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作物学报

作物学报 ›› 2020, Vol. 46 ›› Issue (5): 645-660.doi: 10.3724/SP.J.1006.2020.94133

• 作物遗传育种·种质资源·分子遗传学 •    下一篇

亚洲棉短绒突变体纤维发育及其差异基因表达分析

王晓阳1,王丽媛1,潘兆娥1,何守朴1,王骁1,龚文芳1,3,*(),杜雄明1,2,*()   

  1. 1中国农业科学院棉花研究所 / 棉花生物学国家重点实验室, 河南安阳455000
    2棉花生物学国家重点实验室郑州研究基地 / 郑州大学, 河南郑州 450001
    3中南林业科技大学 / 经济林培育与保护教育部重点实验室, 湖南长沙 410004
  • 收稿日期:2019-09-02 接受日期:2019-12-26 出版日期:2020-05-12 网络出版日期:2020-01-15
  • 通讯作者: 龚文芳,杜雄明
  • 作者简介:E-mail: wangxiaoyang198806@126.com
  • 基金资助:
    本研究由国家自然科学基金项目(31601353);国家重点研发计划项目资助(2017YFD0101601-03)

Analysis of differentially expressed genes and fiber development in Gossypium arboreum fuzzless mutant

Xiao-Yang WANG1,Li-Yuan WANG1,Zhao-E PAN1,Shou-Pu HE1,Xiao WANG1,Wen-Fang GONG1,3,*(),Xiong-Ming DU1,2,*()   

  1. 1Institute of Cotton Research, Chinese Academy of Agricultural Sciences / State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
    2Zhengzhou Research Base, State Key Laboratory of Cotton Biology / Zhengzhou University, Zhengzhou 450001, Henan, China
    3Key Laboratory of Cultivation and Protection for Non-wood Forest, Ministry of Education / Central South University of Forestry and Technology, Changsha 410004, Hunan, China
  • Received:2019-09-02 Accepted:2019-12-26 Published:2020-05-12 Published online:2020-01-15
  • Contact: Wen-Fang GONG,Xiong-Ming DU
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31601353);the National Key Technology R&D Program(2017YFD0101601-03)

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摘要：

棉花纤维是重要的天然纺织材料, 是最长的单细胞, 是研究纤维发育的良好材料。本研究以亚洲棉短绒突变体(FZ)及其野生型(fz)为材料, 结合扫描电镜、石蜡切片、RNA-seq技术, 解析棉花短绒起始的可能机制。与野生型(fz)的0DPA时期胚珠相比, 突变体的胚珠在该时期仅有少量的纤维起始。在+3DPA时, 突变体没有短绒细胞起始, 仅有长纤维细胞, 而野生型有大量的短纤维细胞和长纤维细胞。对这2个材料的0DPA、+3DPA、+5DPA和+8DPA胚珠差异基因分析结果显示, 在短绒突变体(FZ)和野生型(fz)的4个纤维发育时期共挖掘出3780个差异表达基因, 其中0DPA时差异基因数目最少, 随着胚珠发育时间的延长, 差异基因的数目逐渐增加。KEGG分析发现这些基因主要参与蜡质、角质生物合成, 以及苯丙烷代谢和植物信号传导过程。共表达趋势分析显示, 在突变体+3DPA上调的差异基因中, 参与离子结合、MAPK级联反应、氧化还原活性和转录调控的基因表达受到正影响(表达水平提高), 造成突变体短绒纤维不能正常起始。这些结果描述了二倍体亚洲棉短绒起始的动态变化, 可为进一步研究棉纤维发育提供参考。

关键词: 亚洲棉, 短绒突变体, 差异表达基因, 共表达趋势

Abstract:

Cotton fiber, one of main nature textile and longest single cell, is a good material for researching the cotton fiber development. In this study, fuzz mutant (FZ) and wild-type (fz) which belong to diploid Gossypium arboreum species were used for unraveling molecular mechanism of fuzz fiber initiation by scanning electron microscopy (SEM), paraffin section and RNA sequencing technology. It was found that any fibers scarcely initiated on the ovule surface of the mutant at 0DPA, compared with that of the wild-type. Only lint fiber cells emerged on the ovule surface of fuzz mutant, while abundant fuzz and lint fiber cells appeared in wild-type at +3DPA stage. The transcriptome analysis of FZ and fz across the four fiber development stages (0DPA, +3DPA, +5DPA, and +8DPA) indicated that the number of differentially expressed gene was 3780. There were litter differentially expressed genes at 0DPA in FZ and fz. In the proceed of ovule development, the number of differentially expressed genes was increased gradually. The KEGG enriched pathway analysis illustrated that these differentially expressed genes were involved in cutin, suberine and wax biosynthesis, phenylalanine metabolism pathways and plant hormone signal transduction pathways. The analysis of co-expressed gene trend lines indicated that the up-regulated genes in mutant at +3DPA were all involved in metal ion binding, MAPK cascade, oxidoreductase activity and transcription regulation, resulting in failed fuzz fiber cells initiation in mutant. These findings elaborated a dynamic variation about fuzz fiber initiation in diploid G. arboreum, which provides a reference for further research in the cotton fiber development.

