Mapping QTL underlying plant height at three development stages and its response to density in soybean [Glycine max (L.) Merri.]

Figures & data

Table 1. QTL for plant height at pod bearing stage.

QTL	Left Marker	Right Marker	Genomic position † cM	Environment ‡	Population §	LOD ¶	a ǁ	PVE or R^2 lll
qPH-A2-1	Satt424	Sat_294	60.59-131.97	HD2	RIL3613	2.8/*/1.4/*	6.30/*/3.33/*	10.21/*/0.04/*
qPH-B2-1	satt577	Satt070	6.05-72.80	HD1	RIL6013	8.4/*/1.2/*	19.11/*/4.19/*	5.19/*/0.02/*
qPH-C1-2	Satt396	Sat_140	24.11-41.43	KD1	RIL3613	*/3.0/1.0/*	*/5.17/3.20/*	*/0.08/0.04/*
qPH-D1a-1	Sat_413	Sat_160	5.93-104.27	KD1	RIL6013	3.6/2.6/*/*	13.98/12.93/*/*	9.99/ 0.42/*/*
qPH-E-1	Satt720	Satt651	20.79-32.09	HD1	RIL3613	*/6.0/2.0/1.4	*/-8.59/-3.74/-3.36	*/0.38/0.07/0.05
qPH-I-1	satt367	satt330	27.98-77.83	HD1	RIL6013	3.2/3.1/*/2.2	15.37/13.78/*/5.92	2.00/0.25/*/0.00
qPH-I-2	Satt239	Satt354	36.93-46.22	HD1	RIL3613	*/3.3/1.5/0.9	*/6.22/3.89/2.93	*/0.13/0.05/0.01
qPH-K-1	Sat_243	satt673	50.79-86.77	HD1	RIL6013	5.3/*/1.0/*	−18.41/*/-4.21/*	4.98/*/0.03/*
qPH-L-2	Satt497	Sat_099	33.70-78.23	HD2	RIL3613	3.3/2.6/1.8/2.5	7.53/6.50/3.62/7.10	9.84/0.15/0.05/0.08
qPH-M-1	Satt567	Satt346	33.47-112.79	HD2	RIL3613	3.8/*/2.4/3.2	−5.87/*/-3.88/-4.46	10.65/*/0.08/0.09
qPH-M-2	Satt567	Satt697	33.47-85.34	KD1	RIL3613	3.0/3.2/2.5/*	−6.86/-7.04/-4.20/*	9.13/0.24/0.09
	Satt567	Satt697		KD2	RIL3613	3.9/2.9/3.5/*	−7.82/-5.33/-4.98/*	12.63/0.15/0.12/*
qPH-M-3	Satt346	Sat_121	103.98-112.79	HD2	RIL3613	*/3.2/*/1.0	*/-4.15/*/-2.48	*/0.12/*/0.03
qPH-N-1	Satt584	Sat_166	37.98-38.59	HD1	RIL6013	*/2.5/*/1.0	*/13.91/*/10.24	*/0.10/*/0.03
qRDPH-A2-1	Satt424	Sat_294	60.59-131.97	HRB	RIL3613	2.8/*/2.0/*	6.19/*/3.60/*	10.99/*/0.07/*
qRDPH-F-1	satt343	satt030	3.04-3.95	HRB	RIL6013	*/3.6/*/1.3	*/6.20/*/2.92	*/0.18/*/0.02
qRDPH-G-1	satt570	AW734137	12.74-15.63	KS	RIL6013	*/3.5/1.1/1.5	*/-3.96/-2.30/-2.65	*/0.09/0.02/0.01
qRDPH-G-2	sat_210	AW734137	3.71-5.63	KS	RIL6013	*/6.8/2.2/*	*/-7.21/-3.18/*	*/0.25/*/*
qRDPH-M-1	Satt567	Satt346	33.47-112.79	HRB	RIL3613	3.1/4.4/1.5/2.2	−5.28/-5.89/-2.91/-3.48	9.30/0.13/0.06/0.08

†: Genomic position means the genetic area in soybean public genetic map [42].

