Scientia Agricultura Sinica ›› 2022, Vol. 55 ›› Issue (8): 1492-1502.doi: 10.3864/j.issn.0578-1752.2022.08.002

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

Unconditional and Conditional QTL Analysis of Wheat Spike Length in Common Wheat Based on 55K SNP Array

TANG HuaPing1(),CHEN HuangXin1(),LI Cong1,GOU LuLu1,TAN Cui2,MU Yang1,TANG LiWei3,LAN XiuJin1,WEI YuMing1,MA Jian1()   

  1. 1Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130
    2Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130
    3PanZhiHua Academy of Agricultural and Forestry Sciences, Panzhihua 617061, Sichuan
  • Received:2021-10-20 Accepted:2021-12-16 Online:2022-04-16 Published:2022-05-11
  • Contact: Jian MA E-mail:707952940@qq.com;1252153393@qq.com;jianma@sicau.edu.cn

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Abstract:

【Objective】This study is to excavate spike length (SL)-related quantitative trait loci (QTL) with potential breeding value, explore the genetic relationship between SL and other important agronomic traits in wheat, and aim at laying a foundation for fine mapping and molecular-assisted selection breeding. 【Method】A total of 126 F7 recombinant inbred lines (RIL) constructed by crossing 20828 and SY95-71 were used in this study. The RIL population including their parents were planted in seven different environments for phenotypic evaluation: Wenjiang, Chongzhou, Ya'an of Sichuan Province in China, and Khulna in Bangladesh during 2016-2017 and 2017-2018 growing seasons. Unconditional QTL mapping was performed using a genetic linkage map constructed using the wheat 55K SNP array, and QTLs’ effects were further analyzed. Conditional QTL analysis was performed to analyze the relationship between SL and other agronomic traits including plant height (PH), spike extension length (SEL), spikelet number per spike (SNS) and thousand-kernel weight (TKW). 【Result】Thirteen QTLs controlling SL were identified using unconditional QTL mapping, and they were located on chromosomes 1A, 1D, 2B, 2D, 4B, 6D, and 7A. The LOD values ranged from 2.79 to 6.19, and the phenotypic variation rate ranged from 5.35% to 12.77%. Three stable and major QTLs (QSl-sau-2SY-2B, QSl-sau-2SY-2D.5 and QSl-sau-2SY-4B) were identified, and they explained 6.54% to 11.72%, 10.16% to 12.57%, and 5.35% to 10.92% of phenotypic variation rate, respectively. Furthermore, these three major QTLs could be also detected in multi-environment analysis. Moreover, aggregation analysis suggested that the SL of lines polymerizing the positive allels at these three major QTLs was significantly longer than that of those with any two ones or those carrying only one. Meanwhile, it was found that QSl-sau-2SY-2B had no significant effect on PH, SEL, SNS and TKW. QSl-sau-2SY-2D.5 had a significant effect on improving TKW (3.98%), but no significant effect on PH, SEL and SNS. QSl-sau-2SY-4B had a significant effect on decreasing PH (-12.28%) and SEL (-22.26%), but no significant effect on SNS and TKW. The conditional QTL analysis showed that QSl-sau-2SY-2B was independent of PH and SEL, whereas, affected by SNS and TKW. QSl-sau-2SY-2D.5 was independent of SEL, SNS and TKW, but affected by PH. QSl-sau-2SY-4B was independent of SEL and TKW, but affected by PH and SNS. 【Conclusion】In this study, three stable and major QTLs were identified for SL: QSl-sau-2SY-2B, QSl-sau-2SY-2D.5, and QSl-sau-2SY-4B, among which QSl-sau-2SY-2B may be a novel QTL independent of PH and SEL.

Key words: common wheat, 55K SNP array, spike length, unconditional QTL, conditional QTL

Fig. 1

The spike length of parents and selected lines in the 2SY population"

Table 1

Phenotypic variation of spike length for parents and RIL in 2SY population"

环境
Environment		 亲本Parent (cm) 重组自交系RIL
20828 SY95-71 范围
Range (cm)		 均值
Mean (cm)		 标准差
SD		 偏度
Skewness		 峰度
Kurtosis		 遗传力
H2
E1 15.60** 9.50 8.10—16.80 12.63 1.68 -0.03 0.06
E2 15.43** 9.83 7.83—17.20 12.28 1.95 0.34 -0.07
E3 14.70** 9.80 6.57—15.50 11.49 1.51 -0.08 0.36
E4 12.55** 8.42 7.41—14.65 10.90 1.47 -0.07 -0.47
E5 13.15** 8.46 7.10—16.12 10.73 1.56 0.20 0.15
E6 11.28** 7.54 5.84—15.62 9.91 1.80 0.29 0.12
E7 15.13** 8.55 6.08—16.33 10.71 1.96 0.64 0.56
BLUP 13.65 9.15 8.70—14.27 11.23 1.14 0.18 -0.02 0.63

