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作物学报 ›› 2021, Vol. 47 ›› Issue (6): 1054-1069.doi: 10.3724/SP.J.1006.2021.04078

• 专题：主要麻类作物基因组学与遗传改良 • 上一篇    下一篇

大麻GRAS转录因子家族的全基因组鉴定及镉胁迫下表达分析

尹明(), 杨大为, 唐慧娟, 潘根, 李德芳, 赵立宁, 黄思齐*()   

  1. 中国农业科学院麻类研究所/农业农村部麻类生物学与加工重点实验室, 湖南长沙 410205
  • 收稿日期:2020-03-27 接受日期:2020-11-13 出版日期:2021-06-12 网络出版日期:2020-12-28
  • 通讯作者: 黄思齐
  • 作者简介:E-mail: 1586887698@qq.com
  • 基金资助:
    国家现代农业产业技术体系建设专项(CARS-16-E02)

Genome-wide identification of GRAS transcription factor and expression analysis in response to cadmium stresses in hemp (Cannabis sativa L.)

YIN Ming(), YANG Da-Wei, TANG Hui-Juan, PAN Gen, LI De-Fang, ZHAO Li-Ning, HUANG Si-Qi*()   

  1. Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture and Rural Affairs, Changsha 410205, Hunan, China
  • Received:2020-03-27 Accepted:2020-11-13 Published:2021-06-12 Published online:2020-12-28
  • Contact: HUANG Si-Qi
  • Supported by:
    The China Agriculture Research System(CARS-16-E02)

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摘要：

GRAS转录因子在植物生长发育及抗逆境胁迫中具有重要作用。本文对大麻GRAS转录因子家族进行了全基因组鉴定, 对其理化性质、系统进化发育、基因结构、基因间的共线性关系进行了分析, 并利用云麻1号及内蒙古小粒大麻的转录组数据分析其在镉胁迫下的表达量变化。结果表明, 大麻基因组中鉴定出54个GRAS基因, 96.30%的基因编码酸性蛋白, 长度为415~757 aa, 分子质量为46,405.05~85,748.52 kD, 等电点为4.77~8.54, 划分为9个亚家族, 其中PAT1、LS、SHR、HAM保守性较高, PAT1、LISCL、CsGRASA出现大量基因串联重复, CSGRAS12基因在5种植物的共线性分析中均存在。将2个大麻品种进行镉胁迫处理发现, 云麻1号株高下降10.48%, 鲜重下降6.33%; 内蒙古小粒大麻株高下降66.07%, 鲜重下降42.67%, 表明云麻1号较内蒙古小粒大麻更耐镉胁迫。云麻1号的54个GRAS基因中, 42个(77.78%)基因表达上调1.05~18.10, 11个(20.37%)基因表达下调0.13~0.91; 内蒙古小粒大麻的54个GRAS基因中, 27个(50.00%)基因表达上调1.01~6.46, 27个(50.00%)基因表达下调0.30~0.96。将两者GRAS基因进行同源基因鉴定并分析其表达情况发现, 耐镉品种云麻1号中40个同源GRAS基因较内蒙古小粒大麻在镉胁迫下的上调或下调幅度更明显, 表明这些GRAS基因与镉胁迫有明显相关性。本文可为挖掘和验证大麻GRAS基因提供参考。

关键词: 大麻, GRAS转录因子, 系统发育分析, 基因结构分析, 表达分析

Abstract:

GRAS transcription factors play important roles in plant growth, development and stress responses. In order to systematically analyze the GRAS transcription factor family in hemp, we performed a genome-wide identification of hemp GRAS genes, analyzed their physical and chemical properties, phylogenetic development, gene structure, and GRAS gene expression under cadmium stress in two hemp varieties (Yunma 1 and Inner Mongolia Xiaolidama). The results showed that there were 54 GRAS transcription factors in hemp genome, with the protein length from 415 to 757, encoding 96.30% of acidic proteins, the molecular weight from 46,405.05 to 85,748.52 kD and the isoelectric point from 4.77 to 8.54. These transcription factors were divided into nine subfamilies, among which, PAT1, LS, SHR, and HAM were more conserved, PAT1, LISCL, and CsGRASA had a large number of tandem repeats of genes, and CSGRAS12 genes were all present in collinearity analysis of five plants. Yunma 1 and Inner Mongolia Xiaolidama were treated with cadmium stress. Plant height and the fresh weight decreased in Yunma 1 and Inner Mongolia Xiaolidama, by 10.48%, 6.33% and 66.07%, 42.67%, respectively, indicating that Yunma 1 was more tolerant than Inner Mongolia Xiaolidama under cadmium stress. Among 54 GRAS genes in Yunma 1, 42 genes (77.78%) were up-regulated by 1.05-18.10, and 11 genes (20.37%) were down-regulated by 0.13-0.91. Among 54 GRAS genes in small-grain cannabis in Inner Mongolia, 27 genes (50.00%) were up-regulated by 1.01-6.46, and 27 genes (50.00%) were down-regulated by 0.30-0.96. This study showed that the 40 homologous GRAS gene in Yunma 1 were significanlty up- or down-regulated than those in Inner Mongolia Xiaolidama under cadmium stress, indicating that these GRAS genes were significantly related to cadmium stress. This study can provide a reference for subsequent mining and verification of GRAS genes in hemp.

Key words: hemp, GRAS transcription factors, phylogenetic analysis, gene structure analysis, expression analysis

表1

GRAS基因及相关信息"

基因名称
Gene name		 NCBI基因登录号
NCBI gene accession		 蛋白长度
Length (aa)		 等电点
pI		 分子量
Molecular weight (kD)
CsGRAS1 LOC115696991 458 4.77 52,006.96
CsGRAS2 LOC115698980 494 5.15 54,901.55
CsGRAS3 LOC115698988 724 5.99 81,047.24
CsGRAS4 LOC115700662 455 5.66 49,596.06
CsGRAS5 LOC115701004 454 6.68 50,178.21
CsGRAS6 LOC115702418 528 5.24 57,541.56
CsGRAS7 LOC115703632 559 6.21 62,215.78
CsGRAS8 LOC115705736 722 5.77 78,760.91
CsGRAS9 LOC115705815 722 5.72 78,817.91
CsGRAS10 LOC115705915 721 5.74 78,730.89
CsGRAS11 LOC115706185 539 5.51 59,352.41
CsGRAS12 LOC115707313 544 6.33 61,258.62
CsGRAS13 LOC115710202 582 4.92 64,716.73
CsGRAS14 LOC115710247 582 4.92 64,716.73
CsGRAS15 LOC115710247 582 4.92 64,716.73
CsGRAS16 LOC115710247 582 4.92 64,716.73
CsGRAS17 LOC115710247 582 4.92 64,716.73
CsGRAS18 LOC115710247 582 4.92 64,716.73
CsGRAS19 LOC115710247 582 4.92 64,716.73
CsGRAS20 LOC115710262 514 4.93 57,833.13
CsGRAS21 LOC115711337 467 5.82 52,554.66
CsGRAS22 LOC115711473 549 6.13 61,322.10
CsGRAS23 LOC115712444 497 5.28 56,735.16
CsGRAS24 LOC115712525 504 5.68 56,355.13
CsGRAS25 LOC115712712 613 5.08 67,527.83
CsGRAS26 LOC115712875 508 6.30 56,609.53
CsGRAS27 LOC115714404 622 5.33 68,325.01
CsGRAS28 LOC115714408 600 5.95 66,439.36
CsGRAS29 LOC115715793 628 5.08 71,316.90
CsGRAS30 LOC115716239 617 6.03 68,009.17
CsGRAS31 LOC115716331 700 5.99 76,887.41
CsGRAS32 LOC115716409 616 6.19 67,882.02
CsGRAS33 LOC115716431 752 6.29 82,128.85
CsGRAS34 LOC115717012 697 5.36 77,185.61
CsGRAS35 LOC115718811 645 6.73 73,634.61
CsGRAS36 LOC115718865 746 5.80 85,106.83
CsGRAS37 LOC115718865 709 5.66 80,996.82
CsGRAS38 LOC115718866 630 7.24 72,454.10
CsGRAS39 LOC115718867 621 5.69 71,491.35
CsGRAS40 LOC115718867 551 6.37 63,913.20
CsGRAS41 LOC115718867 506 8.54 58,824.80
CsGRAS42 LOC115719316 749 5.03 84,965.93
CsGRAS43 LOC115719656 757 5.10 85,748.52
CsGRAS44 LOC115719656 636 5.20 73,211.22
基因名称
Gene name		 NCBI基因登录号
NCBI gene accession		 蛋白长度
Length (aa)		 等电点
pI		 分子量
Molecular weight (kD)
CsGRAS45 LOC115719730 698 5.68 78,688.43
CsGRAS46 LOC115722004 577 4.94 66,178.24
CsGRAS47 LOC115723037 575 5.14 64,688.92
CsGRAS48 LOC115723133 436 5.58 49,164.54
CsGRAS49 LOC115723500 454 6.00 51,420.59
CsGRAS50 LOC115724710 577 6.05 64,503.06
CsGRAS51 LOC115724919 548 5.14 61,008.73
CsGRAS52 LOC115724919 415 5.20 46,405.05
CsGRAS53 LOC115725148 463 5.64 52,596.41
CsGRAS54 LOC115725491 756 6.16 85,229.91

