Recent Trend of Genome-Wide Multigene Family Analysis and Their Role in Plant Drought Tolerance

Kakar KU¹, Akram Ali Baloch¹, Nawaz Z² and Ahmed J¹*

¹Department of Biotechnology, Faculty of Life Sciences & Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan

²Department of Botany, University of Central Punjab, Rawalpindi, Pakistan

*Corresponding author: Prof. Dr. Jamil Ahmed, Department of Biotechnology, Faculty of Life Sciences & Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan. Tel: +923456789775; Email: jamil. ahmad@buitms.edu.pk

Received: July 24, 2019; Accepted: July 30, 2019; Published: August 06, 2019

Short Communication

Drought stress is a major abiotic stress that have devastating impact on world agriculture. Drought not only reduces the crop productivity and yield but also leads to lower incomes for farmers and weaken global food security [1]. Recent data from numerous independent studies have demonstrated that water stress reduced the average yield by 40% for Maize in 2016, 21% for Wheat in 2016 and 34-68% for cowpea in 2017 [2,3]. The speedy development and adoption of climate-resilient crop genotypes is imperative to ensure global food security [4].

Plants display stress resistance or stress tolerance through acclimation and adaptation mechanisms. To lessen the damages from drought stress, plant breeders, geneticists and farmers are exploring new approaches for resistance breeding in crops. The need to access and investigate genetic diversity on an unprecedented scale in plant genomes and discovery of new resistant genes has become inevitable. In this scenario, latest developments in plant genomics have provided additional resources to accelerate the pace of genetic improvement [5].

Current researches in plant genomics have largely focused on the genomewide identification, characterization and expression profiling of novel multigene families in sequenced organisms. These multigene families are being continuously reported in almost every known and important agricultural crop, including, rice, tomato, maize, citrus, papaya, Brassica, tobacco etc. To the best of our knowledge, more than 100 articles have been published in various journals this year, and the number is increasing gradually. The focus of such studies is to find one or more novel candidate gene(s) associated with plant growth, development and response to environmental stimuli. Examples of the newly identified gene families associated with drought stress response in plants include Mitogen-Activated Protein Kinases (MAPKs), Superoxide Dismutase (SOD), GRAS, Brassinazole-Resistant (BZR), Auxin Response Factors (ARFs), Alternative Oxidase (AOX), WRKY transcription factors, Metacaspase (MC), Cyclic Nucleotide-Gated Ion Channels (CNGCs), Catalases (CATs), Heat shock transcription factors (Hsfs), Expansin (EXP), NAC family, Multiple Organellar RNA editing Factor (MORF), IQ67-domain (IQD), Teosintebranched 1/Cycloidea/Proliferating (TCP), Aquaporins (AQPs), Calmodulin-binding Transcription Activators (CAMTAs), Late Embryogenesis Abundant (LEAs) and trihelix etc (Table 1). Many of these gene families have been systematically characterized in multiple plant species, while, others have been reported in particular species only. For example, BZR family of Transcription Factors (TFs), regulating the biosynthesis of brassinosteroids and drought resistance, is comprised of 16 genes in Glycine max (soybean), 11 genes in Zea Mays (Maize), 7 in Medicago truncatula (Barrel medic) and Phaseolus vulgaris (common bean), 6 in Cajanus cajan (pigeon pea) and Cicer arietinum (chickpea), and 5 genes in Lotus japonicus (Bridsfoot Trefoil) and Vigna radiate (mung bean) [6]. Similarly, the CNGC family genes involved in ion transport, calcium signaling, plant growth and stress response have been identified in Rice, tomato, Chinese cabbage and tobacco [7-9]. Depending on plant species and/or gene family, the proteins of each gene family have their own distinctive roles by using specific mechanism. For instance, MAPKs play central roles in hormone signaling transduction in cassava [10], while ARFs are critical components of the auxin-signaling pathway in chickpea, Medicago and Arabidopsis [11-13]. However, due to complex gene regulatory networks, crossed signaling pathways and protein-protein interactions, individual gene(s) or gene family contribute to various biological functions including plant growth, development, and biotic and abiotic stress resistance.

Table 1: A summary of some of the recently identified drought stress responsive multigene families through genome-wide analysis.




