Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (4): 627-637.doi: 10.3864/j.issn.0578-1752.2024.04.001

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

Genome-Wide Association Studies for Canopy Activity Related Traits and Its Genetic Effects on Yield-Related Traits

LI FaJi1(), CHENG DunGong1, YU XiaoCong2, WEN WeiE3, LIU JinDong4, ZHAI ShengNan1, LIU AiFeng1, GUO Jun1, CAO XinYou1, LIU Cheng1, SONG JianMin1, LIU JianJun1, LI HaoSheng1()   

  1. 1 Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Key Laboratory of Wheat Biology and Genetics and Breeding in Northern Huang-Huai River Plain, Ministry of Agriculture and Rural Affairs/Shandong Technology Innovation Center of Wheat/Jinan Key Laboratory of Wheat Genetic Improvement, Jinan 250100
    2 College of Agricultral and Biological Engineering (College of Tree Peony), Heze University, Heze 274015, Shandong
    3 Department of Cell Biology, Zunyi Medical University, Zunyi 563099, Guizhou
    4 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081
  • Received:2023-07-17 Accepted:2023-09-12 Online:2024-02-16 Published:2024-02-20
  • Contact: LI HaoSheng

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Abstract:

【Objective】Canopy activity is an important indicator of wheat growth and development. Identification the loci for canopy activity related traits and their relationships with grain yield (GY) related traits can provide theoretical support for the dissection of genetic structure of yield trait and assisted wheat breeding.【Method】A total of 166 wheat varieties originating from both domestic and international sources were planted in Anyang of Henan province and Suixi of Anhui province in cropping seasons. With the integrated physical map containing 326 570 SNP markers from the wheat 90K and 660K chips, genome-wide association studies for normalized difference vegetation index at seedling stage (NDVI-S) and 10 days after flowering (NDVI-10), and chlorophyll content in flag leaf at 10 days after flowering (Chl-10) were carried out. The results were compared with the previous study for GY related traits using the same material. 【Result】Analysis of variance (ANOVA) showed highly significant effects (P<0.01) of genotypes, environments and genotype×environment interactions on NDVI-S, NDVI-10 and Chl-10, with broad-sense heritabilities (h2 b) of 0.81, 0.81 and 0.91, respectively. Thirteen, 12 and 15 loci were detected to be significantly correlated with NDVI-S, NDVI-10 and Chl-10, respectively, among which 12, 11 and 12 were new, and five loci were associated with two or more traits. The number of favorable alleles for NDVI-S, NDVI-10 and Chl-10 ranged from 4 to 11, 3 to 11 and 4 to 12, respectively, in the 166 wheat varieties, and the phenotypic values increased with the accumulation of favorable alleles. NDVI-S showed significant (P<0.01) and positive correlations with thousand-kernel weight, kernel length and kernel width. Chl-10 was significant positively correlated with GY and flag leaf width (P<0.01), whereas significant negatively correlated with spike number per unit area, plant height and uppermost internode length (P<0.01). Seven pleiotropic loci were detected co-related with both GY and canopy activity related traits.【Conclusion】NDVI-S can be directly used for selection of yield traits. The stable and pleiotropic loci detected in this study can be used for marker-assisted selection.

Key words: Triticum aestivum, canopy activity, grain yield, normalized difference vegetation index, chlorophyll content, genome- wide association studies

Table 1

Analysis of variance and broad-sense heritabilities (h2 b) for canopy activity related traits"

性状
Trait		 均方值Mean square 遗传力
h2 b
基因型
Genotype (G)		 环境
Environment (E)		 重复
Replicate		 基因型×环境
G×E		 误差
Error
NDVI-S 0.003** 0.047** 0.003** 0.001** 0.001 0.81
NDVI-10 0.009** 0.048** 0.001 0.002** 0.001 0.81
Chl-10 74.25** 1212.76** 26.24** 7.47** 1.64 0.91

Fig. 1

Frequency distribution histogram for the BLUE values of NDVI-S, NDVI-10 and Chl-10"

Table 2

Mean, standard deviation (SD), and range of canopy activity related traits in 166 wheat varietie"

性状 Trait 环境 Environment 平均值 Mean 标准差 SD 范围 Range 变异系数 CV
NDVI-S E1 0.20 0.013 0.17-0.24 0.056
E2 0.18 0.018 0.15-0.25 0.072
E3 0.21 0.021 0.14-0.27 0.079
E4 0.20 0.023 0.11-0.26 0.087
E5 0.20 0.015 0.15-0.24 0.063
NDVI-10 E1 0.75 0.028 0.66-0.80 0.035
E2 0.76 0.027 0.66-0.84 0.032
E3 0.75 0.046 0.63-0.87 0.053
E4 0.74 0.040 0.58-0.83 0.048
E5 0.75 0.026 0.68-0.82 0.032
Chl-10 E1 54 2.6 46-61 0.043
E2 53 2.8 45-59 0.047
E3 53 2.8 45-60 0.047
E4 50 3.1 43-57 0.055
E5 53 2.5 46-59 0.042

