Morphological variability and genetic diversity of wheat genotypes grown on saline soil and identification of new promising molecular markers associated with salinity tolerance

Figures & data

Table 1. Name, origin, and pedigree and/or selection history of eleven bread wheat genotypes tested.

Name	Origin	Pedigree and/or selection history
L1 (I-3)	ICARDA^†	CM59456-3AP-1AP-2AP-1AP-0AP
L2 (L-606^††)	Egypt	RCB-61// (Atlas 66 / Nap Hall) /2* RCB-61Su606-13Su-2Su-5Su-0Su-18Su
L3 (A 305)	ACSAD^‡	Bb / Nar 67//Kal 1227 A / Bb /3/ JBE4-Toluca 73
L4 (S8/17^††)	Egypt	R8 tissue culture-regenerated double-haploid plant
L5 (Gomam)	CIMMYT^§	SWM 11619-2 AP-4 AP-1 AP-2 AP-0AP
L6 (I-6)	ICARDA^†	Dove ‘S’ / Buc ‘S’ CM58808-6AP-2AP-1AP-1AP-0AP
L7 (Nesser)	CIMMYT^§/ICARDA^†	ICW85-0024-06AP-300AP-300L-1AP-0AP
L8 (L-263^††)	Egypt	Sids 1 // CM 33204 7Su-26SW-3SW-1SW-0SW
L9 (Siwa5)	Egypt	Newly bred line selected under Siwa Oasis conditions
Sids12	Egypt	BUS//7C//ALD/5/MAYA74/ON//1160.147/3/BB/GLL/4/CHAT‘S’/6/MAYA/VUL//CMH74A.630/4*SX.- SD720096-4SD-1SD-1SD-0SD
GIZA 171	Egypt	SAKHA 93/GEMMEIZA 9 - S.6-1GZ-4GZ-1GZ-2GZ-0S

^†ICARDA: International Center for Agricultural Research in the Dry Areas.

^‡ACSAD: The Arab Center for the Studies for Arid zones and Dry lands.

^§CIMMYT: Centro International de Mejoramiento de Maize Y Trigo (Mexico) = International Maize and Wheat Improvement Center.

^††Newly bred lines released through the Desert Research Center wheat breeding program.

Table 2. Soil physical analysis of the two experimental sites at Ashmon – Menofya, and Siwa Oasis during 2016/2017 growing season.

Location	Physical analysis (%)				Texture
	Course sand	Fine sand	Silt	Clay
Ashmon	6.35	12.8	16.4	64.5	Clay
Siwa Oasis	9.8	12.4	60.82	16.98	Sandy loam

Table 3. Chemical analysis of soil saturation extract and irrigation water during 2016/2017 growing seasons.

Location	OM (%)	CaCO3 (%)	PH	EC (dSm^−1)	Anions (meq/L)			Cations (meq/L)
					Cl^−	${\mathrm{H}\mathrm{C}\mathrm{O}}_3^{-}$	${\mathrm{S}\mathrm{O}}_4^{2-}$	Na^+	K^+	Ca^2+	Mg^2+
Soil analysis (0–30 cm)
Ashmon	1.7	1.6	7.5	1.8	9.8	1.15	7.1	8.7	0.35	5.7	3.2
Siwa Oasis	0.53	17.5	7.9	12.3	83.6	2.3	36.2	68.9	1.60	34.5	17.4
Irrigation water analysis
Ashmon	–	–	7.6	1.35	1.87	3.56	6.92	12.3	0.32	1.15	1.18
Siwa Oasis	–	–	7.3	3.96	18.6	10.8	7.48	22.1	0.45	8.3	8.7

Table 4. Mean performance combined over the two environments (under stress and adequate) as well as under each environment for yield and its components of eleven bread wheat genotypes tested.

