Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (1): 17-28.doi: 10.3864/j.issn.0578-1752.2026.01.002

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Identification, Validation and Genetic Effect Analysis of Major QTL for Spike Density in Wheat

YE MeiJin1(), CHEN JiaTing2(), ZHOU JieGuang2, YIN Li2, HU XinRong2, LAN YuXin2, CHEN Bin2, SU LongXing2, LIU JiaJun3, LIU TianChao1, LI XiaoYu4(), MA Jian2()   

  1. 1 College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu 611130
    2 Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130
    3 Sichuan University of Arts and Science/Dazhou Key Laboratory of Agricultural Resources Development and Ecological Conservation in Daba Mountain, Dazhou 635000, Sichuan
    4 Nanchong Academy of Agricultural Sciences, Nanchong 637000, Sichuan
  • Received:2025-07-22 Accepted:2025-09-01 Online:2026-01-07 Published:2026-01-07
  • Contact: LI XiaoYu, MA Jian

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Abstract:

【Objective】Spike density (SD) is an important agronomic trait in wheat, and elucidating its genetic regulatory mechanisms is crucial for constructing ideal spike architecture and achieving yield breakthroughs. This study aimed to identify and genetically characterize key genetic loci controlling SD, providing a theoretical basis for molecular design breeding of wheat spike morphology. 【Method】A recombinant inbred line (RIL) population consisting of 198 F6 lines derived from a cross between the natural mutant msf and cultivar Chuannong16 was used. Combined with a genetic linkage map based on the wheat 16K SNP array, quantitative trait loci (QTL) associated with SD were systematically identified using phenotypic data from four environments. Furthermore, two populations with different genetic backgrounds were employed to validate the major and stably expressed QTL. The genetic effects of the stable QTL on yield-related traits were analyzed, and their potential for yield improvement was evaluated. 【Result】The SD of the RIL population ranged from 0.62 to 2.35, with a heritability of 0.71. SD showed a significant positive correlation with productive tiller number and spikelet number, while exhibiting a highly significant negative correlation with grains per spike, grain weight per spike, and spike length. Nine QTLs controlling SD were identified, distributed on chromosomes 1A, 1D, 5A (2 QTLs), 5B, 7A (3 QTLs), and 7B. Among them, QSd.sicau-MC-1A was mapped between flanking markers 1A_1208254 and 1A_3911208 on chromosome 1A and detected in two environments and in the best linear unbiased prediction (BLUP) dataset, explaining 9.05%-15.84% of the phenotypic variation. This QTL, with its positive allele derived from Chuannong 16, was considered a major and stably expressed locus, and its effect was further validated in two independent genetic backgrounds. QSd.sicau-MC-7A.1 was located between markers 7A_671413788 and 7A_672390144 on chromosome 7A and also detected in two environments and BLUP. Although stably expressed, this QTL had a relatively minor effect (7.06%-10.39% phenotypic variation), with its positive allele originating from msf. The remaining seven QTLs were minor-effect loci. Genetic effect analysis revealed that the positive allele of QSd.sicau-MC-1A had negative effects on major yield-related traits, whereas QSd.sicau-MC-7A.1 exhibited positive effects. Additive effect analysis demonstrated that lines carrying both QSd.sicau-MC-1A and QSd.sicau-MC-7A.1 positive alleles had significantly higher SD (9.01% increase) compared to those carrying only one or no positive alleles. Lines with only QSd.sicau-MC-1A or QSd.sicau-MC-7A.1 showed 5.03% and 4.19% increases in SD, respectively, over lines without any positive alleles. Comparative analysis with previously reported SD QTLs suggested that QSd.sicau-MC-1A might be a novel locus. 【Conclusion】Two stably expressed QTLs for SD, QSd.sicau-MC-1A and QSd.sicau-MC-7A.1, were identified in wheat. The latter shows greater potential for breeding applications.

