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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (6): 1346-1356.doi: 10.3724/SP.J.1006.2022.11055


Molecular mapping and validation of quantitative trait loci for spike-related traits and plant height in wheat

HU Wen-Jing1,2,*(), LI Dong-Sheng1, YI Xin1,3, ZHANG Chun-Mei1, ZHANG Yong1,2,*()   

  1. 1Lixiahe Institute of Agricultural Sciences / Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Yangzhou 225007, Jiangsu, China
    2Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Yangzhou University, Yangzhou, Jiangsu 225009, China
    3Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake / Huaiyin Normal University, Huai’an 223300, Jiangsu, China
  • Received:2021-06-18 Accepted:2021-10-19 Online:2022-06-12 Published:2021-11-15
  • Contact: HU Wen-Jing,ZHANG Yong E-mail:huren2008@126.com;zy@wheat.org.com
  • Supported by:
    National Natural Science Foundation of China(31901544);National Key Research and Development Program of China(2017YFD0100801);National Key Research and Development Program of China(2017YFD0101802)


Spike-related traits and plant height are important target traits in wheat breeding. In the present study, a population of 198 recombinant inbred lines (RILs) derived from the cross between a CIMMYT wheat line C615 and Yangmai 13 (YM13) was constructed, followed by genotyping with Wheat 90K SNP array and phenotyping of spike-related traits and plant height in three environments to excavate QTLs (quantitative trait loci) for these traits. Using composite interval mapping method, we identified one QTL for total spikelet number per spike (TSS), two QTLs for spike length (SL), two QTLs for spikelet compactness (SC), and three QTLs for plant height (PH). QSN.yaas-3B and QPH.yaas-3B overlapped on the chromosome 3B. QSL.yaas-5A, QSC.yaas-5A and QPH.yaas-5A overlapped on the chromosome 5A. QSL.yaas-6A and QSC.yaas-6A overlapped on the chromosome 6A. QSN.yaas-3B/QPH.yaas-3B and QSL.yaas-6A/QSC.yaas-6A had not been reported yet, and were likely to be novel loci. The SNP marker closely linked to QSL.yaas-5A/QSC.yaas-5A/QPH.yaas-5A was then converted into one Kompetitive Allele Specific PCR (KASP) marker (QC615-5A-KASP), and validated in a panel of 105 wheat lines. The results would be useful for improvement of yield related traits in wheat breeding.

Key words: wheat, 90K SNP, spike-related traits, plant height, QTLs, KASP markers, marker-assisted selection

Table 1

Phenotypic variation of spike traits and plant height in the parents and RIL population of C615/Yangmai 13"

亲本 Parent RIL群体 RIL population
C615 YM13 平均值 Mean 最大值
每穗结实总小穗数 TSS 20.56 A 19.02 A 19.36 22.25 16.34 -0.04 0.49 0.68
穗长 SL (cm) 10.51 A 11.30 A 11.61 13.78 9.80 0.30 -0.23 0.79
结实小穗着生密度 SC (No. cm-1) 1.96 A 1.69 B 1.68 2.06 1.40 0.10 -0.41 0.81
株高 PH (cm) 121.52 A 88.92 B 106.71 134.10 81.66 0.06 -0.35 0.90

Table 2

QTLs for total spikelet number per spike, spikelet length, spikelet compactness, and plant height"

