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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (2): 363-372.doi: 10.3724/SP.J.1006.2024.33022

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

Genome-wide association study of yield traits and special combining ability in maize hybrid population

MA Juan*(), CAO Yan-Yong   

  1. Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China
  • Received:2023-04-06 Accepted:2023-09-13 Online:2024-02-12 Published:2023-09-28
  • 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:

Increasing yield is the long-term goal of maize breeding. It is important to analyze the genetic basis of yield-related traits and combining ability for breeding new maize varieties with high yield. In this study, 123 maize inbred lines and eight tester lines were selected as the experimental parents, and 540 hybrids were obtained according to NCII (North Carolina design II). The F1 hybrids were investigated at the Xinxiang and Zhoukou experimental fields for eight yield and component traits, including kernel weight per ear, ear weight, 100-kernel weight, and kernel number per row. Parental genotypes were detected using maize 5.5K liquid breeding chip, and the genotypes of F1 hybrids were inferred. The additive and dominant models of BLINK (Bayesian information and links-disequilibrium iteratively nested keyway) were used to conduct genome-wide association study of the F1 hybrid phenotypes and special combining ability (SCA). The results showed that 10 and 31 significant association loci were detected by additive and dominant models for F1 hybrids, respectively. Eight SNPs (single nucleotide polymorphisms) were significantly associated with SCA using the dominant model. There were seven co-detected loci among different traits and models, and one of them was co-detected between ear weight and SCA. A total of 26 candidate genes were identified by scanning the major-effect and co-detected SNPs. Among them, transcription factors MYBR85, NLP9, PHD3, auxin up-regulated small RNA (SAUR11 and SAUR12), and FCS-like zinc finger protein gene FLZ16 may be important candidate genes for controlling yield traits and SCA of F1 hybrid.

Key words: maize, hybrid, special combining ability, genome-wide association study

Fig. 1

Principal component analysis"

Table 1

Correlation coefficient among different traits"

性状Trait 单穗粒重KWE 单穗重EW 百粒重HKW 行粒数KNR 穗长EL 穗粗ED 粒长KL 粒宽KW
单穗粒重KWE 0.62*** 0.98*** 0.63*** 0.41*** 0.53*** 0.46*** 0.59*** 0.61***
单穗重EW 0.96*** 0.61*** 0.64*** 0.39*** 0.55*** 0.49*** 0.56*** 0.60***
百粒重HKW 0.32*** 0.33*** 0.72*** 0.10* 0.23*** 0.34*** 0.49*** 0.69***
行粒数KNR 0.42*** 0.43*** 0.02 0.87*** 0.64 -0.04 0.04 0.28***
穗长EL 0.57*** 0.60*** 0.13** 0.62*** 0.84*** -0.01 -0.03 0.33***
穗粗ED 0.43*** 0.44*** 0.28*** 0.01 0.04 0.77*** 0.38*** 0.15***
粒长KL 0.51*** 0.48*** 0.25*** 0.00 -0.01 0.42*** 0.70*** 0.43***
粒宽KW 0.24*** 0.28*** 0.45*** 0.12* 0.19*** 0.13*** 0.18*** 0.65***

Table 2

Significant SNPs for F1 hybrid traits and special combining ability"