  
    Gene family
    Plant Species
    Common name
    No. of genes
    Reference
  
  
    Mitogen-activated protein kinases (MAPKs)
    Cassava
     
     
    [10]
  
  
    Superoxide dismutase (SOD)
    Vitis    vinifera (Grapevine)
     
    10
    [34]
  
  
    GRAS genes 
    Citrus    sinensis
    Sweet orange
    50
    [33]
  
  
    BRASSINAZOLE-RESISTANT (BZR)
    Cajanus cajan 
    Pigeon pea
    6
    [6]
  
  
    Cicer arietinum
    Chickpea 
    6
     
  
  
    Glycine max
    Soybean 
    16
     
  
  
    Lotus japonicus (Bridsfoot Trefoil)
     
    5
     
  
  
    Medicago truncatula
    Barrel medic
    7
     
  
  
    Phaseolus vulgaris
    Common bean
    7
     
  
  
    Vigna radiata
    Mung bean
    5
     
  
  
    Zea Mays
    Maize
    11
    [43]
  
  
    Auxin Response Factors (ARFs)
    Cicer arietinum
    Chickpea 
    24
    [11]
  
  
    ALTERNATIVE OXIDASE 
      (AOX)
    Triticum aestivum
    Hexaploid wheat
    20
    [40]
  
  
    WRKY
    Ananas comosus
    Pineapple
    54
    [45]
  
  
    Metacaspase (MC)
    Cucumis sativus
    Cucumber
    5
    [14]
  
  
    cyclic nucleotide-gated channels (CNGCs)
    Nicotiana tabacum
    Common tobacco
    35
    [9]
  
  
     
    Nicotiana sylvestris
     
     
     
  
  
     
    Nicotiana tomentosiformis
     
     
     
  
  
     
    Brassica oleracea
    Cabbage, cauliflower, broccoli, Brussels    Sprout, kohlrabi and kale
    26
     
  
  
    Catalases (CATs)
    Gossypium hirsutum L
    Cotton
    7
    [44]
  
  
    Heat stress transcription factors (Hsfs)
    Brassica oleracea
    Cabbage, cauliflower, broccoli, Brussels    sprout, kohlrabi and kale
    35
    [42]
  
  
    Expansin (EXP)
    Triticum aestivum L
    Common bread wheat
    241
    [19]
  
  
    NAC family
    T. aestivum L
    Common bread wheat
    361
     
  
  
    Multiple organellar RNA editing factor    (MORF)
    Populus trichocarpa
    Black cottonwood
    9
    [21]
  
  
    IQD (IQ67-domain)
    Brassica rapa ssp. pekinensis
    Chinese cabbage
    35
    [20]
  
  
    Teosinte-branched    1/Cycloidea/Proliferating (TCP)
    Zea mays
    Maize
    46
    [41]
  
  
    Aquaporins (AQPs)
    Citrus sinensis
    Sweet orange
    34
    [30]
  
  
     
    Vicia sativa sub sp. sativa
    Common vetch
    21
    [31]
  
  
    Calmodulin-binding Transcription Activator    CAMTA
    Musa acuminata
    Banana
    5
    [29]
  
  
    Late Embryogenesis Abundant (LEA)
    Vitis vinifera
    Grape
    60
    [26]
  
  
    Trihelix
    Gossypium hirsutum 
     
    102
    [27]
  
  
    Gossypium arboreum
     
    51
     
  
  
    Gossypium raimondii
     
    51



Table 1: A summary of some of the recently identified drought stress responsive multigene families through genome-wide analysis.

The primary and secondary functions of a newly identified gene(s) can be initially assessed by studying their functional domains followed by gene expression patterns or transcript abundances in plants against hormonal, biotic and abiotic stress through Real-Time Quantitative Polymerase Chain Reaction (qRT-PCR), Microarray or RNA-sequencing. Latest transcriptome-wide studies and expression profiling analyses have demonstrated the role of genome wide identified genes in plant drought tolerance. The qRT-PCR of cucumber (Cucumis sativus) Metacaspase (CsMC) family that encodes caspases like proteins involved in programmed cell death genes showed that the expression levels of CsMC2-CsMC5 were down-regulated by drought stress [14]. Huang et al. and Liu et al. noted similar responses for MC genes in rice and rubber tree (Hevea brasiliensis), indicating that some MC genes may play negative regulatory roles in drought stress and it’s induced programmed cell death [15,16]. The overexpression of Arabidopsis catalase gene AtCAT3, and rice OsCatA and OsCatC improved drought stress tolerance in Arabidopsis [17] and conferred systematic resistance in transgenic rice [18]. The genome-wide expression profiles of Hsfs genes in B. napus revealed that many members of BnaHsf family respond to drought stress. The artificially induced drought stress via PEG treatment induced greater response in wheat expansin (TaEXPs) genes [19] and BrIQD5 in B. rapa, where BrIQD5-overexpressed plants showed more tolerance to drought stress than wild-type plants [20]. Wang et al. [21] identified nine drought responsive genes through expression profiling of water deficient black poplar (Populus×euramericana cv. ‘Neva’). The NAC family is the largest of the plant-specific transcription families comprising 488 genes in Triticum aestivum only [22]. The RNA-seq based expression data exhibited that 23 TaNAC genes were differentially expressed under drought stress treatment [22]. Moreover, NAC genes such as MlNAC9 (Miscanthus lutarioriparius) [23], SlNAC3 (Solanum lycopersicum) [23], ONAC022 (Oryza sativa) [24], GmNAC3 and GmNAC4 (Soybean) [25], have already been profiled as to be involved in drought stress tolerance. The microarray expression profiles of the grape LEA family genes (VvLEAs) exhibited strong response to drought stress [26]. Following RNA sequencing and qRT-PCR analysis, Magwanga et al. [27], overexpressed GT2 gene from Gossypium hirsutum in cotton that enhanced the tolerance to maximum level. The transcriptome-wide profiles and functional analysis have also shown the regulatory roles of AQPs, CAMTAs, CNGCs in enhancing drought tolerance in rice, banana, citrus, vetches, tobacco and cabbages [28-31,7-9].

