Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (20): 3917-3930.doi: 10.3864/j.issn.0578-1752.2023.20.001


Analysis of Genetic and Breeding Selection Effects of A Major QTL-qSl-2D for Wheat Spike Length

DONG JiZi(), CHEN LinQu(), GUO HaoRu, ZHANG MengYu, LIU ZhiXiao, HAN Lei, TIAN ZhaoSaShuang, XU NingHao, GUO QingJie, HUANG ZhenJie, YANG AoYu, ZHAO ChunHua, WU YongZhen, SUN Han, QIN Ran(), CUI Fa()   

  1. School of Agriculture, Ludong University/Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Yantai 264025, Shandong
  • Received:2023-04-10 Accepted:2023-05-23 Online:2023-10-16 Published:2023-10-31


【Objective】By analyzing the genetic and breeding selection effects of the stable major QTL for spike length in wheat, its genetic effects on yield-related traits were clarified, and the future breeding application potential was evaluated. The results could provide a basis for subsequent gene mining and molecular breeding of wheat. 【Method】A major QTL for spike length, named qSl-2D, was detected in multiple environments using a recombinant inbred lines population derived from the cross of Kenong9204 and Jing411, denoted as KJ-RIL; Two molecular markers closely linked to qSl-2D were developed by using the InDel sites in target interval. The genetic effects of yield-related traits based on KJ-RIL, MY-F2, NILs and natural mapping populations, were analyzed by combining genotype data of molecular markers or wheat 55K array, respectively. By genotyping the natural mapping population, the breeding selection effect of qSl-2D haplotype was parsed across different wheat regions and different ages. 【Result】QTL mapping results showed that qSl-2D could be detected in 7/10 sets of environmental data, and could explain 4.02%-10.10% of the phenotypic variation. The peak LOD of 5/10 sets of environmental data was positioned at 608.75 Mb. The results of genetic effect analysis showed that the enhancing allele of qSl-2D could significantly increase spike length in the four populations with different genetic backgrounds. In addition, it has positive effects on kernel number per spike and plant height, but has negative effects on thousand kernel weight, kernel weight per spike and yield per plant in most population backgrounds. Further analysis of plant height in KJ-RIL population showed that the enhancing allele had rod lowering effect on all internode lengths except the internode length below spike, which resulted in the insignificant increase in plant height. The results of qSl-2D haplotype analysis showed that the utilization rates of the long-spike haplotype Hap-AA-GG varied greatly in different wheat regions, with the highest utilization rate in the northern winter wheat region, accounting for 24%; while the short-spike haplotype Hap-CC-CC accounted for more than 30% in most wheat regions. Moreover, the utilization rate of qSl-2D long-spike haplotype showed a gradual decrease over time, while that of short-spike haplotype consistently maintained a higher selection trend. 【Conclusion】A stable major QTL-qSl-2D for spike length was identified, the enhancing allele of qSl-2D could significantly increase spike length under different genetic backgrounds, and had certain genetic effects on yield-related traits. The closely linked molecular markers developed in the target region can be used for the genetic improvement of wheat spike length and yield-related traits in wheat.

Key words: wheat (Triticum aestivum L.), spike length, major QTL, genetic effects analysis, molecular marker

Table 1

Primary mapping analysis of qSl-2D in multiple environments"

Position (Mb)
Left marker
Right marker
LOD 表型变异率
PVE (%)
E1 608.75 AX-111528013 AX-95178308 10.13 4.02 -0.20
E3 608.75 AX-111528013 AX-95178308 9.07 10.10 -0.24
E4 608.75 AX-111528013 AX-95178308 9.07 8.73 -0.25
E7 577.75 AX-109437399 AX-94823865 5.72 8.31 -0.22
E8 608.75 AX-111528013 AX-95178308 5.63 7.93 -0.21
LN-BLUE 609.75 AX-95178308 AX-108752409 8.42 9.85 -0.19
HN-BLUE 608.75 AX-111528013 AX-95178308 9.82 8.49 -0.20

Fig. 1

LODs distribution of spike length QTL-qSl-2D in multiple environments The abscissa indicates the physical position of wheat 660K SNP array in KN9204 genome. The red chromosome segment below indicates the location interval"

