Mapping the major quantitative trait loci of the heading date trait in Qingke barley (Hordeum vulgare L.) from the Qinghai-Tibetan Plateau via genotyping by sequencing

Figures & data

Figure 1. Phenotypic comparison of the two parents in terms of the heading date. (a) Dazhangzi, an early-maturing parent, shows early heading, whereas (b) Kunlun 10, a late-maturing parent, shows late heading.

Figure 2. Heading date comparison and distribution of the parents and the F_2:3 populations derived from a cross between Dazhangzi and Kunlun 10, which were measured under three spring ecological conditions and environments in 2020 consisting of 20QW (Quanwan), 20MY (Menyuan), and 20XN (Xining).

Table 1. Summary statistics of the heading date trait of the parents and the F_2:3 populations across 20QW (Quanwan), 20MY (Menyuan), and 20XN (Xining).

	Parents			F2:3
Environment ^a	Dazhangzi	Kunlun 10	Range	Mean ± SD^b	Skewness	Kurtosis
20QW	39.33 ± 0.58	53.80 ± 0.84**	35.00-58.00	44.13 ± 3.96	0.44	0.02
20MY	59.00 ± 0.82	75.63 ± 1.30**	54.00-91.00	67.79 ± 4.86	1.04	3.72
20XN	46.67 ± 0.58	58.80 ± 0.84**	46.00-70.00	53.18 ± 2.61	0.15	0.63

** represents the 0.01 level of significance between both parents within the same environment based on the Student’s t-test, where ‘a’ represents the environment and ‘b’ represents standard deviation (SD).

Table 2. Analysis of variance and broad-sense heritability of the heading date.

Source of variation	DF	SS	MS	F value	h^2 (%)
Environment (E)	2	263101.073	131550.537	20627.432**	83.61
Genotype (G)	130	19111.016	147.008	23.051**
Genotype × environment (E × G)	244	6635.015	27.193	4.264**
Error	3456	22040.488	6.377
Corrected total	3833	12896405.000

DF: degrees of freedom; SS: sum of squares; MS: mean square; F value: F test value; E × G: genotype by environment interaction; h²: broad-sense heritability; and ** represents a 0.01 significance level.

Figure 3. QTL mapping of the heading date trait in the F_2:3 population derived from a cross between Dazhangzi and Kunlun 10. Ten heading date QTL that were identified in the three environments are distributed among four chromosomes. The colored lines represent the QTL detected in each environment, and the line with two colors represents the QTL detected in different environments simultaneously. The two consensus QTL are located on the chromosome 2, while the six specific QTL were identified by the single-environment analysis across the three environments.

Table 3. Consensus, specific, and identified quantitative trait loci (QTL) of the heading date trait within the F_2:3 population in 2020.

Consensus/Specific QTLs	Peak (cM)	CI (cM)	Identified QTLs	LG	LOD	R^2 (%)	ADD	Peak (cM)	CI (cM)	QTL type
cqHD2H-1	49.00	48.64-49.35	qHD2H-20MY1	2H	15.22	13.36	3.65	49.00	48.50-49.50	Major
			qHD2H-20XN1	2H	19.54	16.13	3.49	49.00	48.50-49.50
cqHD2H-2	52.99	52.63-53.36	qHD2H-20MY2	2H	24.62	25.35	−4.97	53.00	52.50-53.50	Major
			qHD2H-20XN2	2H	29.22	29.65	−4.65	53.00	52.50-53.50
sqHD2H-1	51.00	50.50-51.50	qHD2H-20QW1	2H	18.92	25.94	−3.49	51.00	50.50-51.50	Major
sqHD5H-1	100.00	99.50-100.50	qHD5H-20QW1	5H	3.36	3.82	−1.16	100.00	99.50-100.50	Minor
sqHD7H-1	96.00	95.50-96.50	qHD7H-20QW1	7H	4.20	5.43	−1.53	96.00	95.50-96.50	Minor
sqHD3H-1	55.00	52.50-57.50	qHD3H-20MY1	3H	3.16	2.37	−1.03	52.50	52.50-57.50	Minor
sqHD7H-2	98.00	97.50-98.50	qHD7H-20MY1	7H	3.53	2.64	−1.53	98.00	97.50-98.50	Minor
sqHD3H-2	82.00	80.50-82.50	qHD3H-20XN1	3H	2.62	1.51	−0.81	82.00	80.50-82.50	Minor

Three environments of QW (Quanwan), MY (Menyuan), and XN (Xining); planting year: 2020; CI: confidence interval of the QTL; LG: specific linkage group; R²: phenotypic variation explained by the QTL; ADD: additive effect of the QTL; LOD: logarithm of odds score at the QTL peak; and QTL type: whether the QTL is major or minor.

Figure 4. Genetic and comparative mapping of the cqHD2H-2. (a) Linkage map of markers of cqHD2H-2. (b) A partial physical map of the linkage markers surrounding cqHD2H-2. The red region indicates the cqHD2H-2 candidate interval, which corresponds to 590,448,597 bp and 674,532,202 bp. (c) HORVU2Hr1G087460 gene corresponding homologous genes of DTH8 of rice.

Data availability statement

The data that support the findings of this study are openly available in figshare.com at https://doi.org/10.6084/m9.figshare.14866248.v4.