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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (6): 1562-1572.doi: 10.3724/SP.J.1006.2023.23042

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

Multi-locus genome-wide association study and prediction for general combining ability of maize ear length

MA Juan*(), ZHU Wei-Hong, LIU Jing-Bao, YU Ting, HUANG Lu, GUO Guo-Jun   

  1. Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China
  • Received:2022-05-18 Accepted:2022-11-25 Online:2023-06-12 Published:2022-12-05
  • Contact: *E-mail: majuanjuan85@126.com
  • Supported by:
    Science and Technology Project of Henan Province(222102110043);Science-Technology Foundation for Outstanding Young Scientists of Henan Academy of Agricultural Sciences(2020YQ04)

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Abstract:

Ear length is an important agronomic trait, which is closely related with yield. General combining ability (GCA) is an important index to evaluate excellent inbred lines. Therefore, the dissection of genetic basis of ear length GCA and formulation of corresponding breeding strategies is of great significance to improve maize yield. In this study, 537 F1 hybrids as the experimental materials were obtained from 123 maize inbred lines and eight tester lines according to North Carolina II genetic mating design, and phenotyped under two environments. A total of 11,734 single nucleotide polymorphisms (SNPs) identified using the maize 5.5 K liquid breeding chip were used to conduct multi-locus genome-wide association study (MGWAS) and genomic prediction for ear length GCA in two environments and combined environment. A total of 11 SNPs significantly associated with ear length GCA were detected using seven MGWAS, and the variation of GCA effect explained by a single locus was 8.06%-28.23%. Five SNPs were co-located using different MGWAS. Locus 7_178103602 was repeatedly detected using mrMLM (multi-locus random-SNP-effect mixed linear model) in Zhoukou and combined environment, explaining 26.02%-28.23% of variation of ear length GCA, which was an environment-stable and major-effect SNP. 11 candidate genes were identified, among which auxin amido synthetase 9 and EID1-like F-box protein 2 may be key genes for GCA of ear length. The accuracy of five random effect models for predicting ear length GCA ranged from 0.53 to 0.69 in the three environments, and there were minor differences among these models. In Xinxiang and Zhoukou environments, GBLUP (genomic best linear unbiased prediction) and RKHS (reproducing kernel Hilbert space) incorporating different significant loci as fixed effects could improve the accuracy of genomic estimated breeding value for GCA of ear length, with a percentage increase of 2.34%-14.98%. In the combined environment, except that the accuracy was slightly reduced using one significant locus derived from FarmCPU (fixed and random model circulating probability unification) or BLINK (Bayesian-information and linkage-disequilibrium iteratively nested keyway) as fixed effects, the addition of significant loci derived from the other two MGWAS methods could improve the genomic prediction ability, with a percentage increase of 2.80%-6.84%. Therefore, the incorporation of significant loci from MGWAS into the prediction models as fixed effects is helpful to improve the accuracy of the genomic estimated breeding value for ear length GCA, which could be used to effectively predict and select GCA of maize parental ear length.

Key words: ear length, general combining ability, multi-locus genome-wide association study, fixed effect model, genomic selection

图A

Distribution of general combining ability of ear length (A) and correlations among different environments (B) In Fig. 1-A, × represents means. In Fig. 1-B, *** represents there is significant difference at the 0.001 probability level."

Table 1

Analysis of variance and heritability of general combining ability of ear length"

来源
Source		 自由度
Degree of freedom		 均方
Mean of square		 F值
F-value		 P值
P-value
环境 Environment 1 1452.1 1182.02 0
重复 Replicate 1 0.3 0.24 0.62
GCAP1 122 11.4 9.25 0
GCAP2 7 26.7 21.77 0
SCA 407 3.6 2.93 0
环境: GCAP1 Environment: GCAP1 122 3.1 2.54 3.82E-15
环境: GCAP2 Environment: GCAP2 7 3 2.46 0.017
环境: SCA Environment: SCA 358 3 2.44 0
残差 Residuals 1020 1.2
GCA遗传力 Heritability of GCA 0.82

Table 2

Significant SNPs and candidate genes for the general combining ability of ear length"

