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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (3): 590-602.doi: 10.3724/SP.J.1006.2024.31034


QTL mapping and GWAS analysis of coleoptile length in bread wheat

HAO Qian-Lin1(), YANG Ting-Zhi1, LYU Xin-Ru1, QIN Hui-Min1, WANG Ya-Lin1, JIA Chen-Fei1, XIA Xian-Chun2, MA Wu-Jun1, XU Deng-An1,*()   

  1. 1College of Agronomy, Qingdao Agricultural University, Qingdao 266109, Shandong, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2023-05-18 Accepted:2023-09-13 Online:2024-03-12 Published:2023-09-27
  • Contact: *E-mail: xudengan200@126.com
  • Supported by:
    High-level Talents Project of Qingdao Agricultural University(663/1122023);Shandong Provincial Natural Science Foundation(ZR202103020229);National Natural Science Foundation of China(32101733)


Under drought conditions, the emergence rate of wheat (Triticum aestivum L.) can be improved by proper deep sowing. The maximum sowing depth of wheat is determined by the length of the coleoptile, so it is very important to cultivate wheat varieties with long coleoptile. In this study, a recombinant inbred line (RIL) population consisting of 275 lines derived from the cross of Doumai and Shi 4185, and 186 natural population materials were used as the experimental materials. Genotyping results of 90K SNP chip were used to identify QTL for wheat coleoptile length in three different environments. The results showed that two stable QTL sites were identified by inclusive composite interval mapping in the RIL population. The two QTL located on Chromosome 4BS (30.17-40.59 Mb) and 6BL (700.08-703.53 Mb), respectively, and explained 26.29%-28.46% and 4.16%- 4.36% of the phenotypic variance, respectively. A total of 36 stable QTL were identified in the genome-wide association study (GWAS) using the mixed linear model. They were located on Chromosome 1A (3), 1B (3), 1D (2), 2A (1), 3A (2), 3B (2), 4B (11), 5A (1), 5B (3), 6B (4), 7A (2), and 7B (2), respectively. Seven significant association loci were repeatedly detected in the three environments, three of which overlapped or were adjacent to reported loci, and the other four loci were presumed to be new loci. They were located on Chromosomes 1A (499.03 Mb), 3A (73.06 Mb), 4B (648.74-648.87 Mb), and 7A (36.31 Mb), respectively. Five candidate genes (TraesCS1A03G0748300, Rht1, TraesCS4B03G0110000, TraesCS4B03G0112200, and TraesCS7A03G0146600) were predicted. A major QTL locus on Chromosome 4BS (30.17-40.59 Mb) was identified in both RIL and natural populations, and the candidate gene Rht1 at this locus had been shown to reduce the length of wheat coleoptile. The results of this study lay a foundation for the identification of genes controlling the length of coleoptile in wheat and the maker-assisted selection breeding.

Key words: wheat, coleoptile length, QTL mapping, GWAS

Table 1

Basic statistics of coleoptile length of two parents and 275 lines of the Doumai/Shi 4185 RIL population"

亲本 Parents RIL家系 RIL lines
Shi 4185
CV (%)
E1 5.41 4.49 2.88 6.33 4.32 0.57 13.31
E2 5.65 4.57 3.23 6.16 4.29 0.56 13.06
E3 5.16 4.54 3.10 6.21 4.27 0.58 13.50
BLUE 5.40 4.54 3.14 6.20 4.29 0.55 12.76

Fig. 1

Seedlings of two parents (Shi 4185 and Doumai)"

Fig. 2

Distributions of coleoptile length for the parents and 275 lines of the Doumai/Shi 4185 RIL population E1, E2, and E3 represent the length of coleoptile measured by seeds were collected from Qingdao in 2020 and 2021, Qingdao in 2021 and 2022, and Xinxiang in 2020 and 2021, respectively."

Table 2

Correlations across environments and broad-sense heritability for coleoptile length of the parents and 275 lines of the Doumai/Shi 4185 RIL population"

相关系数 Correlation coefficient 广义遗传力
E1 E2 E3
E1 1 0.92
E2 0.89** 1
E3 0.80** 0.88** 1

Fig. 3

QTL for coleoptile length identified in the Doumai/Shi 4185 RIL population Only partial of the markers in the presented linkage interval are showed in the maps. The “Green Revolution” gene Rht1 showed on linkage groups 4BS, was not used for linkage map construction, and it was arranged on the map based on its and the neighboring markers’ physical positions in Chinese Spring reference genome IWGSC RefSeq v2.1 (http://www.wheatgenome.org/[40])."

Table 3

QTL for coleoptile length identified in the Doumai/Shi4185 RIL population"

Flanking marker
Physiol interval (Mb) b
LOD value c
PVE (%)
QCL.qau-4BS E1 IWA102-IWB54814 30.17-40.59 18.43 27.84 0.32
E2 IWA102-IWB54814 30.17-40.59 15.51 26.29 0.30
E3 IWA102-IWB54814 30.17-40.59 16.99 26.66 0.31
BLUE IWA102-IWB54814 30.17-40.59 19.32 28.46 0.31
QCL.qau-6BL E1 IWB19986-IWB35852 702.16-703.53 3.15 4.16 -0.12
E3 IWB63870-IWB19986 700.08-702.16 3.02 4.36 -0.12
BLUE IWB19986-IWB35852 702.16-703.53 15.03 20.97 -0.25

Table 4

Statistical analysis on coleoptile length evaluated on 186 natural population materials"

CV (%)
相关系数 Correlation coefficient 遗传力
E1 E2 E3
E1 3.98 0.55 13.74 1 0.91
E2 4.01 0.56 14.07 0.94** 1
E3 4.03 0.57 14.25 0.93** 0.93** 1
BLUE 4.01 0.55 13.70

Fig. 4

Distributions of coleoptile length of the 186 natural population materials E1, E2, and E3 represent the length of coleoptile measured by seeds collected from Qingdao in 2020 and 2021, Qingdao in 2021 and 2022, and Xinxiang in 2020 and 2021, respectively."