Fig. 2

The frequency distribution of spike length in 2SY population E1: Wenjiang experiment base, Chengdu, Sichuan Province, China in 2017; E2: Chongzhou experiment base, Sichuan Province, China in 2017; E3: Ya'an experiment base, Sichuan Province, China in 2017; E4: Wenjiang experiment base, Chengdu, Sichuan, China in 2018; E5: Chongzhou experiment base, Sichuan Province, China in 2018; E6: Ya'an experiment base, Sichuan Province, China in 2018; E7: Experiment field in Khulna, Bangladesh in 2018"

Table 2

Correlation analysis of spike length in different environments in 2SY population"

环境Environment E1 E2 E3 E4 E5 E6 E7 BLUP
E1 1
E2 0.696** 1
E3 0.755** 0.699** 1
E4 0.581** 0.568** 0.539** 1
E5 0.642** 0.591** 0.571** 0.731** 1
E6 0.545** 0.636** 0.488** 0.570** 0.607** 1
E7 0.329** 0.424** 0.383** 0.231* 0.192* 0.279** 1
BLUP 0.838** 0.867** 0.817** 0.767** 0.788** 0.772** 0.556** 1

Table 3

Unconditional QTL for spike length in 2SY population"

非条件QTL
Unconditional QTL		 环境
Environment		 染色体
Chromosome		 位置
Position (cM)		 标记区间
Marker interval		 LOD 贡献率
PVE (%)		 加性效应
Add
QSl-sau-2SY-1A E7 1A-1 59 AX-110961101—AX-108871459 2.93 11.30 0.69
QSl-sau-2SY-1D.1 E5 1D 44 AX-94498629—AX-89319035 4.78 9.32 0.54
QSl-sau-2SY-1D.2 E4 1D 84 AX-111087365—AX-110640947 4.80 9.41 0.48
QSl-sau-2SY-1D.3 E2 1D 116 AX-110766802—AX-111575769 2.97 7.26 0.56
QSl-sau-2SY-2B E4 2B-2 141 AX-111019809—AX-109451490 5.91 11.72 -0.53
E5 2B-2 147 AX-94441014—AX-109521609 3.49 6.54 -0.46
BLUP 2B-2 147 AX-94441014—AX-109521609 3.97 9.86 -0.37
QSl-sau-2SY-2D.1 BLUP 2D-1 19 AX-86163393—AX-109785183 3.23 10.04 0.37
QSl-sau-2SY-2D.2 E5 2D-2 47 AX-110977542—AX-109417243 5.85 12.53 0.63
QSl-sau-2SY-2D.3 E6 2D-3 25 AX-108767381—AX-111722527 3.44 12.77 0.65
QSl-sau-2SY-2D.4 E2 2D-3 35 AX-111722527—AX-109421761 4.44 12.66 0.73
QSl-sau-2SY-2D.5 BLUP 2D-3 70 AX-109291628—AX-111093303 3.93 11.28 0.39
E1 2D-3 72 AX-111093303—AX-109338052 2.96 10.16 0.55
E4 2D-3 74 AX-109338052—AX-111656957 6.19 12.57 0.55
QSl-sau-2SY-4B E4 4B-2 0 AX-110928817—AX-111620391 2.88 5.35 0.36
E5 4B-2 0 AX-110928817—AX-111620391 5.43 10.92 0.59
E3 4B-2 4 AX-111573292—AX-111233094 3.04 10.08 0.54
QSl-sau-2SY-6D E2 6-D 31 AX-111026969—AX-109353709 2.79 9.59 0.64
QSl-sau-2SY-7A E2 7A-2 27 AX-109417084—AX-108776518 3.00 7.63 -0.58

Table 4

Multi-environment QTL for spike length in 2SY population"