Key words: Gossypium arboreum, fuzzless mutant, differentially expressed gene, co-expressed trend

表1

用于荧光定量PCR验证的基因和引物"

基因编号 Gene 正向引物
Forward primer (5'-3')		 反向引物
Reverse primer (5'-3')		 log2RT-QPCR log2FPKM 功能注释
Functional annotations
Ga02G0173 GTGCTCGGAAGAAAACGCTC CGCACCTGCCAAAGTTGTTA 1.31 1.10 谷胱甘肽转移酶 Glutathione S-transferase
Ga03G0324 ACAGCAAAAGGCAATCGAGAAC CGTGGGAAGCTATCGGCTTT 2.85 1.65 谷胱甘肽转移酶 Glutathione S-transferase
Ga04G0014 CTTTCGGGTCAGGTCGAAGG GTTGTGTTACTCGGGGGACC 3.52 2.89 细胞色素氧化酶 Cytochrome P450
Ga05G3679 GAGCCATCGCTAAGTTCTGGGC TCCAACAATTTCAGGCACGCAA -1.19 -1.40 谷胱甘肽转移酶 Glutathione S-transferase
Ga05G3965 CCTGCTATTGCCATCAACACTT TTGTGCTGGACTTGTTCTTGCT -2.00 -1.24 分子伴侣 Molecular chaperone
Ga07G0568 CAACGGCGAAAACAACACGGAA TGCACTGGTCTCCTTCTGTGGA 1.31 1.18 甲基转移酶Methyltransferase
Ga07G1530 GGTGGTAACCCTAGCTTGTGGC GCGCGTTATGTGTAACTTGCGA 1.26 1.11 转录因子WD40
Ga07G1742 GCCGTGCTAACTTATTCCCTTGC AGCACCCCAAGTAGTAACCAAGC -1.54 -1.20 钙联蛋白 Calnexin 1
Ga07G2088 TTGCATCAGAGCAGCCTGCATA TCTGCTGCCCAAGATTTGCCAT -1.54 -1.32 转录因子 MYB108
Ga07G2611 GCAGAGGCAGCTTTAAGTTTGGG GCATCCCACCAGGCCTAAGTTC -1.61 -1.55 网状蛋白 Reticulon-like protein
Ga08G0121 TGTCTTCGGAACCCGGAGATGA GGCATCCCACTAGCAGCATTGA 4.47 6.69 蛋白受体激酶 Receptor-like protein kinase
Ga09G0409 TACCGGTGCACTGATCGACCTA TTCTGAGTCGACTGTTCGTCGC 2.03 1.55 功能未知 Unknown
Ga09G0435 TGCAGGGTTGTTAAGGTGTGGG TGATTTCGTTATCGGTCCGCCC 1.14 1.05 假定蛋白 Predicted protein
Ga09G0661 CGCCATGCTTGCCATCTTCATC CACTGAAGGCAGCTTGATCCGA 1.28 1.31 还原酶 Dihydroflavonol-4-reductase
Ga10G0810 ATGAGCCGCCCTATTGACTGCC TGGTAGATGCCTTCGTTGCTGA 2.24 2.51 RNA加工 RNA processing
Ga10G1419 CCAACAAGGGCCCAAGTGCTAT TCTTGTTCCCTTGGCCGACTTG -1.22 -1.20 NADH脱氢酶 NADH dehydrogenase
Ga11G2832 TAAGATCGGTTCGGCTTCGG ATGCTCCACCCTAACTTGCC 2.01 2.45 假定蛋白 Hypothetical protein
Ga11G2833 CACTTCTCGTGTGATGACCTGT CATCTTCTAACGCTGGAATCTG 3.70 5.20 谷胱甘肽转移酶 Glutathione S-transferase
Ga11G3625 ATGCTTCTCAACTGCGCAGGAA GCTGTTGTCGAACTTTATGGGGC 2.45 2.86 谷胱甘肽转移酶 Glutathione S-transferase
Ga11G3670 GACCGATGAAGAGGAACCCAGC CCATGTGGTGTCCCGGTATGAC -2.88 -1.78 NADH脱氢酶 NADH dehydrogenase
Ga12G0113 TCGACGTCGCCCTGTTTTTCAT CTGACGTGGACGCCATGTTGAT 1.53 1.58 假定蛋白 Hypothetical protein
Ga10G0013 TACCAGTTGAAGCCGAAGGCTG CCATTGTAAGGCCTGCGCTTTG 2.18 1.81 甲基转移酶N-methyltransferase

图1

野生型fz和短绒突变体FZ材料中短纤维发育过程的形态学观察 A: 野生型、短绒突变体的种子以及扫描电镜下看到的短绒纤维起始; B: 石蜡切片所示短绒纤维起始。红色箭头所示长纤维, 黑色箭头所示短纤维细胞。"

