Assessment of genetic diversity in Triticum urartu Thumanjan ex Gandilyan accessions using start codon targeted polymorphism (SCoT) and CAAT-box derived polymorphism (CBDP) markers

Figures & data

Table 1. Geographical characteristics of sampling locations of Iranian T. urartu accessions in this study.

Population	Code	Province	n	Elevation (m)	Latitude (N)	Longitude (E)
Bashmagh	1-14	Kurdistan	14	1509	34°27′22″	46°16′18″
Kerend-e-Gharb	15-27	Kermanshah	13	1971	33°17′52″	46°19′24″
Sisakht-Pataveh	28-37	Kohgiluyeh and Boyer Ahmad	10	1673	33°53′30″	50°51′29″
Farokhshahr	38-50	Chaharmahal and Bakhtiyari	13	1796	33°53′30″	51°11′34″
Bisetoon	51-62	Kermanshah	12	1551	36°25′26″	47°25′22″
Songhor	63-72	Kermanshah	10	1637	34°25′26″	47°52′33″
Marvian	73-85	Kurdistan	13	1518	35°37′34″	42°19′31″

Table 2. Start Codon Targeted (SCoT) and CAAT-box derived polymorphism (CBDP) primers and their amplification results generated in the 85 T. urartu accessions.

Primer	Sequence (5′→3′)	Ta (^◦C)	TAB	NPB	PIC	Rp	MI
SCoT-1	CAACAATGGCTACCACCA	53.7	10	10	0.49	9.83	4.99
SCoT-2	CAACAATGGCTACCACCC	56.0	9	9	0.47	8.30	4.47
SCoT-3	CAACAATGGCTACCACCG	56.0	9	9	0.48	8.70	4.45
SCoT-4	CAACAATGGCTACCACCT	53.7	12	12	0.44	12.40	5.99
SCoT-5	CAACAATGGCTACCACGA	53.7	10	10	0.46	10.28	4.99
SCoT-6	CAACAATGGCTACCACGG	56.0	11	11	0.41	12.40	5.41
SCoT-7	CAACAATGGCTACCACGT	53.7	13	13	0.48	12.30	6.48
SCoT-8	CAACAATGGCTACCAGCA	53.7	10	10	0.43	11.10	4.93
SCoT-9	CAACAATGGCTACCAGCC	56.0	9	9	0.49	8.87	4.49
SCoT-10	AAGCAATGGCTACCACCA	53.7	10	10	0.48	9.45	4.98
SCoT-11	ACGACATGGCGACCAACG	58.2	7	7	0.45	7.57	3.47
SCoT-12	ACGACATGGCGACCATCG	58.2	9	9	0.50	6.72	4.46
SCoT-13	ACGACATGGCGACCACCG	60.5	7	7	0.45	6.72	3.49
SCoT-14	ACGACATGGCGACCGCGA	60.5	13	13	0.50	12.89	6.49
SCoT-15	CCATGGCTACCACCGGCC	62.8	10	10	0.44	9.43	4.98
SCoT-16	CATGGCTACCACCGGCCC	62.8	12	12	0.43	12.44	5.99
SCoT-17	CACCATGGCTACCACCAT	56.0	8	8	0.50	8.16	3.99
SCoT-18	CCATGGCTACCACCGCCA	60.5	8	8	0.48	8.65	3.97
SCoT-19	ACAATGGCTACCACCATC	53.7	8	8	0.48	8.65	3.97
	Mean		9.74	9.74	0.47	9.73	4.84
CBDP-1	TGAGCACGATCCAATAGC	52.0	10	10	0.48	11.76	4.84
CBDP-2	TGAGCACGATCCAATAAT	45.8	9	9	0.49	9.55	4.48
CBDP-3	TGAGCACGATCCAATACC	59.1	9	9	0.40	10.25	4.41
CBDP-4	TGAGCACGATCCAATAAG	61.5	10	10	0.43	11.10	4.93
CBDP-5	TGAGCACGATCCAATCTA	73.0	9	9	0.43	9.88	4.45
CBDP-6	TGAGCACGATCCAATCGA	50.0	9	9	0.47	13.64	4.28
CBDP-7	TGAGCACGATCCAATCGA	50.9	12	12	0.49	13.64	4.41
CBDP-8	TGAGCACGATCCAATCGG	50.0	9	9	0.43	10.23	4.41
CBDP-9	TGAGCACGATCCAATGAT	56.9	9	9	0.48	10.61	4.35
CBDP-10	TGAGCACGATCCAATGTT	54.1	10	10	0.49	11.29	4.91
CBDP-11	TGAGCACGATCCAATTGC	50.0	8	8	0.45	8.23	3.99
CBDP-12	TGAGCACGATCCAATATA	44.8	11	11	0.48	13.03	5.31
CBDP-13	TGAGCACGATCCAATGAG	33.6	9	9	0.46	10.25	4.41
CBDP-14	TGAGCACGATCCAATGCG	35.9	9	9	0.41	9.41	4.49
CBDP-15	TGAGCACGATCCAATTGA	54.9	8	8	0.45	7.03	3.94
	Mean		9.40	9.40	0.45	10.66	4.51

Note. MI: marker index; NPB: number of polymorphic bands; PIC: polymorphism information content; Rp: resolving power; Ta: temperature annealing; TAB: total amplified bands.

