis and cross-species amplification of custard apple (Annona squamosa) using simple sequence repeats developed via next-generation sequencing technology

Open Access
|Jul 2025

Figures & Tables

Table 1.

Distribution of microsatellite types in A. squamosa genome.

Motif typesNumber of SSRsFrequency (%)
Mono-nucleotide10065856.20
Di-nucleotide4649325.96
Tri-nucleotide155908.70
Tetra-nucleotide22661.26
Penta-nucleotide4950.27
Hexa-nucleotide2020.11
Compound nucleotide133767.4
Total179080

1 SSR, simple sequence repeat.

Table 2.

Genetic analysis of SSR primers data using. A. squamosa genotypes.

LocusForward sequence and reverse sequence 5′–3′Repeat motif*Tm (°C)No. of alleles per locus (k)HoHePICPI
ASIIHR01 F
ASIIHR01 R
ACATGCCCTCAATCATCTCC
AGTTAAAAATTAATGAATGAGCCAGG
(TA)655230.500.930.910.0103
ASIIHR02 F
ASIIHR02 R
CTGAATTCTAACAGATGTGCTGGG
GCTTTGGACGTCTACGCAT
(TA)860200.600.910.900.0150
ASIIHR03 F
ASIIHR03 R
TCAGACTTCAACTCAAGTCGATCC
TAATACCCAAGTCATGAAGACCAA
(AT)855250.620.930.910.0114
ASIIHR04 F
ASIIHR04 R
ACTCGTACTGCTATAAAAGTGGGT
ATGAGAGCTGCCCACGAC
(AT)755370.650.970.950.0032
ASIIHR05 F
ASIIHR05 R
AAAACTGTCGGCTTCCATGT
AGA AC C A AC AC AGC TTC C ATT
(TA)655200.800.840.820.0364
ASIIHR06 F
ASIIHR06 R
CTTCTGTTGTCATCACTCGCA
CACGATAGAAATCGAAGAACAGA
(TA)655220.520.900.880.0186
ASIIHR07 F
ASIIHR07 R
AAATATCAAGTTTAAAGCAGTATTTGC
TACAAGCGGGACATAGAAGC
(TA)655300.970.950.930.0064
ASIIHR08 F
ASIIHR08 R
GATAGGAAGACAAACAGTTAGTTTAGG
CGGCAGCTTTCTTCTTGTTC
(AG)655280.920.910.900.0143
ASIIHR09 F
ASIIHR09 R
CCAAGAAATCTCACGTTCGC
TCTTTCTTTAGCAAGTAGTGGTTTTT
(AG)1360300.820.950.930.0065
ASIIHR10 F
ASIIHR10 R
TGTGGGTTTATATTGACCATCATT
GTGGAGCTAGGGTTCTTCGTC
(GA)860310.970.930.940.0057
ASIIHR11 F
ASIIHR11 R
ACGCTTTTCTTCTCCGGC
CTCGCCTGCTCCTCTCAC
(GA)955260.520.950.910.0110
ASIIHR12 F
ASIIHR12 R
GCTTTGAGAGAAAATGAGAGACAA
CTACCTTTCCGGCGAATCC
(AG)1155300.920.910.930.0065
ASIIHR13 F
ASIIHR13 R
GATATTCAAAGAGCACGAGAGGA
AAAAGTTAGTCGGCAAATCCC
(GA)655330.700.880.890.0147
ASIIHR14 F
ASIIHR14 R
GTGAGAGAGAGAGAAGGAAGGC
GCGAATCTCTCTTCCGACAG
(GA)1055190.700.930.850.0284
ASIIHR15 F
ASIIHR15 R
TTTTCTCTTTTCTTCGTTCTTGC
GAGGGGGCTGGTGACCTAT
(GA)1260250.820.920.910.0107
ASIIHR16 F
ASIIHR16 R
CCTAATCGGAAAGGTGCAAA
TGGCTTTATTGGATGTGTTTGA
(AC)755230.700.850.910.0126
ASIIHR17 F
ASIIHR17 R
GCTAAGACGGGGCCAACC
TGCCTTATTTCTTTAAACAGGGTC
(AC)660160.750.870.830.0388
ASIIHR18 F
ASIIHR18 R
CTCTCTCTTGTGCTTCTCCCA
CTTTCTCTCTCTCCCCCTCC
(AC)655180.820.970.840.0338
ASIIHR19 F
ASIIHR19 R
TGACGAGATCGAATTAAGTACCC
TGATGCCTATAAAAGGGGCA
(CA)860460.920.940.960.0022
ASIIHR21 F
ASIIHR21 R
ACCAGCAAATCCTGGGAAG