表2

样品测序数据与参考基因组序列比对结果分析"

编号 No 过滤后的序列数
Clean reads		 GC
GC (%)		 Q30
Q30 (%)		 原始数
Total reads		 比对到参考基因组的总数
Mapped reads		 比对到参考基因组唯一位置的数目
Uniq mapped reads		 比对到参考基因组多个位置的数目
Multiple mapped reads		 比对到正链数
Reads map to “+”		 比对到负链数
Reads map to “-“
L01 6E+07 42.75 88.41 1.13E+08 100098347(88.79%) 95615963 (84.82%) 4482384 (3.98%) 49356770 (43.78%) 49542917 (43.95%)
L02 7E+07 42.89 87.89 1.49E+08 132564763(88.84%) 126665191 (84.88%) 5899572 (3.95%) 65411403 (43.84%) 65613688 (43.97%)
L03 6E+07 43.73 88.21 1.29E+08 114781600(89.23%) 109876069 (85.42%) 4905531 (3.81%) 56731466 (44.10%) 56901283 (44.24%)
L04 7E+07 43.32 87.93 1.31E+08 115706679(88.26%) 109946001 (83.86%) 5760678 (4.39%) 57037850 (43.51%) 57182987 (43.62%)
L05 6E+07 43.45 88.18 1.15E+08 101447417(88.47%) 96871049 (84.47%) 4576368 (3.99%) 50115129 (43.70%) 50235739 (43.81%)
L06 7E+07 43.65 88.41 1.36E+08 119977298(88.23%) 114195412 (83.98%) 5781886 (4.25%) 59276583 (43.59%) 59413894 (43.69%)
L07 9E+07 43.47 88.41 1.85E+08 164355512(88.86%) 156168989 (84.43%) 8186523 (4.43%) 81092741 (43.84%) 81289251 (43.95%)
L08 6E+07 43.21 87.12 1.24E+08 108363137(87.68%) 102760244 (83.15%) 5602893 (4.53%) 53406006 (43.21%) 53552268 (43.33%)
L09 6E+07 43.53 88.53 1.25E+08 110741117(88.61%) 105077371 (84.08%) 5663746 (4.53%) 54559214 (43.66%) 54711263 (43.78%)
L10 6E+07 43.93 88.53 1.12E+08 95982638(85.64%) 89277314 (79.66%) 6705324 (5.98%) 47006407 (41.94%) 47142478 (42.06%)
L11 6E+07 43.62 87.74 1.24E+08 106630817(85.76%) 99506038 (80.03%) 7124779 (5.73%) 52250173 (42.03%) 52415958 (42.16%)
L12 7E+07 43.65 88.90 1.45E+08 125095168(86.41%) 116813022 (80.69%) 8282146 (5.72%) 61391019 (42.41%) 61584013 (42.54%)
L13 6E+07 43.78 89.76 1.28E+08 109195486(85.27%) 104512429 (81.62%) 4683057 (3.66%) 53869063 (42.07%) 54027240 (42.19%)
L14 7E+07 43.40 90.20 1.31E+08 115537224(88.07%) 110898150 (84.53%) 4639074 (3.54%) 57057026 (43.49%) 57220578 (43.61%)
L15 8E+07 43.20 90.60 1.63E+08 144883755(88.62%) 139117996 (85.09%) 5765759 (3.53%) 71628619 (43.81%) 71848062 (43.94%)
L16 7E+07 44.19 89.70 1.44E+08 122786455(85.34%) 116535579 (80.99%) 6250876 (4.34%) 60495477 (42.04%) 60621983 (42.13%)
L17 8E+07 44.14 90.20 1.56E+08 130032853(83.13%) 123871138 (79.19%) 6161715 (3.94%) 64115657 (40.99%) 64295623 (41.10%)
L18 7E+07 43.38 90.49 1.44E+08 127237888(88.61%) 121687992 (84.75%) 5549896 (3.87%) 62876344 (43.79%) 63029624 (43.90%)
L19 6E+07 43.32 91.03 1.19E+08 106495539(89.28%) 101489480 (85.08%) 5006059 (4.20%) 52555236 (44.06%) 52649155 (44.14%)
L20 6E+07 43.38 91.29 1.16E+08 101384931(87.60%) 96799488 (83.64%) 4585443 (3.96%) 50050156 (43.24%) 50157927 (43.34%)
L21 6E+07 43.63 91.17 1.12E+08 98144438(87.78%) 93630910 (83.74%) 4513528 (4.04%) 48444159 (43.33%) 48541604 (43.42%)
L22 6E+07 44.24 87.94 1.22E+08 100479675(82.20%) 92865206 (75.98%) 7614469 (6.23%) 49048631 (40.13%) 49206041 (40.26%)
L23 6E+07 44.06 87.32 1.23E+08 102829882(83.46%) 95769710 (77.73%) 7060172 (5.73%) 50222205 (40.76%) 50359879 (40.87%)
L24 6E+07 44.39 86.86 1.14E+08 96749028(84.55%) 90393952 (79.00%) 6355076 (5.55%) 47365502 (41.39%) 47485322 (41.50%)