Fig. 2

Manhattan (left) and quantile-quantile (right) plots for the BLUE values of NDVI-S、NDVI-10 and Chl-10"

Table 3

Loci for canopy activity related traits in the diverse panel of wheat varieties and comparisons with previous studies"

性状
Trait		 标记a
Marker		 染色体
Chr.		 物理位置b
Physical position (bp)		 环境
Environment		 SNPc P
 贡献率
R2 (%)		 QTL/标记/基因d
QTL/marker/gene
苗期归一化
植被指数
NDVI-S		 AX-109973814 1A 553879787-556989408 E1/E4/E5 A/G 3.76E-04-9.45E-04 7.2-8.8
AX-89581383 2A 31905918-31954704 E1/E5 C/T 1.92E-04-9.38E-04 7.3-8.9
AX-95099338 2B 794345863-794501909 E2/E3/E5 C/T 2.30E-05-9.94E-04 6.9-12.5
AX-108780837 3B 800187839-803762562 E2/E3/E4/E5 G/T 2.37E-04-9.92E-04 6.9-9.8
AX-111488372 4A 688477376-692653638 E1/E4/E5 C/T 4.42E-04-9.97E-04 7.0-8.5
AX-108817291 4B 32178420-42912748 E1/E3/E4/E5 A/G 4.67E-05-9.70E-04 7.0-11.1
AX-109416328 5A 511336844-516799817 E3/E4/E5 C/T 7.41E-05-9.99E-04 7.0-10.5
AX-108827844 5B 584820626-587603152 E1/E2/E5 C/T 2.25E-05-9.21E-04 7.0-11.7
AX-95010007 5D 479879394-483521914 E2/E4/E5 C/T 1.02E-04-7.72E-04 7.7-10.0
AX-108871828 6B 705307814-705307884 E1/E5 A/G 2.65E-04-6.98E-04 7.6-8.8 QNDVI-S.caas-6BL[24]
AX-110399902 7A 511044701-514432331 E2/E4/E5 A/C 1.14E-04-9.79E-04 6.9-10.0
AX-109353477 7B 53647905-59320644 E1/E4/E5 C/T 9.49E-06-9.99E-04 6.8-13.5
AX-111483621 7B 700393032-704402945 E2/E3/E5 G/T 1.81E-04-9.82E-04 7.1-9.2
花后10 d归一
化植被指数NDVI-10		 AX-89581383 2A 31905918-31958182 E2/E3/E5 C/T 5.03E-06-9.14E-04 7.9-11.4
AX-110065934 3A 20031674-24754209 E1/E2/E4/E5 C/T 1.28E-05-9.82E-04 7.3-13.7
AX-111066255 4A 3156028-4485378 E3/E4/E5 G/T 3.83E-05-9.39E-04 7.1-12.1
IWB9838 5A 444529778-444893234 E1/E4/E5 A/G 1.26E-04-7.27E-04 7.7-9.4 QNDVI-10.caas-5AL [24]
AX-111085648 5A 509652100-509992242 E2/E3/E4 A/G 6.29E-04-9.85E-04 7.5-8.6
AX-110413050 5A 538001880-540914319 E2/E3/E4/E5 G/T 3.99E-05-9.99E-04 7.0-11.5
AX-110910427 5B 416212499-420974307 E1/E2/E5 A/G 3.33E-05-9.95E-04 7.2-11.7
AX-108831704 5B 571816645-572547249 E2/E4/E5 A/G 8.35E-05-6.95E-04 8.0-10.4
AX-110458337 5D 512761945-515042348 E2/E3/E5 C/T 8.47E-05-5.92E-04 8.1-11.3
IWA497 7A 515006880-517518517 E1/E4/E5 A/G 2.26E-05-9.29E-04 7.1-11.7
IWA5912 7A 674272175-674276806 E1/E2/E5 A/G 3.94E-05-7.05E-04 7.4-10.8
AX-111094331 7B 720812571-725728459 E2/E4/E5 A/G 2.86E-07-9.10E-04 6.7-18.5
花后10 d旗叶
叶绿素含量
Chl-10		 AX-89478051 1A 10746438-11665198 E1/E3/E4/E5 C/T 1.15E-04-8.89E-04 7.3-9.8
AX-110019816 1A 572240419-574819040 E2/E3/E4/E5 A/G 2.21E-04-6.48E-04 7.7-8.8
AX-109271027 1B 14147203-14149354 E1/E3/E4/E5 C/T 3.72E-05-9.09E-04 7.4-10.5
IWB34618 1B 39590913-41642839 E1/E2/E3/E4/E5 C/T 1.49E-05-9.73E-04 6.9-11.7
AX-110906318 1B 464709853-465687627 E3/E4/E5 A/G 2.36E-05-9.71E-04 6.6-9.3
AX-111696227 1B 562234252-563750279 E3/E4/E5 G/T 6.29E-06-9.62E-04 6.8-13.9
AX-111592648 2B 670837387-674035196 E1/E2/E3/E4/E5 C/T 5.71E-05-8.91E-04 6.8-10.1
AX-108767341 2D 79064947-79552104 E1/E2/E3/E4/E5 A/C 4.79E-05-8.80E-04 6.9-11.0 QChl-A.caas-2DS[11]
AX-111709018 4A 3126102-3126172 E1/E2/E5 C/T 5.19E-04-9.10E-04 6.8-7.7
AX-109356891 4A 688401664-690885158 E1/E2/E3/E5 C/G 3.89E-04-9.72E-04 6.4-8.4
AX-110921829 4A 726314392-729886306 E1/E2/E3/E4/E5 C/T 1.74E-04-9.42E-04 6.8-9.7
IWB31092 5A 510096358-514153660 E1/E2/E3/E4/E5 A/G 1.33E-05-9.76E-04 6.5-12.1 IWB21197[21]
AX-111078602 5B 576574518-576574588 E3/E4/E5 C/T 4.38E-04-4.82E-04 7.7-8.1
AX-110462661 6A 26782691-26782761 E1/E2/E4/E5 C/T 2.28E-04-9.14E-04 7.1-9.8 QChl-10.caas-6AS[11];
QChl-6A[20]; Qchl-saw-6A[22]
AX-110587099 7A 6330314-12989016 E1/E2/E3/E4/E5 C/T 8.19E-05-9.97E-04 6.7-10.3

