柱状苹果Co基因的筛选与候选基因分析

doi:10.3864/j.issn.0578-1752.2019.23.015

Abstract

Abstract:

【Objective】Columnar growth in apple (Malus × domestica Borkh.) is a special type of dwarf mutation. Due to short internodes and lateral branches, a limited canopy and minimal pruning, columnar apple trees are well adapted to high density plantings. Based on the fine mapping of Co, the genes in the localization interval were screened, which laid a foundation for elucidating the molecular mechanism of columnar apple formation and breeding new varieties of columnar apples.【Method】Based on the latest apple genome data and transcriptome information, the buds, stem tips and leaves of columnar apple Wujia, Runtai No.1 and standard apple Fuji and Huashuo were used as test materials, and the genes between the fine mapping Co gene in interval from 27.66 Mb to 29.05 Mb were annotated and predicted. The coding sequence of the target gene was selected to detect primer specificity by RT-PCR, the real-time quantitative PCR was used to analyze the expression characteristics of target genes in different tissues and organs, and differential genes were screened out as candidate genes.【Result】The results showed that there were 67 genes between 27.66 Mb and 29.05 Mb in chromosome 10, 12 of which were non-coding RNAs (ncRNA), and the rest were genes with encoding proteins. According to the columnar and standard apple RNA-seq, there were 25 genes with more than 1 fold difference, 13 of which were up-regulated, and 12 genes were down-regulated in columnar apples. Among the 14 predicted genes, there were significant differences in the relative expression of the four genes MD10G1184100, MD10G1185400, MD10G1185600 and MD10G1190500 between shoot tips and lateral shoot tips in columnar and standard apples. The relative expression levels of MD10G1184100 and MD10G1185600 in the tip of terminal bud of two columnar apples were significantly higher than those of both standard apples. The relative expression of MD10G1185400 and MD10G1190500 genes in the tip of lateral bud of two columnar apples was significantly higher than that of two standard apples, while the expression of MD10G1184100 gene in two columnar apples was significantly lower than that of standard apples. The gene expression patterns of different tissues or organs of four candidate genes were analyzed. The result showed that the expression of MD10G1184100 gene in the roots of columnar apples was significantly higher than that in other tissues. The MD10G1185400 and D10G1185600 genes were significantly expressed in lateral tips in columnar apples, while MD10G1190500 gene was prominently expressed in the terminal bud of columnar apples.【Conclusion】4 genes with significant differences in columnar and standard apple could be regarded as Co candidate genes, which laid a foundation for gene cloning and functional verification and apple tree-oriented genetic improvement.

Key words: apple, columnar trait, gene mapping, gene expression, candidate gene analysis

BAI TuanHui,LI Li,ZHENG XianBo,WANG MiaoMiao,SONG ShangWei,JIAO Jian,SONG ChunHui. Screening and Expression Analysis of Co Candidate Genes in Columnar Apple[J].Scientia Agricultura Sinica, 2019, 52(23): 4350-4363.

Figures/Tables 6

Table 1

Table 2

Preliminary screening of genes in apple Co region"