图2

所有样本间皮尔逊相关系数分析 A和B分别代表fz和FZ"

图3

fz及其短绒突变体FZ不同纤维发育时期共有的差异基因 A: 在fz和FZ材料中不同纤维发育时期差异基因韦恩图; B: 在fz和FZ两个材料中4个纤维发育时期91个共有的差异基因热图。"

表3

在fz和FZ两个材料中4个纤维发育时期91个共有的差异基因及其表达情况"

基因编号 Gene ID 基因注释Gene annotation 0DPA +3DPA +5DPA +8DPA
Ga11G2831 含有WD40结构的蛋白 WD40 repeat-like superfamily protein 2.00 2.70 3.00 1.72
Cotton_newGene_517935 假定蛋白 Hypothetical protein 2.55 2.94 1.88 1.84
Ga03G0324 谷胱甘肽S-转移酶 Glutathione S-transferase 1.33 1.65 1.63 1.05
Ga11G0115 假定蛋白 Hypothetical protein -1.25 -1.28 -1.42 -1.05
Ga07G1809 硫代硫酸盐ATP结合蛋白 Sulfate/thiosulfate ATP-binding protein 2.35 2.34 2.40 0.95
Cotton_newGene_190500 未鉴定蛋白 Uncharacterized protein 2.37 2.67 0.97 1.16
Cotton_newGene_217366 未鉴定蛋白 Uncharacterized protein 2.03 2.44 1.33 1.65
Ga11G3311 葡萄糖基转移酶 UDP-glycosyltransferase 83A1 1.25 1.98 1.50 1.85
Ga09G2202 乙烯响应因子 AP2/ERF 1.95 1.31 2.13 -1.42
Ga09G0608 亮氨酸拉链蛋白 Leucine-rich repeat protein kinase -1.90 -1.49 -0.70 -0.20
Cotton_newGene_190685 假定蛋白 Hypothetical protein 1.39 1.60 0.94 0.89
Cotton_newGene_184413 假定蛋白 Hypothetical protein 0.86 0.82 0.68 0.20
Cotton_newGene_216530 假定蛋白 Hypothetical protein 1.42 1.92 0.70 1.48
Ga06G0475 泛素连接酶 E3 ligase -0.74 -0.80 -0.53 -0.61
Cotton_newGene_206595 假定蛋白 Hypothetical protein 0.62 0.51 0.22 0.08
Cotton_newGene_188033 假定蛋白 Hypothetical protein -3.18 -2.89 -2.89 -1.50
Ga14G2119 谷氨酸受体 Glutamate receptor 3.94 3.27 3.11 1.92
Cotton_newGene_206588 假定蛋白 Hypothetical protein 2.13 2.00 1.73 0.92
Ga11G2832 自噬相关蛋白 Autophagy-related protein 2.42 2.45 2.66 1.38
Ga06G1674 锌依赖的包外多肽酶蛋白 Zn-dependent exopeptidases protein -1.22 -0.78 -0.75 -0.57
Cotton_newGene_313214 TMV抗性蛋白 TMV resistance protein 0.42 1.14 1.27 0.73
Ga04G1219 乙酰基葡萄糖转移酶 UDP-GlcNAc 1.21 1.37 1.40 0.78
Cotton_newGene_383086 ATP合成酶 ATP synthase 1.29 1.00 1.15 0.57
Cotton_newGene_336363 核酸内切酶 Endonuclease 1.47 1.00 1.30 0.46
Cotton_newGene_521387 功能未知 Unknown 1.87 1.81 1.73 1.36
Ga04G0915 功能未知 Unknown 1.43 1.30 1.23 0.32
Cotton_newGene_190683 细胞色素氧化酶 P450 Cytochrome P450 2.78 3.25 2.09 1.73
Cotton_newGene_94861 核酸酶 Putative nuclease -1.00 -0.86 -0.93 -0.65
Cotton_newGene_195900 功能未知 Unknown -3.47 -3.50 -3.45 -2.85
Ga10G0013 甲基转移酶 Histone-lysine N-methyltransferase 1.78 1.81 2.10 1.35
Ga11G0121 木糖梅 Alpha-xylosidase 1 -1.64 -0.77 -0.92 -1.26
Ga11G0187 假定蛋白 Hypothetical protein -0.85 -0.74 -0.81 -0.48
Ga11G0110 假定蛋白 Hypothetical protein 0.82 1.21 0.71 0.84
Ga06G1755 脯氨酸受体蛋白激酶Proline-rich receptor-like protein kinase -1.00 -0.52 -0.98 -0.95
Ga05G2954 天冬氨酸酶 Asparticase 0.65 0.58 1.25 0.24
Cotton_newGene_572274 假定蛋白 Hypothetical protein 2.24 2.62 1.48 1.69
Cotton_newGene_353692 假定蛋白 Hypothetical protein -0.56 -0.63 -0.71 -0.49
Cotton_newGene_483966 假定蛋白 Hypothetical protein 2.77 2.77 2.71 2.30
Ga11G0111 微丝蛋白 Fb17 -0.31 -0.75 -1.21 -2.11
Cotton_newGene_99176 丝氨酸/苏氨酸蛋白磷酸酶 Serine/threonine protein phosphatase 1.08 0.85 0.97 1.10
Ga12G1137 乙烯受体蛋白 AP2/ERF 1.25 1.53 1.81 -1.25
Ga11G2354 假定蛋白 Hypothetical protein 1.73 1.58 1.68 0.31
Cotton_newGene_517938 细胞色素氧化酶 P450 Cytochrome P450 4.11 4.65 3.60 3.14
Cotton_newGene_300782 核酸内切酶亚基 Endonuclease subunit 1.47 1.44 1.06 1.14