标记
Marker name		 方法
Method		 P值
P-value		 r2 (%) 环境
Environment		 候选基因
Candidate gene
7_178103514 mrMLM 3.09E-08 24.29 新乡Xinxiang Zm00001d022457 (peroxidase 3, PX3)
2_216138581 FASTmrEMMA 6.12E-10 23.09 Zm00001d006761 (EID1-like F-box protein 2, EDL2)
8_126983650 FASTmrEMMA 6.73E-08 19.25 Zm00001d010756
2_216138581 pLARmEB 1.41E-07 15.63 Zm00001d006761 (EID1-like F-box protein 2, ELD2)
8_126983650 pLARmEB 3.43E-09 16.01 Zm00001d010756
6_84476172 BLINK 3.99E-10 — Zm00001d036328
6_84476172 FarmCPU 3.86E-08 — Zm00001d036328
7_178103602 mrMLM 5.24E-07 26.02 周口Zhoukou Zm00001d022457 (peroxidase 3, PX3)
7_178327031 FASTmrMLM 1.68E-08 10.64 Zm00001d022473 (auxin amido synthetase 9, AAS9)
7_178327031 pLARmEB 3.91E-07 11.29 Zm00001d022473 (auxin amido synthetase 9, AAS9)
10_139481397 ISIS EM-BLASSO 4.56E-08 11.69 Zm00001d026137
10_149653708 ISIS EM-BLASSO 7.45E-07 11.25 Zm00001d026668
1_192956360 FarmCPU 1.43E-07 — 综合环境Combined
environment		 Zm00001d031527
1_192956360 BLINK 1.57E-08 — Zm00001d031527
7_178103602 mrMLM 7.14E-12 28.23 Zm00001d022457 (peroxidase 3, PX3)
7_106761824 mrMLM 1.82E-11 18.49 Zm00001d020325 (potassium high-affinity transporter23, HAK23)
5_194917385 pLARmEB 7.33E-08 8.06 Zm00001d017399 (vacuolar processing enzyme 1, VPE1)

Table S1

Relative expression level of candidate genes for general combining ability of ear length and known genes for ear length obtained from MaizeGDB"

