中国农业科学 ›› 2019, Vol. 52 ›› Issue (4): 579-590.doi: 10.3864/j.issn.0578-1752.2019.04.001
• 作物遗传育种·种质资源·分子遗传学 • 下一篇
收稿日期:
2018-10-30
接受日期:
2018-12-09
出版日期:
2019-02-16
发布日期:
2019-02-27
通讯作者:
邹枨
作者简介:
杨宇昕,基金资助:
Received:
2018-10-30
Accepted:
2018-12-09
Online:
2019-02-16
Published:
2019-02-27
Contact:
Cheng ZOU
摘要:
【目的】玉米起源于热带地区,经过自然和人工选择,广泛的种植于温带地区。开花是玉米生长发育的中心环节,也是热带玉米向温带环境种植的主要适应性性状。鉴定玉米在驯化过程中出现的受选择基因区段,并进一步挖掘开花候选基因,为玉米的群体改良、开花遗传机理解析提供数据支撑。【方法】首先单独分析30份温带玉米自交系和21份热带玉米自交系的单倍型数据,通过过滤高缺失和等位基因频率较低的变异位点,得到高质量的SNP(single nucleotide polymorphism)标记,利用SnpEff软件对温带和热带玉米群体的基因组多态性位点进行了功能预测。其次过滤得到同时存在于温带和热带玉米的高质量SNP标记,对温带和热带玉米的基因型数据进行主成分分析(principle component analysis,PCA)以确定其群体结构,之后利用群体分化指数(fixation index,FST)和群体间扩展单倍型纯合度(cross population extended haplotype homozygosity,XP-EHH)法分析温带和热带玉米群体间的选择信号分布情况,选择FST和XP-EHH值的top 1%为阈值,筛选得到受选择位点。通过对SNP进行功能注释得到温热带玉米群体受到选择的基因。利用agriGO工具对候选驯化基因进行功能富集分析。利用相关的生物信息学数据库对候选基因进行功能注释,进一步鉴定玉米驯化过程中的开花候选基因。【结果】通过对温热带玉米群体的高测序深度的SNP进行分析,发现热带玉米群体的SNP数目为14 123 408个,温带玉米群体的SNP数目为8 791 673个,鉴定到的SNP主要分布于基因间区。2个群体中均存在的SNP标记数目是204 752个。主成分分析表明温带和热带玉米可以显著的分为两个类群。FST选择信号的top 1%是0.3593,共鉴定到557个候选驯化基因,XP-EHH选择信号法的top 1%是3.2681,共鉴定到1 913个候选基因。鉴定到多个候选基因与玉米的开花调控密切相关,包括ZmCCT9、COL1、GRMZM2G387528。如ZmCCT9抑制开花基因ZCN8的表达,导致玉米在长日照环境下出现晚花表型,是一个重要的开花调控基因;COL1与开花促进因子FT蛋白互作,加速玉米开花以适应长日照环境;GRMZM2G387528的功能注释揭示该基因是一个光敏色素互作因子,与光周期基因ZmphyB1互作。【结论】热带玉米群体具有更高的遗传多态性,筛选到一系列参与了热带玉米和温带玉米的分化候选基因,并且重点挖掘了参与其中的玉米开花调控相关基因。
杨宇昕,邹枨. 基于温带和热带玉米群体全基因组FST和XP-EHH的选择信号检测[J]. 中国农业科学, 2019, 52(4): 579-590.
YANG YuXin,ZOU Cheng. Genome-Wide Detection of Selection Signal in Temperate and Tropical Maize Populations with Use of FST and XP-EHH[J]. Scientia Agricultura Sinica, 2019, 52(4): 579-590.