Cotton_newGene_252500 Copia型多蛋白 Copia-type polyprotein 2.74 2.88 2.52 2.00
Cotton_newGene_517934 功能未知 Unknown 3.19 3.84 2.65 1.73
Cotton_newGene_353671 缬氨酸-tRNA连接酶 Valine-tRNA ligase -0.39 -0.95 -0.65 -0.94
Ga05G3965 功能未知 Unknown -1.55 -1.24 -1.95 -1.34
Ga09G1652 丝氨酸/苏氨酸蛋白磷酸酶 Serine/threonine protein phosphatase -1.61 -1.34 -1.01 -1.25
Ga04G1773 转录因子 NAC1 1.20 0.98 2.02 -1.43
Ga09G1364 乙酰辅酶A氧化酶 Acyl-coenzyme A oxidase 2.66 2.52 2.53 2.06
Cotton_newGene_213765 假定蛋白 Hypothetical protein -1.28 -1.29 -1.89 -1.22
Ga04G0280 富含脯氨酸蛋白 Proline-rich protein 0.71 0.77 1.46 1.21
Cotton_newGene_217374 假定蛋白 Hypothetical protein 1.56 1.89 0.72 1.26
Ga10G0798 细胞壁受体激酶 Wall-associated receptor kinase 0.44 0.41 0.30 0.13
Ga03G0640 功能未知 Unknown 1.88 1.62 1.14 1.16
Cotton_newGene_577041 功能未知 Unknown 3.08 1.66 3.58 0.40
Ga07G1742 含有CBS结构域的蛋白 CBS domain-containing protein -1.45 -1.20 -1.17 -0.69
Ga07G2703 丝氨酸/苏氨酸蛋白磷酸酶 Serine/threonine-protein kinase -0.81 -0.59 -0.39 -0.26
Ga07G0566 转录因子 bHLH137 1.05 1.03 3.13 -0.50
Cotton_newGene_190686 假定蛋白 Hypothetical protein 1.42 1.61 0.84 0.86
Ga04G1342 未鉴定蛋白 Uncharacterized protein 0.80 0.30 0.17 0.37
Cotton_newGene_563611 未鉴定蛋白 Uncharacterized protein 2.35 2.52 1.44 1.83
Cotton_newGene_592029 丝裂原活化蛋白激酶 Mitogen-activated protein kinase MMK1 -1.65 -1.23 -0.87 -0.46
Ga01G1687 富含半胱氨酸/组氨酸蛋白 Cysteine/histidine-rich protein 0.74 0.58 0.54 0.48
Cotton_newGene_54250 功能未知 Unknown 2.88 2.87 2.67 1.88
Cotton_newGene_353710 假定蛋白 Hypothetical protein 1.50 1.25 1.10 1.44
Cotton_newGene_474685 未鉴定蛋白 Uncharacterized protein 2.45 2.75 1.40 1.79
Cotton_newGene_67170 假定蛋白 Hypothetical protein 3.06 2.61 2.59 1.44
Cotton_newGene_353674 芳香类多肽 Pentafunctional arom polypeptide 1.41 1.31 1.33 1.02
Ga03G1055 木聚糖糖基化酶 Xyloglucan endotransglucosylase 0.83 2.34 -1.71 0.96
Ga11G0123 甲硫氨酸tRNA转移酶 Methionine-tRNA ligase -2.16 -1.98 -1.73 -1.21
Ga07G0272 咖啡酸盐酯酶 Caffeoylshikimate esterase -1.59 -1.52 -1.82 -1.20
Cotton_newGene_57872 假定蛋白 Hypothetical protein 0.51 0.71 0.36 0.36
Ga03G2383 受体蛋白 Receptor -0.81 -1.43 -2.23 1.21
Ga02G0173 假定蛋白 Hypothetical protein 1.44 1.10 1.19 1.04
Cotton_newGene_509534 假定蛋白 Hypothetical protein 1.82 2.28 1.03 1.35
Ga11G0124 未鉴定蛋白 Uncharacterized protein -2.92 -4.04 -3.64 -3.84
Ga13G1311 丝氨酸/苏氨酸蛋白磷酸酶 Serine/threonine-protein phosphatase 1.80 1.60 1.61 1.42
Ga10G1419 NADH脱氢酶 NADH dehydrogenase -0.99 -1.20 -1.37 -1.31
Cotton_newGene_190499 未鉴定蛋白 Uncharacterized protein 1.30 1.60 0.80 0.91
Cotton_newGene_217363 假定蛋白 Hypothetical protein 1.69 2.16 0.97 1.75
Ga07G2215 未鉴定蛋白 Uncharacterized protein 1.38 2.23 -2.23 0.98
Ga11G2833 谷胱甘肽S-转移酶 Glutathione S-transferase 4.06 5.20 5.45 1.92
Cotton_newGene_473974 功能未知 Unknown 1.76 1.56 1.46 0.69
Ga07G0353 富含脯氨酸蛋白 Proline-rich protein 1.48 1.61 1.06 0.36
Cotton_newGene_99000 假定蛋白 Hypothetical protein 0.73 0.61 0.46 0.92
Ga07G1792 CBL9 -1.33 -1.33 -1.07 -0.68
Cotton_newGene_190497 假定蛋白 Hypothetical protein 2.55 2.89 2.28 1.86
Ga09G1540 蛋白YLS9 YLS9 protein 0.88 1.12 -0.82 0.66
Ga09G1216 川芎嗪-3 Tetraspanin-3 -1.02 -1.53 -0.94 -2.15