组织
Tissue		 Zm00001d028915 Zm00001d031527 Zm00001d026137 Zm00001d026668 Zm00001d006761 Zm00001d017399 Zm00001d036328 Zm00001d036602 Zm00001d020325 Zm00001d020686 Zm00001d022457 Zm00001d022473 Zm00001d010756
YIGE1 EDL2 VPE1 KNR6 HAK23 ZmACO2 PX3 AAS9
B73_16DAP_Embryo 23.8 9.3 0 16.2 18.3 45.9 23.8 1.6 3.9 0.7 0 2 0
B73_18DAP_Embryo 18.8 9 0 4.3 17.9 52.5 25.9 1.9 4.8 0.9 0 1.8 0
B73_20DAP_Embryo 20.5 9 0 4.9 16.7 71 32 1.9 4.1 1 0 2.5 0
B73_22DAP_Embryo 23.1 8.2 0.1 5.3 19.4 91 26.6 2.2 3.7 1.4 0 2.7 0
B73_24DAP_Embryo 20.5 6 0 7 16.9 125.5 26.7 2.1 1.4 2.8 0 2.1 0
B73_16DAP_Endosperm 15.2 7.5 0.2 7.1 18.2 0.4 17.5 2.1 3.8 0 0 0.2 0
B73_18DAP_Endosperm 12.9 7.4 0.1 2.4 15.4 0.6 21.3 1.8 3 0.1 0 0.2 0
B73_20DAP_Endosperm 9.8 4 0 1.9 9.5 0.6 14.6 1.6 2.2 0 0 0.2 0
B73_22DAP_Endosperm 10.6 3.1 0 1.7 9.6 0.6 13.5 1.6 2 0 0 0.3 0
B73_24DAP_Endosperm 8.6 3.5 0.2 1.7 8 0.8 11.6 1.7 1.5 0 0 0.1 0
run_0_NOPOL_INT 12.8 6.9 10.9 5.6 9.9 0.1 7.7 9 25.9 46.3 13.2 0.8 0.2
run_12_NOPOL_INT 13.7 6.3 8 7.6 10 0.1 14.8 4.6 10 16.8 0.2 0.7 0.1
run_18_NOPOL_INT 19.9 7.4 11.2 5.8 8.8 0 5.1 5.9 40.3 4.8 10.5 0.3 0
run_24_NOPOL_INT 11.7 8.8 33.2 8.9 13.6 0.1 9 9.3 18.1 8.9 4.7 0.6 0.3
run_30_NOPOL_INT 12.5 6.7 7.5 6.9 9.3 0.1 15.6 4.5 9.3 49.4 1.6 0.8 0
run_6_NOPOL_INT 14.6 6.2 12.6 5.9 12.2 0.1 12.8 3.3 9.9 5.8 2.4 1.1 0.1
run_0_DAP_NOPOL_LEAF 70 2.9 6.2 0.5 6.5 0 2.6 2.1 7.3 24.2 0.7 0.2 0.2
run_12_DAP_NOPOL_LEAF 56.9 7.7 2 0.6 3.6 0 4.8 2.7 8.6 38.2 0.2 0.2 0.1
run_18_DAP_NOPOL_LEAF 51.3 6.8 2.7 1.2 3.3 0.1 6.6 3.6 11.3 27.9 0.4 0.2 0.3
run_24_DAP_NOPOL_LEAF 37.1 11.1 1.8 1.4 7.3 0.1 5.1 4.1 10.3 18 0.1 0.3 0.2
run_30_DAP_NOPOL_LEAF 19.1 31.1 4.2 2.5 6.3 0.1 4.6 9 3.3 7.2 0.1 0.1 1
run_0_POL_INT 14.3 7 13.9 5.8 9.9 0.2 8.5 5.8 27.7 56.2 9.1 0.7 0
run_12_POL_INT 14.6 5.4 23.4 5.1 8.7 0.3 12.5 9.4 10.1 12 21.3 0.8 0.3
run_18_POL_INT 18 5 17.3 3.5 10.7 0.1 9.8 7.3 9.1 38.2 1.4 1.2 0
run_24_POL_INT 18.9 6.7 42.3 4 13 0.1 7.2 9.3 17 6.6 4.7 0.7 0.3
run_30_POL_INT 15.2 7.4 29.6 4.2 13.4 0.1 9.2 6.5 9.6 9.4 9.4 0.7 0.3
run_6_POL_INT 15.5 6.6 21.5 3.9 15.1 0 9.9 5.4 9.8 49 4.3 1 0
run_0_DAP_POL_LEAF 71.1 3.9 6.5 0.4 5.7 0 2.3 1.9 7.8 27.6 0.2 0.2 0.2
run_12_DAP_POL_LEAF 55.2 7.3 2.1 0.8 3 0.1 5.7 2 8.7 41.8 0.5 0.2 0.3
run_18_DAP_POL_LEAF 51.2 7.7 3.5 0.7 3.4 0.1 7.1 3.1 11.2 33 0.7 0.2 0.1
