Open Access

Genetic diversity and structure analysis of Croatian garlic collection assessed by SSR markers

Danijela Poljuha
Danijela Poljuha
, 
Mario Franić
Mario Franić
, 
Ines Kralj
Ines Kralj
, 
Tim Weber
Tim Weber
, 
Zlatko Šatović
Zlatko Šatović
, 
Dean Ban
Dean Ban
, 
Nina Toth
Nina Toth
, 
Gvozden Dumičić
Gvozden Dumičić
, 
Snježana Kereša
Snježana Kereša
, 
Camila Pinto da Cunha
Camila Pinto da Cunha
 and 
Smiljana Goreta Ban
Smiljana Goreta Ban
   | May 13, 2021
Folia Horticulturae's Cover Image
About this article
Previous Article
Next Article
Cite
Article Category: Original Article
Published Online: May 13, 2021
Page range: 157 - 171
Received: Dec 15, 2020
Accepted: Mar 31, 2021
DOI: https://doi.org/10.2478/fhort-2021-0011
Keywords
© 2021 Danijela Poljuha et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

UPGMA tree (A) based on SSR marker data of 80 garlic accessions and its proportion of membership in each cluster as defined by STRUCTURE (B) and BAPS (C). Region of origin of each accession is indicated as follows: P1 – continental Croatia, P2 – Istria, P3 – Dalmatian and P4 – foreign (followed by three-letter country codes). Bootstrap support values >50% of 1,000 replicates are given above branches. Each accession is represented by a single horizontal rectangle divided into colours. Each colour represents one cluster, and the length of the coloured segments shows the estimated proportion of membership in that cluster. SSR, simple sequence repeat.
UPGMA tree (A) based on SSR marker data of 80 garlic accessions and its proportion of membership in each cluster as defined by STRUCTURE (B) and BAPS (C). Region of origin of each accession is indicated as follows: P1 – continental Croatia, P2 – Istria, P3 – Dalmatian and P4 – foreign (followed by three-letter country codes). Bootstrap support values >50% of 1,000 replicates are given above branches. Each accession is represented by a single horizontal rectangle divided into colours. Each colour represents one cluster, and the length of the coloured segments shows the estimated proportion of membership in that cluster. SSR, simple sequence repeat.

Figure S1

Inference of the most likely number of clusters based on the results of STRUCTURE by analysing SSR data of 80 garlic accessions. SSR, simple sequence repeat.
Inference of the most likely number of clusters based on the results of STRUCTURE by analysing SSR data of 80 garlic accessions. SSR, simple sequence repeat.

AMOVA’s pairwise φST values among groups of garlic accessions.

Group of accessions Region P1 P2 P3 P4
P1 Continental Croatia * ns ns
P2 Istria 0.103 *** **
P3 Dalmatia 0.049 0.189 ns
P4 Foreign accessions −0.006 0.115 0.048

Number of SSR electropherogram peaks per marker per number of accessions observed in the set of 80 accessions.

Locus Number of peaks
1 2 3 4 5
AS2655 33 38 7 0 2
AS449 27 51 1 1 0
AS5944 13 62 4 1 0
AS623 37 43 0 0 0
AS6389 12 68 0 0 0
AS739 1 78 0 1 0
AS96 0 78 1 0 0
Asa14 4 44 23 2 0
GB-ASM-040 12 64 3 1 0
GB-ASM-053 4 26 49 1 0
GB-ASM-059 8 68 3 1 0
GB-ASM-072 36 27 14 0 0
GB-ASM-080 52 28 0 0 0

Allelic diversity of 13 microsatellite loci scored in 80 garlic accessions.

No. Locus Repeat motif Size range Na
1 Asa14 (GT)7 221–243 5
2 GB-ASM-040 (AC)6, (AC)14-(AT)5 253–283 6
3 GB-ASM-053 (CA)15, (AC)8 156–214 8
4 GB-ASM-059 (TG)11, (TG)5 264–295 5
5 GB-ASM-072 (TA)7-(TG)5GC(GT)9T(TG)8 161–273 6
6 GB-ASM-080 (CCG)5 142–155 4
7 AS739 (AGC)10 196–212 6
8 AS623 (GCT)6 289–292 2
9 AS2655 (AGAAA)5 239–262 6
10 AS96 (AACGGC)4 123–141 5
11 AS449 (AGATGG)5 195–221 6
12 AS6389 (AGCCTG)5 100–235 5
13 AS5944 (AC)28 159–231 7
Average 5.46

List of accessions.