图1

大麻、拟南芥的GRAS基因系统进化树 不同颜色表示不同的亚家族, 同一颜色的不同基因均属同一亚家族。"

图2

大麻GRAS基因结构分析"

图3

大麻GRAS基因基序"

图4

大麻GRAS基因的染色体定位"

图5

大麻染色体间GRAS基因共线性分析"

图 6

雷蒙德氏棉、大麻、水稻间GRAS基因共线性分析"

图7

大豆、大麻、玉米间GRAS基因共线性分析"

表2

云麻1号GRAS基因表达"

基因名称
Gene name		 云麻1号对照组
Yunma 1
control check		 云麻镉胁迫组
Yunma 1
cadmium stress		 变化值
Fold change		 基因名称
Gene name		 云麻对照组
Yunma 1
control check		 云麻镉胁迫组
Yunma 1
cadmium stress		 变化值
Fold change
CsGRAS24 2.44 0.33 0.13* CsGRAS28 2.31 4.07 1.76*
CsGRAS46 4.02 0.58 0.14* CsGRAS13 4.74 9.76 2.06*
CsGRAS25 42.77 20.24 0.47* CsGRAS32 13.12 27.08 2.06*
CsGRAS33 6.56 3.12 0.48* CsGRAS52 8.33 18.67 2.24*
CsGRAS2 1.62 0.78 0.48 CsGRAS1 0.21 0.46 2.24
CsGRAS11 30.07 14.91 0.50* CsGRAS29 0.21 0.46 2.24
CsGRAS22 1.63 0.91 0.56 CsGRAS12 19.52 44.15 2.26*
CsGRAS54 6.20 4.59 0.74 CsGRAS30 7.67 18.41 2.40*
CsGRAS6 0.32 0.28 0.88 CsGRAS5 0.37 0.97 2.65
CsGRAS42 9.74 8.87 0.91 CsGRAS7 1.00 2.68 2.69*
CsGRAS48 0.25 0.26 1.05 CsGRAS38 2.22 6.10 2.75*
CsGRAS9 6.16 6.88 1.12 CsGRAS43 0.74 2.10 2.85*
CsGRAS4 8.31 9.43 1.14 CsGRAS47 0.04 0.11 2.91
CsGRAS21 2.66 3.16 1.19 CsGRAS40 0.31 0.99 3.19
CsGRAS20 0.76 0.93 1.21 CsGRAS17 3.35 11.74 3.51*
CsGRAS10 7.49 9.54 1.27 CsGRAS37 12.42 61.52 4.95*
CsGRAS36 8.79 11.82 1.34 CsGRAS41 0.21 1.19 5.59*
CsGRAS31 14.46 19.51 1.35 CsGRAS26 0.04 0.21 5.64
CsGRAS23 0.20 0.27 1.37 CsGRAS50 8.33 57.94 6.96*
基因名称
Gene name		 云麻1号对照组
Yunma 1
control check		 云麻镉胁迫组
Yunma 1
cadmium stress		 变化值
Fold change		 基因名称
Gene name		 云麻对照组
Yunma 1
control check		 云麻镉胁迫组
Yunma 1
cadmium stress		 变化值
Fold change
CsGRAS15 3.04 4.43 1.46 CsGRAS3 0.01 0.14 10.50*
CsGRAS49 0.97 1.44 1.49 CsGRAS39 0.03 0.60 18.10*
CsGRAS8 8.98 13.70 1.53* CsGRAS18 0.00 0.30 0.30*
CsGRAS27 18.49 28.66 1.55* CsGRAS19 0.00 0.17 0.17*
CsGRAS44 4.33 6.75 1.56 CsGRAS34 0.00 0.03 0.03
CsGRAS16 0.32 0.51 1.59 CsGRAS35 0.00 0.32 0.32*
CsGRAS14 0.76 1.24 1.62* CsGRAS45 0.00 0.00 0.00
CsGRAS51 6.82 11.11 1.63* CsGRAS53 0.27 0.00 -0.27*