run_24_DAP_POL_LEAF 48.2 7.6 2.1 1.2 4.4 0.1 5.2 2 10 26.7 0.4 0.3 0.1
run_30_DAP_POL_LEAF 52.5 14 4 0.9 3.4 0 6.9 3.8 13.7 22.8 0.4 0.2 0.2
B73_18DAP_Pericarp 14.4 9.8 3.1 7.3 17.7 0.6 9 6 3.1 3.5 0 0.4 0.4
B73_10DAP_Whole_seed 16.9 11 5.4 10.8 15.8 0.4 16 4.2 10.5 4.1 0.9 0.8 0.3
B73_12DAP_Whole_seed 20.4 9.3 3.5 4.9 20 0.4 20.7 2.9 8.6 0.8 0 0.6 0.2
B73_14DAP_Whole_seed 17.7 13.6 2.4 2.6 23.3 0.9 26.5 2.2 6.6 1.1 0 0.3 0.1
B73_18DAP_Whole_Seed 13.1 8.3 0.7 4 15.4 2 20.9 2.7 3.5 0.8 0 0.4 0
B73_2DAP_Whole_seed 20.7 14.1 0.9 23.6 14.4 0.7 15.4 4.2 16.9 2.9 0.2 2.7 0
B73_20DAP_Whole_Seed 11.6 5.7 0.7 2.4 11.1 5.2 16.7 2.2 2.4 0.5 0 0.3 0
B73_22DAP_Whole_Seed 12.6 5.5 0.9 2.7 13.4 8.1 16.5 2 2.5 0.4 0 0.8 0.1
B73_24DAP_Whole_Seed 10.9 6 1.1 2.8 11.8 12.9 15.1 2.5 1.6 0.5 0 0.4 0
B73_4DAP_Whole_Seed 21.8 12.8 1.1 23.7 15.5 0.6 16.1 5 16.4 3.5 0.6 2.3 0
B73_6DAP_Whole_seed 21.8 8.8 3.3 13.6 16.5 0.6 9.8 4.7 15.1 2.8 0.5 2.5 0.1
B73_8DAP_Whole_seed 18.9 11 5.1 11 13.4 0.4 12.7 5 11.8 3.5 0.4 1.6 0.2
B73_R1_Anthers 16.4 43 5 1.8 9.3 0 4.5 1.5 25 2 0.9 5 0.2
BraceRoot_Node6_abvgrnd_V13 12.8 3.9 1.7 8.3 13.8 0.1 15.7 3.5 7.1 15.2 2.1 1.1 0
B73_6_DAS_GH_Coleoptile 10.8 10.6 4 8.1 9 0.2 17.2 4.7 14.9 89 18.5 1 0
CortPar_3d 12.1 8.9 7.5 6.7 11.9 0.1 6.7 7.7 44.5 13 11.2 0.5 0
CrownRoot_Node4_V7 13.5 5 27.2 5.8 10.7 0.4 13 10.3 10.8 6.9 22.1 0.9 0.6
CrownRoot_Node5_V13 13.2 5.6 31.5 9.3 13.8 0.1 8.5 5.6 13.4 14.6 3.7 0.9 0.1
CrownRoot_Node5_V7 12.7 7.6 22.2 7.9 9.9 0.1 8.9 5.3 13.2 3.1 10.4 0.9 0
CrownRoot_Nodes_1_3_V7 15.2 5.3 25.9 5 8 0.2 12.9 10.5 9.4 10.5 19.9 0.7 1.1
DifferentiationZone_3d 10 9.9 13.6 7.5 9 0.2 5.8 7.9 39.5 3.6 20.9 0.4 0.1
Mz_Ez_3d 8.4 8.7 0.6 10 10.5 0.1 18.8 1.8 9.5 0.5 0.7 0.6 0.1
B73_R1_Pre_pollination_cob 24.3 14.4 1 22.2 15.5 0.7 17.6 2.9 20.5 2.6 0 3.7 0
run_6DAS_GH_Primary_Root 7.8 9.6 14.8 7.7 7.8 0.2 12.1 4.2 28.3 1.7 7 0.7 0
Seminal_7d 10.7 8.3 30.8 9.7 10.8 0.1 13.1 6.3 19.2 1.9 13.6 0.6 0.4
B73_R1_Silks 21.9 9 1.6 15.3 11.1 0.1 11.1 5.1 14.7 2.2 0 0.3 0
Stele_3d 11 8.5 12.5 6.2 9.3 0.1 10.9 3.8 10.6 2.5 10.3 1 0
TapRoot_Z1_7d 12.3 7.9 13.2 4.7 11.9 0 15.1 4.9 9.8 5.9 1.8 1.2 0
TapRoot_Z2_7d 12.5 7.2 18.4 8.9 11.4 0.1 11.6 5.9 21 6 13.9 0.8 0.1
TapRoot_Z3_7d 43.2 5.7 31.9 4.3 10.5 0.1 5.6 5.8 12.5 14.5 20.8 1.1 0.1