‡: HD1 means planting density of 2.2 × 10⁵ plants/hm² in Harbin; HD2 means planting density of 3.1 × 10⁵ plants/hm² in Harbin; KD1 means planting density of 2.6 × 10⁵ plants/hm² in Keshan; KD2 means planting density of 3.5 × 10⁵ plants/hm² in Keshan. HRB represent Location Harbin and KS represent Keshan.

§: RIL3613 refers to recombinant inbred lines population derived from Dongnong L13 × Heihe36; RIL6013 refers to recombinant inbred lines population derived from Dongnong L13 × Henong60.

¶: In LOD₁/ LOD ₂/ LOD ₃/ LOD ₄, LOD ₁ refer to log of odd (LOD) of inclusive compositive interval mapping methods (ICIM); LOD ₂ refer to log of odd (LOD) of compositive interval mapping methods (CIM); LOD ₃ refer to log of odd (LOD) of single marker analysis methods (SMA) for left marker; LOD ₄ refer to log of odd (LOD) of single marker analysis methods (SMA) for right marker. * represent that the QTL could not be detected the corresponding method.

ǁ: In a₁/ a₂/ a₃/a ₄, a₁ refer to additive effects derived from inclusive composite interval mapping methods (ICIM); a₂ refer to additive effects derived from composite interval mapping methods (CIM); a₃ refer to additive effects derived from single marker analysis methods (SMA) for left marker; a₄ refer to additive effects derived from single marker analysis methods (SMA) for right marker. * represent that the QTL could not be detected the corresponding method.

lll:In PVE/ R²₁/ R²₂/ R²₃, PVE refer to PHenotypic variation ratio of explanation of the QTL computed by inclusive composite interval mapping methods (ICIM); R²₁ refer to determination coefficient of the QTL computed by composite interval mapping methods (CIM); R²₂ refer to determination coefficient of the QTL computed by single marker analysis methods (SMA) for left marker; R²₃ refer to determination coefficient of the QTL computed by single marker analysis methods (SMA) for right marker. * represent that the QTL could not be detected the corresponding method.

Table 2. QTL for plant height at seed filling period.

QTL	Left Marker	Right Marker	Genomic position † cM	Environment ‡	Population §	LOD ¶	a ǁ	PVE or R^2 lll
qPH-B1-1	Sat_270	Satt359	21.99-102.55	HD1	3613	*/3.3/2.0/*	*/9.00/7.69/*	*/0.14/0.07/*
qPH-C1-1	satt565	Satt713	0.00-88.94	KD2	6013	2.9/4.1/1.2/1.8	6.39/7.89/3.02/3.62	7.21/0.24/0.00/0.02
qPH-F-1	sat_039	Sat_417	27.87-135.94	HD1	6013	*/3.0/1.9/*	*/12.18/5.75/*	*/0.32/0.00/*
qPH-G-1	AZ254740	Satt688	8.23-12.54	HD2	3613	*/3.9/2.2/1.1	*/-6.63/-4.79/-3.63	*/0.12/0.07/0.04
qPH-L-1	Satt182	Satt497	14.03-33.7	HD2	3613	*/3.2/* /1.1/	*/6.03/*/3.59	*/0.13/*/0.03
qPH-M-2	Satt567	Satt697	33.47-85.34	HD2	3613	2.6/3.2/2.1/*	−6.56/-7.36/-4.56/*	11.80/0.19/0.07/*
qPH-M-4	Satt536	Satt655	62.13-76.41	KD1	3613	3.4/*/1.7/2.6	5.11/*/3.50/4.33	9.12/*/0.06/0.09
qPH-N-2	Satt675	Satt080	34.65-45.13	HD2	3613	2.9/3.9/ 0.9/2.7	5.17/5.30/3.00/5.06	7.29/0.17/0.03/0.08
qRDPH-D1b-1	AI856451	Satt041	50.11-84.04	HRB	3613	*/3.2/*/2.8	*/-5.05/*/-5.03	*/0.12/*/0.08
qRDPH-M-2	Satt536	Satt655	62.13-76.41	HRB	3613	*/3.3/1.8/*	*/4.78/3.48/*	*/0.14/0.07/*

†: Genomic position means the genetic area in soybean public genetic map [42].

