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作物学报 ›› 2024, Vol. 50 ›› Issue (2): 363-372.doi: 10.3724/SP.J.1006.2024.33022

所属专题： 玉米：遗传育种·种质资源·分子遗传学

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

玉米杂交群体产量性状及其特殊配合力全基因组关联分析

马娟*(), 曹言勇   

  1. 河南省农业科学院粮食作物研究所, 河南郑州 450002
  • 收稿日期:2023-04-06 接受日期:2023-09-13 出版日期:2024-02-12 网络出版日期:2023-09-28
  • 通讯作者: *马娟, E-mail: majuanjuan85@126.com
  • 基金资助:
    河南省科技攻关项目(222102110043);河南省农业科学院优秀青年基金项目(2020YQ04)

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 Published:2024-02-12 Published online: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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摘要：

提高产量是玉米育种的长期目标, 解析产量相关性状及其配合力的遗传基础对选育高产玉米新品种具有重要意义。本研究选用123份玉米自交系和8份测验种作为亲本, 根据NCII (North Carolina design II)获得540份杂交种为材料, 在新乡和周口试验田调查F1杂交种的单穗粒重、单穗重、百粒重、行粒数等8个产量及构成性状, 利用玉米5.5K液相育种芯片检测亲本基因型, 推断F1杂交种的基因型, 利用BLINK (Bayesian information and linkage-disequilibrium iteratively nested keyway)加性和显性模型开展F1杂交种表型与其特殊配合力(special combining ability, SCA)的全基因组关联分析。结果表明, 利用加性和显性模型对F1杂交种分别检测到10个和31个显著关联位点。利用显性模型检测到8个SNPs (single nucleotide polymorphisms)与SCA显著关联。不同性状和模型间共定位位点有7个, 其中1个为单穗重与其SCA同时关联位点。通过对主效和共定位SNPs的扫描, 共鉴定到26个候选基因, 其中转录因子MYBR85、NLP9、PHD3、生长素上调小RNA (SAUR11和SAUR12)、FCS-like锌指蛋白基因FLZ16等可能是控制F1杂交种产量性状与其SCA的重要候选基因。

关键词: 玉米, 杂交种, 特殊配合力, 全基因组关联分析

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

图1

主成分分析"

表1

不同性状之间的相关系数"

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***

表2

F1杂交种性状和特殊配合力显著关联SNPs"

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

表3

主效和共定位SNPs挖掘的候选基因"

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

图2

主效和共定位SNPs优异等位基因分析 缩略词同表1。"

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