Key words: wheat, QTL, spike density, genetic effect, yield

Fig. 1

Spike phenotype of the parents"

Table 1

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

环境
Environment		 亲本Parents 重组自交系RIL
msf 川农16 CN16 范围Range (SNS/cm) 平均值Mean 标准差SD 变异系数Variance 遗传力H2
2021WJ 1.98（14.33） 1.99（10.24**） 1.89-1.95 1.92 0.21 0.05 0.71
2021CZ N（9.84） N（8.90**） 2.28-2.35 2.32 0.26 0.07
2022WJ 1.68（14.36） 1.87*（9.74**） 0.62-1.87 0.82 0.24 0.03
2022CZ 1.81（13.08） 1.78（10.68**） 1.80-1.87 1.84 0.22 0.05

Fig. 2

Frequency distribution of spike density for MC population in various environments"

Table 2

Correlations between spike density and other yield related traits in MC population"

性状 Trait 穗密度 Spike density
株高Plant height 0.067
有效分蘖数Effective tiller number 0.402**
小穗数Spikelet number per spike 0.215**
每穗籽粒数Kernel number per spike -0.316**
每穗粒重Kernel weight per spike -0.311**
千粒重Thousand kernel weight -0.122
旗叶长Flag leaf length 0.006
旗叶宽Flag leaf width 0.001
穗长Spike length -0.666**

Table 3

QTL related to spike density in MC population"

数量性状位点
QTL		 环境
Environment		 遗传位置
Genetic position (cM)		 区间
Interval		 阈值
LOD		 表型变异率
PVE (%)		 加性效应
Add
QSd.sicau-MC-1A 2022WJ 0 1A_1208254-1A_3911208 6.82 13.09 -0.07
2022CZ 2 1A_3911208-1A_10060497 8.30 15.84 -0.09
BLUP 0 1A_1208254-1A_3911208 6.61 9.05 -0.05
QSd.sicau-MC-7A.1 2021CZ 106 7A_671413788-7A_672390144 4.54 10.39 0.08
2021WJ 113 7A_675589691-7A_677881538 3.44 8.05 0.06
BLUP 105 7A_671413788-7A_672390144 5.18 7.06 0.04
QSd.sicau-MC-5A.1 2022WJ 43 5A_688174533-5A_691403852 2.99 6.45 -0.05
BLUP 41 5A_688174533-5A_691403852 3.16 4.44 -0.03
QSd.sicau-MC-7A.2 2022WJ 54 7A_78127897-7A_80137450 3.18 5.86 0.05
QSd.sicau-MC-7A.3 2022CZ 74 7A_540052478-7A_544573026 3.01 5.17 0.05
QSd.sicau-MC-1D 2021WJ 47 1D_279525304-1D_252822346 3.00 6.09 -0.10
QSd.sicau-MC-5A.2 BLUP 74 5A_512433953-5A_523864082 2.61 3.42 -0.03
QSd.sicau-MC-5D 2021WJ 24 5D_544232381-5D_520844905 3.08 10.16 -0.12
QSd.sicau-MC-7B BLUP 57 7B_113156591-7B_122267814 3.20 4.23 0.03

Fig. 3

Genetic effect analysis of QSd.sicau-MC-1A THE P-VALUES OBTAINED FROM THE T-TEST ARE INDICATED BELOW THE ENVIRONMENT NAMES, WHERE P<0.05 REPRESENTS SIGNIFICANCE; THE PERCENTAGE DIFFERENCE BETWEEN LINES CARRYING THE TWO ALLELES IN EACH ENVIRONMENT IS LABELED ABOVE THE HORIZONTAL LINE. THE SAME AS BELOW"

Fig. 4

Genetic effect analysis of QSd.sicau-MC-7A.1"

Fig. 5

Additive effect (a) and genetic analyses (b) of QSd.sicau-MC-1A and QSd.sicau-MC-7A.1"

Fig. 6

Effect of QSd.sicau-MC-1A on other yield related traits THE NUMBER BELOW THE ASTERISK REPRESENTS THE PERCENTAGE DIFFERENCE BETWEEN LINES CARRYING THE TWO ALLELES. THE SAME AS BELOW"

Fig. 7

Effect of QSd.sicau-MC-7A.1 on other yield related traits"

Fig. 8

Validation of QSd.sicau-MC-1A in two populations"

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