TGAATCTGCAACTCAAAACTGA
(AC)655291.000.780.930.0076
ASIIHR21 F
ASIIHR21 R
TTGATGCAATTCTTCAGTTTGA
TACAAGGGTTGGGAATTTGG
(AC)855160.920.920.740.0758
ASIIHR22 F
ASIIHR22 R
CATACATTTTGCCCACGACC
CACAGATACACACACACGAACAA
(GT)860250.770.950.900.0132
ASIIHR23 F
ASIIHR23 R
AAAAAGTCCATTCTTTTTCTCCA
TCATTTCTTCATCCCATTGC
(GT)655280.920.940.930.0066
ASIIHR24 F
ASIIHR24 R
CACATCACCCATATAAAAAGCG
GTTGGGACAACTCTTCACCC
(TG)660350.820.930.930.0065
ASIIHR25 F
ASIIHR25 R
CAGCGATGGTTGCTTAATTTG
AGTAGGTGGAGAGACCCACG
(GT)655250.770.930.920.0099
ASIIHR26 F
ASIIHR26 R
AGCAAAAGTGGTCATCCGAA
TTTTAGATCGCTAAGAAGATCACA
(TG)1360300.800.960.910.0102
ASIIHR27 F
ASIIHR27 R
TCGCTATTTCAAAATTAAGTAAAAGAA
TGTTTTAGTTGAGCAAGGCTAGG
(TG)855370.820.960.950.0044
ASIIHR28 F
ASIIHR28 R
TCTTGTTTTTGCCAGTTCCC
GCTTGAACTCAAAGCATGTTG
(GT)860340.870.870.950.0038
ASIIHR29 F
ASIIHR29 R
TGTTACTGTTGGGCATGGAA
GGTTGGGTTGAAAATTTAAGCA
(GT)655230.670.950.850.0263
ASIIHR30 F
ASIIHR30 R
CCTTCCACCCTTGGATCTTA
GATCAATGTGGATAAAACTTCGC
(CT)655330.820.970.940.0058
ASIIHR31 F
ASIIHR31 R
CTTTTCTTCTCCATTTTCCCG
CGTTGGAGATTCCAAGAGAAA
(CT)855440.950.950.950.0031
ASIIHR32 F
ASIIHR32 R
AGGTGGATCGCTTAAGATGAA
TCTGAGCAGGTGTGTAGTCCT
(TC)655290.800.920.930.0069
ASIIHR33 F
ASIIHR33 R
ACTGGCCGAGGAAAGGGT
GAGAGGGAGGAAAAAGTTAATCG
(TC)1255280.970.970.910.0117
ASIIHR34 F
ASIIHR34 R
CTCCCCGTTACCCAACTG
GGTTCCTTCCGTCCTCCTG
(CT)955350.720.960.950.0034
ASIIHR35 F
ASIIHR35 R
TTTC ATAGC TTTTATTGC TTTCTTAG
AGTCGGGTCGAATCCACA
(GA)855400.850.960.950.0036
ASIIHR36 F
ASIIHR36 R
CTTCTGTCTTCCTCATTTTCTCG
TGGGAGAGAAGTGAGAGAGC TT
(AG)860350.770.940.940.0047
ASIIHR37 F
ASIIHR37 R
GGCCACACTTGCTCAAAAAT
TTCTTATTGATGCGTAGCGG
(GC)755190.920.900.920.0090
ASIIHR38 F
ASIIHR38 R
GGGAGGAAACTTGATCCCTT
AAAATTATGGTGCAGTGGCG
(GC)660150.270.940.880.0196
ASIIHR39 F
ASIIHR39 R
GGCCACACTTGCTCAAAAAT
TTCTTATTGATGCGTAGCGG
(GC)755280.270.970.920.0087
ASIIHR40 F
ASIIHR40 R
CCAATCCCTTTATCCAAGCA
GTGCAATTTGAAAAGCAGCA
(GC)755350.270.930.960.0027
ASIIHR41 F
ASIIHR41 R
CATCTCCGCAACACCAGATA
GCCAGAAGAGGCAGTGATTC
(GC)855270.670.940.920.0092
ASIIHR42 F
ASIIHR42 R
AGAGGAAAACTTACAAAAACATAGACG
GCCCTAAGAGAGCAGTTTACCC
(ATG)655260.300.930.920.0089
ASIIHR43 F
ASIIHR43 R
GTATGTCATGGAGGATACAGGGA
CATCCTCATCATCTCCCACA
(GAA)555230.250.900.920.0091
ASIIHR44 F
ASIIHR44 R
ACTGCTGCTGAGATGTGCG
CTGCTGCTGCTGTTGACG
(GAT)755230.300.920.910.0112
ASIIHR45 F
ASIIHR45 R
TTATTGTATAAAACACCCCAAAGAA
TTCTTATCATTTTGCCCGTCT
(TTC)1060180.450.960.890.0183
ASIIHR46 F
ASIIHR46 R
TTGGCAACCATCAGAATAAGA
ACAACCCTGCTTCCATTCAA
(AAT)560170.350.940.900.0152
ASIIHR47 F
ASIIHR47 R
AAAAACCTTGGGCTTGTGC