Genotypes	Plant height (cm)	Spikes no./Plant	Spike length (cm)	Spikelets no/spike	1000-grain weight(g)	Grains no./plant	Grain yield (g)	Straw yield (g)
Adequate environment	106.59	2.81	17.12	20.67	32.43	123.89	3.34	8.28
Salt stressed environment	103.10	2.54	16.78	19.23	29.64	107.40	2.87	6.39
LSD (5 %)	NS^†	NS^†	NS^†	NS^†	NS^†	NS^†	NS^†	0.37
Combined data over environments
(L1)	91.78	2.43	14.64	19.11	29.37	100.87	2.90	7.11
(L2)	95.57	3.40	20.08	21.59	40.74	177.53	4.78	10.65
(L3)	113.12	2.02	18.37	22.18	22.59	101.22	2.07	4.92
(L4)	104.88	3.07	15.18	22.17	35.61	164.08	4.31	9.16
(L5)	121.88	2.54	20.99	16.61	35.30	95.26	2.91	7.06
(L6)	105.82	3.81	15.05	22.15	34.54	137.00	3.91	10.53
(L7)	96.12	2.58	14.43	18.84	21.02	106.96	2.67	6.16
(L8)	95.33	2.59	15.63	18.73	23.91	131.06	3.21	6.70
(L9)	97.29	1.82	16.08	21.81	35.21	81.31	2.09	4.94
Sids12	108.21	2.52	19.20	18.42	26.23	108.48	2.70	7.05
GIZA 171	123.29	2.60	16.81	17.85	36.88	88.31	2.63	6.42
LSD (5 %)	7.63	0.28	2.15	1.52	8.00	15.80	0.57	1.06
Adequate environment
(L1)	92.07	2.48	14.61	19.61	29.71	107.23	3.03	7.54
(L2)	96.73	3.73	20.46	22.27	47.30	167.73	5.23	11.90
(L3)	117.00	2.13	19.09	23.28	23.11	109.77	2.20	4.91
(L4)	105.17	3.26	15.26	23.46	39.37	184.87	4.74	10.08
(L5)	125.13	2.68	21.42	17.51	34.62	112.47	3.22	8.25
(L6)	109.40	4.06	15.63	23.21	36.07	147.67	4.30	13.52
(L7)	96.37	2.73	14.33	19.24	20.38	106.73	2.86	6.55
(L8)	98.23	2.69	15.86	19.56	25.08	140.83	3.47	7.22
(L9)	98.23	1.89	15.89	22.66	37.31	86.07	2.23	5.45
Sids12	110.60	2.65	19.40	18.66	26.55	111.17	2.79	8.34
GIZA 171	123.53	2.59	16.39	17.93	37.17	88.27	2.70	7.28
LSD 5%	12.38	0.35	3.38	2.47	12.49	28.22	1.05	1.69
Salt stressed environment
(L1)	91.49	2.38	14.67	18.61	29.02	94.50	2.77	6.68
(L2)	94.41	3.06	19.70	20.90	34.17	147.33	4.32	9.40
(L3)	109.23	1.92	17.65	21.08	22.06	92.67	1.94	4.92
(L4)	104.59	2.89	15.10	20.88	31.85	143.28	3.88	8.23
(L5)	118.63	2.41	20.56	15.72	35.97	78.06	2.60	5.87
(L6)	102.24	3.57	14.47	21.09	33.01	126.34	3.52	7.54
(L7)	95.88	2.42	14.53	18.44	21.66	107.19	2.48	5.77
(L8)	92.43	2.49	15.41	17.89	22.74	121.29	2.96	6.18
(L9)	96.35	1.75	16.26	20.96	33.11	76.56	1.94	4.42
Sids12	105.81	2.40	18.99	18.18	25.90	105.78	2.61	5.75
GIZA 171	123.05	2.61	17.22	17.78	36.58	88.36	2.56	5.55
LSD 5%	9.73	0.45	2.89	1.93	10.80	16.33	0.50	1.40

^†NS, nonsignificant at the 0.05 probability level.

Figure 1. Unweighted pair group method arithmetic average (UPGMA) dendrogram for eleven wheat genotypes based on the allelic data of 33 SSR and 31 EST-SSR combinations.

Table 5. The levels of genetic diversity in eleven wheat genotypes by SSR and EST- SSR markers.

Source of primers	No. of primers	No. of loci	No. of alleles	Allele ̸ Loci		Similarity coefficient		PIC value
				Range	Average	Range	Average	Range	Average
SSR	50	33	45	1–3	1.36	0.19–0.7	0.46	0–0.987	0.203
EST-SSR	46	31	38	1–5	1.23	0.22–0.882	0.575	0 to.740	0.08
Combinations	96	64	83	1–5	1.29	0.32–0.7	0.6113	–	–

Table 6. Specific SSR and EST-SSR markers in eleven wheat genotypes under salt stress.

Source of primers	Salt category	Markers	Chromosome number	Size (bp)	Genotypes	Coefficient of determination (R^2)	Significance level
SSR	Salt tolerant	Barc63	6A	210	L6	65	0.00114
		Barc124	5B	100	L1	41	0.01656
		Barc125	7D,3D,4B,5A	130	L1, L2, L4, L6, L8	63	0.00097
		Barc144	5D,5A	250	L2	41	0.01656
		Barc210	1D,2B	200	L2	41	0.01656
EST-SSR	Salt tolerant	Xcwem9	1D,1A,3A	390	L2, L4, L6	78	0.00004
		Xcwem40	5B,5A	120	L2, L4	65	0.00067
		Xcwem45	5B	225	L2, L6	47	0.00780
		Xcwem54	7A,1B,2B	220	L1, L2, L4, L6	63	0.00097