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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (12): 3188-3203.doi: 10.3724/SP.J.1006.2023.31014

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

Mapping and effect analysis of QTL for phenology traits in wheat using 55K chip technology

WEN Ming-Xing1,2,*(), XIAO Jin2, XU Tao2, SUN Li2, WANG Zong-Kuan2, WANG Hai-Yan2, WANG Xiu-E2   

  1. 1Zhenjiang Institute of Agricultural Science, Jurong 212400, Jiangsu, China
    2State Key Laboratory of Crop Genetics and Germplasm Enhancement / Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
  • Received:2023-02-26 Accepted:2023-05-24 Online:2023-12-12 Published:2023-05-31
  • Contact: * E-mail: wmxcell2007@163.com
  • Supported by:
    Open Fund of the State Key Laboratory of Crop Genetics and Germplasm Enhancement(ZW20202009)

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Abstract:

Phenology is an important agronomic trait for common wheat, which has a great impact to explore its genetic mechanism and effect for wheat breeding and application. In this study, 240 recombinant inbred lines (RILs) derived from Yangmai 158 and Hiller were used to identify the phenology traits in 2-4 environments. A total of 52 QTL were detected on chromosomes 2A, 2D, 3D, 4B, 4D, 5A, 5B, 5D, 6A, 6B, 7A, 7B, and 7D by using the constructed high-density genetic map. QJS/BS/HS/FS/MS.nau-5D.2, QJS/BS/HS/FS/MS.nau-2D.1, and QJS/BS/HS/FS/MS.nau-7B.1 were detected for several years, which explained 4.56%-46.86%, 1.32%-33.40%, and 2.37%-13.27% of phenotypic variation, respectively. QBS/HS.nau-2A.3, QHS/FS.nau-5B.2, QFS.nau-2A.5, QBS.nau-6A.2, QJS.nau-4D.2, QJS.nau-6A.3, QBS.nau-2A.2, QBS/HS.nau-6A.1, QFS.nau-7A.2, QMS.nau-3D, QMS.nau-4D.1, and QMS.nau-6B.1 were new QTL. Pyramiding of multiple phenology loci with large effects or repeated is an effective approach to shorten the growth period in different degrees, which could be used to cultivate early-maturing and high-yield wheat varieties.

Key words: Triticum aestivum L., phenology traits, QTL, SNP markers

Table 1

Phenotypic analysis of main phenology traits"

性状
Trait		 环境
Environment		 亲本Parent RIL群体RIL population 遗传力Heritability
扬麦158
Y158		 密穗小麦HL 均值Mean 标准差SD 最大值Max. 最小值Min. 峰度Kurtosis 偏度Skewness 变异系数CV (%)
拔节期 Jointing stage (d) E2 114 119 114 5.59 125 106 -1.26 0.43 4.90 0.97
E3 94 97 96 3.08 106 89 0.75 0.60 3.21
BLUP 104 108 105 3.99 116 99 -0.83 0.50 3.80
孕穗期 Booting stage (d) E1 161 167 105 2.59 112 97 0.26 0.05 2.47 0.93
E2 143 149 147 4.42 157 137 -0.85 -0.07 3.01
E3 136 150 141 5.58 156 114 1.67 0.23 3.96
E4 141 149 147 3.34 158 139 0.79 0.66 2.28
BLUP 145 154 147 3.14 155 140 -0.35 0.21 2.14
抽穗期 Heading stage (d) E1 159 163 109 2.50 116 100 1.21 -0.07 2.29 0.79
E2 152 155 153 3.56 163 145 -0.35 0.50 2.33
E3 144 157 150 5.94 164 139 -0.89 -0.08 3.96
E4 146 157 154 4.12 167 145 -0.10 0.21 2.68
BLUP 149 158 146 3.98 157 138 -0.56 0.16 2.73
开花期 Flowering stage (d) E1 165 170 111 2.53 118 103 0.87 0.33 2.28 0.82
E2 157 164 161 3.21 169 153 -0.53 0.18 2.00
E3 155 166 161 4.84 173 147 -0.36 0.08 3.01
E4 156 167 164 3.46 174 155 -0.07 0.12 2.11
BLUP 159 167 155 3.42 164 147 -0.35 0.17 2.21
成熟期Maturity stage (d) E1 189 195 148 2.53 153 140 0.33 -0.44 1.71 0.75
E2 197 203 199 2.89 209 170 3.29 -3.44 1.45
E3 184 190 203 3.15 209 196 -0.76 -0.23 1.55
BLUP 189 195 190 2.33 197 179 1.92 -0.09 1.23