‡: HD1 means planting density of 2.2 × 10⁵ plants/hm² in Harbin; HD2 means planting density of 3.1 × 10⁵ plants/hm² in Harbin; KD1 means planting density of 2.6 × 10⁵ plants/hm² in Keshan; KD2 means planting density of 3.5 × 10⁵ plants/hm² in Keshan. HRB represent Location Harbin and KS represent Keshan.

§: RIL3613 refers to recombinant inbred lines population derived from Dongnong L13 × Heihe36; RIL6013 refers to recombinant inbred lines population derived from Dongnong L13 × Henong60.

¶: In LOD₁/ LOD₂/ LOD₃/ LOD₄, LOD₁ refer to log of odd (LOD) of inclusive compositive interval mapping methods (ICIM); LOD ₂ refer to log of odd (LOD) of compositive interval mapping methods (CIM); LOD ₃ refer to log of odd (LOD) of single marker analysis methods (SMA) for left marker; LOD ₄ refer to log of odd (LOD) of single marker analysis methods (SMA) for right marker. * represent that the QTL could not be detected the corresponding method.

ǁ: In a₁/ a₂/ a₃/a ₄, a₁ refer to additive effects derived from inclusive composite interval mapping methods (ICIM); a₂ refer to additive effects derived from composite interval mapping methods (CIM); a₃ refer to additive effects derived from single marker analysis methods (SMA) for left marker; a₄ refer to additive effects derived from single marker analysis methods (SMA) for right marker. * represent that the QTL could not be detected the corresponding method.

lll: In PVE/ R²₁/ R²₂/ R²₃, PVE refer to PHenotypic variation ratio of explanation of the QTL computed by inclusive composite interval mapping methods (ICIM); R²₁ refer to determination coefficient of the QTL computed by composite interval mapping methods (CIM); R²₂ refer to determination coefficient of the QTL computed by single marker analysis methods (SMA) for left marker; R²₃ refer to determination coefficient of the QTL computed by single marker analysis methods (SMA) for right marker. * represent that the QTL could not be detected the corresponding method.

Table 3. QTL for plant height at maturity period.

QTL	Left Marker	Right Marker	Genomic position † cM	Environment ‡	Population §	LOD ¶	a ǁ	PVE or R^2 lll
qPH-B1-2	Satt197	Satt359	46.38-102.55	KD1	3613	2.9/2.9/1.9/1.0	−5.68/-5.98/ −3.84/-2.94	5.31/0.13/ 0.07/0.04
				KD2	3613	2.6/*/1.8/*	−5.22/*/-3.82/*	8.62/*/0.06/*
qPH-C1-1	satt565	Satt713	0-88.94	KD2	6013	*/3.0/*/1.8	*/5.65/*/4.02	*/0.10/*/0.00
qPH-C1-3	Satt396	Sat_367	24.11-28.04	KD1	3613	*/3.0/1.7/1.2	*/5.47/4.25/3.27	*/0.10/0.05/0.04
qPH-G-2	Satt503	Satt288	68.76-76.76	KD1	3613	2.7/*/0.9/*	−8.16/*/-2.62/*	11.69/*/0.03/*
	Satt503	Satt288		KD2	3613	*/2.7/0.9/*	*/-8.53/-2.61/*	*/0.30/0.03/*
qPH-H-1	satt293	Satt181	89.08-91.12	HD1	6013	*/4.6/2.2/*	*/7.92/5.37/*	*/0.11/0.00/*
qPH-M-4	Satt536	Satt655	62.13-76.41	KD2	3613	2.7/4.4/1.8/2.5	5.07/5.67/3.75/4.35	8.50/0.15/0.06/0.09
qRDPH-B1-1	Sat_247	Satt484	49.73-118.52	KS	3613	*/4.6/3.1/*	*/5.33/3.79/*	*/0.23/0.04/*

†: Genomic position means the genetic area in soybean public genetic map [42].

‡: HD1 means planting density of 2.2 × 10⁵ plants/hm² in Harbin; HD2 means planting density of 3.1 × 10⁵ plants/hm² in Harbin; KD1 means planting density of 2.6 × 10⁵ plants/hm² in Keshan; KD2 means planting density of 3.5 × 10⁵ plants/hm² in Keshan. HRB represent Location Harbin and KS represent Keshan.