TapRoot_Z4_7d 14 8.4 29.1 8 9.8 0.3 12.6 9.9 17.7 13 4 1 0.2
B73_R2_Thirteenth_Leaf 57.4 4.6 2.3 3.5 2 0.1 2.9 2.1 10.2 84.6 5.5 0.2 1
B73_V1_4D_PE_Pooled_Leaves 123.1 2 28.1 2.2 6.3 0 1.1 1.2 8.5 18.6 26.4 0 0
B73_V1_4D_PE_Primary_root 22.6 7.8 10.3 17.7 17.4 0.7 12 4.2 16.5 14.7 1.8 2.5 0.2
B73_V1_4D_PE_Stem__SAM 18.7 15 9.8 11 14.2 0.4 18.4 4.3 12.9 16.4 14.7 1.4 0.1
B73_V13_Immature_tassel 28.7 12.7 0.5 9.1 14.2 0.8 14.8 5 15.3 0.3 0 3.9 0
B73_V18_Immature_cob 35.6 18.5 0.3 7.7 15.9 0.9 16.2 3.9 19.8 2 0 4.4 0
B73_V18_Meiotic_tassel 28.5 7.9 15.9 6.4 11.4 0.1 5.6 3.9 19.3 1 0.1 2.6 0.2
V3_Stem_andSAM 17.6 13.7 7.9 18.3 12.9 0.4 16.7 3.8 11 22.2 13.1 1.1 0
B73_V3_Topmost_leaf 93.1 4.2 15.9 3.8 7.7 0 1.7 1.7 10.8 11.7 16.9 0.1 0.1
B73_V5_Bottom_of_transition_leaf 31.3 11.5 1.2 10.3 10.7 0.1 8.2 0.4 12.8 9 0 0.6 0
B73_V5_First_elonagetd_internode 19.1 10.3 7.6 25.9 15.9 0.7 17.7 3.5 12.2 33.5 1.2 1.7 0
B73_V5_Shoot_tip 17.7 15.3 3.4 22.5 16.1 0.7 18.1 2.1 14.1 23.1 0.8 0.9 0
V5_Tip_ofStage_2_Leaf 108.4 2.3 10.6 0.9 2.1 0 0.9 0.6 5.8 15.7 5.9 0.1 0
B73_V7_Bottom_of_transition_leaf 29.7 10.9 2 9.2 12.5 0.2 12.5 1.2 13.2 1.6 0 1.2 0
B73_V7_Tip_of_transition_leaf 139.1 2 22.2 0.5 8.3 0.1 0.6 0.8 9.8 1.2 0 0 0.1
B73_V9_Eighth_Leaf 64.6 3 7.7 1.7 5.5 0.1 1.4 2.4 8 18.1 0.6 0.1 0.6
B73_V9_Eleventh_Leaf 44.1 8.4 28.9 8.9 10.2 0.1 1.3 5.5 9.9 5.4 8.5 0.2 0.6
B73_V9_Fourth_elongated_internode 27.3 10.3 1.7 14 20.4 0.5 15.6 1.5 16 2.7 0 1 0
B73_V9_Immature_Leaves 30.1 5.9 5.3 48.8 11 0.1 4.2 1.6 9.3 1.9 0.1 0.4 0.2
B73_V9_Thirteenth_Leaf 42.6 9.1 21.7 20 7.8 0.1 1.9 2.3 11.1 1.1 2.3 0.2 0.1
B73_VT_Thirteenth_Leaf 68.9 3 2.5 1.8 1.6 0.2 1.7 1.8 11.4 47 0.3 0.3 0.5
WholePrimaryRoot_7d 13.5 7.9 57.3 8.2 10.8 0.1 9.5 10.4 21.5 6.2 31.8 0.7 0.5
WholeRootSystem_3d 9.4 8 9.2 9.4 9.8 0 12 4.4 34.1 1 15.9 0.8 0
WholeRootSystem_7d 12.9 9.9 45.4 8.2 11.3 0.2 8.9 9.7 25.9 3.6 23.4 0.7 0.5
Reproductive_Control 22.1 7.4 1.7 22.9 12 0.7 9 6.8 14.1 0.6 0.2 2.2 0
Reproductive_Drought 23.5 12.6 11.8 6.1 9.8 0.3 5.7 8 30.5 4.8 0 1 0
Vegetative_Control 24.9 4.8 22.4 2.2 13.8 0.1 3 7.3 9.4 19 0.5 0.2 0.7
Vegetative_Drought 20.5 13.1 17.2 2.8 14.5 0.1 2.6 7.6 8.2 10.2 0.1 0.2 0.7
wtL_1_wild_type 7.37 13.14 0.41 7.96 5 0.78 15.75 0.67 5.5 0.02 0 0.94 0