Table 2

Correlation of main phenology traits"

性状
Trait		 拔节期
Jointing stage		 孕穗期
Booting stage		 抽穗期
Heading stage		 开花期
Flowering stage
孕穗期 Booting stage 0.724**
抽穗期 Heading stage 0.683** 0.948**
开花期 Flowering stage 0.701** 0.941** 0.971**
成熟期 Maturity stage 0.464** 0.682** 0.743** 0.757**

Fig. 1

Phenotype of main phenology traits The best linear unbiased estimations across 2-4 environments for each trait was used."

Table 3

Main QTL for phenology traits mapped in this study"

性状
Trait		 QTL 环境
Environment		 物理位置
Physical position (Mb)		 标记区间
Marker interval		 LOD值
LOD value		 贡献率
PVE (%)		 加性效应
Add.b		 已知基因/QTL/标记
Known gene/QTL/Marker
拔节期
Jointing stage		 QJS.nau-2D.1 E2 32.97‒35.02 AX-111096297‒AX-109422526 4.33 2.21 ‒0.87 PPD-D1[8]
BLUP 7.18 3.80 ‒0.82
E3 35.02‒37.27 AX-109422526‒AX-110452779 6.73 6.02 ‒0.82
QJS.nau-2D.3 E2 414.99‒422.88 AX-110558888‒AX-110558245 4.11 2.00 ‒0.83 qHd-2D.1[27]
BLUP 3.93 1.92 ‒0.58
QJS.nau-5B.1 E3 572.17‒575.24 AX-110961703‒AX-110490429 13.23 11.75 1.15 PhyC[28]
BLUP 22.19 13.49 1.55
QJS.nau-5D.2 E2 468.16‒469.56 AX-108861262‒AX-109428027 55.03 46.86 ‒4.00 PhyC[28]
E3 21.62 21.08 ‒1.54
BLUP 51.52 42.61 ‒2.74
QJS.nau-7B.1 E2 9.75‒14.76 AX-111090034‒AX-111635682 4.62 2.37 ‒0.90 TaVRN3-7B[7]
E3 3.15 2.49 ‒0.53
BLUP 7.34‒9.75 AX-111636399‒AX-111090034 6.31 3.22 ‒0.75
孕穗期
Booting stage		 QBS.nau-2A.3 E3 611.88‒666.62 AX-109283226‒AX-110464869 2.77 2.33 ‒0.83
E4 611.71‒611.82 AX-110711634‒AX-108837102 2.98 2.52 ‒0.53
BLUP 5.23 1.84 ‒0.54
QBS.nau-2D.1 E1 32.97‒35.02 AX-111096297‒AX-109422526 19.62 22.89 ‒1.22 PPD-D1[8]
E2 26.47 18.09 ‒1.99
E3 25.64 26.29 ‒2.77
E4 28.45 31.32 ‒1.87
BLUP 34.49 16.42 ‒1.60
QBS.nau-5D.1 E3 449.29‒451.17 AX-109855976‒AX-109453419 4.66 3.81 ‒1.06 PhyC[28]
BLUP 453.23‒456.31 AX-108843804‒AX-109042166 6.53 2.39 ‒0.61
QBS.nau-5D.2 E1 465.11‒465.86 AX-110717870‒AX-111262507 7.95 8.00 ‒0.72 PhyC[28]
E3 7.21 6.02 ‒1.33
E2 468.16‒469.56 AX-108861262‒AX-109428027 34.95 26.52 ‒2.42
E4 6.61 5.91 ‒0.81
BLUP 14.40 5.67 ‒0.94
QBS.nau-7A.3 E3 54.90‒55.33 AX-111665118‒AX-111639706 4.30 3.48 ‒1.01 VRN-A3/FT-A1[7]
E1 66.18‒68.32 AX-110952157‒AX-108820762 3.38 3.27 ‒0.46
E2 3.01 1.60 ‒0.59
E4 4.51 3.93 ‒0.67
BLUP 4.69 1.65 ‒0.51
QBS.nau-7B.1 E1 9.75‒14.76 AX-111090034‒AX-111635682 8.72 8.84 ‒0.76 TaVRN3-7B[7]
E2 16.77 10.17 ‒1.49
E3 12.99 11.45 ‒1.83
E4 10.19 9.13 ‒1.01
BLUP 7.34‒9.75 AX-111636399‒AX-111090034 18.04 7.32 ‒1.07
QBS.nau-7D.1 E1 63.48‒66.54 AX-108882010‒AX-111061288 3.18 3.14 0.45 VRN-D3/FT-D1[7]
E2 6.76 4.03 0.94
E4 6.94 6.58 0.86
BLUP 7.74 3.10 0.69
抽穗期
Heading stage		 QHS.nau-2A.3 E4 611.71‒611.82 AX-110711634‒AX-108837102 3.78 2.83 ‒0.69
BLUP 3.24 1.86 ‒0.55
QHS.nau-2D.1 E1 32.97‒35.02 AX-111096297‒AX-109422526 26.07 27.08 ‒1.33 PPD-D1[8]
E2 23.33 17.29 ‒1.50
E3 30.21 28.27 ‒3.14
E4 33.09 33.40 ‒2.34
BLUP 36.68 29.45 ‒2.18