表1
温带和热带玉米群体的SNP在基因组区间的分布比例"
类型 Type | 温带 Temperate | 热带 Tropical | ||
---|---|---|---|---|
数目 Count | 百分比 Percent (%) | 数目 Count | 百分比 Percent (%) | |
Downstream | 2722265 | 18.14 | 4507749 | 18.54 |
Exon | 326417 | 2.18 | 463543 | 1.91 |
Intergenic | 7686519 | 51.22 | 12389340 | 50.97 |
Intron | 1257112 | 8.38 | 2046559 | 8.42 |
Splice_Site_Acceptor | 647 | 0.00 | 1005 | 0.00 |
Splice_Site_Donor | 602 | 0.00 | 977 | 0.00 |
Spice_Site_Region | 28482 | 0.19 | 45454 | 0.19 |
Upstream | 2667996 | 17.78 | 4376510 | 18.00 |
UTR_3_Prime | 192736 | 1.28 | 297085 | 1.22 |
UTR_5_Prime | 124412 | 0.83 | 180849 | 0.74 |
表2
FST选择信号得到的基因进行GO富集分析的结果"
GO条目 GO term | 通路 Ontology | 描述 Description | P值 P-value | 错误发现率 FDR |
---|---|---|---|---|
GO:0008064 | P | 肌动蛋白聚合或解聚的调节 Regulation of actin polymerization or depolymerization | 1.30E-06 | 0.00011 |
GO:0032271 | P | 蛋白质聚合的调节Regulation of protein polymerization | 1.30E-06 | 0.00011 |
GO:0030832 | P | 微丝长度的调节Regulation of actin filament length | 1.30E-06 | 0.00011 |
GO:0030833 | P | 微丝聚合反应的调节Regulation of actin filament polymerization | 1.30E-06 | 0.00011 |
GO:0032970 | P | 肌动蛋白丝的调控过程Regulation of actin filament-based process | 1.30E-06 | 0.00011 |
GO:0044087 | P | 细胞组分生物合成的调节Regulation of cellular component biogenesis | 1.30E-06 | 0.00011 |
GO:0030041 | P | 肌动蛋白丝的聚合Actin filament polymerization | 2.20E-06 | 0.00014 |
GO:0008154 | P | 激动蛋白丝的聚合或者解聚Actin polymerization or depolymerization | 2.20E-06 | 0.00014 |
GO:0007015 | P | 肌动蛋白丝组织Actin filament organization | 2.20E-06 | 0.00014 |
GO:0032535 | P | 细胞组分大小的调节Regulation of cellular component size | 3.10E-06 | 0.00016 |
GO:0090066 | P | 解剖学结构大小的调节Regulation of anatomical structure size | 3.10E-06 | 0.00016 |
GO:0033043 | P | 细胞器组织的调节Regulation of organelle organization | 4.20E-06 | 0.00021 |
GO:0051128 | P | 细胞成分组织的调节Regulation of cellular component organization | 1.20E-05 | 0.00057 |
GO:0030036 | P | 肌动蛋白细胞骨架组织Actin cytoskeleton organization | 0.00071 | 0.029 |
GO:0030029 | P | 肌动蛋白丝基过程Actin filament-based process | 0.00071 | 0.029 |
GO:0006996 | P | 细胞器组织Organelle organization | 0.0012 | 0.046 |
表3
选择信号鉴定得到的候选基因功能注释"
基因 Gene | 染色体 Chromosome | 物理位置 Position (Mb) | FST值a FST value | XP-EHH值b XP-EHH value | 注释c Annotation |
---|---|---|---|---|---|
GRMZM2G366434d | 5 | 17.336—17.338 | 0.3688** | 4.6263** | AP2-ErEBP转录因子206,ereb206 AP2-EREBP-transcription factor 206, ereb206 |
GRMZM2G145579d | 4 | 47.618—47.620 | 0.5071** | 3.8724* | bHLH转录因子165,bhlh165 bHLH-transcription factor 165, bhlh165 |
GRMZM2G023325 | 1 | 66.506—66.507 | 0.7845** | 氧氮杂萘酮合成12,bx12 Benzoxazinone synthesis12,bx12 | |