图4

fz及其短绒突变体FZ不同纤维发育时期差异基因概况 A: 在fz和FZ材料中不同纤维发育时期差异基因数目; 红色代表上调的基因, 绿色代表下调基因。B: 1783个差异基因在fz和FZ材料4个短绒纤维发育时期的表达趋势。C: fz和FZ材料4个短绒纤维发育时期差异基因KEGG 富集通路。"

表4

角质、软木质、蜡质生物合成途径以及苯丙烷代谢途径的差异基因及其表达情况"

基因编号Gene ID 基因功能
Gene function		 0DPA +3DPA +5DPA +8DPA KEGG_pathway_annotation
Ga01G2133 ω-羟基棕榈酸酯-乙酰酰转移酶
Omega-hydroxypalmitate-feruloyl transferase		 0.05 0.52 -0.11 1.07 Cutin, suberine, and wax biosynthesis
Ga12G0500 细胞色素氧化酶 P450 Cytochrome P450 -0.06 0.18 -1.22 -1.24 Cutin, suberine, and wax biosynthesis
Ga07G2444 细胞色素氧化酶 P450 Cytochrome P450 0.06 1.06 -0.18 -0.40 Cutin, suberine, and wax biosynthesis
Ga08G1573 细胞色素氧化酶 P450 Cytochrome P450 -0.81 -0.68 -0.63 1.02 Cutin, suberine, and wax biosynthesis
Ga08G2220 细胞色素氧化酶 P450 Cytochrome P450 -1.95 -2.11 -2.22 0.14 Cutin, suberine, and wax biosynthesis
Ga10G2228 ω-羟基棕榈酸酯-乙酰酰转移酶
Omega-hydroxypalmitate-feruloyl transferase		 0.59 -1.55 0.32 0.59 Cutin, suberine, and wax biosynthesis
Ga04G1297 脂肪酸羟化酶 Fatty acid hydroxylase -0.95 -0.15 0.31 2.10 Cutin, suberine, and wax biosynthesis
Ga07G2443 细胞色素氧化酶 P450 Cytochrome P450 0.05 1.16 -0.09 -0.37 Cutin, suberine, and wax biosynthesis
Ga05G2018 过氧化物酶Peroxidase 0.34 0.88 1.20 -0.25 Phenylalanine metabolism
Ga14G0143 肉桂醇脱氢酶
Cinnamyl alcohol dehydrogenase		 -0.06 0.47 0.77 -1.41 Phenylpropanoid biosynthesis
Ga10G0561 甲基转移酶 Caffeic acid-methyltransferase 0.08 -0.02 -0.19 -1.30 Phenylalanine metabolism
Ga11G3625 过氧化物酶 Peroxidase 0.65 2.86 1.37 1.11 Phenylalanine metabolism
Ga12G1737 甲基转移酶 Caffeic acid-methyltransferase -1.18 -0.54 -0.96 1.15 Phenylpropanoid biosynthesis
Ga05G1817 过氧化物酶 Peroxidase -0.05 0.33 -0.17 -2.71 Phenylalanine metabolism
Ga12G2843 过氧化物酶 Peroxidase -1.71 -1.17 -0.29 -0.02 Phenylalanine metabolism
Ga12G0336 甲基转移酶 Caffeic acid-methyltransferase 0.35 0.44 -0.05 -1.12 Phenylpropanoid biosynthesis
Ga03G0366 花青素葡萄糖基转移酶
Anthocyanidin-glucosyltransferase		 0.25 0.72 -0.22 1.45 Phenylpropanoid biosynthesis
Ga05G0239 乙烯脱氢酶 Aldehyde dehydrogenase -0.01 0.02 0.37 -3.41 Phenylpropanoid biosynthesis
Ga09G0681 葡萄糖苷酶 Glucosidase -0.18 0.30 -0.15 -1.20 Phenylpropanoid biosynthesis
Ga04G1983 过氧化物酶 Peroxidase 0.08 0.33 0.23 -1.16 Phenylalanine metabolism
Ga09G1700 苯丙氨酸氨裂合酶
Phenylalanine ammonia-lyase		 -0.19 0.37 -1.21 -0.84 Phenylalanine metabolism
Ga01G2475 过氧化物酶 Peroxidase 68 0.42 2.69 0.60 -0.49 Phenylalanine metabolism
Ga10G0968 肉桂酸4-羟化酶 Cinnamate 4-hydroxylase 0.24 -0.26 -1.28 -0.01 Phenylalanine metabolism
Ga11G1671 过氧化物酶 Peroxidase 17 0.13 0.46 0.05 -2.06 Phenylalanine metabolism
Ga10G1786 过氧化物酶 Cationic peroxidase 1 0.46 1.38 0.50 -0.25 Phenylalanine metabolism
Ga10G1772 莽草酸O-羟基肉桂酰基转移酶
Shikimate O-hydroxycinnamoyltransferase		 0.04 1.14 1.78 1.38 Phenylpropanoid biosynthesis
Ga11G2088 过氧化物酶 Peroxidase 72 0.42 0.22 0.79 -2.38 Phenylalanine metabolism
Ga13G0640 细胞色素氧化酶 P450 Cytochrome P450 -0.09 0.15 0.12 -1.35 Phenylpropanoid biosynthesis
Ga12G1739 氨基甲酸N-甲基转移酶
Anthranilate N-methyltransferase		 -1.30 -0.86 -0.68 0.34 Phenylpropanoid biosynthesis
Ga04G0842 苯丙氨酸裂解酶
Phenylalanine ammonia-lyase		 -0.12 0.06 -1.08 -0.88 Phenylalanine metabolism
Ga04G1242 过氧化物酶 Peroxidase 51 0.44 1.08 -0.02 0.17 Phenylalanine metabolism

表5

植物激素转导途径中的差异基因及其表达情况"