表3

内蒙古小粒大麻GRAS基因表达"

基因名称
Gene name		 内蒙大麻对照组
Inner Mongolia Xiaolidama
control check		 内蒙大麻镉胁迫组
Inner Mongolia Xiaolidama
cadmium stress		 变化值
Fold change		 基因名称
Gene name		 内蒙大麻对照组
Inner Mongolia Xiaolidama
control check		 内蒙大麻镉胁迫组
Inner Mongolia Xiaolidama
cadmium stress		 变化值
Fold change
CsGRAS24 5.40 1.61 0.30* CsGRAS31 20.57 20.70 1.01
CsGRAS53 0.84 0.37 0.44* CsGRAS40 0.60 0.62 1.02
CsGRAS22 2.70 1.35 0.50* CsGRAS39 0.31 0.33 1.05
CsGRAS48 0.34 0.17 0.50 CsGRAS42 9.72 10.66 1.10
CsGRAS25 49.36 28.23 0.57* CsGRAS4 8.38 9.73 1.16
CsGRAS21 2.54 1.61 0.63 CsGRAS44 4.87 5.91 1.21
CsGRAS33 12.12 7.76 0.64* CsGRAS52 12.38 15.14 1.22
CsGRAS36 10.98 7.07 0.64 CsGRAS13 6.41 8.78 1.37
CsGRAS41 1.27 0.97 0.76 CsGRAS47 0.08 0.11 1.38
CsGRAS17 8.55 6.64 0.78 CsGRAS28 1.85 2.58 1.39
CsGRAS11 37.71 29.54 0.78 CsGRAS30 12.06 17.68 1.47*
CsGRAS18 0.22 0.18 0.78* CsGRAS9 6.75 9.90 1.47*
CsGRAS20 0.28 0.23 0.79 CsGRAS51 14.04 21.05 1.50*
CsGRAS7 1.70 1.39 0.82 CsGRAS38 2.68 4.34 1.62
CsGRAS6 0.28 0.23 0.82 CsGRAS12 17.93 31.35 1.75*
CsGRAS1 0.48 0.40 0.83 CsGRAS15 1.82 3.65 2.00
CsGRAS29 0.48 0.40 0.83 CsGRAS45 0.04 0.10 2.73
CsGRAS14 1.08 0.94 0.87 CsGRAS16 0.10 0.30 3.00
CsGRAS27 20.63 18.12 0.88 CsGRAS50 13.12 41.91 3.19*
CsGRAS23 0.29 0.26 0.89 CsGRAS3 0.01 0.05 3.38
CsGRAS49 1.10 0.99 0.89 CsGRAS5 0.31 1.20 3.87*
CsGRAS32 13.96 12.66 0.91 CsGRAS37 8.00 34.34 4.29*
CsGRAS8 14.56 13.35 0.92 CsGRAS43 2.10 9.65 4.59*
CsGRAS10 4.19 3.87 0.92 CsGRAS26 0.08 0.50 6.46*
CsGRAS54 7.36 6.96 0.94 CsGRAS19 0.00 0.17 0.17*
CsGRAS46 1.17 1.12 0.95 CsGRAS34 0.00 0.23 0.23*
CsGRAS2 2.82 2.71 0.96 CsGRAS35 0.00 0.89 0.89*

图8

两个大麻品种在正常环境与镉胁迫环境的生长状况"

图9

GRAS同源基因表达"

图10

12个基因的qPCR验证表达 *, **, ***分别表示在0.05、0.01和0.001水平显著差异。"

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