Table 3. Estimated genetic diversity parameters for different Iranian T. urartu populations using SCoT and CBDP markers.

Marker	Population	Na	Ne	I	H	PPL
SCoT	Bashmagh	1.89 ± 0.03	1.54 ± 0.02	0.47 ± 0.02	0.32 ± 0.01	91.89
	Kerend-e-Gharb	1.91 ± 0.03	1.65 ± 0.02	0.53 ± 0.01	0.36 ± 0.01	93.51
	Sisakht-Pataveh	1.89 ± 0.03	1.59 ± 0.02	0.50 ± 0.02	0.34 ± 0.01	92.43
	Farokhshahr	1.90 ± 0.02	1.55 ± 0.02	0.48 ± 0.02	0.32 ± 0.01	91.89
	Bisetoon	1.91 ± ± 0.02	1.58 ± 0.02	0.50 ± 0.01	0.33 ± 0.01	94.05
	Songhor	1.88 ± 0.03	1.59 ± 0.02	0.51 ± 0.01	0.34 ± 0.01	92.43
	Marvian	1.87 ± 0.03	1.57 ± 0.02	0.49 ± 0.02	0.33 ± 0.01	90.27
	Mean	1.89 ± 0.01	1.58 ± 0.009	0.50 ± 0.006	0.33 ± 0.004	92.36 ± 3.46
CBDP	Bashmagh	1.85 ± 0.04	1.58 ± 0.02	0.49 ± 0.02	0.33 ± 0.02	87.94
	Kerend-e-Gharb	1.88 ± 0.03	1.65 ± 0.02	0.53 ± 0.01	0.36 ± 0.02	92.91
	Sisakht-Pataveh	1.86 ± 0.05	1.66 ± 0.03	0.53 ± 0.02	0.37 ± 0.02	90.07
	Farokhshahr	1.85 ± 0.04	1.60 ± 0.02	0.50 ± 0.01	0.34 ± 0.02	90.78
	Bisetoon	1.84 ± 0.05	1.62 ± 0.02	0.51 ± 0.01	0.35 ± 0.02	88.65
	Songhor	1.81 ± 0.05	1.58 ± 0.03	0.48 ± 0.02	0.33 ± 0.01	85.11
	Marvian	1.80 ± 0.04	1.50 ± 0.02	0.44 ± 0.01	0.29 ± 0.02	85.11
	Mean	1.84 ± 0.01	1.60 ± 0.01	0.50 ± 0.01	0.34 ± 0.01	88.65 ± 10.90
Pooled data	Bashmagh	1.89 ± 0.02	1.59 ± 0.01	0.50 ± 0.01	0.33 ± 0.01	92.33
	Kerend-e-Gharb	1.88 ± 0.02	1.63 ± 0.02	0.53 ± 0.02	0.36 ± 0.01	91.10
	Sisakht-Pataveh	1.88 ± 0.02	1.62 ± 0.01	0.52 ± 0.02	0.35 ± 0.01	91.41
	Farokhshahr	1.88 ± 0.02	1.57 ± 0.01	0.49 ± 0.01	0.33 ± 0.01	91.41
	Bisetoon	1.88 ± 0.02	1.60 ± 0.02	0.50 ± 0.01	0.34 ± 0.01	91.72
	Songhor	1.85 ± 0.02	1.59 ± 0.02	0.49 ± 0.02	0.33 ± 0.01	89.26
	Marvian	1.84 ± 0.02	1.54 ± 0.02	0.47 ± 0.02	0.31 ± 0.01	88.04
	Mean	1.87 ± 0.02	1.59 ± 0.01	0.50 ± 0.01	0.33 ± 0.01	90.75 ± 0.58

Note. Na: observed number of alleles; Ne: effective number of alleles; I: Shannon’s information index; H: Nei’s gene diversity; PPL: the percentage of polymorphic loci.

Table 4. Analysis of molecular variance (AMOVA) in T. urartu populations.

Source of variation	SCoT		CBDP		SCoT + CBDP
	Between populations	Within populations	Between populations	Within populations	Between populations	Within populations
df	6	78	6	78	6	78
SS	302.24	2821.24	285.67	2025.05	587.71	4846.061
MS	50.37	36.17	47.61	25.96	97.95	62.13
Est.Var	1.17	36.17	1.78	25.96	2.95	62.13
Var	3%	97%	6%	94%	5%	95%
GST	0.07		0.11		0.23
Nm	6.20		4.16		5.44

Note. SS: sum of squares; MS: mean squares; Est. Var estimated variance components; Var: total variance, Gst: inter-population differentiation; Nm: gene flow.

Figure 1. Fan-dendrogram generated using neighbour-joining clustering based on SCoT (A), CBDP (B) and SCoT + CBDP (C) data. See Table 1 for codes of genotypes.

Figure 2. Biplot derived from the PCoA of the 85 Iranian T. urartu accessions based on SCoT (A), CBDP (B) and SCoT + CBDP (C) data.

Figure 3. Population structure of 85 accessions of T. urartu based on SCoT (A), CBDP (B) and SCoT + CBDP (C) primers inferred by STRUCTURE analysis. See Table 1 for codes of genotypes.