Fig. 5

Kinships and population structure of the 186 natural population materials used in this study A: phylogenetic relationship; B: principal component analysis; C: Neighbor-Jointing tree analysis."

Table 5

CL-associated loci detected in at least two environments by MLM"

Environment a
Marker name
Allele b
Physical position (Mb) c
P-value min. d
P-value max. d
E1/BLUE IWB30674 G/A 1A:48.36 1.59E-04 3.16E-05
E1/E2/E3/BLUE IWB50788 G/A 1A:499.03 6.07E-04 1.40E-04
E3/BLUE IWA7871 G/A 1A:505.76 5.98E-04 1.23E-04
E1/E3/BLUE IWB21039 G/A 1B:30.67 9.25E-04 1.99E-04
E3/BLUE IWB53874 G/A 1B:588.25 2.83E-04 2.28E-04
E3/BLUE IWB74028 G/A 1B:690.58 8.03E-04 7.03E-04
E1/BLUE IWB18554 G/A 1D:42.77 1.00E-03 4.68E-04
E1/BLUE IWA830 G/A 1D:43.07 1.00E-03 4.68E-04
E1/E2/BLUE IWB64018 G/A 2A:757.65 3.83E-04 1.30E-05
E2/E3/BLUE IWB2733 G/A 3A:72.88 8.60E-04 6.15E-04
E1/E2/E3/BLUE IWB53051 G/A 3A:73.06 5.40E-04 1.52E-04
E1/E2/E3/BLUE IWB24605 G/A 3B:19.95 2.26E-04 1.17E-04
E1/BLUE IWB39644 G/A 3B:75.98 7.11E-04 5.20E-04
E1/E2/E3/BLUE IWB49875 G/A 4B:24.28 8.57E-04 5.50E-05
E1/E2/E3/BLUE IWB70449 G/A 4B:40.43 7.36E-04 9.01E-05
E1/E2/E3/BLUE IWB54814 G/A 4B:40.59 3.42E-05 7.35E-06
E1/BLUE IWA6850 G/A 4B:40.76 9.74E-04 8.55E-04
E1/E3/BLUE IWB4719 G/A 4B:40.77 5.04E-04 1.79E-04
E1/E3/BLUE IWB25737 G/A 4B:41.02 5.55E-04 2.55E-04
E1/BLUE IWB40899 G/A 4B:574.98 7.29E-04 5.86E-04
E1/BLUE IWB59718 G/A 4B:577.08 8.58E-04 8.18E-04
E1/BLUE IWB71859 G/A 4B:578.54 9.42E-04 7.17E-04
E1/E2/E3/BLUE IWB53155 G/A 4B:648.74 3.86E-04 5.06E-05
E1/E2/E3/BLUE IWB42023 G/A 4B:648.87 5.14E-04 6.61E-05
E1/E3 IWB35845 G/A 5A:710.07 5.69E-04 5.66E-04
E1/BLUE IWA6527 G/A 5B:211.64 7.49E-04 2.81E-04
E1/BLUE IWB71849 G/A 5B:607.90 9.62E-04 2.43E-04
E/E2 IWB63425 G/A 5B:75.60 9.64E-04 9.60E-04
E2/E3 IWB62054 G/A 6B:123.26 7.01E-04 6.74E-04
E2/BLUE IWB56800 G/A 6B:128.10 6.75E-04 4.32E-04
E2/E3 IWB68130 G/A 6B:146.70 9.96E-04 5.02E-04
E2/E3 IWB65561 G/A 6B:683.94 8.99E-04 7.31E-04
E2/E3 IWB22879 G/A 7A:31.41 7.50E-04 5.52E-04
E1/E2/E3/BLUE IWB11001 G/A 7A:36.31 8.74E-04 4.53E-05
E3/BLUE IWB72566 G/A 7B:203.84 9.80E-04 4.88E-04
E1/E3/BLUE IWB11945 G/A 7B:204.38 7.06E-04 1.98E-04

Fig. 6

Genome wide association study of coleoptile length in 186 natural population materials A: the manhattan plot for the BLUE of coleoptile length based on the mixed linear models, X-axis shows SNP markers along each wheat chromosome, Y-axis is the -log10 (P-value); B: the quantile-quantile plot for the BLUE of coleoptile length based on the mixed linear models, the X-axis shows -log10 transformed expected P-values and Y-axis shows -log10 transformed observed P-values."

Table 6

Candidate genes for the loci associated with CL"

Marker name
Position (Mb) a
Gene name b
Position (Mb) c
Homologs d
Gene function
IWB50788 1A:499.03 1A03G0748300 1A:496.71 OsEXP4[48] Alpha-expansin OsEXPA4
IWB70449 4B:40.43 Rht1 4B:33.61 DELLA protein
IWB54814 4B:40.59 4B03G0110000 4B:42.02 AT5G39760[50] Zinc finger homeodomain protein
IWB54814 4B:40.59 4B03G0112200 4B:43.56 AT1G09570[51] Phytochrome A
IWB11001 7A:36.31 7A03G0146600 7A:32.23 AT5G13320[52] Auxin-responsive GH3 protein
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