基因编号 Gene ID		预测功能 Putative function	基因表达量Gene expression
基因编号 Gene ID		预测功能 Putative function	普通型Normal	柱状Columnar
MD10G1183600		肽酶S24/S26A/S26B/S26C家族蛋白 Peptidase family protein	1040.4	1080.7
MD10G1183700		染色体(SMC)家族蛋白的结构维持 (SMC) family protein	777.0	1174.6
MD10G1183800		非编码RNA ncRNA	-	-
MD10G1183900		非编码RNA ncRNA	-	-
MD10G1184000		前mRNA剪接Prp 18-相互作用因子 Pre-mRNA splicing Prp18-interacting factor	949.5	1446.9
MD10G1184100		MYB结构域蛋白15 MYB domain protein 15	11.4	230.1
MD10G1184200		非编码RNA ncRNA	-	-
MD10G1184300		未知功能蛋白 Protein of unknown function	331.7	335.6
MD10G1184400		未知功能蛋白 Protein of unknown function	270.1	240.6
MD10G1184500		肌动蛋白解聚因子6 Actin depolymerizing factor 6	1209.1	1275.9
MD10G1184600		磷酸盐转运蛋白1 Phosphate transporter 1	-	-
MD10G1184700		磷酸盐转运蛋白1 Phosphate transporter 1	472.8	519.2
MD10G1184800		乙烯响应因子1 Ethylene response factor 1	2.8	0.0
MD10G1184900		非编码RNA ncRNA	-	-
MD10G1185000		整合酶型DNA结合超家族蛋白 Integrase-type DNA-binding superfamily protein	2.8	0.0
MD10G1185100		整合酶型DNA结合超家族蛋白 Integrase-type DNA-binding superfamily protein	-	-
MD10G1185200		未知功能蛋白 Protein of unknown function	518.3	640.6
MD10G1185300		环/U盒超家族蛋白 RING/U-box superfamily protein	-	-
MD10G1185400		2-氧戊二酸（2OG）和铁（II）依赖性加氧酶超家族蛋白 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein	0.0	26.4
MD10G1185500		2-氧戊二酸（2OG）和铁（II）依赖性加氧酶超家族蛋白 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein	-	-
MD10G1185600		环/U盒超家族蛋白RING/U-box superfamily protein	0.9	3.2
MD10G1185700		四三肽重复序列（TPR）样超家族蛋白 Tetratricopeptide repeat (TPR)-like superfamily protein	-	-
MD10G1185800		四三肽重复序列（TPR）样超家族蛋白 Tetratricopeptide repeat (TPR)-like superfamily protein	-	-
MD10G1185900		自噬9 Autophagy 9 (APG9)	420.7	515.0
MD10G1186000		结节蛋白MTN21/EAMA样转运蛋白家族 Nodulin MTN21/EAMA-like transporter family protein	84.3	108.7
MD10G1186100		无顶端分生组织结构域转录调节超家族蛋白 NAC (No Apical Meristem) domain transcriptional regulator superfamily protein	-	-
MD10G1186200		非编码RNA ncRNA	-	-
MD10G1186300		开放阅读框7上游保守肽 Conserved peptide upstream open reading frame 7	966.5	1175.6
MD10G1186400		2-氧戊二酸（2OG）和铁（II）依赖性加氧酶超家族蛋白 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein	41.7	11.6
MD10G1186500		糖基水解酶9B6 Glycosyl hydrolase 9B6	-	-
MD10G1186600		糖基水解酶9B1 Glycosyl hydrolase 9B1	-	-
MD10G1186700		2-氧戊二酸（2OG）和铁（II）依赖性加氧酶超家族蛋白 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein	-	-
MD10G1186800		碱性螺旋-环-螺旋（bHLH）DNA结合超家族蛋白 Basic helix-loop-helix (bHLH) DNA-binding superfamily protein	-	-
MD10G1186900		碱性螺旋-环-螺旋（bHLH）DNA结合超家族蛋白 Basic helix-loop-helix (bHLH) DNA-binding superfamily protein	-	-
MD10G1187000		2-氧戊二酸（2OG）和铁（II）依赖性加氧酶超家族蛋白 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein	0.9	11.6
MD10G1187100		非编码RNA ncRNA	-	-
MD10G1187200		α/β水解酶超家族蛋白Alpha/beta-Hydrolases superfamily protein	2.8	0.0
MD10G1187300		侧生器官边界结构域29 Lateral organ boundaries-domain 29	-	-
MD10G1187400		锌指Zinc finger	-	-
MD10G1187500		光系统I亚单位H2 Photosystem I subunit H2	-	-
MD10G1187600		侧生器官边界结构域29 Lateral organ boundaries-domain 29	-	-
MD10G1187700		侧生器官边界结构域16 Lateral organ boundaries-domain 16	1.9	0.0
MD10G1187800		多聚ADP核糖聚合酶2 Poly(ADP-ribose) polymerase 2	869.9	577.3
MD10G1187900		ARM重复超家族蛋白 ARM repeat superfamily protein	560.0	506.6
MD10G1188000		BET1P/SFT1P样蛋白14A BET1P/SFT1P-like protein 14A	915.4	391.5
MD10G1188100		C2H2和C2HC锌指超家族蛋白C2H2 and C2HC zinc fingers superfamily protein	5.7	12.7
MD10G1188200		C2H2和C2HC锌指超家族蛋白C2H2 and C2HC zinc fingers superfamily protein	-	-
MD10G1188300		核糖体S17家族蛋白 Ribosomal S17 family protein	0.0	2.1
MD10G1188400		具有Dil结构域的肌球蛋白家族蛋白 Myosin family protein with Dil domain	110.9	186.8
MD10G1188500		半乳糖氧化酶/kelch重复超家族蛋白 Galactose oxidase/kelch repeat superfamily protein	-	-
MD10G1188600		未知Unknown	-	-