Accession no. IPTPO accession ID Universal accession ID Landrace Origin of accession Region State MLG UPGMA Structure K3 BAPS K5
P1S01 IJK18NB – – Vojnić P1 Croatia G01 B B B
P1S02 AFZ014NB – Unski Unčani P1 Croatia G06 A A A
P1S03 AFZ013NB – Kerestinečki Kerestinec P1 Croatia U01 C C C
P1S04 AFZ015B – Bjelovarski Bjelovar P1 Croatia U02 A A A
P1S05 AGRE8NB – – Sesvetski Kraljevec P1 Croatia U03 B B B
P1S06 AGRE9NB – – Cerje Lekeničko P1 Croatia U04 A A A
P1S07 AFZ011NB – – Bjelovar P1 Croatia U05 C C C
P1S08 IPT246NB – VGUK1,2-710 Križevci P1 Croatia U06 A A A
P1S09 IPT249NB VEG00093 VGUK Šokac Cerić P1 Croatia G02 A A A
P1S10 IPT250NB – VGUK675 Bakovčice P1 Croatia G02 A A A
P1S11 IPT251NB – VGUK Đakovački Đakovo P1 Croatia G02 A A A
P1S12 IPT252NB – VGUK Sremski Srijem P1 Croatia U07 B BM B
P1S13 IPT272B – Bilogorski Donji Mosti P1 Croatia U08 C C C
P1S14 IPT273NB – Mraclinski Mraclin P1 Croatia U09 B B B
P1S15 IPT274NB – Kerestinečki Kerestinec P1 Croatia G07 C C C
P1S16 IPT275NB – Unski Unčani P1 Croatia G07 C C C
P2S17 IJK7NB – Tinjanski Tinjan P2 Croatia G08 A A A
P2S18 IPTO10B VEG00095 Domaći ozimi crveni Pazin P2 Croatia U10 D C D
P2S19 IPTO11B VEG00096 Domaći ozimi Kaštelir P2 Croatia G03 A A A
P2S20 IPTO12B VEG00097 Domaći ozimi with stalk Kaštelir P2 Croatia G03 A A A
P2S21 IPTO13B VEG00098 Istarski crveni Lindar P2 Croatia G03 A A A
P2S22 IPTO14NB VEG00094 Domaći jari Tinjan P2 Croatia U11 A A A
P2S23 IPTO15NB VEG00099 Istarski bijeli Pazin P2 Croatia U12 A A A
P2S24 IPTO16B VEG00100 Istarski domaći Ograde P2 Croatia U13 A A A
P2S25 IPTO17NB VEG00101 Istarski bijeli Ograde P2 Croatia U14 A A A
P2S26 IPTO19B VEG00102 Brgujski Brgud (Opatija) P2 Croatia U15 D C D
P2S27 IPTO20B VEG00103 Brsečki Brseč P2 Croatia U16 A A A
P2S28 IPT224NB VEG00104 – Ližnjan P2 Croatia U17 A AM A
P2S29 IPT338NB – Istarski bijeli Lindar P2 Croatia U18 A A A
P2S30 IPT339B – Music Lindar P2 Croatia U19 X CM D
P2S31 IPT341B – Istarski crveni Pićan P2 Croatia U20 A A A
P2S32 IPT342NB – Mješavina Tinjan P2 Croatia G04 A A A
P2S33 IPT343B – Istarski crveni Gračišće P2 Croatia G04 A A A
P2S34 IPT344NB – Istarski bijeli Gračišće P2 Croatia G04 A A A
P2S35 IPT345NB – Istarski crveni Beram P2 Croatia U21 A A A
P2S36 IPT347B – Istarski crveni (with stalk) Oprtalj P2 Croatia U22 A A A
P2S37 IPT348NB – Istarski crveni (without stalk) Oprtalj P2 Croatia U23 D C D
P2S38 IPT349B – Istarski crveni (with stalk) Oprtalj P2 Croatia U24 A A A
P3S39 IJK3NB VEG00223 – Zmijavci P3 Croatia U25 A A A
P3S40 IJK4NB VEG00224 – Rastok (Vrgorac) P3 Croatia G09 B B B
P3S41 IJK8NB VEG00225 – Kurtovići P3 Croatia U26 A A A
P3S42 IJK9NB VEG00227 – Obrovac Sinjski P3 Croatia G05 A A A
P3S43 IJK10NB VEG00226 – Stija P3 Croatia U27 A A A
P3S44 IJK13NB VEG00229 – Primorski dolac P3 Croatia G08 A A A
P3S45 IJK14B VEG00230 – Trnbusi 1 P3 Croatia G05 A A A
P3S46 IJK17NB VEG00231 – Opuzen (Raba) P3 Croatia U28 B B B
P3S47 IJK19NB VEG00232 – Metković P3 Croatia G01 B B B
P3S48 IJK20NB VEG00236 – Trnbusi 2 P3 Croatia G01 B B B
