Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (24): 4814-4825.doi: 10.3864/j.issn.0578-1752.2023.24.002


Identification and Genetic Analysis of QTL for Spike Length in Wheat

YAO QiFu1(), ZHOU JieGuang2(), WANG Jian2, CHEN HuangXin2, YANG YaoYao2, LIU Qian2, YAN Lei2, WANG Ying2, ZHOU JingZhong3, CUI FengJuan3, JIANG Yun4(), MA Jian2()   

  1. 1 College of Agroforestry Engineering and Planning, Tongren University/Guizhou Key Laboratory of Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren 554300, Guizhou
    2 Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130
    3 Tongliao Institute of Agriculture and Animal Husbandry Sciences, Tongliao 028015, Inner Mongolia
    4 Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu 610000
  • Received:2023-08-11 Accepted:2023-10-10 Online:2023-12-16 Published:2023-12-21
  • Contact: JIANG Yun, MA Jian


【Objective】Spike length (SL) plays an important role in determining spike structure and yield potential of wheat. Quantitative trait loci (QTL) for spike length were excavated and their genetic effects were further analyzed to provide theoretical basis for molecular breeding. 【Method】This study consisted of a population of 198 F6 recombinant inbred lines (RIL) derived from the cross between the natural mutant msf and the cultivar Chuannong 16 (MC population). The MC population and its parents were planted in five different environments including Wenjiang in 2021 and 2022 (2021WJ and 2022WJ); Chongzhou in 2021 and 2022 (2021CZ and 2022CZ); and Ya’an in 2021 (2021YA) for spike length measurement. The 16K SNP chip-based constructed high-quality and high-density genetic linkage maps were used to map QTL for spike length. Additionally, the genotype of the flanking markers for the major spike length QTL was used to analyze its genetic effect on yield-related traits and thus to evaluate its potentiality for yield improvement.【Result】A total of 14 QTL for spike length were identified and they were mainly distributed on chromosomes 1A (one), 1B (one), 2B (one), 3D (three), 4A (one), 4D (two), 5A (one), 5B (one), 7A (one), 7B (one), and 7D (one). Among them, QSl.sau.1A was detected in four environments and the best linear unbiased prediction (BLUP) value, explained 6.46% to 20.12% of the phenotypic variation, and thus was regarded as a major QTL. The positive allele at QSl.sau.1A came from the parental line msf. QTL analysis across multiple environments also detected QSl.sau.1A, indicating it exhibits minimal environmental influence and represents a major and stably expressed QTL. The effect of QSl.sau.1A was successfully verified in two populations with different genetic backgrounds. Genetic effects analysis showed that the positive allele of QSl.sau.1A showed a significant effect on improving grain number per spike (12.68%), grain weight per spike (14.99%), 1000-grain weight (5.79%), flag leaf width (2.94%), spikelet number (1.48%), and flowering date (0.61%), and a significant effect of reducing plant height (-6.47%) and effective tiller number (-36.11%).【Conclusion】A major and stably expressed spike length QTL, QSl.sau.1A, was detected on chromosome 1A. Its positive allele significantly increased grain number per spike, grain weight per spike, thousand grain weight, and spikelet number per spike, indicating its great breeding value.

Key words: wheat, 16K SNP array, QTL, spike length, yield

Table 1

Phenotypic distribution of spike length for parents and RIL in MC population"

亲本Parents 重组自交系RIL
msf 川农16
Spike length (cm)
2021WJ 14.33** 10.24 8.95-18.68 12.16±1.29 0.97 2.87
2021CZ 9.84** 8.90 7.29-14.70 9.93±1.21 1.04 1.96
2021YA 12.40N 8.60 7.05-15.50 11.1±1.65 0.14 -0.19
2022WJ 14.36** 9.74 8.03-16.59 11.47±1.35 0.52 0.71
2022CZ 13.08** 10.68 8.17-16.95 11.76±1.50 0.19 -0.01
BLUP 12.44 10.03 9.71-14.38 11.29±0.75 0.35 0.51

Fig. 1

Spike phenotype of MC population"

Fig. 2

Frequency distribution and correlations of spike length for MC population in different environments **: Significant difference at level 0.01. The same as below"

Table 2

Analysis of variance for spike length in MC population"

G×E interaction
自由度Degrees of freedom 197 4 734 5.00 905
均方Mean square 9.28 282.26 2.33 0.07 0.31
F临界值F value 29.73 903.66 7.46 0.23
PP value <0.001 <0.001 <0.001 0.95

Table 3

Correlations between spike length and yield related traits in MC population"

Spike length
株高Plant height 0.06
有效分蘖数Effective tiller number -0.45**
小穗数Spikelet number per spike 0.43**
每穗籽粒数Kernel number per spike 0.64**
每穗粒重Kernel weight per spike 0.50**
千粒重Thousand kernel weight -0.02
旗叶长Flag leaf length 0.04
旗叶宽Flag leaf width 0.11
开花期Flowering date 0.13

Table 4

QTL related to spike length in MC population"