Genetic position (cM)
Physical position (Mb)
Marker interval
LOD 表型贡献率
PVE (%)
每穗结实总小穗数 TSS QSN.yaas-3B 17YZ 72.10 31.11 Excalibur_c24391_321-BS00070455_51 3.00 6.12 -0.38
穗长 SL QSL.yaas-5A 17YZ 146.10 519.89 wsnp_Ex_c5626_9897389-BS00069175_51 10.70 16.78 -0.43
QSL.yaas-6A 15YZ 214.10 0.62 wsnp_Ku_c7471_12865307-wsnp_Ku_c34036_43438136 9.11 13.66 -0.40
结实小穗着生密度 SC QSC.yaas-5A 15YZ 145.70 519.89 RAC875_c8690_446-wsnp_Ex_c5626_9897389 5.59 12.90 0.05
16YZ 146.20 wsnp_Ex_c5626_9897389-BS00069175_51 9.21 19.34 0.06
17YZ 144.40 BS00068178_51-RAC875_c8690_446 11.59 25.31 0.07
QSC.yaas-6A 15YZ 213.60 0.62 wsnp_Ku_c7471_12865307-wsnp_Ku_c34036_43438136 3.98 12.05 0.05
株高 PH QPH.yaas-3B 15YZ 73.20 31.11 Excalibur_c24391_321-BS00070455_51 5.35 7.07 3.89
16YZ 76.00 Excalibur_c24391_321-BS00070455_51 6.26 6.43 4.00
17YZ 76.00 Excalibur_c24391_321-BS00070455_51 2.61 2.85 2.51
QPH.yaas-4D 16YZ 61.00 18.72 Kukri_rep_c101259_81-Rht-D1_SNP 8.41 13.08 7.10
17YZ 62.80 Kukri_rep_c101259_81-Rht-D1_SNP 9.66 14.42 7.62
QPH.yaas-5A 16YZ 144.60 519.89 RAC875_c8690_446-wsnp_Ex_c5626_9897389 11.93 14.54 -5.15
17YZ 144.40 BS00068178_51-RAC875_c8690_446 11.12 12.33 -5.03

Fig. 1

Genetic map of QTLs for spike traits and plant height Markers' names are shown on the right of linkage groups, and their genetic positions are shown on the left (cM). LOD values are shown on the right side of QTL. 15YZ, 16YZ, and 17YZ represent environments of 2015, 2016, and 2017, respectively. TSS, SL, SC, and PH represent total spikelet number per spike, spike length, spikelet compactness, and plant height, respectively."

Table 3

t-test of different alleles of QTLs in the RIL population for for spike traits and plant height"

Linked marker
SL (cm)
小穗着生密度SC (No. cm-1) 株高
PH (cm)
QSN.yaas-3B BS00070455_51 C615等位变异
C615 allele
19.21 B 11.57 A 1.66 A 108.60 A 140
QPH.yaas-3B 扬麦13等位变异 Yangmai 13 allele 19.74 A 11.68 A 1.69 A 101.01 B 54
tt-value -3.52 -0.89 -1.44 4.60
PP-value 5.41E-04 3.76E-01 1.51E-01 7.73E-06
QPH.yaas-4D Rht-D1_SNP C615等位变异
C615 allele
19.30 A 11.60 A 1.67 A 108.27 A 171
Linked marker
SL (cm)
小穗着生密度SC (No. cm-1) 株高
PH (cm)
扬麦13等位变异 Yangmai 13 allele 19.84 A 11.76 A 1.70 A 97.31 B 14
tt-value 1.98 0.72 0.61 -3.89
PP-value 4.90E-02 4.75E-01 5.40E-01 1.42E-04
QSL.yaas-5A RAC875_c8690_446 C615等位变异
C615 allele
19.56 A 11.33 B 1.73 A 102.97 B 110
QSC.yaas-5A 扬麦13等位变异 Yangmai 13 allele 19.09 B 11.97 A 1.60 B 111.26 A 83
QPH.yaas-5A tt-value 3.50 -5.82 8.01 -5.68
PP-value 5.82E-04 2.44E-08 1.13E-13 4.89E-08
QSL.yaas-6A wsnp_Ku_c34036_43438136 C615等位变异
C615 allele
19.58 A 11.38 B 1.73 A 105.59 A 101
QSC.yaas-6A 扬麦13等位变异 Yangmai 13 allele 19.13 B 11.85 A 1.62 B 108.11 A 94
tt-value 3.37 -4.26 6.31 -1.63
PP-value 9.20E-04 3.13E-05 1.92E-09 1.04E-01

Fig. 2

Genotyping RIL population by using QC615-5A-KASP marker Blue indicates the T allele of C615, red indicates the C allele of YM 13, and black indicates the blank control."

Table 4

t-test of different alleles of QSL.yaas-5A/QSC.yaas-5A/QPH.yaas-5A in 105 wheat lines"

Analysis type
穗数 TSS
SL (cm)
密度SC (No. cm-1)
PH (cm)
C615等位变异 C615 allele 19.30 A 10.51 B 1.84 A 86.62 B 48
扬麦13等位变异 YM13 allele 18.95 A 11.13 A 1.71 B 89.03 A 57
tt-value 2.15 -5.42 5.38 -2.91
PP-value 0.03 3.89E-07 4.64E-07 4.44E-03
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doi: 10.3389/fpls.2021.694023
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