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Current Journal of Applied Science and Technology

33(1): 1-11, 2019; Article no.CJAST.46931


ISSN: 2457-1024
(Past name: British Journal of Applied Science & Technology, Past ISSN: 2231-0843,
NLM ID: 101664541)

Biotechnology: An Advanced Tool for Crop


Improvement
Tinee Adlak1, Sushma Tiwari1*, M. K. Tripathi1, Neha Gupta1,
Vinod Kumar Sahu1, Punamchand Bhawar1 and V. S. Kandalkar1
1
Department of Plant Molecular Biology and Biotechnology, College of Agriculture, RVSKVV, Gwalior,
Madhya Pradesh, India.

Authors’ contributions

This work was carried out in collaboration between all authors. Authors TA and ST wrote the first draft
of the manuscript. Author ST checked and corrected final manuscript. Author NG managed the
literature search and references. In joint efforts all authors MKT, PB and VSK structured the final
version of the manuscript. All authors read and approved the final manuscript.

Article Information

DOI: 10.9734/CJAST/2019/v33i130081
Editor(s):
(1) Dr. Farjana Sultana, Professor, College of Agricultural Sciences, International University of Business Agriculture and
Technology (IUBAT University), Bangladesh.
Reviewers:
(1) Dr. M. Thangaraj, CAS in Marine Biology Annamalai University, India.
(2) Dr. R. K. Lal, CSIR-CIMAP, Lucknow, U.P. India.
Complete Peer review History: http://www.sdiarticle3.com/review-history/46931

Received 16 November 2018


Review Article Accepted 20 February 2019
Published 05 March 2019

ABSTRACT
Plant breeding is mainly concerned with genetic improvement of crops through hybridization,
screening and selection of advance lines. The conventional methods give advance varieties with
desirable traits but take consume more time (6 to 12 years) to achieve. Biotechnology tools makes
breeding methods more advance by reducing the time to get improved varieties. Other than
conventional methods varietal advancement can be achieved by applying plant tissue culture,
transgenic approaches and molecular breeding methods. Crop improvement by using
biotechnology approaches is mostly concerned with protoplast fusion to get somatic hybrids, gene
transfer to get genetically modified organisms and use of DNA markers to select trait of interests.
Variety with improved biotic and abiotic stress resistance can be developed in less time and more
accuracy using recent biotechnological approaches. Several advance tools are being utilized for
that purpose including, nanotechnology, bioinformatics tools offers new era of genomics assisted
molecular breeding. Next Generation Sequencing and high throughput genotyping approaches are
increasing efficiency and output of biotechnological tools in agriculture. Current review focused on
overview of biotechnological tools being applied for crop improvement.
_____________________________________________________________________________________________________

*Corresponding author: E-mail: sushma2540@gmail.com;


Adlak et al.; CJAST, 33(1): 1-11, 2019;; Article no.CJAST.46931
no.

Keywords: Crop improvement; genomics; molecular breeding; plant tissue culture; transgenics.

1. INTRODUCTION culture, haploid production, somaclonal


hybridization or somaclonal variations. Another
Plant breeding plays a major role in increasing major application of biotechnology is transfer of
crop yield for over a century. Continue efforts gene from one organism to another which could
have been made to inculcate desirable trait like be done by direct method (physical or chemical
diseases tolerant, higher yield, abiotic stress transfer) or indirect method (agrobacterium
tolerant etc. in a single line or genotype. Crop mediated gene transfer). Most popular and used
improvement is based on the criteria novelty, method for crop improvement is molecular
stability, uniformity and utility; which a breeder breeding method, where we use DNA markers
achieve by combined application of conventional and improve variety by marker assisted selection.
breeding and tools of biotechnology, this Agriculture biotechnological aspects may hhelp in
emphasis of plant biotechnology supplements getting improved varieties according to changing
breeding for crop improvement. Thus, the th climate [1,2] and for biotic and abiotic stress
integration of both plant breeding and resistant
ant variety development [3]
[3]. Moose and
biotechnology, overcome the increasingly Mumm [4] emphasize how the application of
sophisticated, and staggering breeding molecular plant breeding is now contributing to
procedure in easiest way. Continuous varietal discoveries of genes
nes and their functions which
improvement through conventional breeding could be helpful for new avenues for basic plant
needs biotechnology to maximize the probability biology research. Recently,, Watson et al al. [5]
of success. Tissue culture and genetic focused on integration of speed breeding with
engineering are the two major approaches other modern crop breeding technologies,
dealing with crop improvement via biotechnology. including high-throughput
throughput genotyping, genome
In plant breeding, biotechnology is more than editing and genomic selection for accelerating
genetic engineering which address problems in the rate of crop improvement. Crossa et al. [6]
all areas of agricultural production
producti and emphasized on Genomic selection (GS) and said
processing. This includes raise and stabilize that it facilitates the selection of superior
yields; to improve resistance to pests, diseases genotypes in less time and thus accelerates the
and abiotic stresses such as drought and cold; breeding cycle. Crop improvement applying
and to enhance the nutritional content of foods biotechnological tools could be done in faster
like protein in pulses, etc. There are three major way by high throughput phenotyping, high
aspects of biotechnology in crop breeding i.e., throughput genotyping, genomics assisted
Plant tissue culture, transgenic approaches and breeding and genome editing. Fig Figs. 1 and 2,
molecular breeding methods. Culturing of plant clearly indicating different approaches of
cell/ tissue in synthetic medium is known as plant biotechnology which h are being applied in plant
tissue culture and it may be applied for breeding practices of crop improvement.
micropropagation, embryo rescue, ue, protoplast

Fig. 1. Different approaches of crop improvement using biotechnological tools

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Fig. 2. Applications of biotechnology in plant breeding practices

