QTL for yield per plant under water deficit and well-watered conditions and drought susceptibility index in soybean (Glycine max (L.) Merr.)

Figures & data

Table 1. Analysis of variance (ANOVA) of soybean seed yield per plant (YP) under drought stressed and full irrigation conditions for 149 soybean accessions.

Source^a	DF^b	Sum of squares	Mean square	F value	Pr > F
Block (Env × Treatment)	12	613.1578	51.0965	11.19	<0.0001
Treatment	1	10259.0812	10259.0812	2246.78	<0.0001
Env	2	19780.1371	9890.0686	2165.97	<0.0001
Env × Treatment	2	1031.5607	515.7803	112.96	<0.0001
Geno	148	5221.2699	35.2789	7.73	<0.0001
Geno × Treatment	148	1210.2212	8.1772	1.79	<0.0001
Geno × Env	296	4956.8638	16.7462	3.67	<0.0001
Geno × Env × Treatment	295	1795.3308	6.0859	1.33	0.0004

^aBlock (Env × Treatment) means the block is nested within Environment × Treatment; Env means environment; Geno means genotype; and Geno × Env means genotype by environment interaction.

^bDegrees of freedom.

Table 2. Descriptive statistics of seed yield per plant (YP) under drought stressed and full irrigation conditions and DSI-YP values for 149 soybean cultivars.

Traits	Minimum	Maximum	Mean	SD^d	CV^e
YP-W^a	4.9127	13.1329	7.2484	0.9676	13.35
YP-S^b	2.9344	6.4222	4.0045	0.6324	15.79
DSI^c	0.5745	1.2719	0.9964	0.1439	14.43

^aYP-W is seed yield per plant under full irrigation conditions.

^bYP-S is seed yield per plant under drought stressed conditions.

^cDSI is drought susceptibility index.

^dSD is standard deviation.

^eCV is coefficient of variation.

Table 3. Phenotypic BLUP (best linear unbiased prediction) correlations between seed yield per plant (YP) under drought stressed and full irrigation conditions and DSI-YP in the 149 soybean cultivars.

Seed yield per plant	YP-S	DSI^c
YP-W^a	0.6950***	0.1865*
YP-S^b		−0.5711***

*** Significance level <0.0001 in Pearson correlation test

*Significance level <0.05 in Pearson correlation test.

^aYP-W is soybean yield under full irrigation conditions.

^bYP-S is soybean yield under drought stressed conditions.

^cDSI is drought susceptibility index.

Figure 1. Frequency distributions of YP-W (A), YP-S (B) and DSI (C) in the 149 soybean accessions.

Figure 2. Genetic structure and relatedness of the 149 soybean accessions. (A) Evolution of the natural logarithm probability of the data against K and the magnitude of Δk for each k value. (B) Clustering using k = 2 for the entire panel of soybean accessions. Each accession is represented by a vertical bar, partitioned into colored segments with the length of each segment representing the proportion of each individual genome contributed by either group when k = 2. (C) Unrooted neighbor-joining tree constructed using SNP data; soybean accessions from Heilongjiang are shown in red; from Jilin are shown in black; from Beijing are shown in purple; and from Japan are shown in blue. (D) Principal component analysis for the entire panel of soybean accessions.

Table 4. SNPs significantly associated with YP under drought stressed and full irrigation conditions and DSI-YP.

Marker	Chr.	Position	Associated Traits (R^2 %)	Method	−log10(P)	Reported QTLs/genes
ss244375521	1	5369218	YP-W(4.71/6.60)	FASTmrMLM/ pLARmEB	4.7878/ 6.2699
ss244871057	2	47979951	DSI-YP(1.70)/YP-S(2.33)	pLARmEB/ pLARmEB	4.0728/ 4.2563	Seed coat hardness [56]; Lateral root density [57]; Root dry weight [58]; Seed weight [59]; Plant dry weight [58]; Seed protein [60]; Seed oil [60]
ss245133420	3	33143761	YP-S(4.00)	pLARmEB	4.2432
ss245630456	5	8589397	YP-W(26.65)	FASTmrEMMA	11.5589
ss245842048	6	8979504	DSI-YP(12.02/7.68)	mrMLM/ FASTmrEMMA	4.8821/ 4.0254	Seed isoflavone [61]
ss245889259	6	15057987	YP-W(5.78)	FASTmrMLM	4.2239	Seed weight [62]; Seed set [63]; Seed protein [64]; Pod maturity [65]; Sudden death syndrome [66]
ss246509299	8	10755506	YP-S(2.18)	pLARmEB	3.997	Canopy wilt [34]; Seed coat hardness [56]; Root dry weight [67]; Root fresh weight [67]; Seed weight [62]; Seed set [63]; Seed oil [60]; Soybean cyst nematode [68]
ss246573652	8	17927603	YP-S(4.58)	pLARmEB	4.4939
ss246821668	9	6300834	YP-W(5.67)	pLARmEB	7.2029
ss247081352	10	2715719	YP-W(8.49/13.73)	FASTmrMLM/ pLARmEB	4.487/ 8.3561	Seed yield [69–70]; Seed set [71]; Root to shoot weight ratio [72]
ss247927074	13	9019809	YP-S(3.13)	pLARmEB	3.904	Phytophthora root rot [73]; Seed stearic acid [74]
ss248616287	15	12547291	YP-W(4.41)	pLARmEB	6.6676
ss249310678	17	9428953	YP-W(2.61)	pLARmEB	3.9854	Canopy wilt [33, 35, 36]; Drought index [9]; Seed weight [75]; Seed yield [76]; Seed oil [77]
ss249576244	18	7314370	YP-W(4.26)	FASTmrMLM	4.9919
ss249600231	18	9265696	YP-S(8.15/5.07)	mrMLM/ FASTmrMLM	4.0758/ 4.6635
ss249889306	18	55508285	YP-S(3.51)	ISIS EM-BLASSO	4.0714	Seed yield [9]; Seed weight [78]; Plant height [79]; Soybean cyst nematode [80]
ss250063822	19	8965290	YP-S(4.83)	FASTmrMLM	4.6180	Plant height [81]; Seed oil [60]
ss250170677	19	35475642	YP-S(10.05/5.72)	mrMLM/ ISIS EM-BLASSO	5.6023/ 4.1864	Plant height [81]; Seed oil [82]
ss250223327	19	40292810	YP-S(4.94)	pLARmEB	4.0462	Seed weight [77]; Seed protein [60, 83]; Seed oil [60]

Figure 3. Manhattan plots from the Q + K model across YP-W (A), YP-S (B) and DSI-YP (C). The names of candidate genes that are hit by significant SNPs are labeled on the top.

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Data availability statement

The data that support the findings of this study are available from the corresponding author, [LJQ], upon reasonable request.