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

No.	Locus	Repeat motif	Size range	N_a
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

[i] N_a is the number of alleles.

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.

Table 2

Molecular diversity of 80 garlic accessions.

No	Origin	n	N_g	N_gr	N_pr	N_par	% 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

[i] n is the number of accessions; N_g is the number of distinct genotypes; N_gr is the genotypic richness; N_pr is the number of private genotypes; N_par is the private genotypic richness; % P is the percentage of polymorphic loci; I is the Shannon’s information index.

Table 3

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

[i] AMOVA, analysis of molecular variance.

Table 4

AMOVA’s pairwise φ_S_T 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

Below diagonal: pairwise φ_ST values.

Above diagonal: P(φ_ST).

AMOVA, analysis of molecular variance; ns, non-significant.

* Significant at p < 0.05.

** Significant at p < 0.01.

*** Significant at p < 0.001.

Table S1

List of accessions.

Accession no.	IPTPO accession ID	Universal accession ID	Landrace	Origin of accession	Region	State	MLG	UPGMA	Structure K3	BAPS K5
P1S01	IJK18^NB	–	–	Vojnić	P1	Croatia	G01	B	B	B
P1S02	AFZ014^NB	–	Unski	Unčani	P1	Croatia	G06	A	A	A
P1S03	AFZ013^NB	–	Kerestinečki	Kerestinec	P1	Croatia	U01	C	C	C
P1S04	AFZ015^B	–	Bjelovarski	Bjelovar	P1	Croatia	U02	A	A	A
P1S05	AGRE8^NB	–	–	Sesvetski Kraljevec	P1	Croatia	U03	B	B	B
P1S06	AGRE9^NB	–	–	Cerje Lekeničko	P1	Croatia	U04	A	A	A
P1S07	AFZ011^NB	–	–	Bjelovar	P1	Croatia	U05	C	C	C
P1S08	IPT246^NB	–	VGUK1,2-710	Križevci	P1	Croatia	U06	A	A	A
P1S09	IPT249^NB	VEG00093	VGUK Šokac	Cerić	P1	Croatia	G02	A	A	A
P1S10	IPT250^NB	–	VGUK675	Bakovčice	P1	Croatia	G02	A	A	A
P1S11	IPT251^NB	–	VGUK Đakovački	Đakovo	P1	Croatia	G02	A	A	A
P1S12	IPT252^NB	–	VGUK Sremski	Srijem	P1	Croatia	U07	B	BM	B
P1S13	IPT272^B	–	Bilogorski	Donji Mosti	P1	Croatia	U08	C	C	C
P1S14	IPT273^NB	–	Mraclinski	Mraclin	P1	Croatia	U09	B	B	B
P1S15	IPT274^NB	–	Kerestinečki	Kerestinec	P1	Croatia	G07	C	C	C
P1S16	IPT275^NB	–	Unski	Unčani	P1	Croatia	G07	C	C	C
P2S17	IJK7^NB	–	Tinjanski	Tinjan	P2	Croatia	G08	A	A	A
P2S18	IPTO10^B	VEG00095	Domaći ozimi crveni	Pazin	P2	Croatia	U10	D	C	D
P2S19	IPTO11^B	VEG00096	Domaći ozimi	Kaštelir	P2	Croatia	G03	A	A	A
P2S20	IPTO12^B	VEG00097	Domaći ozimi with stalk	Kaštelir	P2	Croatia	G03	A	A	A
P2S21	IPTO13^B	VEG00098	Istarski crveni	Lindar	P2	Croatia	G03	A	A	A
P2S22	IPTO14^NB	VEG00094	Domaći jari	Tinjan	P2	Croatia	U11	A	A	A
P2S23	IPTO15^NB	VEG00099	Istarski bijeli	Pazin	P2	Croatia	U12	A	A	A
P2S24	IPTO16^B	VEG00100	Istarski domaći	Ograde	P2	Croatia	U13	A	A	A
P2S25	IPTO17^NB	VEG00101	Istarski bijeli	Ograde	P2	Croatia	U14	A	A	A
P2S26	IPTO19^B	VEG00102	Brgujski	Brgud (Opatija)	P2	Croatia	U15	D	C	D
P2S27	IPTO20^B	VEG00103	Brsečki	Brseč	P2	Croatia	U16	A	A	A
P2S28	IPT224^NB	VEG00104	–	Ližnjan	P2	Croatia	U17	A	AM	A
P2S29	IPT338^NB	–	Istarski bijeli	Lindar	P2	Croatia	U18	A	A	A