P3S49 IJK22B VEG00234 – Rama (Vinjani g.) P3 Croatia G05 A A A
P3S50 IJK23NB VEG00235 – Kijevo P3 Croatia U29 A A A
P3S51 IJK24NB VEG00236 – Golubić 2 P3 Croatia U30 C C C
P3S52 IJK25NB VEG00237 – Golubić 1 P3 Croatia G01 B B B
P3S53 IJK26NB VEG00130 Ljubitovački šarac Ljubitovica P3 Croatia U31 A AM AM
P3S54 IJK27B VEG00238 – Unešić Plameni P3 Croatia U32 D CM D
P3S55 IJK28B – – Unešić Jaki P3 Croatia U33 B B B
P3S56 AFZ024NB – Bruški 1 Bruška P3 Croatia U34 B B B
P3S57 AFZ025NB – Lisičićki 1 Lisičić P3 Croatia G01 B B B
P3S58 AFZ026NB – Rodaljički Rodaljice P3 Croatia U35 B B B
P3S59 VEG00010NB VEG00010 Brgudski ozimi syn. Benkovački Brgud P3 Croatia G01 B B B
P3S60 IPT268NB – Cabrunski Cabrun P3 Croatia U36 B B B
P3S61 IPT269NB – Bruški Brusje P3 Croatia U37 B B B
P3S62 IPT270NB – Lisički Lisje P3 Croatia G10 B B B
P3S63 IPT271NB Rodaljički Rodaljice P3 Croatia G10 B B B
P3S64 IPT276NB – Brgudski ozimi syn. Benkovački 1 Brgud P3 Croatia U38 B BM B
P4S65 B_2 0033* Chinês real China P4 Brazil U39 E CM E
P4S66 B_5 0077* Peruano Peru P4 Brazil U40 A AM AM
P4S67 B_9 0089* Ugarte Brazil P4 Brazil U41 E CM E
P4S68 IPT177B VEG00118/W610735** B92-22 Bulgaria P4 Bulgaria U42 B B B
P4S69 IPT182B VEG00124/PI493116** 174 Czech Republic U43 Czech Republic U43 D C D
P4S70 IJK2NB – Pinčić (Skadar) P4 Montenegro G09 B B B
P4S71 IPT181B VEG00123/PI497945)** – Poland P4 Poland U44 C C C
P4S72 IPT185B VEG00126/PI540351** 0525-85-76 Poland P4 Poland U45 C C C
P4S73 IPT179NB VEG00128/PI383817** Domasen Serbia P4 Serbia U46 A A A
P4S74 IPT189NB VEG00129 – Subotica P4 Serbia U47 B B B
P4S75 AGRE11NB – Semenarna Ljubljana P4 Slovenia G06 A A A
P4S76 IPT186NB VEG00119/PI615422** Blanco de Huelma Zamora I Spain P4 Spain U48 B B B
P4S77 IPT188NB VEG00122/PI3497951** Kisswani Syria P4 Syria U49 X CM DM
P4S78 IPT180NB VEG00125/PI3515971** Chet’s USA P4 USA G01 B B B
P4S79 IPT187B VEG00120/W612832** 870825 USA P4 USA U50 A AM A
P4S80 IPT178B VEG00127/PI576914** UO86 Uzbekistan P4 Uzbekistan U51 D C D

Molecular diversity of 80 garlic accessions.

No Origin n Ng Ngr Npr Npar % P I
1 Croatia 64 48 – 45 – 84.51 0.508
1.1 Continental Croatia 16 13 13.00 11 11.00 64.79 0.493
1.2 Istria 22 18 13.61 17 12.88 67.61 0.412
1.3 Dalmatia 26 19 12.66 16 10.43 70.42 0.420
2 Foreign 16 16 16.00 13 13.00 94.37 0.626
Total 80 61

AMOVA for the partition of the total molecular diversity between and within Croatian and foreign garlic accessions (A), among and within three Croatian regions (B) and among and within three Croatian regions including foreign accessions as a fourth group.

Analysis Source of variation df Variance components % total variation φ-statistics P(φ)
(A) Among groups 1 0.244 2.75 0.027 0.099
Within groups 62 8.639 97.25
(B) Among groups 2 1.023 12.29 0.123 <0.0001
Within groups 47 7.304 87.71
(C) Among groups 3 0.790 8.89 0.089 <0.0001
Within groups 62 8.090 91.11
eISSN:
2083-5965
Language:
English
Publication timeframe:
2 times per year
Journal Subjects:
Life Sciences, Plant Science, Zoology, Ecology, other
Journal RSS Feed