wtL_2_wild_type 11.12 13.59 0.13 6.39 7.75 0.71 14.16 0.56 5.64 0 0 0.95 0
wtL_3_wild_type 10.48 15.97 0.5 5.61 6.55 0.44 15.08 0.51 5.57 0 0 0.71 0
lg1_1_lg1_R_mutant 8.31 10.52 0.4 7.22 3.76 0.69 12.15 0.44 5.31 0 0 1.17 0
lg1_2_lg1_R_mutant 9.23 10.71 0.4 6.95 5.57 0.69 12.94 0.5 5.98 0 0 1.14 0
lg1_3_lg1_R_mutant 10.28 11.1 1.5 8.69 5.7 0.76 13.07 0.69 6.22 0.02 0 1.14 0
B_L1_1_preblade_adaxial 4.48 10.2 0 10.95 0.72 0 20.02 0.5 1.83 0.02 0 1.54 0
B_L1_2_preblade_adaxial 3.39 11.42 0 18.03 2.45 0 12.63 0.3 2.27 0 0 0.7 0
B_L1_3_preblade_adaxial 4.16 7.96 0 12.38 1.35 0.1 10.28 0.24 2.26 0 0 2.9 0
B3_preblade 6.96 13.48 0.55 3.64 3.1 0.26 21.37 0.72 2.02 0 0 0.99 0
B4_preblade 6.02 10.89 0.79 9.61 1.51 0.32 15.05 0.57 2.42 0.06 0 1.38 0
B5_preblade 7.8 11.63 0.52 9.28 1.43 0.39 17.44 1 3.16 0 0 0.9 0
L_L1_1_preligule_adaxial 3.92 15.24 0 16.14 0.63 0 8.48 0 2.37 0 0 6.53 0
L_L1_2_preligule_adaxial 6.73 14.35 0 17.52 1.53 0 10.74 0.37 2.13 0 0 7.28 0
L_L1_3_preligule_adaxial 8.18 12.46 0 17.1 0.79 0.64 9.54 0.19 2.27 0 0 9.02 0
L3_preligule 10.56 11.2 0.57 4.73 2.65 0.18 13.94 0.65 2.95 0 0 2.68 0
L4_preligule 7.85 10.18 0.56 15.38 2.02 0.32 8.36 0.28 3.79 0 0 2.87 0
L5_preligule 7.09 11.57 0.58 11.11 4.42 0.57 11.75 0.28 3.85 0 0 2.24 0
S_L1_1_presheath_adaxial 2.48 10 0 10.44 0 0 9.49 0.9 2.24 0 0 5.13 0
S_L1_2_presheath_adaxial 5.47 10.34 0 22.09 0.39 0 6.58 0.08 3.88 0 0 5.02 0
S_L1_3_presheath_adaxial 4.4 9.94 0 15.78 0.13 0.04 10.32 0.56 2.9 0 0 4.82 0
S3_presheath 6.18 8.75 1.04 13.21 2.09 0.39 11.88 0.59 3.7 0 0 2.01 0
S4_presheath 6.26 14.43 0.36 3.67 1.04 0.36 17.65 0.42 3.91 0 0 1.38 0
S5_presheath 8.23 12.12 0.92 12.28 4.17 0.27 10.54 0.19 3.65 0 0 1.13 0
rmr6_Control_T0 20.8 2.5 9.4 2.1 4.4 0.2 1.5 1.2 9.3 2.5 0 0.2 0.2
rmr6_Control_T7 19.4 3.3 9.2 1.6 5 0.2 1.5 1.6 7.6 5.1 0 0.3 0.2
rmr6_Drought_Salt_T0 7.4 1.3 2.3 0.4 1.9 0.1 0.7 1 3.5 1.5 0 0.1 0
rmr6_Drought_Salt_T7 19.8 3.6 11.9 2.1 5.3 0.1 2.1 2.1 10.2 3.4 0 0.2 0.5
rmr6_Drought_T0 17.6 3.6 8.7 1.1 4.9 0.2 1.7 2.7 8.6 3.1 0.1 0.3 0.1
rmr6_Drought_T7 18.6 2.4 10.4 1.2 4.9 0.1 1.3 1.6 8.5 3.5 0.1 0.2 0.4
rmr6_Salt_T0 18.9 3.3 11.8 1.8 4.9 0.2 2 2.4 10 2.7 0 0.3 0.5
rmr6_Salt_T7 19.4 3 6.7 1.3 5.9 0.1 1.9 1.7 9 4.6 0 0.2 0.3
wt_Control_T0 31.9 3.8 13.5 2.6 6.3 0.1 2.2 1.3 11 3.7 0 0.2 0.3