MD10G1188700		2-氧戊二酸（2OG）和铁（II）依赖性加氧酶超家族蛋白 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein	-	-
MD10G1188800		2-氧戊二酸（2OG）和铁（II）依赖性加氧酶超家族蛋白 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein	-	-
MD10G1188900		未知Unknown	34.1	51.7
MD10G1189000		未知Unknown	292.8	93.9
MD10G1189100		未知Unknown	154.5	228.0
MD10G1189200		光合电子转移C Photosynthetic electron transfer C	-	-
MD10G1189300		未知Unknown	145.0	162.5
MD10G1189400		2-氧戊二酸（2OG）和铁（II）依赖性加氧酶超家族蛋白 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein	-	-
MD10G1189500		未知Unknown	37.9	19.0
MD10G1189600		2-氧戊二酸（2OG）和铁（II）依赖性加氧酶超家族蛋白 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein	-	-
MD10G1189700		半乳糖氧化酶/kelch重复超家族蛋白 Galactose oxidase/kelch repeat superfamily protein	-	-
MD10G1189800		未知Unknown	-	-
MD10G1189900		2-氧戊二酸（2OG）和铁（II）依赖性加氧酶超家族蛋白 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein	-	-
MD10G1190000		碱性螺旋-环-螺旋（bHLH）DNA结合超家族蛋白 Basic helix-loop-helix (bHLH) DNA-binding superfamily protein	668.0	853.8
MD10G1190100		未知Unknown	245.4	51.7
MD10G1190200		细胞色素P450 Cytochrome P450	531.6	331.4
MD10G1190300		未知Unknown	-	-
MD10G1190400		细胞色素P450 Cytochrome P450	661.4	798.9
MD10G1190500		未知功能蛋白 Protein of unknown function	69.2	180.5
MD10G1190600		非编码RNA ncRNA	6.6	5.3
MD10G1190700		IND1（NADH脱氢酶所需的铁硫蛋白）-类 IND1(iron-sulfur protein required for NADH dehydrogenase)-like	225.5	520.3
MD10G1190800		类pfkb碳水化合物激酶家族蛋白 Pfkb-like carbohydrate kinase family protein	193.3	224.8
MD10G1190900		Mudr家族转座酶 Mudr family transposase	389.5	707.1
MD10G1191000		非编码RNA ncRNA	1.9	3.2
MD10G1191100		含核苷三磷酸水解酶超家族蛋白的P环 P-loop containing nucleoside triphosphate hydrolases superfamily protein	2.8	9.5
MD10G1191200		翼螺旋DNA结合转录因子家族蛋白 Winged-helix DNA-binding transcription factor family protein	10231.9	5165.8
MD10G1191300		乙烯响应元件结合因子3 Ethylene responsive element binding factor 3	1089.7	547.7
MD10G1191400		WRKY DNA结合蛋白21 WRKY DNA-binding protein 21	839.5	546.7
MD10G1191500		信号识别粒子 Signal recognition particle	508.8	376.8
MD10G1191600		跨膜氨基酸转运体家族蛋白 Transmembrane amino acid transporter family protein	—	—
MD10G1191700		PRA1家族蛋白 PRA1 (Prenylated rab acceptor) family protein	321.2	246.9
MD10G1191800		DREB2A相互作用蛋白2 DREB2A-interacting protein 2	338.3	338.8
MD10G1191900		镁转运蛋白9 Magnesium transporter 9	364.8	421.1
MD10G1192000		半乳糖醛糖基转移酶6 Galacturonosyltransferase 6	188.6	193.1
MD10G1192100		光系统II反应中心W Photosystem II reaction center W	6877.5	1885.9
MD10G1192200		非编RNA ncRNA	7.6	2.1
MD10G1192300		谷胱甘肽还原酶 Glutathione reductase	665.2	1506.0
MD10G1192400		Transferin/WD 40重复超家族蛋白 Transducin/WD40 repeat-like superfamily protein	11.4	58.0
MD10G1192500		α/β水解酶超家族蛋白 Alpha/beta-Hydrolases superfamily protein	303.2	237.4
MD10G1192600		非编码RNA ncRNA
MD10G1192700		非编码RNA ncRNA	-	-
MD10G1192800		类RNI超家族蛋白 RNI-like superfamily protein	1226.2	1437.4
MD10G1192900		吲哚-3-乙酸7 Indole-3-acetic acid 7	3281.4	8731.8
MD10G1193000		AUX/IAA转录调节家族蛋白 AUX/IAA transcriptional regulator family protein	-	-
MD10G1193100		原体prib/单链DNA结合 Primosome prib/single-strand DNA-binding	302.3	378.9
MD10G1193200		碱性螺旋-环-螺旋（bHLH）DNA结合超家族蛋白 Basic helix-loop-helix (bHLH) DNA-binding superfamily protein	525.0	624.8
MD10G1193300		色氨酸合酶α链 Tryptophan synthase alpha chain	329.8	215.3
MD10G1193400		碱性亮氨酸拉链25 Basic leucine zipper 25	145.9	575.2
MD10G1193500		GNAT家族1组蛋白乙酰转移酶 Histone acetyltransferase of the GNAT family 1	547.7	491.8
MD10G1193600		非编码RNA ncRNA	-	-
MD10G1193700		泛素结合酶11 Ubiquitin-conjugating enzyme 11	-	-
MD10G1193800		SOUL血红素结合家族蛋白 SOUL heme-binding family protein	1072.7	1758.2
MD10G1193900		泛素特异性蛋白酶15 Ubiquitin-specific protease 15	810.2	1333.9
MD10G1194000		阳离子氨基酸转运蛋白8 Cationic amino acid transporter 8	532.5	255.4
MD10G1194100	拟南芥赤霉素2-氧化酶1 Arabidopsis thaliana gibberellin 2-oxidase 1	1936.8	795.7