Fig. 3

Effects of the number of alleles for increasing phenotypic values of NDVI-S, NDVI-10 and Chl-10"

Table 4

Correlation analysis between canopy activity related traits and grain yield related traits in our previous study[25] in the diverse panel of wheat varieties"

性状Trait NDVI-S NDVI-10 Chl-10
产量GY -0.001 0.170* 0.405**
每平方米穗数SN -0.052 0.154* -0.367**
穗粒数KNS -0.034 -0.190* 0.220**
千粒重TKW 0.370** 0.082 0.290**
粒长KL 0.293** 0.148 0.037
粒宽KW 0.321** 0.035 0.245**
穗长SL -0.002 -0.211** 0.071
穗干重SDW 0.312** -0.179* 0.346**
抽穗期HD -0.237** 0.142 0.159*
株高PH 0.243** -0.287** -0.381**
穗下节长UIL 0.209** -0.249** -0.362**
旗叶长FLL 0.231** -0.034 -0.291**
旗叶宽FLW -0.092 0.091 0.514**

Table 5

Pleiotropic loci for both canopy activity related traits in the present study and grain yield related traits in our previous study[25] in the diverse panel of wheat varieties"

染色体
Chr.		 物理位置
Physical interval (bp)		 冠层活性相关性状显著性位点
Significant loci for canopy activity related traits		 产量相关性状显著性位点
Significant loci for grain yield related traits
1A 8291180-11950637 AX-89478051 (Chl-10) IWB6999 (KW); AX-109621606 (FLL)
2A 27328522-31954704 AX-89581383 (NDVI-S; NDVI-10) AX-94546135 (GY); AX-111037158 (KW; HD); AX-110988136 (PH)
5A 509652100-516799817 AX-109416328 (NDVI-S); AX-111085648 (NDVI-10); IWB31092 (Chl-10) AX-109367907 (SL)
5A 538001880-547648338 AX-110413050 (NDVI-10) AX-110919697 (SL); AX-110675353 (PH)
5B 571816645-587603152 AX-108827844 (NDVI-S); AX-108831704 (NDVI-10); AX-111078602 (Chl-10) AX-110995303 (GY); AX-110971192 (SL); AX-108921249 (PH)
6B 696641914-709221403 AX-108871828 (NDVI-S) AX-95260682 (SN); AX-109820966 (KW); AX-109459603 (FLL)
7A 511044701-517518517 AX-110399902 (NDVI-S); IWA497 (NDVI-10) AX-110127979 (GY); AX-109921812 (HD)
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