P2S30	IPT339^B	–	Music	Lindar	P2	Croatia	U19	X	CM	D
P2S31	IPT341^B	–	Istarski crveni	Pićan	P2	Croatia	U20	A	A	A
P2S32	IPT342^NB	–	Mješavina	Tinjan	P2	Croatia	G04	A	A	A
P2S33	IPT343^B	–	Istarski crveni	Gračišće	P2	Croatia	G04	A	A	A
P2S34	IPT344^NB	–	Istarski bijeli	Gračišće	P2	Croatia	G04	A	A	A
P2S35	IPT345^NB	–	Istarski crveni	Beram	P2	Croatia	U21	A	A	A
P2S36	IPT347^B	–	Istarski crveni (with stalk)	Oprtalj	P2	Croatia	U22	A	A	A
P2S37	IPT348^NB	–	Istarski crveni (without stalk)	Oprtalj	P2	Croatia	U23	D	C	D
P2S38	IPT349^B	–	Istarski crveni (with stalk)	Oprtalj	P2	Croatia	U24	A	A	A
P3S39	IJK3^NB	VEG00223	–	Zmijavci	P3	Croatia	U25	A	A	A
P3S40	IJK4^NB	VEG00224	–	Rastok (Vrgorac)	P3	Croatia	G09	B	B	B
P3S41	IJK8^NB	VEG00225	–	Kurtovići	P3	Croatia	U26	A	A	A
P3S42	IJK9^NB	VEG00227	–	Obrovac Sinjski	P3	Croatia	G05	A	A	A
P3S43	IJK10^NB	VEG00226	–	Stija	P3	Croatia	U27	A	A	A
P3S44	IJK13^NB	VEG00229	–	Primorski dolac	P3	Croatia	G08	A	A	A
P3S45	IJK14^B	VEG00230	–	Trnbusi 1	P3	Croatia	G05	A	A	A
P3S46	IJK17^NB	VEG00231	–	Opuzen (Raba)	P3	Croatia	U28	B	B	B
P3S47	IJK19^NB	VEG00232	–	Metković	P3	Croatia	G01	B	B	B
P3S48	IJK20^NB	VEG00236	–	Trnbusi 2	P3	Croatia	G01	B	B	B
P3S49	IJK22^B	VEG00234	–	Rama (Vinjani g.)	P3	Croatia	G05	A	A	A
P3S50	IJK23^NB	VEG00235	–	Kijevo	P3	Croatia	U29	A	A	A
P3S51	IJK24^NB	VEG00236	–	Golubić 2	P3	Croatia	U30	C	C	C
P3S52	IJK25^NB	VEG00237	–	Golubić 1	P3	Croatia	G01	B	B	B
P3S53	IJK26^NB	VEG00130	Ljubitovački šarac	Ljubitovica	P3	Croatia	U31	A	AM	AM
P3S54	IJK27^B	VEG00238	–	Unešić Plameni	P3	Croatia	U32	D	CM	D
P3S55	IJK28^B	–	–	Unešić Jaki	P3	Croatia	U33	B	B	B
P3S56	AFZ024^NB	–	Bruški 1	Bruška	P3	Croatia	U34	B	B	B
P3S57	AFZ025^NB	–	Lisičićki 1	Lisičić	P3	Croatia	G01	B	B	B
P3S58	AFZ026^NB	–	Rodaljički	Rodaljice	P3	Croatia	U35	B	B	B
P3S59	VEG00010^NB	VEG00010	Brgudski ozimi syn. Benkovački	Brgud	P3	Croatia	G01	B	B	B
P3S60	IPT268^NB	–	Cabrunski	Cabrun	P3	Croatia	U36	B	B	B
P3S61	IPT269^NB	–	Bruški	Brusje	P3	Croatia	U37	B	B	B
P3S62	IPT270^NB	–	Lisički	Lisje	P3	Croatia	G10	B	B	B
P3S63	IPT271^NB		Rodaljički	Rodaljice	P3	Croatia	G10	B	B	B
P3S64	IPT276^NB	–	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	IPT177^B	VEG00118/W610735**	B92-22	Bulgaria	P4	Bulgaria	U42	B	B	B
P4S69	IPT182^B	VEG00124/PI493116**	174	Czech Republic	U43	Czech Republic	U43	D	C	D
P4S70	IJK2^NB		–	Pinčić (Skadar)	P4	Montenegro	G09	B	B	B
P4S71	IPT181^B	VEG00123/PI497945)**	–	Poland	P4	Poland	U44	C	C	C
P4S72	IPT185^B	VEG00126/PI540351**	0525-85-76	Poland	P4	Poland	U45	C	C	C
P4S73	IPT179^NB	VEG00128/PI383817**	Domasen	Serbia	P4	Serbia	U46	A	A	A
P4S74	IPT189^NB	VEG00129	–	Subotica	P4	Serbia	U47	B	B	B
P4S75	AGRE11^NB		–	Semenarna Ljubljana	P4	Slovenia	G06	A	A	A
P4S76	IPT186^NB	VEG00119/PI615422**	Blanco de Huelma Zamora I	Spain	P4	Spain	U48	B	B	B
P4S77	IPT188^NB	VEG00122/PI3497951**	Kisswani	Syria	P4	Syria	U49	X	CM	DM
P4S78	IPT180^NB	VEG00125/PI3515971**	Chet’s	USA	P4	USA	G01	B	B	B
P4S79	IPT187^B	VEG00120/W612832**	870825	USA	P4	USA	U50	A	AM	A
P4S80	IPT178^B	VEG00127/PI576914**	UO86	Uzbekistan	P4	Uzbekistan	U51	D	C	D