wt_Control_T7 29.4 4.8 12.2 1.8 4.8 0.1 1.7 1.3 9.6 3.3 0.1 0.3 0.2
wt_Drought_Salt_T0 28.3 5.1 8.6 1.5 6.7 0.2 1.6 1.7 9.4 2.4 0 0.3 0.1
wt_Drought_Salt_T7 29.8 4.1 11.1 2.4 5.1 0.1 1.6 1.2 9.6 2.6 0.1 0.2 0.3
wt_Drought_T0 28.1 5.4 9.5 1.4 7.3 0.1 1.8 1.9 9.1 4.6 0 0.2 0.1
wt_Drought_T7 28.7 3.8 10.5 1.8 5.4 0.1 1.3 1.1 7.6 2.7 0.1 0.1 0.4
wt_Salt_T0 30.3 5.8 12.4 2.2 6 0.1 2.1 1.4 10 2.7 0.1 0.4 0.2
wt_Salt_T7 31.8 4.4 11.5 1.9 7.5 0.1 1.7 2 9.8 3.7 0 0.2 0.2
B73_cold 47.7 33.1 7.4 8 7.8 0 1.9 1.6 7.1 30 1.1 0.1 0.2
B73_control 43.9 5.1 20.3 10.9 5 0.2 2.9 1.8 12.8 28.3 0.3 0.2 0.1
B73_heat 41.1 1.3 9.5 1.5 2 0.1 0.7 0.8 8.4 37.7 0.4 0.5 0
B73_salt 50.01 4.3 2 4.11 2.17 0.12 1.9 1.63 12.43 13.69 0.24 0.73 0
B73_UV 30.98 5.29 6.63 11.44 2.88 0.23 3.76 1.36 7.82 10.43 52.72 0.69 0.99
endosperm_12DAP 28.9 11.9 1.7 5.1 41.2 1.2 20 3 9.1 0 0 1.7 0.1
pericarp_aleurone 17.2 8.4 12.4 6.3 17.8 137.9 10.5 6.7 1.4 0 0.3 1.8 1.1
endosperm_crown 6.3 3.9 2.3 5.4 19.6 4.3 6.5 1.1 1.5 0 0 0.2 0.5
SYMMETRICAL_DIVISION_ZONE 49.2 24 2.3 17.5 28.1 0.9 16.3 7 30.5 0.1 0 9.6 0
GROWTH_ZONE 43.3 28.5 6 26.9 21.5 0.5 10.6 1.1 21.2 5.3 0 3.9 0
embryos_20DAP 30.4 7.8 0.4 5.9 35.4 145.1 13.5 5.6 12.8 5.6 0 8.8 0
EMBRYOS 33.4 7.6 0.2 26.4 18.7 314.7 36 4.5 2.9 4.9 1.3 12.1 0
MATURE_LEAF_TISSUE_leaf_8 122.3 9.5 36.5 2.1 18.9 0.7 2 5.1 18 19.8 0.5 1.6 0.3
run_6_8_mm_from_tip_of_ear_primordium 51 35.2 2.1 11.2 40.5 2.1 10.5 13.8 35.7 9 0 9.7 0
run_2_4_mm_from_tip_of_ear_primordium 46.1 34.6 1.2 11.7 42.5 1.6 11.7 13.3 37.1 10.6 0 8.1 0
MZ 19 28.7 0.1 11.6 24.5 0.3 59.3 1.9 7.1 0 0.1 2.5 0
EZ 8.8 13.8 0.3 42.6 20.2 0.1 24.3 1.2 7.6 0.9 0.4 1.2 0.2
Cortex 11 12.2 6.8 15.8 27.7 0.1 4.4 12.9 73.4 26.6 41.3 0.3 0.6
PR 12.6 18.5 2.7 38.6 24.4 0.2 36 5.5 32.3 8.4 24.9 0.9 0.1
SR 13.4 21.1 2.6 39.6 23.6 0.1 35.2 6.3 24.3 8 83.5 1.2 0.2
Mature_pollen 0.8 23.8 0 0.1 7.2 0 0.3 0.2 21.2 0 0.1 0.7 0
silks 22.1 11.2 13.2 13.5 30 0.2 5 13.2 9.7 13.5 0.3 0.3 0
mature_female_spikelets 38 29.1 8.1 38 53.3 2.3 13.3 10.8 15.4 3.5 0.2 2.7 0.1
Internode_6_7 36.5 39.8 18 103.5 40.5 0.5 27.4 5.2 20.5 12.1 0 0.7 0
Internode_7_8 41.1 48.9 15.6 103 46.4 1.2 28.5 6.5 25.1 7.4 0 0.7 0
Vegetative_Meristem_and_surrounding_Tissue 37.2 30.6 7 29.2 42.4 1.1 22.2 9.3 20.7 2.9 0 4.9 0