Table 2

Fig. 1

Fig. 2

Fig. 3

Fig. 4

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编号 No	基因名称 Gene name	正向及反向引物序列 Forward and reverse primer sequences (5'-3')		扩增产物大小 Amplified product size (bp)
A	MD10G1184100	F：	AGCAGGGAAGAAGAAGAAGACGC	201
A	MD10G1184100	R：	GGTCGTGACAGATGACGTGT	201
B	MD10G1185400	F：	CTTGCTGAAGGGTTGGGACTGAG	218
B	MD10G1185400	R：	GAAATAGGCTCAACACCAATCCAA	218
C	MD10G1185600	F：	TCAACCACCTCTGCCAAGTC	244
C	MD10G1185600	R：	GACTGATTTGTCAAGCCCGC	244
D	MD10G1186300	F：	CATGAACTCCGGAGATGTGCTTGA	237
D	MD10G1186300	R：	CTTGTCACCACGGGCTTCTGTC	237
E	MD10G1186400	F：	CACAACCAAGCATTCGGATCCT	259
E	MD10G1186400	R：	TTTGAATCTTTGCGTAGCACTTGGA	259
F	MD10G1187000	F：	CGATCTCGGCTTTCTAACCTTGCT	232
F	MD10G1187000	R：	GTCGTCCGTGCCAACAAAACAT	232
G	MD10G1190500	F：	TTCAGTCACCCACAATCGTAAACAA	204
G	MD10G1190500	R：	ACCTGCCACTACTCCAAACAAAAAC	204
G	MD10G1190700	F：	TTGTTGGCGAGATACCGTTAGAAAT	264
G	MD10G1190700	R：	AGATTACAAAGGCATGAACAAGGGA	264
I	MD10G1191100	F：	AGGGTGGGCAGGCTAAATGAC	209
I	MD10G1191100	R：	GAAGTTTAAAATGCTACCTGGCTGG	209
J	MD10G1192300	F：	CACCCGACAGCCGCAGAAG	232
J	MD10G1192300	R：	GTCATGCCGAATACTCCAATACCAG	232
K	MD10G1192400	F：	CAGAGGAACCTTCTAATGGTCCGATA	247
K	MD10G1192400	R：	TTCGCCTTCACTAAGTCAAAGCTGTAA	247
L	MD10G1192900	F：	GAAACGCGCAGATGGATTGAG	201
L	MD10G1192900	R：	AAGCAAACACCAAGCCGTCCT	201
M	MD10G1193400	F：	CGCAGCAGTAGCTCTCTCTC	213
M	MD10G1193400	R：	GGAGTTCTCCTCTGAGCTGC	213
N	MD10G1194200	F：	CTCGAGCAGCCCACCATGATG	222
N	MD10G1194200	R：	GAGGTGGAAGCAGAAGCAGTCG	222
	MdActin	F：	GGATTTGCTGGTGATGATGCT	178
	MdActin	R：	AGTTGCTCACTATGCCGTGC	178

Screening and Expression Analysis of Co Candidate Genes in Columnar Apple

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