[i] MLG, multilocus genotype; NPGS, National Plant Germplasm System.

[ii] Accession No.: Accession number; IPTPO Accession ID: Institute of Agriculture and Tourism Collection ID (flowering behaviour (^B – bolting, ^NB – non-bolting); Universal Accession ID: CPGRD (Croatian Plant Genetic Resources Database; cpgrd.hapih.hr), CENARGEN, Embrapa, Brazil*, and GRIN, NPGS, USA** Collection ID; Landrace: traditional name or name listed in the collection; Origin of Accession: original collecting site; Region: Region of origin (P1 – continental Croatia, P2 – Istria, P3 – Dalmatia, P4 Foreign accessions); State: State of origin; MLG: Multilocus genotype (G group of identical accessions, U – unique genotype); UPGMA: Cluster on UPGMA tree (X – separate lineage); Structure K3: Cluster based on STRUCTURE analysis at K = 3 (M – accession of mixed origin: the proportion of membership lower than 0.75 in any cluster); BAPS K5: Cluster based on BAPS analysis at K = 5 (M – accession of mixed origin: the proportion of membership lower than 0.75 in any cluster).

Table S2

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

Locus	Number of peaks
Locus	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

[i] 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.

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DOI: https://doi.org/10.2478/fhort-2021-0011 | Journal eISSN: 2083-5965 | Journal ISSN: 0867-1761

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Language: English

Page range: 157 - 171

Submitted on: Dec 15, 2020

Accepted on: Mar 31, 2021

Published on: May 13, 2021

Published by: Polish Society for Horticultural Sciences (PSHS)

In partnership with: Paradigm Publishing Services

Publication frequency: 2 issues per year

Keywords:

collections management,

garlic,

genetic diversity,

genetic structure,

plant genetic resources,

SSR

Related subjects:

Life sciences,

Plant science

© 2021 Danijela Poljuha, Mario Franić, Ines Kralj, Tim Weber, Zlatko Šatović, Dean Ban, Nina Toth, Gvozden Dumičić, Snježana Kereša, Camila Pinto da Cunha, Smiljana Goreta Ban, published by Polish Society for Horticultural Sciences (PSHS)
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Volume 33 (2021): Issue 1 (June 2021)

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

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Table 1

Figure 1

Table 2

Table 3

Table 4

Table S1

Table S2

Figure S1

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