中国农业科学 ›› 2019, Vol. 52 ›› Issue (23): 4350-4363.doi: 10.3864/j.issn.0578-1752.2019.23.015
收稿日期:
2019-07-17
接受日期:
2019-09-06
出版日期:
2019-12-01
发布日期:
2019-12-01
通讯作者:
白团辉,宋春晖
基金资助:
BAI TuanHui(),LI Li,ZHENG XianBo,WANG MiaoMiao,SONG ShangWei,JIAO Jian,SONG ChunHui()
Received:
2019-07-17
Accepted:
2019-09-06
Online:
2019-12-01
Published:
2019-12-01
Contact:
TuanHui BAI,ChunHui SONG
摘要:
【目的】柱状苹果是一种特殊的矮生突变类型,其节间短、短枝多、侧生分枝少、主干粗壮直立,是苹果实行矮化密植栽培的重要资源。本研究在前期Co精细定位的基础上,对定位区间的基因进行筛选,为阐明柱状苹果形成的分子机制和选育柱状苹果新品种奠定基础。【方法】以柱状苹果‘舞佳’和‘润太一号’,普通型苹果‘富士’和‘华硕’的芽、茎尖和叶片为试材,根据最新的苹果基因组以及与柱状相关的转录组信息,对Co精细定位区间27.66—29.05 Mb的基因进行注释分类,选择目标基因,查找其CDS序列,使用RT-PCR技术检测引物特异性,利用实时荧光定量PCR分析预测基因在不同组织器官中的表达特征,筛选出差异基因并将其作为候选基因。【结果】在苹果第10号染色体27.66—29.05 Mb区域内包含67个基因,其中12个为非编码RNA(ncRNA),其余为编码蛋白质的基因。根据RNA-seq分析,柱状和普通型苹果基因相对表达差异倍数在1倍以上的有25个基因,其中13个基因在柱状苹果中上调表达,12个基因在柱状苹果中下调表达。在预测的14个基因中,发现4个基因MD10G1184100、MD10G1185400、MD10G1185600和MD10G1190500在柱状和普通型苹果的主枝茎尖或侧枝茎尖中相对表达存在显著差异。其中,MD10G1184100和MD10G1185600在两个柱状苹果主枝茎尖中的相对表达量均显著高于两个普通型苹果。MD10G1185400和MD10G1190500在两个柱状苹果侧枝茎尖的表达量显著高于两个普通型苹果,而MD10G1184100在两个柱状苹果中的表达量显著低于普通型苹果。进一步对这4个候选基因进行不同组织或器官的基因表达特征进行分析,发现基因MD10G1184100在柱状苹果根部的表达显著高于其他部位,MD10G1185400和MD10G1185600在柱状苹果的侧枝茎尖中显著高表达,而MD10G1190500在柱状苹果的顶芽中显著高表达。【结论】在柱状和普通型苹果茎尖中筛选到4个表达显著差异的基因,可作为Co候选基因,为该基因的克隆和功能验证及苹果树树型定向遗传改良奠定了基础。
白团辉,李莉,郑先波,王苗苗,宋尚伟,焦健,宋春晖. 柱状苹果Co基因的筛选与候选基因分析[J]. 中国农业科学, 2019, 52(23): 4350-4363.
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.
表1
14个预测基因相对表达实时荧光定量PCR引物序列"
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 |
R: | GGTCGTGACAGATGACGTGT | |||
B | MD10G1185400 | F: | CTTGCTGAAGGGTTGGGACTGAG | 218 |
R: | GAAATAGGCTCAACACCAATCCAA | |||
C | MD10G1185600 | F: | TCAACCACCTCTGCCAAGTC | 244 |
R: | GACTGATTTGTCAAGCCCGC | |||
D | MD10G1186300 | F: | CATGAACTCCGGAGATGTGCTTGA | 237 |
R: | CTTGTCACCACGGGCTTCTGTC | |||
E | MD10G1186400 | F: | CACAACCAAGCATTCGGATCCT | 259 |
R: | TTTGAATCTTTGCGTAGCACTTGGA | |||
F | MD10G1187000 | F: | CGATCTCGGCTTTCTAACCTTGCT | 232 |
R: | GTCGTCCGTGCCAACAAAACAT | |||
G | MD10G1190500 | F: | TTCAGTCACCCACAATCGTAAACAA | 204 |
R: | ACCTGCCACTACTCCAAACAAAAAC | |||
G | MD10G1190700 | F: | TTGTTGGCGAGATACCGTTAGAAAT | 264 |
R: | AGATTACAAAGGCATGAACAAGGGA | |||
I | MD10G1191100 | F: | AGGGTGGGCAGGCTAAATGAC | 209 |
R: | GAAGTTTAAAATGCTACCTGGCTGG | |||
J | MD10G1192300 | F: | CACCCGACAGCCGCAGAAG | 232 |
R: | GTCATGCCGAATACTCCAATACCAG | |||
K | MD10G1192400 | F: | CAGAGGAACCTTCTAATGGTCCGATA | 247 |
R: | TTCGCCTTCACTAAGTCAAAGCTGTAA | |||
L | MD10G1192900 | F: | GAAACGCGCAGATGGATTGAG | 201 |
R: | AAGCAAACACCAAGCCGTCCT | |||
M | MD10G1193400 | F: | CGCAGCAGTAGCTCTCTCTC | 213 |
R: | GGAGTTCTCCTCTGAGCTGC | |||
N | MD10G1194200 | F: | CTCGAGCAGCCCACCATGATG | 222 |
R: | GAGGTGGAAGCAGAAGCAGTCG | |||
MdActin | F: | GGATTTGCTGGTGATGATGCT | 178 | |
R: | AGTTGCTCACTATGCCGTGC |
表2
苹果Co定位区间的基因初步筛选"
基因编号 Gene ID | 预测功能 Putative function | 基因表达量Gene expression | ||
---|---|---|---|---|
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 |
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