QHS.nau-5B.2 E1 593.48‒595.05 AX-108736770‒AX-109321892 3.17 2.60 0.42
E3 3.79 2.77 0.99
BLUP 4.24 2.52 0.64
QHS.nau-5D.2 E1 465.11‒465.86 AX-110717870‒AX-111262507 5.45 4.56 ‒0.55 PhyC[28]
E2 28.25 21.59 ‒1.69
E3 20.21 17.02 ‒2.45
BLUP 21.59 14.79 ‒1.56
E4 463.25‒465.11 AX-109924594‒AX-110717870 8.56 7.30 ‒1.10
QHS.nau-7A.3 E1 66.18‒68.32 AX-110952157‒AX-108820762 4.54 3.79 ‒0.50 VRN-A3/FT-A1[7]
E2 6.70 4.11 ‒0.74
E3 4.37 3.14 ‒1.05
E4 4.37 3.40 ‒0.75
BLUP 6.66 3.99 ‒0.81
QHS.nau-7B.1 E1 9.75‒14.76 AX-111090034‒AX-111635682 11.26 9.98 ‒0.81 TaVRN3-7B[7]
E2 19.19 13.27 ‒1.32
E3 11.96 9.24 ‒1.79
E4 13.47 10.95 ‒1.34
BLUP 18.40 12.17 ‒1.40
QHS.nau-7D.1 E1 63.48‒66.54 AX-108882010‒AX-111061288 5.44 4.63 0.55 VRN-D3/FT-D1[7]
E2 7.92 5.27 0.83
E3 4.25 3.48 1.10
E4 7.09 5.84 0.98
BLUP 9.92 6.58 1.03
开花期
Flowering stage		 QFS.nau-2A.5 E1 557.00‒568.31 AX-111140902‒AX-108927651 3.44 3.47 ‒0.46
BLUP 3.08 2.01 ‒0.46
QFS.nau-2D.1 E1 32.97‒35.02 AX-111096297‒AX-109422526 17.27 20.19 ‒1.10 PPD-D1[8]
E2 27.27 16.10 ‒1.29
E3 26.25 26.64 ‒2.46
E4 32.56 32.00 ‒1.91
BLUP 33.93 28.29 ‒1.76
QFS.nau-2D.2 E1 370.12‒406.29 AX-109417243‒AX-110515536 3.87 3.90 ‒0.49 C[24]
E4 3.25 2.37 ‒0.52
QFS.nau-2D.3 E2 414.99‒422.88 AX-110558888‒AX-110558245 5.37 2.55 ‒0.51 qHd-2D.1[27]
E3 2.63 2.11 ‒0.69
BLUP 4.72 2.98 ‒0.57
QFS.nau-5B.2 E1 593.48‒595.05 AX-108736770‒AX-109321892 3.02 3.03 0.43
E3 5.44 4.53 1.02
BLUP 6.32 4.02 0.67