QTL 染色体 Chromosome 标记区间
Marker interval
Position (cM)
LOD 表型变异率
PVE (%)
Addition effect
QSl.sau.1A 1A 1A_1208254-1A_39112087 0 2021CZ 3.06 6.46 0.31
1A 1A_1208254-1A_3911208 0 2022CZ 6.77 11.70 0.49
1A 1A_3911208-1A_10060497 1 2021WJ 8.42 13.06 0.51
1A 1A_1208254-1A_3911208 0 2022WJ 11.44 20.12 0.59
1A 1A_1208254-1A_3911208 0 BLUP 10.53 17.51 0.31
QSl.sau.1B 1B 1B_627919768-1B_643249550 50 2021WJ 2.60 3.90 -0.28
QSl.sau.2B 2B 2B_703728317-2B_712659058 209 2021WJ 4.18 6.23 0.35
QSl.sau.3D.1 3D 3D_604256246-3D_610079701 27 2021CZ 2.58 5.57 0.29
QSl.sau.3D.2 3D 3D_70735603-3D_84658486 56 2022CZ 3.49 6.09 0.35
QSl.sau.3D.3 3D 3D_345120579-3D_350582175 67 2022WJ 5.12 8.40 0.38
3D 3D_345120579-3D_350582175 67 BLUP 3.00 4.57 0.16
QSl.sau.4A 4A 4A_639942192-4A_679248111 31 2022CZ 4.38 7.52 0.39
4A 4A_639942192-4A_679248111 31 BLUP 4.45 7.07 0.20
QSl.sau.4D.1 4D 4D_10917137-4D_54598748 6 BLUP 2.59 6.08 -0.19
QSl.sau.4D.2 4D 4D_481390193-4D_484488681 54 2021YA 2.52 7.35 0.45
QSl.sau.5A 5A 5A_667964439-5A_671488533 29 2022WJ 2.75 4.36 0.27
QSl.sau.5B 5B 5B_541684640-5B_530691925 71 2021WJ 3.69 5.50 0.33
QSl.sau.7A 7A 7A_62032879-7A_67671869 48 2022WJ 3.73 6.06 -0.32
7A 7A_62032879-7A_67671869 48 2022CZ 3.51 5.90 -0.35
QSl.sau.7B 7B 7B_43849-7B_3090779 2 2022CZ 4.23 7.57 0.39
7B 7B_43849-7B_3090779 2 BLUP 3.02 4.90 0.17
QSl.sau.7D 7D 7D_70115592-7D_86750000 17 2021WJ 3.20 5.02 0.31

Table 5

Multi-environment QTL related to spike length in MC population"

QTL 标记区间
Marker interval
PVE (%)
QSl.sau.1A 1A_1208254-1A_3911208 39.37 28.42 10.95 10.51 9.31 1.20 0.38
-- 2A_53613442-2A_82027007 5.58 4.31 1.27 1.42 1.28 0.14 0.14
-- 2A_564267619-2A_561241398 5.48 4.70 0.78 1.49 1.42 0.06 0.15
-- 2A_605590450-2A_631788025 6.67 5.54 1.13 1.77 1.61 0.15 0.16
QSl.sau.4A 4A_639942192-4A_679248111 15.41 11.29 4.12 3.81 3.46 0.35 0.23
-- 5A_470176289-5A_471914902 5.17 3.09 2.08 1.44 0.93 0.50 0.12
-- 5A_512433953-5A_523864082 5.12 2.98 2.15 1.26 0.91 0.35 0.12
-- 5A_691403852-5A_693635094 7.64 4.29 3.35 1.57 1.31 0.26 0.14
QSl.sau.7A 7A_62032879-7A_67671869 7.91 4.75 3.15 2.10 1.44 0.66 -0.15
QSl.sau.2B 2B_703728317-2B_712659058 6.06 3.78 2.29 1.52 1.16 0.37 0.14
-- 5B_496582254-5B_505769526 6.31 2.99 3.32 1.40 0.86 0.54 0.12
QSl.sau.5B 5B_530691925-5B_547522719 5.17 3.23 1.94 1.40 0.99 0.42 0.13
QSl.sau.7B 7B_43849-7B_3090779 11.48 6.95 4.53 2.98 2.11 0.87 0.18
-- 7B_90885206-7B_99090151 5.07 2.65 2.42 0.98 0.81 0.17 -0.11
QSl.sau.3D.2 3D_68039763-3D_70735603 9.99 5.94 4.04 2.49 1.84 0.65 0.17
QSl.sau.3D.3 3D_350582175-3D_352155972 6.73 2.59 4.14 1.94 0.79 1.15 0.11
QSl.sau.3D.1 3D_604256246-3D_610079701 8.57 6.68 1.89 2.24 2.02 0.21 0.18
-- 5D_506205528-5D_483300147 5.92 2.67 3.25 1.47 0.77 0.70 -0.11
QSl.sau.7D 7D_70115592-7D_86750000 6.08 4.68 1.40 1.53 1.37 0.16 0.15
-- 7D_91560930-7D_113753770 5.82 4.74 1.08 1.61 1.44 0.17 0.15

Fig. 3

Genetic effect of major QTL for spike length in MC population Chr.: Chromosome; + and −: Lines carrying and not carrying the positive allele of corresponding QTL; n: Lines. The same as below"

Fig. 4

Validation of the major QTL QSl.sau.1A for spike length + and −: Individual plants carrying and not carrying the positive allele of corresponding QSl.sau.1A. The same as below"

Fig. 5

Effect of the major QTL QSl.sau.1A for spike length on yield related traits *: Significant difference at level 0.05; a-i: Effects of QSl.sau.1A on other agronomic traits"

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