基因编号
Gene ID		 基因注释
Gene annotation		 基因名称Gene name 激素Hormone 0DPA +3DPA +5DPA +8DPA
Ga06G1125 乙烯响应因子 EIN3-binding F-box protein 1 EIN3 ETH 1.1 1.1 4.6 0.4
Ga01G1781 生长素响应因子Auxin response factor 9 ARF9 IAA 1.0 1.2 2.4 0.6
Ga09G2536 生长素诱导蛋白Auxin-induced protein 22D AUX22D IAA 1.6 1.0 2.6 1.6
Ga02G1198 脱落酸不敏感蛋白Abscisic acid-insensitive protein ABI3 ABA 0.7 0.8 2.1 0.4
Ga01G2735 转录因子MYC4 Transcription factor MYC4 MYC4 JA 1.7 1.4 4.1 0.5
Ga13G1098 生长素诱导蛋白Auxin-induced protein X10A AIP10A IAA 1.0 1.0 0.6 2.2
Ga03G2153 吲哚乙酸合成酶Indole-3-acetic acid-amido synthetase IAA IAA 0.9 5.0 2.7 0.6
Ga05G2728 生长素诱导蛋白Auxin-induced protein 6B AIP6B IAA 1.2 0.9 3.2 1.0
Ga11G1087 生长素响应蛋白Auxin-responsive protein IAA16 IAA16 IAA 0.8 1.1 4.2 0.4
Ga07G0242 脱落酸受体Abscisic acid receptor PYL2 ABA 1.2 1.7 1.5 0.7
Ga01G0771 吲哚乙酸合成酶 Indole-3-acetic acid-amido synthetase IAA IAA 1.4 1.3 3.0 0.5
Ga08G2804 乙烯响应因子 Ein3-binding F-box protein 4 EIN3 ETR 1.4 1.2 4.6 0.7
Ga06G2183 磷酸转移蛋白Histidine-containing phosphotransfer protein 4 AHP4 CK 1.0 1.0 0.6 0.4
Ga10G2395 生长素响应蛋白 Auxin-responsive protein IAA26 SRK2I IAA 0.8 1.4 2.3 0.7
Ga10G3077 生长素诱导蛋白Auxin-induced protein X15 AIPX15 IAA 0.3 0.4 0.7 1.0
Ga08G2252 生长素响应蛋白Auxin-responsive protein IAA11 IAA11 IAA 1.2 0.9 2.5 0.6
Ga03G2608 生长素诱导蛋白Auxin-induced protein X10A AIP10A IAA 2.2 0.8 1.3 1.0
Ga03G0428 乙烯受体Ethylene receptor 2 ETR2 ETH 1.3 0.9 2.6 0.7
Ga11G1046 乙烯受体Ethylene receptor EIN4 ETH 1.3 1.2 2.2 0.8
Ga07G0142 蛋白磷酸酶 Protein phosphatase 2C PP2C ABA 1.5 1.6 4.0 0.8
Ga05G0163 乙烯响应蛋白EIN3-binding F-box protein 1 EIN3 ETH 0.9 1.2 3.6 0.4
Ga09G2537 生长素响应蛋白 Auxin-responsive protein IAA14 IAA14 IAA 1.0 0.5 0.4 1.2
Ga12G2846 赤霉素受体 Gibberellin receptor GID1B GID1B GA 1.2 1.8 2.1 0.4
Ga08G2885 蛋白磷酸酶 Protein phosphatase 2C PP2C77 ABA 1.4 1.3 3.9 0.4