检测到的QTL
Detected QTL		 标记区间
Marker interval		 LOD LOD
(A)		 LOD
(AbyE)		 贡献率
PVE (%)		 PVE
(A)		 PVE
(AbyE)		 加性效应
Add
QSl-sau-2SY-2B AX-94498629—AX-89319035 7.11 3.60 3.51 1.23 0.76 0.47 0.21
AX-111019809—AX-109451490 9.82 5.55 4.27 1.63 1.16 0.47 -0.25
AX-94441014—AX-109521609 9.01 7.40 1.60 1.86 1.55 0.31 -0.29
AX-110872666—AX-110373068 7.01 5.87 1.13 1.54 1.21 0.33 0.26
AX-110977542—AX-109417243 11.93 8.66 3.27 1.99 1.77 0.22 0.31
AX-111722527—AX-109421761 7.68 5.65 2.03 1.64 1.16 0.48 0.25
QSl-sau-2SY-2D.5 AX-109338052—AX-111656957 12.32 7.68 4.65 1.97 1.60 0.37 0.30
QSl-sau-2SY-4B AX-110928817—AX-111620391 10.59 4.14 6.45 1.80 0.88 0.92 0.22

Fig. 3

Pyramiding effect of major QTL for spike length in 2SY population + and -: The lines carrying and not carrying the positive allele of target QTL; #RILs: Number of corresponding lines; a, b, c and d represent significant difference. The same as below"

Fig. 4

Effects of major QTL for spike length on other agronomic traits a—d: Effects of QSl-sau-2SY-2B on plant height, spike extension length, spikelet number per spike and thousand-kernel weight, +: Contains 50 lines, -: Contains 60 lines; e—h: Effects of QSl-sau-2SY-2D.5 on plant height, spike extension length, spikelet number per spike and thousand-kernel weight, +: Contains 40 lines, -: Contains 46 lines; i—l: Effects of QSl-sau-2SY-4B on plant height, spike extension length, spikelet number per spike and thousand-kernel weight, +: Contained 43 lines, -: Contained 61 lines; * and **: The significant difference at 0.05 and 0.01 levels"

Table 5

Conditional QTL for spike length in 2SY population"

T1|T2 染色体
Chromosome		 位置
Position (cM)		 标记区间
Marker interval		 LOD 贡献率
PVE (%)		 加性效应
Add		 非条件QTL
Unconditional QTL		 LOD 贡献率
PVE (%)		 加性效应
Add
SL|PH 2B-2 147 AX-94441014—AX-109521609 3.66 8.50 -0.32 QSl-sau-2SY-2B 3.97 9.86 -0.37
SL|PH 2D-2 48 AX-110977542—AX-109417243 2.87 6.80 0.29 -
SL|PH 2D-3 74 AX-109338052—AX-111656957 3.35 8.05 0.31 QSl-sau-2SY-2D.5 3.93 11.28 0.39
SL|PH 4B-2 3 AX-111573292—AX-111233094 4.49 12.29 0.39 QSl-sau-2SY-4B
SL|PH 7D 20 AX-109130875—AX-109379249 3.52 9.68 0.34 -
SL|SEL 2B-2 147 AX-94441014—AX-109521609 3.62 9.15 -0.37 QSl-sau-2SY-2B 3.97 9.86 -0.37
SL| SEL 2D-1 18 AX-86163393—AX-109785183 3.32 10.94 0.40 -
SL| SEL 2D-3 71 AX-109291628—AX-111093303 4.02 10.92 0.40 QSl-sau-2SY-2D.5 3.93 11.28 0.39
SL|SNS 2B-2 147 AX-94441014—AX-109521609 2.85 6.47 -0.29 QSl-sau-2SY-2B 3.97 9.86 -0.37
SL|SNS 2D-2 47 AX-110977542—AX-109417243 3.09 7.70 0.31 -
SL|SNS 2D-3 72 AX-111093303—AX-109338052 4.01 9.30 0.34 QSl-sau-2SY-2D.5 3.93 11.28 0.39
SL|SNS 4B-2 3 AX-111573292—AX-111233094 2.57 6.44 0.29 QSl-sau-2SY-4B
SL|SNS 7A-2 103 AX-110518554—AX-110442528 3.79 9.35 -0.35 -
SL|TGW 2B-2 146 AX-108758148—AX-94441014 3.09 7.40 -0.29 QSl-sau-2SY-2B 3.97 9.86 -0.37
SL|TGW 2D-3 72 AX-111093303—AX-109338052 4.02 9.47 0.33 QSl-sau-2SY-2D.5 3.93 11.28 0.39
SL|TGW 6B-1 83 AX-89344223—AX-110472291 2.59 6.07 0.27 -
SL|TGW 7A-2 27 AX-109417084—AX-108776518 4.05 10.10 -0.35 -
SL|TGW 7D 20 AX-109130875—AX-109379249 3.98 11.30 0.36 -
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