CCTTGCCCCTATTATTTTCC
(TCT)655320.370.950.950.0037
ASIIHR48 F
ASIIHR48 R
TTGGTGAAGCATTCAAAAATTC
CCTTGCCCCTATTATTTTCC
(ATG)1055320.520.930.930.0072
ASIIHR49 F
ASIIHR49 R
TCAAACGCCCGCATATTTA
GCTGGAGAAAGACGGCAAG
(AGC)555260.400.940.930.0070
ASIIHR50 F
ASIIHR50 R
ACCTCAAAGCTAGGGGGTAAA
CCGAAGTAGAGATACGCCTCTT
(GAA)555260.350.930.920.0103
ASIIHR51 F
ASIIHR51 R
AAAATGAGCATGAAGAAAAGAAAAA
GATTGTAAGACAAATTGAGATGTAATG
(ATT)1055220.300.940.930.0081
ASIIHR52 F
ASIIHR52 R
TCCCATTTTCTGATCGAGTTG
TAACCCTCGCCGTGAATAG
(TCA)555230.420.930.920.0101
ASIIHR53 F
ASIIHR53 R
AGACTAATCTAAGTTTAAAGCAAGCAA
TGATC TTTGTTGAAGCGTCTCT
(AAG)555210.450.940.920.0090
ASIIHR54 F
ASIIHR54 R
TTCAAGAATCATCTTTTAAGTCAACC
TTTTCATGGAAACAACCAAATG
(GTG)555300.450.940.920.0079
ASIIHR55 F
ASIIHR55 R
TCACTTGGAATAATGTGGAACG
CAGTCCCCAGCTCCAAAC
(GTC)1155190.400.910.890.0181
ASIIHR56 F
ASIIHR56 R
CCCCAATCCCAATCCTTAGT
GGAGTTCGTGTGCTTTACCG
(AGC)555280.750.960.940.0047
ASIIHR57 F
ASIIHR57 R
GACGTGCTGCTG
GGATTCTTCACCAGGCAGTT
(CGA)555240.350.920.900.0134
ASIIHR58 F
ASIIHR58 R
AAAATGCATGCCTTGTTTGT
TAGTCCTTGAGCAACACATGC
(ATTC)760230.550.910.900.0146
ASIIHR59 F
ASIIHR59 R
AAGGGCATGTTGTCTTCTCAA
TTTGCAAGTTTATTTCTGCTCAA
(TTGT)660290.450.950.930.0070
ASIIHR60 F
ASIIHR60 R
TCCCGACCTTTCTTACGGAT
TTTATCTCTATCTCTCCACCGGA
(ATCTC)660220.670.870.850.0276
ASIIHR61 F
ASIIHR61 R
AATATGTTAACCCGAAACTCAACC
AATAATTACATAATTGATGAGGGTCAA
(TAGGGT)555160.600.950.780.0571
ASIIHR62 F
ASIIHR62 R
CTCTGTTTCTATCTCTCTCAAACTCA
GGAATGGGAGAGTATTTGAAGG
(TC)9tgtctctcatt(TC)655340.500.870.940.0058
ASIIHR63 F
ASIIHR63 R
TACCGGATCTCTCATTTTCG
GCTGGGAGAGTGAGCTGAAA
(TC)5cgccatttctatctct ctctccgtcattcct ctctctctttctctgttttccttt ggaaaaatcggca aacccaaat(TC)655240.620.810.900.0139
ASIIHR64 F
ASIIHR64 R
CATGTTGGACATGTGAGCCA
ATGCCTATTTTAGGCTGGGT
(A)10g(A)1055280.850.950.910.0101
ASIIHR65 F
ASIIHR65 R
GGCGTCCAAAAATTGAGATT
TTTGGGGAGTATCTACTCAGGC
(AT)7gtatttgccccatggg ccccaaaaaaaataaa(AT)7 ttttagactttcaa(AT)755310.670.920.920.0082
ASIIHR66 F
ASIIHR66 R
TCTACGCTACCCAGCAAATG
AATGACAATATGATTTGCCTTGA
(T)11(TA)6*55280.670.930.900.0128
ASIIHR67 F
ASIIHR67 R
CCGACTTCAACCTTCTGAGC
TCAATGGAATATTCACTTTTCTAGG
(A)11ttaaaacagattta tcaaaaatgttctta cgagaaagggaaaa taggagaaaaaggt agaatgagggttttc tttttgtgcgtgttttgga(AG)855270.600.940.910.0075
ASIIHR68 F
ASIIHR68 R
GTGGATACTCCCCGACTGG
TTCACATACTTTTGCCTGAGTAGA
(AAT)655260.550.950.920.0066
ASIIHR69 F
ASIIHR69R
TTCACATACTTTTGCCTGAGTAGA
GCCATCTTGGGCTTTTTAGA
(AT)6gacctcttcgctcaatccaagcctcaatgtc(A)1055210.670.920.900.0143
ASIIHR70F
ASIIHR70 R
GAAGGGAGATGCAAACGTTAAG
AACTGCTTGCTTTATGCACTTT
(A)11(T)1055270.600.920.910.0118