§:RIL3613 refers to recombinant inbred lines population derived from Dongnong L13 × Heihe36; RIL6013 refers to recombinant inbred lines population derived from Dongnong L13 × Henong60.

¶: In LOD₁/ LOD ₂/ LOD ₃/ LOD ₄, LOD ₁ refer to log of odd (LOD) of inclusive compositive interval mapping methods (ICIM); LOD ₂ refer to log of odd (LOD) of compositive interval mapping methods (CIM); LOD ₃ refer to log of odd (LOD) of single marker analysis methods (SMA) for left marker; LOD ₄ refer to log of odd (LOD) of single marker analysis methods (SMA) for right marker. * represent that the QTL could not be detected the corresponding method.

ǁ: In a₁/ a₂/ a₃/a ₄, a₁ refer to additive effects derived from inclusive composite interval mapping methods (ICIM); a₂ refer to additive effects derived from composite interval mapping methods (CIM); a₃ refer to additive effects derived from single marker analysis methods (SMA) for left marker; a₄ refer to additive effects derived from single marker analysis methods (SMA) for right marker. * represent that the QTL could not be detected the corresponding method.

lll: In PVE/ R²₁/ R²₂/ R²₃, PVE refer to PHenotypic variation ratio of explanation of the QTL computed by inclusive composite interval mapping methods (ICIM); R²₁ refer to determination coefficient of the QTL computed by composite interval mapping methods (CIM); R²₂ refer to determination coefficient of the QTL computed by single marker analysis methods (SMA) for left marker; R²₃ refer to determination coefficient of the QTL computed by single marker analysis methods (SMA) for right marker. * represent that the QTL could not be detected the corresponding method..

Figure 1. Temporal contribution of QTL.

Temporal development of PVE or R² of the QTL detected at PBS, SFS and MS for PH under low seeding density (Left) and high density (Right)

Figure 2. Venn diagram for QTL related to PH detected under two densities at three developmental stages.

PBS: Pod bearing stage; SFS: Seeds filling stage; MS: Maturity stage

D1: Planting density of 2.2 × 10⁵ plants/hm² in Harbin OR 2.6 × 10⁵ plants/hm² in Keshan; KD2 means planting density of 3.1 × 10⁵ plants/hm² in Harbin OR 3.5 × 10⁵ plants/hm² in Keshan

Figure 3. Additive effects of QTL for PH and AED detected in two populations under two kinds of densities over two location.

In the name of QTL, 36- or 60- represent QTL detected in RIL3613 or RIL6013 population; D1 or D2 indicate QTL detected under the first or second kind of density; qph and qphae represent QTL of PH and AED; B1, I, …, represent linkage groups; the number, i.e., 1,2, 3,4 represent the sequence of QTL in one linkage group.

Figure 4. Additive effects of allelic combination of QTL qph-C1-3, qph-B1-2, qph-G-2 associated with PH at maturity stages.

Q1 and q1 represent allele of qph-C1-3 carried by Dongnong L13 and Heihe36, Q2 and q2 represent allele of qph- B1-2 carried by Dongnong L13 and Heihe36, Q3 and q3 represent allele of qph- G -2 carried by Dongnong L13 and Heihe36.

Figure 5. Theory and sample means of allelic combination of QTL qph-C1-3, qph-B1-2, qph-G-2 associated with PH at maturity stages.

Q1 and q1 represent allele of qph-C1-3 carried by Dongnong L13 and Heihe36, Q2 and q2 represent allele of qph-B1-2 carried by Dongnong L13 and Heihe36, Q3 and q3 represent allele of qph-G-2 carried by Dongnong L13 and Heihe36.

^{a, b, c} indicate the significance of difference between the phenotype means of allelic combination, i.e., no same letter means difference between two allelic combination was significant at 0.05 level, the reverse is also true.

Song QJ, Marek LF, Shoemaker RC, et al. A new integrated genetic linkage map of the soybean. Theor Appl Genet. 2004;109(1):122–128.

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