Fig. 2

Electrophoretic amplification results of molecular markers in Kenong 9204, Jing 411 and some KJ-RIL M: Marker; 1-46: The amplification results of parts of KJ-RIL; K: Kenong 9204; J: Jing 411"

Fig. 3

The association analysis between genotype and spike length of KJ-RIL in different environments Hap-KN9204: Genotype identical to Kenong 9204, Hap-J411: Genotype identical to Jing 411; *, **: Significant differences at P<0.05 and P<0.01 levels, respectively. The same as below"

Fig. 4

Genetic effect analysis of qSl-2D on yield-related traits in KJ-RIL population"

Table 2

Genetic effect analysis of qSl-2D on each internode length in KJ-RIL population"

ILBS (cm)
Hap-KN9204 20.71±3.82 19.78±2.11 13.55±1.37 9.50±1.34 5.78±1.28
Hap-J411 21.16±4.14 19.37±2.13 13.37±1.31 9.33±1.31 5.49±1.40

Table 3

Genetic effect analysis of qSl-2D on yield-related traits in NILs population"

SL (cm)
PH (cm)
TKW (g)
NIL-KN9204 7.73±0.50 61.17±1.92 53.75±3.40 18.50±1.69 8.42±2.37 39.07±3.68 2.93±3.40
NIL-J411 8.5±0.57** 61.58±2.43 55.67±5.68 18.71±2.49 10.14±1.77 38.54±2.96 2.27±0.20

Table 4

Genetic effect analysis of qSl-2D on yield-related traits in MY-F2 population"

SL (cm)
PH (cm)
TKW (g)
Hap-M37 10.08±0.74** 78.33±5.90** 57.89±7.62 20.00±1.12 41.62±2.96 3.95±3.47**
Hap-YN999 9.16±0.93 74.99±5.21 55.26±7.23 19.20±1.46 41.44±4.11 2.13±0.21

Fig. 5

Genetic effects analysis of qSl-2D on yield-related traits in 190 cultivated varieties (lines) Hap-CC-CC: The short-spike haplotype; Hap-AA-GG: The long-spike haplotype; The numbers in the figure represent the mean value of each haplotype"

Fig. 6

Selection effect analysis of qSl-2D haplotype across different wheat regions"

Fig. 7

Selection effect analysis of qSl-2D haplotype in varieties approved in different ages"

Table 5

QTL mapping information of spike length reported on wheat chromosome 2D"

QTL名称 QTL name 左端标记 Left marker 右端标记 Right marker 区间 Interval (Mb) 参考文献 Reference
QSl2D-1 XGWM296 XWMC112 17.61—23.02 [36]
QSl2D-2 XCFD53 XWMC18 23.02—130.83 [36]
QSl2D-3 XGWM296 XGWM261 17.61—19.62 [36]
QSl2D-4 XGWM311.2 XBARC129.2 647.51- [36]
QSl2D-5 XWMC112 XCFD53 —23.02 [36]
QSpl.nau-2D Xcfd53 DG371 23.02— [13]
QTL wmc181 gs2a 593.74— [15]
QTL gwm261 barc168 19.62—44.74 [15]
QTL Xcfd53 Xwmc18 23.02—130.83 [37]
QTL Xwgrc1257 DG371 / [17]
QSl.sau.2D.1 AX-111096297 AX-109422526 32.97—35.02 [18]
QSl.sau.2D.2 AX-110552569 AX-111660432 602.14—606.92 [18]
qSL-2D.1 AX-111939856 AX-111497351 30.49—31.58 [19]
Qsl.nwsuaf-2D tplb0053n05_793 Kukri_c51992_290 20.77—22.45 [20]
QSL-XX.2D AX-111561744 AX-179557748 23.42—31.56 [21]
MQTL-2D-1 2243439--D GDEEGVY02I0IOX_61 2.69—8.98 [10]
MQTL-2D-2 D_contig74612 253--2243548 5.44—10.32 [10]
MQTL-2D-3 3222417--D GA8KES401CIV9Z_240 24.98—28.76 [10]
MQTL-2D-4 1282771 983316 28.88—36.42 [10]
QTL AX-109911369 AX-111087066 18.2—36.89 [38]
QSl.cas-2D.2 AX-110462142 AX-110168677 585.69—601.05 [39]
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