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作物学报

作物学报 ›› 2024, Vol. 50 ›› Issue (3): 603-612.doi: 10.3724/SP.J.1006.2024.33035

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

玉米花序发育基因AFP1的定位及功能研究

薛明1(), 汪晨晨1, 姜露光2, 刘浩1, 张路遥1, 陈赛华1,*()   

  1. 1江苏省作物基因组学和分子育种重点实验室 / 植物功能基因组学教育部重点实验室 / 江苏省作物遗传生理重点实验室, 扬州大学农学院, 江苏扬州 225009
    2作物杂种优势与利用教育部重点实验室 / 国家玉米改良中心 / 中国农业大学农学院与生物技术学院, 北京 100193
  • 收稿日期:2023-05-26 接受日期:2023-09-13 出版日期:2024-03-12 网络出版日期:2023-10-08
  • 通讯作者: *陈赛华, E-mail: chensaihua@yzu.edu.cn
  • 作者简介:E-mail: mxue@yzu.edu.cn
  • 基金资助:
    江苏省种业振兴揭榜挂帅项目(JBGS[2021]002);江苏省重点研发计划项目(BE2022343)

Mapping and functional analysis of maize inflorescence development gene AFP1

XUE Ming1(), WANG Chen-Chen1, JIANG Lu-Guang2, LIU Hao1, ZHANG Lu-Yao1, CHEN Sai-Hua1,*()   

  1. 1Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, Jiangsu, China
    2MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
  • Received:2023-05-26 Accepted:2023-09-13 Published:2024-03-12 Published online:2023-10-08
  • Contact: *E-mail: chensaihua@yzu.edu.cn
  • Supported by:
    Jiangsu Province Government(JBGS[2021]002);Key Research and Development Program of Jiangsu Province(BE2022343)

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摘要：

玉米花序的正常发育是玉米产量的根本保证。鉴定和挖掘调控花序模式建成的基因和代谢通路将有助于揭示花序发育的分子机制, 为提高玉米产量提供理论指导。本研究从Mo17背景的EMS突变体库中筛选到一个玉米花序发育模式改变的材料, 命名为altered flower pattern 1 (afp1)。表型鉴定结果发现, afp1雌穗产生一系列侧生分枝、且无花丝形成; 雄穗上侧生小穗数量显著增多。遗传学分析表明, afp1性状受一对隐性核基因控制。利用afp1与B73构建的F2分离群体进行连锁分析, 该基因被定位在第7号染色体分子标记M150~M176之间。利用该区间内新开发的14对多态性标记进行精细定位, afp1被限定在分子标记M1722和M1725间约300 kb的范围内, 其间包含一个已知调控玉米花序发育基因BD1 (Branched silkless1)。通过测序发现, afp1的BD1发生一处C-T的变异, 引起BD1蛋白的第67位精氨酸(R)变为色氨酸(W), 该突变位于保守的功能域ERF/AP2上。对发育早期的野生型与afp1雌穗进行RNA-seq分析后发现, afp1相比野生型存在274个差异表达基因(differentially expressed genes, DEGs), 其中56.20%基因表达下调, 43.80%基因表达上调。通过KEGG分析发现, 差异表达基因富集到多种代谢通路, 其中富集到植物激素信号转导途径中的83.30%基因表达量都显著下调, 说明afp1可能通过影响激素信号从而改变花序发育模式。

关键词: 玉米, 花序发育, BD1, 激素信号转导

Abstract:

The normal development of maize inflorescence is the foundation of yield. Mining genes and metabolic pathways can reveal the molecular mechanism of inflorescence development, which will provide a theoretical guidance for maize yield improvement. In this study, a mutant with altered flower pattern 1 (named afp1) was screened from a Mo17 EMS mutant library. The afp1 mutant showed excrescent branches with no silk in the ear, while it increased the lateral spikelet number in the tassel. Genetic analysis revealed that the afp1 phenotype was controlled by a single recessive gene. The gene was initially restricted between M150 and M176 on chromosome 7 by linkage analysis in the afp1×B73 F2 population. It was further narrowed into a 300 kb region between M1722 and M1725 with 14 newly developed molecular markers. Within the mapping region, a known gene related to inflorescence development, BD1 (Branched silkless 1), was located. Due to a C-T mutation in afp1, the 67th conserved arginine (R) in the ERF/AP2 domain of the BD1 protein was altered into tryptophan (W). A total of 274 differentially expressed genes (DEGs) were identified between young ears in afp1 and the wild-type by RNA-seq. Among these genes, 56.20% were down-regulated and 43.80% were up-regulated, which were enriched in multiple metabolic pathways by KEGG analysis. Among them, 83.3% of DEGs in phytohormone signaling pathways were significantly down-regulated, suggesting that afp1 may modulate inflorescence development via a hormone-dependent pathway.

Key words: maize, inflorescence development, BD1, hormone signaling

表1

试验中使用的引物序列"

引物名称
Primer name		 正向引物
Forward primer (5'-3')		 反向引物
Reverse primer (5'-3')		 备注
Note
M150 GACATTCCGTCCTTGAAATC AGGGATCGGCGTTTGATG 图位克隆 Map-based cloning
M158 ATGACTCACGATGGGTATTG CCAAGCAGGTCAGGGTTC 图位克隆 Map-based cloning
M168 TCACGAGTCACGCGACAA GGAAGACGACAGCGAGGA 图位克隆 Map-based cloning
M1690 AGGAGTAGTAGCGGGTGG CACCTGATTTGTGCAAGGG 图位克隆 Map-based cloning
M1696 GTTGAGACGGCGACGACA AAGTGGAGGACGAAAGGA 图位克隆 Map-based cloning
M1702 GTATGGTTTGGGCGTTTG TGCTGGCAAGAATCCACT 图位克隆 Map-based cloning
M1705 CTTGTTTTGAGTTTGCTGCTTC TAACTGCTGGCTATGTCGAGC 图位克隆 Map-based cloning
M171 GTAGCGGCGGTGGAGAAT CCGTGGCTGACAAAGGGA 图位克隆 Map-based cloning
M1718 GCGTATGCGTCTTGGTTG TCGGCTTTAATACTTGCTATCT 图位克隆 Map-based cloning
M1721 GATTCTCGTAGAAGCGGACTG CTGGAGCAATGGCTGTCG 图位克隆 Map-based cloning
M1722 CTGTACATGTGCAGTGTCC TGCTACTGGTCGATCTATC 图位克隆 Map-based cloning
M1725 CGCCGCTGCTTTCTACTCAT TCAATCGTTTCTGGTGGG 图位克隆 Map-based cloning
M173 GCGTCGCTTTCGGGTCTT ATCGGCCTGAAATCGTGT 图位克隆 Map-based cloning
M176 AGGGTGGAACGGATAGGG TGTCGTGGCTGGCTCACT 图位克隆 Map-based cloning
BD1-promoter AGTGGGCCGATTGACGTTGC AATGCCGCTCCTTGGTCGTG 测序 Sequencing
BD1-gene TAAACAGCAGGGATCGGAAGA CAGGCCACCCAGCACTCA 测序 Sequencing
Zm00001d039958 ATTGATATGGCGTTCGCTGAG CTCGTTGTTGACCTCGTAGTGC 实时定量PCR qRT-PCR
Zm00001d014840 TCGTCACCGAGCAGTGGACC CGCCAAGGATGTCGCAGAA 实时定量PCR qRT-PCR
Zm00001d047736 GCCCGTCAACAAGGAGG GGAGTCGTGGGAGGAGATG 实时定量PCR qRT-PCR
Zm00001d007464 CTTGCCGAGCAGAGGAG TTCGTTGTTAGCAGGGAC 实时定量PCR qRT-PCR
Zm00001d037737 ACAACCATGAGCCACAA CAACTCCATTTCCCTTCT 实时定量PCR qRT-PCR
Zm00001d028216 GAGATTCAGCGCATCAAAG CAAAGCGTGGCTCAGTT 实时定量PCR qRT-PCR
Zm00001d049641 GTCACCGTCTTTGGCATCAG AGCAGCCTTGTCCTTGTCAGT 实时定量PCR qRT-PCR