Characterization of the novel genes from genome wide analysis have shown that the upstream regions of these genes harbored multiple drought responsive cis-acting regulatory elements i.e., eighty elements in 52 sugarcane Expansin genes [32]; thirty-one in orange CsGRAS genes [33]; four in cucumber CsMC genes [14]; and one in Grapevine VvCSD6 gene [34]. The most widespread cis acting regulatory elements that are involved in drought inducibility include MYB binding sites, dehydration-responsive element (DRE; TACCGACAT), CRT-core motif (A/GCCGAC) and MYCATRD22 (CACATG) [35].

Additionally, studies focusing on genome-wide profiling and analysis of miRNAs have let the scientists identified numerous classes of drought stress responsive mRNAs in different crops [36]. Apart from cis-acting regulatory elements, many classes of microRNAs have been shown to be regulatory of gene expression by targeting endogenous and/or exogenous genes [37]. Growing evidence suggest that miRNA-guided regulation of ROS-related genes at the posttranscriptional level is essential for normal growth, development and adaptation to stress conditions including drought [38,39]. The novel drought responsive genes resulting from genomewide studies can serve as potential candidates for futuristic breeding programs to produce novel drought tolerant transgenic plant cultivars.

References

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Citation:Kakar KU, Ali Baloch A, Nawaz Z and Ahmed J. Recent Trend of Genome-Wide Multigene Family Analysis and Their Role in Plant Drought Tolerance. Ann Agric Crop Sci. 2019; 4(2): 1046.

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Gene family	Plant Species	Common name	No. of genes	Reference
*Mitogen-activated protein kinases (MAPKs)*	Cassava			[10]
*Superoxide dismutase (SOD)*	Vitis vinifera (Grapevine)		10	[34]
*GRAS* genes	Citrus sinensis	Sweet orange	50	[33]
BRASSINAZOLE-RESISTANT (BZR)	Cajanus cajan	Pigeon pea	6	[6]
	Cicer arietinum	Chickpea	6
	Glycine max	Soybean	16
	Lotus japonicus (Bridsfoot Trefoil)		5
	Medicago truncatula	Barrel medic	7
	Phaseolus vulgaris	Common bean	7
	Vigna radiata	Mung bean	5
	Zea Mays	Maize	11	[43]
Auxin Response Factors (ARFs)	Cicer arietinum	Chickpea	24	[11]
*ALTERNATIVE OXIDASE* *(AOX)*	Triticum aestivum	Hexaploid wheat	20	[40]
WRKY	Ananas comosus	Pineapple	54	[45]
Metacaspase (MC)	Cucumis sativus	Cucumber	5	[14]
cyclic nucleotide-gated channels (CNGCs)	Nicotiana tabacum	Common tobacco	35	[9]
	Nicotiana sylvestris
	Nicotiana tomentosiformis
	Brassica oleracea	Cabbage, cauliflower, broccoli, Brussels Sprout, kohlrabi and kale	26
Catalases (CATs)	Gossypium hirsutum L	Cotton	7	[44]
Heat stress transcription factors (Hsfs)	Brassica oleracea	Cabbage, cauliflower, broccoli, Brussels sprout, kohlrabi and kale	35	[42]
Expansin (EXP)	Triticum aestivum L	Common bread wheat	241	[19]
NAC family	T. aestivum L	Common bread wheat	361
Multiple organellar RNA editing factor (MORF)	Populus trichocarpa	Black cottonwood	9	[21]
IQD (IQ67-domain)	Brassica rapa ssp. pekinensis	Chinese cabbage	35	[20]
Teosinte-branched 1/Cycloidea/Proliferating (TCP)	Zea mays	Maize	46	[41]
Aquaporins (AQPs)	Citrus sinensis	Sweet orange	34	[30]
	Vicia sativa sub sp. sativa	Common vetch	21	[31]
Calmodulin-binding Transcription Activator CAMTA	Musa acuminata	Banana	5	[29]
Late Embryogenesis Abundant (LEA)	Vitis vinifera	Grape	60	[26]
Trihelix	Gossypium hirsutum		102	[27]
	Gossypium arboreum		51
	*Gossypium* *raimondii*		51