* Indicates the number of times a particular motif was repeated in the microsatellite locus. For example: (TA6 – means TA has been repeated six times in the sequence results analysed during SSR identification. He, expected heterozygosity; Ho, observed heterozygosity; PI, probability of identity; PIC, polymorphic information content; SSR, simple sequence repeat.

Figure 1.

Dendrogram analysis of A. squamosa genotypes using SSR markers data. SSR, simple sequence repeat.

Figure 2.

Structure analysis of Annona genotypes using SSR data.

Table 3.

Cross species amplification of 70 SSR loci derived from A. squamosa.

No.LocusA. cherimolaA. reticulataA. glabraA. muricataA. atemoya
1ASIIHR01AAAAA
2ASIIHR02AAAAA
3ASIIHR03AAAAA
4ASIIHR04AAAAA
5ASIIHR05AAAAA
6ASIIHR06AAAAA
7ASIIHR07NAANAANA
8ASIIHR08AAAAA
9ASIIHR09AAAAA
10ASIIHR10AAAAA
11ASIIHR11AAAAA
12ASIIHR12AAAAA
13ASIIHR13AAAAA
14ASIIHR14AAAAA
15ASIIHR15AAAAA
16ASIIHR16AAAAA
17ASIIHR17AAAAA
18ASIIHR18AAAAA
19ASIIHR19AAAAA
20ASIIHR20AAAAA
21ASIIHR21AAAAA
22ASIIHR22AAANANA
23ASIIHR23AAAAA
24ASIIHR24AAAAA
25ASIIHR25AAAAA
26ASIIHR26AAAAA
27ASIIHR27NAAAANA
28ASIIHR28AAAAA
29ASIIHR29AAAAA
30ASIIHR30AAAAA
31ASIIHR31AAAAA
32ASIIHR32AAAAA
33ASIIHR33AAAAA
34ASIIHR34AAAAA
35ASIIHR35AAAANA
36ASIIHR36AAAAA
37ASIIHR37AAAAA
38ASIIHR38AAAAA
39ASIIHR39AAAAA
40ASIIHR40AAAAA
41ASIIHR41AANAANA
42ASIIHR42AAAAA
43ASIIHR43AAAAA
44ASIIHR44AAAAA
45ASIIHR45AAAAA
46ASIIHR46AAAAA
47ASIIHR47AAAAA
48ASIIHR48AAAANA
49ASIIHR49AAAAA
50ASIIHR50AAAAA
51ASIIHR51NAAAAA
52ASIIHR52AAANANA
53ASIIHR53NAAAANA
54ASIIHR54AAAAA
55ASIIHR55AAAAA
56ASIIHR56AAAAA
57ASIIHR57AAAAA
58ASIIHR58ANAANANA
59ASIIHR59AAAAA
60ASIIHR60AAANANA
61ASIIHR61AAAAA
62ASIIHR62ANAANANA
63ASIIHR63AAAAA
64ASIIHR64AAAAA
65ASIIHR65AAANANA
66ASIIHR66AAAAA
67ASIIHR67AAAAA
68ASIIHR68ANAANANA
69ASIIHR69AAAAA
70ASIIHR70AAAAA
Transferability %94.295.797.190.0080.00

1 A, amplified, NA, not amplified; SSR, simple sequence repeat.

Table 4.

