Scientia Agricultura Sinica ›› 2019, Vol. 52 ›› Issue (4): 579-590.doi: 10.3864/j.issn.0578-1752.2019.04.001

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

Genome-Wide Detection of Selection Signal in Temperate and Tropical Maize Populations with Use of FST and XP-EHH

YANG YuXin,ZOU Cheng()   

  1. Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081
  • Received:2018-10-30 Accepted:2018-12-09 Online:2019-02-16 Published:2019-02-27
  • Contact: Cheng ZOU E-mail:zoucheng@caas.cn

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Abstract:

【Objective】 Maize was first domesticated in tropical areas, but it has been cultivated widely in the temperate regions after natural and artificial selection. Flowering time is not only the key component of the entire growth period, but also a major adaptive trait during the dispersal process from tropical to temperate conditions. Thus, identifying the selected gene regions responsible for the adaptation to temperate zones, and discovering the genes that are involved in flowering time could provide a molecular basis for improving maize and for dissecting its flowering mechanism. 【Method】 We analyzed the haplotype data of 30 temperate and 21 tropical maize inbred lines. High quality SNP (single nucleotide polymorphism) markers were obtained after filtering out SNPs with high missing rates and low allele frequencies. These high quality SNPs were annotated by SNPeff. Principle component analysis (PCA) of the genotypic data of temperate and tropical maize was performed to further validate the population structure of these samples. Using high quality SNP markers that were present in tropical and temperate populations, we calculated the selection signal using the fixation index (FST) and cross population extended haplotype homozygosity (XP-EHH) methods. The top 1% of values was used as a significant threshold to identify the candidate selected signals. The candidate selected genes that we selected from temperate and tropical maize were identified based on their SNP annotation. The function of these selected genes was characterized furtherly by the GO enrichment analysis using agriGO. To identify the genes for flowering time that were under selection, bioinformatics databases were examined that contained relevant data on maize. 【Result】 By analyzing the high depth resequencing data, we found 14123408 and 8791673 SNPs in tropical and temperate populations, respectively. The identified SNPs were mainly distributed in the intergenic regions. There were 204752 high quality SNPs that coexisted in temperate and tropical populations. PCA indicated that temperate and tropical maize can be divided into two groups. The top 1% of FST value and XP-EHH were 0.3059, 3.2681, and a total of 557 and 1 913 candidate genes were identified by FST and XP-EHH methods, respectively. Many candidate genes were highly related to regulation of flowering time, which included ZmCCT9, COL1 and GRMZM2G387528. ZmCCT9 is a vital gene for regulating flowering time, and it negatively regulated the floral activator gene ZCN8, which cause the late flowering time phenotype under long-day conditions. COL1 positively interacts with the FT protein to promote the transition of flowering time to adapt to the long-day environment. Functional annotations of GRMZM2G387528 revealed that it was a phytochrome interacting factor, and interacts with photoperiod gene ZmphyB1. 【Conclusion】 Our study revealed that tropical maize had higher genetic diversity than temperate maize. A series of genes that were under selection during the adaptation to tropical to temperate conditions were predicted, and we further explored the genes that were involved in flowering during this process.

Key words: maize, selection signal, fixation index, cross population extended haplotype homozygosity, flowering time genes

Fig. 1

The SNP distribution in the temperate and tropical maize genome a: Represents the SNP distribution in temperate chromosomes; b: Represents the SNP distribution in tropical chromosomes. The abscissa represents the physical position of chromosome, and window size is 1 Mb. The darkgreen represents the SNP-poor regions, and red color indicates SNP-rich regions"

Table 1

The distribution proportions of SNP found in genomic regions between temperate and tropical maize"

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

Fig. 2

The phenotype of the temperate (a) and tropical (b) maize inbred line"

Fig. 3

The principle component analysis of temperate and tropical maize"

Fig. 4

Genome-wide FST values between temperate and tropical maize populations The cutoff line represent top 1% of FST"

Fig. 5

Genome-wide distribution of XP-EHH signatures between temperate and tropical maize The cutoff lines represent the top 1% of the XP-EHH selection signal"

Table 2

The results of GO enrichment analysis using the genes, which obtained from the FST selection signatures"

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

Table 3

The function annotation of candidate genes which obtained from the selection signatures"

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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