QFS.nau-5D.2 E1 465.11‒465.86 AX-110717870‒AX-111262507 4.58 4.59 ‒0.53 PhyC[28]
E3 14.96 13.34 ‒1.75
BLUP 19.73 14.11 ‒1.25
E4 463.25‒465.11 AX-109924594‒AX-110717870 10.13 8.20 ‒0.97
E2 468.16‒469.56 AX-108861262‒AX-109428027 37.59 25.12 ‒1.62
QFS.nau-7A.3 E1 66.18‒68.32 AX-110952157‒AX-108820762 4.67 4.67 ‒0.54 VRN-A3/FT-A1[7]
E2 11.46 5.65 ‒0.77
E3 4.14 3.33 ‒0.88
E4 5.08 3.86 ‒0.67
BLUP 6.80 4.34 ‒0.69
QFS.nau-7B.1 E1 9.75‒14.76 AX-111090034‒AX-111635682 8.22 8.89 ‒0.73 TaVRN3-7B[7]
E2 16.43 8.47 ‒0.94
E3 8.44 7.03 ‒1.26
E4 11.54 9.00 ‒1.02
BLUP 14.09 9.54 ‒1.02
QFS.nau-7D.1 E1 63.48‒66.54 AX-108882010‒AX-111061288 5.14 5.22 0.56 VRN-D3/FT-D1[7]
E2 8.20 3.95 0.64
E3 6.48 5.66 1.14
E4 10.62 8.35 0.98
BLUP 10.90 7.24 0.89
成熟期
Maturity stage		 QMS.nau-2D.1 E1 32.97‒35.02 AX-111096297‒AX-109422526 10.41 16.34 ‒1.06 PPD-D1[8]
E3 15.62 18.67 ‒1.42
BLUP 18.79 21.34 ‒1.16
E2 35.02‒37.27 AX-109422526‒AX-110452779 6.52 1.32 ‒0.86
QMS.nau-4B E3 31.88‒40.90 AX-94434500‒AX-109850058 5.39 5.96 ‒0.80 Rht-B1/Rht1[35]
BLUP 4.20 4.23 ‒0.51
QMS.nau-5D.2 E3 465.11‒465.86 AX-110717870‒AX-111262507 5.20 5.45 ‒0.77 PhyC[28]
BLUP 463.25‒465.11 AX-109924594‒AX-110717870 5.63 6.22 ‒0.63
QMS.nau-7B.1 E1 7.34‒9.75 AX-111636399‒AX-111090034 2.87 4.07 ‒0.53 TaVRN3-7B[7]
E2 5.93‒7.34 AX-110953411‒AX-111636399 41.07 11.94 ‒2.60
E2 9.75‒14.76 AX-111090034‒AX-111635682 56.28 19.83 ‒3.35
E3 7.27 7.80 ‒0.92
BLUP 10.23 10.33 ‒0.81