AMOVA analysis of genetic variances within and among populations of 40 custard apple accessions.

Source of variationdfSSMSEstimated variance% Variation
Among populations5213.76942.740.0210
Among individuals341447.24442.569.87030
Within individuals40913.0022.82522.82570
Total100

1 AMOVA, analysis of molecular variance; df, degrees of freedom; MS, mean sum of squares; SS, sum of squares.

Supplementary Table 1.

List of 40 custard apple (A. squamosa) genotypes/cultivars belonging to A. squamosa and different species of Annona used in the study.

Sl. No.Cultivars/accessions No.Place of collectionState
1.BalanagarSangareddyTelangana
2.RaidurgAnanthapurAndhra Pradesh
3.TaiwanTaiwanTaiwan
4.Arka_Sahan (IC No. 0632061)IIHRKarnataka
5.NMK_1GarmaleMaharashtra
6.APK_1AruppukottaiTamil Nadu
7.WASHINGTON_05FloridaUSA
8.BarbadosFloridaUSA
9.Washington_97FloridaUSA
10.19/26 (IC no. 0632061)IIHR, BangaloreKarnataka
11.Arka Neelanchal VikramBhubaneswarOdisha
12.MammothFloridaUSA
13.Red_sitaphalSangareddyTelangana
14.6_8NalakadoddiAndhra Pradesh
15.2_1VengalampalliAndhra Pradesh
16.3_1VengalampalliAndhra Pradesh
17.1_1VengalampalliAndhra Pradesh
18.8_8PythotaAndhra Pradesh
19.8_9PythotaAndhra Pradesh
20.2_2VengalampalliAndhra Pradesh
21.27_1JambugumpalaAndhra Pradesh
22.5_8MolakalmuruKarnataka
23.3_2VengalampalliAndhra Pradesh
24.5_1MolakalmuruKarnataka
25.8_18PythotaAndhra Pradesh
26.1_10VengalampalliAndhra Pradesh
27.8_16PythotaAndhra Pradesh
28.11_8YercaudTamil Nadu
29.3_3VengalampalliAndhra Pradesh
30.4_11MolakalmuruKarnataka
31.8_17PythotaAndhra Pradesh
32.1_5VengalampalliAndhra Pradesh
33.2_13VengalampalliAndhra Pradesh
34.4_1MolakalmuruKarnataka
35.2_10VengalampalliAndhra Pradesh
36.4_10MolakalmuruKarnataka
37.6_10NalakadoddiAndhra Pradesh
38.4_12MolakalmuruKarnataka
39.8_7PythotaAndhra Pradesh
40.RoleniaMoodubidireKarnataka
41.A. cherimolaSangareddyTelangana
42.A. reticulataSangareddyTelangana
43.A. glabraSangareddyTelangana
44.A. muricataSangareddyTelangana
45.A. atemoyaSangareddyTelangana
Supplementary Table 2.

Summary of sample Balanagar assembled genome.

Plant WGSBalanagar
Contigs generated1388525
Maximum contig length21462
Minimum contig length100
Average contig length466.126
Total contigs length647227553 (647.2 MB)
Total number of non-ATGC characters54429
Percentage of non-ATGC characters8.40956E-05
Contigs >100 b:1379816
Contigs >500 b:350135
Contigs >1 Kb:170254
Contigs >10 Kb:19
Contigs >100 Kb:0
n50 value:954
n90_value:151
kmer length89
Total number of scaffolds58528
Total number of identified SSRs1790080

1 SSR, simple sequence repeat.

DOI: https://doi.org/10.2478/fhort-2025-0009 | Journal eISSN: 2083-5965 | Journal ISSN: 0867-1761
Language: English
Page range: 139 - 155
Submitted on: Feb 6, 2025
Accepted on: May 20, 2025
Published on: Jul 10, 2025
Published by: Polish Society for Horticultural Sciences (PSHS)
In partnership with: Paradigm Publishing Services
Publication frequency: 2 issues per year
Related subjects:

© 2025 Abhilasha Krishnamurthy, Thandavarayan Sakthivel, Kundapura V. Ravishankar, published by Polish Society for Horticultural Sciences (PSHS)
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.