性状
Trait		 SNP名称
SNP name		 最小等位基因频率
Minor allele frequency		 P值
P-value		 模型
Model		 表型变异解释率
Phenotypic variance explained (%)
KWE 3_229718911 0.18 2.15E-09 F1_ADD 19.62
KWE 10_2362594 0.21 2.26E-06 F1_ADD 8.59
EW 2_172799260 0.15 8.42E-15 F1_ADD 81.65
EW 4_245349341 0.25 9.06E-07 F1_ADD 1.70
HKW 6_163896721 0.16 1.10E-06 F1_ADD 19.58
HKW 7_180299 0.38 2.59E-06 F1_ADD 16.62
EL 3_223382067 0.33 9.11E-07 F1_ADD 17.64
EL 8_170590897 0.45 3.62E-08 F1_ADD 11.14
KW 9_158819519 0.10 2.38E-09 F1_ADD 27.30
KW 10_140869639 0.47 4.97E-06 F1_ADD 0.34
KWE 1_3495500 0.39 6.77E-08 F1_DOM 2.48
KWE 1_224025559 0.44 2.30E-06 F1_DOM 1.80
KWE 2_35999586 0.41 1.75E-06 F1_DOM 10.33
KWE 3_151476859 0.38 1.74E-10 F1_DOM 15.39
KWE 4_124715480 0.42 1.78E-09 F1_DOM 3.64
KWE 4_245349341 0.25 1.49E-19 F1_DOM 2.06
KWE 7_9222599 0.29 1.12E-09 F1_DOM 0.81
KWE 8_135270440 0.23 1.61E-07 F1_DOM 13.22
EW 10_128608741 0.36 1.32E-09 F1_DOM 33.90
KNR 9_126752677 0.24 4.23E-08 F1_DOM 4.89
HKW 1_263446521 0.34 1.03E-07 F1_DOM 5.90
HKW 4_158534508 0.30 8.54E-08 F1_DOM 1.35
HKW 4_245349341 0.25 9.78E-12 F1_DOM 7.04
HKW 8_173023129 0.38 1.78E-06 F1_DOM 23.62
EL 1_286265360 0.26 4.50E-06 F1_DOM 0.39
EL 2_215919932 0.39 1.66E-09 F1_DOM 0.97
EL 2_240628723 0.45 2.89E-08 F1_DOM 2.51
EL 3_229718911 0.32 5.19E-18 F1_DOM 4.02
EL 3_231983795 0.43 1.28E-10 F1_DOM 2.57
EL 5_25546627 0.20 2.57E-06 F1_DOM 0.92
EL 8_1358238 0.39 2.49E-06 F1_DOM 0.98
EL 8_1358337 0.39 2.49E-06 F1_DOM 0.90
EL 8_11330000 0.39 2.49E-06 F1_DOM 0
EL 8_11330024 0.39 2.49E-06 F1_DOM 0.56
ED 9_126752677 0.24 8.12E-08 F1_DOM 1.23
KL 2_202588564 0.40 5.09E-07 F1_DOM 2.12
KL 4_124715480 0.42 3.11E-08 F1_DOM 5.18
KL 7_23591153 0.34 1.63E-09 F1_DOM 3.37
KL 10_119211470 0.27 7.08E-10 F1_DOM 1.61
KL 10_140869698 0.23 1.87E-07 F1_DOM 2.41
KW 1_263446521 0.34 5.66E-07 F1_DOM 4.41
KW 2_9499620 0.42 1.12E-07 F1_DOM 2.06
KW 3_229718911 0.32 5.27E-06 F1_DOM 0
KW 5_1099333 0.42 2.14E-08 F1_DOM 3.62
KW 6_105844375 0.40 2.78E-06 F1_DOM 3.18
KW 9_158819519 0.40 1.86E-07 F1_DOM 1.86
SCA_EW 2_2038269 0.20 1.48E-07 SCA_DOM 6.15
SCA_EW 4_3412671 0.28 3.44E-07 SCA_DOM 21.19
SCA_EW 6_75433362 0.25 1.03E-07 SCA_DOM 3.16
SCA_EW 10_128608741 0.36 1.40E-06 SCA_DOM 3.86
SCA_EL 2_226466002 0.28 1.32E-10 SCA_DOM 23.09
SCA_ED 7_13827332 0.29 9.09E-07 SCA_DOM 35.86
SCA_ED 8_179883706 0.36 2.54E-07 SCA_DOM 7.85
SCA_KL 6_67818656 0.27 8.19E-07 SCA_DOM 16.80

Table 3

Candidate genes identified from major-effect and co-detected SNPs"

性状
Trait		 SNP名称
SNP name		 候选基因
Candidate gene
KWE_F1_ADD, EL_F1_DOM, KW_F1_DOM 3_229718911 Zm00001d044497 (thioredoxin family Trp26)
EW_F1_ADD 2_172799260 Unknown
HKW_F1_ADD 6_163896721 Zm00001d038753 (ubiquitin domain containing 1)
HKW_F1_ADD 7_180299 Zm00001d018595 (sulfoquinovosyl transferase SQD2)
EL_F1_ADD 3_223382067 Zm00001d044267 (glyoxylate/succinic semialdehyde reductase 2)
EL_F1_ADD 8_170590897 Zm00001d012232, Zm00001d012233 (PHD finger protein)
KW_F1_ADD, KW_F1_DOM 9_158819519 Zm00001d048563
KWE_F1_DOM 2_35999586 Unknown
KWE_F1_DOM 3_151476859 Zm00001d042114, Zm00001d042115, Zm00001d042116 (U-box domain-containing protein 44)
KWE_F1_DOM 8_135270440 Zm00001d010967 (MYB-related-transcription factor 85)
EW_F1_DOM, EW_SCA_DOM 10_128608741 Zm00001d025757 (NLP-transcription factor 9)
HKW_F1_DOM 8_173023129 Zm00001d012361, Zm00001d012362 (O-fucosyltransferase 19)
EW_F1_ADD, KWE_F1_DOM, HKW_F1_DOM 4_245349341 Zm00001d054032, Zm00001d054033 (DNA-directed RNA polymerase II 16 kDa polypeptide), Zm00001d054034
KWE_F1_DOM, KL_F1_DOM 4_124715480 Zm00001d050822 (CLP protease regulatory subunit CLPX3), Zm00001d050823
HKW_F1_DOM, KW_F1_DOM 1_263446521 Zm00001d033463 (small auxin up RNA11), Zm00001d033464 (small auxin up RNA12), Zm00001d033465
KNR_F1_DOM, ED_F1_DOM 9_126752677 Unknown
EW_SCA_DOM 4_3412671 Zm00001d048693 (senescence-associated protein OSA15), Zm00001d048694 (FCS-like zinc finger16)
EL_SCA_DOM 2_226466002 Zm00001d007274 (F-box/kelch-repeat protein At2g44130-like)
ED_SCA_DOM 7_13827332 Zm00001d019039 (PHD-transcription factor 3)
KL_SCA_DOM 6_67818656 Unknown

Fig. 2

Favourable allele analysis of major-effect and co-detected SNPs Abbreviations are the same as those given in Table 1. *: P < 0.05; **: P < 0.01; ***: P < 0.001."

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