Table S1

Main QTLs for phenology traits mapped in this study"

性状
Trait		 QTL 环境
Environ.		 物理位置
Physical position (Mb)		 标记区间
Marker interval		 LOD值
LOD value		 贡献率
PVE (%)		 加性效应Add.b 已知基因/QTL/标记
Known gene/QTL/Marker
拔节期
Jointing stage		 QJS.nau-2A.1 E3 90.93-120.71 AX-108751507-AX-108800384 3.36 2.68 0.55 TaSuSy2[26]
QJS.nau-4D.2 E3 424.86-426.85 AX-110432863-AX-108781235 6.85 5.69 −0.80
QJS.nau-6A.3 E3 559.17-562.47 AX-109456124-AX-111131762 4.74 3.93 0.67
QJS.nau-7B.2 E2 192.97-240.90 AX-109966136-AX-111699859 7.29 3.71 1.12 TaSEP3-B1[29]
孕穗期
Booting stage		 QBS.nau-2A.2 E1 163.10-172.02 AX-110617782-AX-109043229 3.61 3.59 −0.48
QBS.nau-5A.2 E1 396.22-396.68 AX-108757456-AX-110913394 2.87 2.78 −0.42 QFlt.dms-5A.2[30]
QBS.nau-6A.1 E1 6.27-12.23 AX-109498898-AX-110492549 2.78 2.78 −0.43
QBS.nau-6A.2 BLUP 445.61-446.73 AX-109396341-AX-111727948 51.65 29.47 −2.14
QBS.nau-6B.2 E3 705.64-707.18 AX-111502013-AX-89558700 3.07 2.61 −0.88 Xwmc105[31]
抽穗期
Heading stage		 QHS.nau-6A.1 E1 6.27-12.23 AX-109498898-AX-110492549 2.75 2.33 −0.40
QHS.nau-7B.3 E2 553.19-558.93 AX-109902366-AX-108804002 3.42 2.03 0.52 QHD-7B[32]
QHS.nau-7D.2 E4 115.54-122.84 AX-111124984-AX-108895252 3.12 2.28 0.62 TaVRT-2[33]
开花期Flowering stage QFS.nau-5A.1 E2 21.42-26.14 AX-110033504-AX-108986214 3.15 1.47 −0.39 QHD-5A.3[32]
QFS.nau-7A.1 E2 25.54-25.85 AX-111504531-AX-110743905 5.06 2.36 −0.49 QMat.tam-7A[34]
QFS.nau-7A.2 E2 34.72-41.64 AX-110109325-AX-110429273 4.28 2.40 0.50
成熟期
Maturity stage		 QMS.nau-3D E3 553.36-561.17 AX-108730721-AX-110362152 3.48 3.65 −0.63
QMS.nau-4D.1 E3 112.79-119.79 AX-110358075-AX-109071036 3.20 3.29 −0.60
QMS.nau-5D.1 E2 453.23-456.31 AX-108843804-AX-109042166 3.59 0.71 −0.63 PhyC[28]
QMS.nau-6B.1 E1 22.27-25.43 AX-109439077-AX-111106671 2.54 3.76 0.51
QMS.nau-7D.1 BLUP 63.48-66.54 AX-108882010-AX-111061288 2.80 2.92 0.43 VRN-D3/FT-D1[7]

Table 4

QTL clusters associated with two or more than two traits"

染色体Chromosome QTL名称
QTL name		 物理位置
Physical position
(Mb)		 平均LOD值
Average LOD value		 平均贡献率
Average R2 value (%)
2A QBS.nau-2A.3, QHS.nau-2A.3 611.71-611.82 3.60 2.28
2D QJS.nau-2D.1, QBS.nau-2D.1, QHS.nau-2D.1, QFS.nau-2D.1, QMS.nau-2D.1 32.97-35.02 22.31 20.16
2D QJS.nau-2D.3, QFS.nau-2D.3 414.99-422.88 4.15 2.31
5B QHS.nau-5B.2, QFS.nau-5B.2 593.48-595.05 4.33 3.24
5D QBS.nau-5D.1, QMS.nau-5D.1 449.29-456.31 4.93 2.30
5D QJS.nau-5D.2, QBS.nau-5D.2, QHS.nau-5D.2, QFS.nau-5D.2, QMS.nau-5D.2 463.25-469.56 19.06 15.25
6A QBS.nau-6A.1, QHS.nau-6A.1 6.27-12.23 2.77 2.55
7A QBS.nau-7A.3, QHS.nau-7A.3, QFS.nau-7A.3 66.18-68.32 5.25 3.61
7B QJS.nau-7B.1, QBS.nau-7B.1, QHS.nau-7B.1, QFS.nau-7B.1, QMS.nau-7B.1 7.34-14.76 14.41 9.02
7D QBS.nau-7D.1, QHS.nau-7D.1, QFS.nau-7D.1, QMS.nau-7D.1 63.48-66.54 6.89 5.07

Fig. 2

QTL for phenology traits on chromosome 2D, 5D, and 7B"

Fig. 3

Genetic effect of elite alleles for phenology traits in RIL population JS, BS, HS, FS, and MS refer to jointing stage, booting stage, heading stage, flowering stage, and maturity stage, respectively. Lowercases letters indicate significant difference in the 0.05 probability level."

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