图1

Mo17和afp1花序表型 (A): 玉米花序发育示意图。AM: 腋生分生组织; IM: 花序分生组织; SPM: 成对小穗分生组织; BM: 分支分生组织; SM: 小穗分生组织; FM小花分生组织; (B): 雌花花序[8]; (C): 雄性花序[8]; (D): Mo17雌穗; (E): 无苞叶的Mo17雌穗; (F): afp1雌穗; (G): 无苞叶的afp1雌穗; (H): Mo17雄穗及小花; (I): afp1雄穗及小花。"

表2

afp1突变位点的遗传分析"

群体
Population		 总植株数
Total number		 突变体植株数
Mutant plants		 野生型植株数
Wild type plants		 突变体/野生型(1:3)
Mutant plants/wild type plants (1:3)		 χ2 χ2(0.05)
B73×afp1 F2 171 45 126 1:2.8 0.69 3.84

表3

SNP芯片检测数据分析"

样本
Sample		 缺失数
Number of missing genotypes		 缺失率
Missing rate (%)		 杂合数
Number of heterogeneities		 杂合率
Heterogeneity rate (%)
WM1 2865 4.6956 26,377 43.2304
WM2 3056 5.0086 26,126 42.819
MM1 2709 4.4399 26,426 43.3107
MM2 2826 4.6316 26,143 42.8468
Mo17 777 1.2735 4351 7.131
B73 243 0.3969 238 0.3888
afp1 1117 1.8307 5356 8.7782

图2

afp1精细定位及候选基因分析 (A): afp1精细定位; (B): BD1 (Branched silkless 1) 结构及突变位点。BD1基因突变的核苷酸及氨基酸位点, 红色方框为AP2/ERF结构域; (C): 玉米BD1、BD1B蛋白与其他6个物种BD1的AP2/ERF结构域序列比对。"

表4

Illumina测序数据组装概述"

样品
Sample		 过滤后序列
Clean reads		 Q20比例
Q20 (%)		 Q30比例
Q30 (%)		 GC含量
GC (%)		 比对到基因组比例
Total mapping ratio (%)		 单一位置序列比例
Unique mapping ratio (%)
CK1 48,448,700 96.84 91.62 55.74 86.61 84.16
CK2 71,004,610 96.79 91.57 56.21 85.73 83.44
CK3 53,127,902 96.76 91.46 55.26 86.03 83.73
601-1 51,585,326 96.85 91.74 55.60 85.41 82.82
601-4 56,660,540 96.67 91.24 55.40 85.29 82.75
600-3 57,037,362 96.81 91.59 55.13 85.51 83.17

图3

差异表达基因火山图及qRT-PCR分析 (A): 差异表达基因火山图; (B): qRT-PCR分析。"

图4

基于差异表达基因的KEGG分析"

表5

植物激素信号转导路径相关基因"

激素
Hormones		 基因编号
Gene ID		 差异倍数
log2 (Fold Change)		 基因注释
Gene description
生长素信号 Auxin signaling Zm00001d039513 -1.33 生长素响应蛋白 Auxin-responsive protein IAA
Zm00001d043350 -6.38 生长素响应GH3基因家族 Auxin responsive GH3 gene family
水杨酸Salicylic acid Zm00001d018738 6.07 病害相关蛋白1 Pathogenesis-related protein 1
Zm00001d004966 -2.08 调节蛋白NPR1 Regulatory protein NPR1
Zm00001d010658 -5.12 转录因子TGA Transcription factor TGA
乙烯信号Ethylene signaling Zm00001d021687 -2.59 乙烯受体 Ethylene receptor

图5

差异表达基因分析 (A): 已报道参与SM和FM发育基因的表达量变化, FPKM (Fragments Per Kilobase of exon model per Million mapped fragments); (B): MADS-box家族基因的表达量显著变化; (C): 花序特异表达基因在afp1材料中的表达量变化; (D): 雌穗中低表达基因在afp1材料中的表达量变化。"

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