Ga07G0455 生长素响应蛋白 Auxin-responsive protein IAA9 IAA9 IAA 1.6 0.8 2.6 0.3
Ga03G2632 生长素转运蛋白 Auxin transporter-like protein 5 ATP5 IAA 0.9 1.1 2.3 0.8
Ga11G3045 脱落酸受体 Abscisic acid receptor PYL9 ABA 1.6 1.2 4.2 0.4
Ga11G1086 生长素诱导蛋白 Auxin-induced protein 22D AUX22D IAA 1.3 1.8 6.4 0.5
Ga03G2592 生长素诱导蛋白 Auxin-induced protein 15A AUX15A IAA 0.9 0.6 0.5 2.2
Ga05G1344 生长素响应蛋白 Auxin-responsive protein IAA16 IAA16 IAA 1.5 1.0 2.3 0.6
Ga05G2981 细胞分裂素响应蛋白 Cytokinin ARR17 ARR17 IAA 1.0 1.2 1.0 0.5
Ga11G2673 乙烯响应转录因子 Ethylene-responsive transcription factor ERF10 ETH 1.8 1.0 15.7 0.1
Ga12G2331 ABA相关蛋白激酶 ABA-related protein kinase SNF1 ABA 1.2 1.3 2.1 0.9
Ga05G0157 生长素响应蛋白IAA29 Auxin-responsive protein IAA29 IAA29 IAA 1.3 0.8 0.5 0.5
Ga02G1269 水杨酸相关蛋白 Salicylic acid-related protein PRP1 SA 0.8 0.9 0.4 0.5
Ga06G2185 磷酸转移蛋白 Histidine phosphotransfer protein AHP3 CK 1.0 0.9 0.7 0.5
Ga13G2114 生长素诱导蛋白Auxin-induced protein 22B AUX15A IAA 1.4 1.2 2.1 1.9
Ga05G3500 生长素诱导蛋白 Auxin-induced protein X15 AUX15 IAA 3.6 0.7 0.9 0.6
Ga07G1535 吲哚乙酸合成酶 Indole-3-acetic acid-amido synthetase IAA IAA 0.8 1.3 1.5 0.4
Ga09G2560 乙烯受体 Ethylene receptor 2 ETR2 ETH 1.3 1.4 6.3 0.3
Ga03G2582 生长素诱导蛋白 Auxin-induced protein 15A AUX15A IAA 1.0 0.9 2.1 0.8
Ga05G1383 生长素响应蛋白 Auxin-responsive protein IAA27 IAA27 IAA 1.1 1.1 1.3 0.2
Ga11G1865 生长素响应蛋白 Auxin-responsive protein IAA IAA 1.3 0.9 2.0 0.4
Ga05G1988 生长素诱导蛋白 Auxin-induced protein 6B AUX6B IAA 1.1 0.8 2.9 0.3

图5

差异基因共表达趋势 A: 在fz 和FZ两个材料中4个纤维发育时期所有差异表达基因的热图分析。B: 差异基因功能注释; 黑色代表0DPA时期高表达的基因, 蓝色代表+3DPA时期高表达的基因, 橙色代表+5DPA时期高表达的基因, 绿色代表+8DPA时期高表达的基因。"

图6

MYBMIXTA-like基因在亚洲棉中的同源序列比对"

图7

Ga12G1199在FZ和fz材料中的表达差异 * P < 0.05, ** P < 0.01, **** P < 0.0001. "

图8

RT-QPCR (X-轴)结果与RNA-seq (Y-轴)差异基因相关性分析 散点图代表RT-QPCR与RNA-seq的差异基因相对表达量的log2值。"

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