Fig. 2

Cluster analysis (A) and gene network analysis (B) of candidate genes and known genes for ear length"

Table S2

Analysis of variance for prediction accuracy of random effect models and environments"

来源
Source		 自由度
Degree of freedom		 平方和
Sum of square		 均方
Mean of square		 F值
F-value		 P值
P-value
模型Model 4 0.01 0.0034 0.125 0.97
环境Environment 2 4.97 2.49 91.03 <2E-16
残差Residuals 1493 40.79 0.027

Table S3

Duncan multiple comparisons for prediction accuracy of different environments in table S2"

环境
Environment		 准确性均值
Mean of accuracy		 0.05水平显著性
0.05 significant level
综合环境 Combined environment 0.68 a
新乡Xinxiang 0.61 b
周口Zhoukou 0.54 c

Fig. 3

Prediction accuracy of general combining ability of ear length using five random effect models"

Table S4

Analysis of variance for prediction accuracy of fixed effect models and random effect models in different environments"

环境
Environment		 来源
Source		 自由度
Degree of freedom		 平方和
Sum of square		 均方
Mean of square		 F值
F-value		 P值
P-value
新乡Xinxiang 模型 Model 9 0.17 0.02 0.70 0.71
残差 Residuals 990 26.63 0.03
周口Zhoukou 模型Model 9 0.69 0.08 2.16 0.02
残差Residuals 990 35.34 0.04
综合环境Combined environment 模型Model 9 0.38 0.04 2.32 0.01
残差Residuals 990 17.86 0.02

Table S5

Duncan multiple comparisons for prediction accuracy of different models in table S4"

环境
Environment		 模型
Model		 预测准确性
Prediction accuracy		 0.05水平显著性
0.05 significant level
周口Zhoukou ISIS EMBLASSO-GBLUP 0.62 a
ISIS EMBLASSO-RKHS 0.61 ab
mrMLM-GBLUP 0.58 abc
mrMLM-RKHS 0.58 abc
FASTmrMLM-GBLUP 0.56 bc
pLARmEB-GBLUP 0.56 bc
FASTmrMLM-RKHS 0.55 bc
pLARmEB-RKHS 0.55 bc
RKHS 0.54 c
GBLUP 0.54 c
综合环境Combined environment mrMLM-GBLUP 0.73 a
mrMLM-RKHS 0.72 a
pLARmEB-RKHS 0.71 ab
pLARmEB-GBLUP 0.70 ab
RKHS 0.69 ab
GBLUP 0.68 b
BLINK-RKHS 0.68 b
FarmCPU-RKHS 0.68 b
BLINK-GBLUP 0.67 b
FarmCPU-GBLUP 0.67 b

Fig. 4

Prediction accuracy of GBLUP and RKHS incorporating significant loci as fixed effects A, B, and C represent Xinxiang, Zhoukou, and combined environment, respectively. GBLUP and RKHS represent random effect models. Models with GBLUP and RKHS as suffixes represent fixed effect models."

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