GRMZM2G074094 | 1 | 199.519—199.525 | 0.4380** | SET结构域,sdg103 SET domain group 103, sdg103 | |
GRMZM2G092091 | 1 | 220.057—220.061 | 0.4136** | bHLH转录因子27,bhlh27 bHLH-transcription factor 27,bhlh27 | |
GRMZM2G478417 | 1 | 272.109—272.113 | 0.3706** | bZIP转录因子49,bzip49 bZIP-transcription factor 49,bzip49 | |
GRMZM2G174834 | 4 | 159.692—159.694 | 0.3952** | WRI1转录因子,wri2 WRI1 transcription factor2, wri2 | |
GRMZM2G126505 | 4 | 185.907—185.912 | 0.3879** | 脱落酸8'-羟化酶2,abh12 Abscisic acid 8'-hydroxylase2, abh12 | |
GRMZM2G070523 | 5 | 20.219—20.221 | 0.3693** | MYB转录因子129,myb129 MYB-transcription factor 129, myb129 | |
GRMZM2G004334 | 6 | 109.244—109.247 | 0.5006** | 同源框转录因子10,hb10 Homeobox-transcription factor 10, hb10 | |
GRMZM2G170148 | 9 | 110.859—110.870 | 0.3954** | MYB相关转录因子86,mybr86 MYB-related-transcription factor 86, mybr86 | |
GRMZM2G156013 | 10 | 141.014—141.018 | 0.4835** | 丝氨酸-苏氨酸激酶4,stk4 Serine-threonine kinase4, stk4 | |
GRMZM2G143602 | 2 | 8.289—8.295 | 4.1470* | CK2蛋白激酶α1,cka1 CK2 protein kinase alpha 1, cka1 | |
GRMZM2G001289 | 2 | 15.033—15.035 | 3.7898* | 同源框转录因子75,hb75 Homeobox-transcription factor 75, hb75 | |
GRMZM2G102059 | 2 | 236.711—236.716 | 3.6779* | ABI3-VP1转录因子12,abi12 ABI3-VP1-transcription factor 12, abi12 | |
GRMZM2G089638 | 3 | 1.464—1.469 | 4.1762* | TCP转录因子31,tcptf31 TCP-transcription factor 31, tcptf31 | |
GRMZM2G087804 | 3 | 140.859—140.861 | 3.9809* | 金色植物2,g2 Golden plant2, g2 | |
GRMZM2G015875 | 4 | 47.618—47.620 | 4.5721* | NMCP/CRWN同源因子1,nch1 NMCP/CRWN-Homologous1, nch1 | |
GRMZM2G145579 | 4 | 161.101—161.108 | 3.8724* | bHLH转录因子165,bhlh165 bHLH-transcription factor 165, bhlh165 | |
GRMZM5G880069 | 5 | 184.337—184.342 | 3.8136* | WRKY转录因子109,wrky109 WRKY-transcription factor 109, wrky109 | |
GRMZM2G129783 | 6 | 106.637—106.640 | 3.7924* | 五肽重复蛋白346,ppr346 Pentatricopeptide repeat protein346, ppr346 | |
GRMZM2G387528 | 8 | 0.935—0.938 | 4.2271* | 光敏色素作用因子3,pif3 Phytochrome interacting factor3, pif3 | |
GRMZM2G028054 | 8 | 170.725—170.728 | 3.7593* | MYB转录因子74,myb74 MYB-transcription factor 74, myb74 | |
GRMZM2G009808 | 9 | 107.641—107.645 | 5.3817** | 乌头酸梅3,aco30 Aconitase3, aco30 | |
GRMZM2G139082 | 9 | 116.292—116.294 | 4.3570* | 热冲击互补因子1,hscf1 Heat shock complementing factor1, hscf1 | |
GRMZM2G013671 | 9 | 152.030—152.038 | 3.7187* | β扩增蛋白5 Beta expansin5, expb5 | |
GRMZM2G474769 | 10 | 78.160—78.161 | 4.8528** | 下胚轴伸长蛋白1,lhy1 Late hypocotyl elongation protein ortholog1, lhy1 | |
GRMZM2G180168 | 10 | 78.333—78.337 | 4.6254** | ABI3-VP1转录因子23,abi23 ABI3-VP1-transcription factor 23, abi23 |
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