2. GLOBAL SCENARIO ON CROP that there will be over 120 different transgenic
IMPROVEMENT events in biotech crops worldwide, which is about
a four-fold
fold increase in the number of current
The broad applications of biotechnology in transgenic events found in commercially
agriculture, specifically in crops, include the cultivated genetically modified (GM) crops. India
development of gene based markers, is the second largest producer of food grains
biofortification, nanotechnology, use of molecular globally & houses numerous varieties of cereals
markers, tissue culture, and genetic engineering. and pulses that are largely consumed cons
These tools would help in supplying the domestically. As per 3rd advance estimates, the
increasing needs of food to continuously growing production of food grains during 2016 2016-17 is
world population which is estimatedated to reach 9 273.38 million tonnes. According to International
billion by 2050 [7]. Research and development service for the Acquisition of agri-biotech
agri
(R&D) activities in genetics (1960) has wide application (ISAAA), India has the forth position
practical application of transgenic crops started under area for genetically modified crop planting.
only during the 1980s with the success of Field trials for 21 GM food crops, including GM
experiments done in tobacco. Several transgenic vegetables and cereals have been approved by
crops were later developed and commercialized the many countries but commercial cultivation of
starting in tomato with delayed ripening, on GM food has not been permitted by any State
agronomic and field crops such as canola, cotton, government in India ia till now [8].
[8] Transgenic
maize, soybean, sugar beet, papaya, and squash approach can be a valid alternative for the
rendering with traits such as herbicide tolerance, development of biofortified crops (nutritionally
virus and insect resistance. In 2004, it was enhanced food crop) when there is a limited or
estimated that more than 50 other species of no genetic variation in nutrient content
cont among
transgenic fruits, vegetables, field crops,
c and plant varieties [9].. Among micronutrients,
other plants were under research in the minerals, vitamins,
ins, several essential amino acids,
laboratory and confined facilities with a long term and desirable fatty acids have been targeted by
goal of eventual commercialization. It is likely genes from different sources to enhance

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nutritional level of food crops. Some of the 3.1 Micropropagation


ssuccessful examples of transgenic food crops
are maize (high lysine), soybean (high Micropropagation is mass production of clonal
unsaturated fatty acid), cassava (high provitamin progeny from very small plant parts (0.2-10 mm)
A and iron rich), and Golden rice (high provitamin in the laboratory, followed by their establishment
A). Biofortified cereals, legumes, vegetables, in soil under greenhouse conditions. Nowadays
fruits, oilseeds, and fodder crops have also been more than 500 million plants belonging to diverse
reported. Molecular breeding approaches are species are now being annually produced
most efficient in enhancing the biotic and abiotic through micropropagation in the world. Banana,
stress adaptation of crop plants, and recent strawberries, citrus, timber trees like Delbergia
advances in high throughput genotyping, sisso, planting material can certainly improve the
sequencing and phenotyping platforms yield potentials of vegetatively propagated.
(phenomics) have transformed molecular Micropropagated plants are true to type, disease
breeding to genomics assisted breeding (GAB). free, high quality and super elite planting material
Most commonly used approaches for genomics for further seed production. This technology
assisted breeding are marker assisted selection possesses tremendous potential for making
(MAS) and genomic selection (GS). MAS, environment clean and green.
includes marker assisted backcrossing, gene
pyramiding, mapping for associated targeted 3.2 Somaclonal Variation
traits by specific genes or QTLs, fine mapping of
QTL region etc. GS, on the other hand, uses all Somaclonal variation is the variation among
available marker data for a population to predict callus-derived plants, is a potent force for
breeding value. The development of improved broadening the genetic base. Several interesting
breeding lines for commercial crop cultivation by and potentially useful novel traits have been
traditional methods is time consuming and recovered that either do not exist or are rare in
expensive task. With the deployment of the natural gene pool using this technique —for
genomics assisted breeding, the generation of example, atrazine resistance in maize,
improved breeding lines has become easier and glyphosate resistance in tobacco, improved
faster. lysine and methionine contents in cereals,
increased seedling vigor in lettuce, jointless
3. PLANT TISSUE CULTURE pedicels in tomato are much significant
recovered traits. In India, a somaclonal variant of
Plant tissue culture broadly refers to the Invitro a medicinal plant, Citronella java has been
cultivation of living plant cells, tissues or organs released as a commercial variety, B-3, which
(seeds, embryos, single cells, protoplasts) on gives higher yield and oil content than the
nutrient media under closely controlled and original variety. Likewise, Pusa Jai Kishan is a
aseptic environment. Depending upon the plant variety of Brassica juncea released as a
part used as explant (part of plant used for somaclonal variant of Varuna variety.
regeneration), plant tissues culture techniques
are micropropagation, somatic embryogenesis, 3.3 Haploids Production
somaclonal variation, meristem culture, anther
culture, embryo culture, protoplast culture, Haploids production through anther or pollen
cryopreservation, and production of secondary culture is an attractive method, where pollen
metabolites. Table 1 is indicating list of crops grains incubate under optimum conditions leads
being studied by different research groups in to growth of microspores into sporophytes. Wide
plant tissue culture area. crossing, irradiation, chemical treatment is other
principal methods for haploid production.

Table 1. List of tissue cultured crop in India (listed by Agri-farming)

Fruit crops Apple, banana, fig, grape, pineapple, strawberry, citrus


Spice crops Turmeric, ginger, vanilla, cardamom, black pepper
Cash crops Potato and sugarcane
Medicinal crops Stevia, patchouli, neem, aloevera
Ornamental crops Gerbera, syngonium, lily
Biofuel Jatropha, pongamia
Woody plants Teak, populous, bamboo, eucalyptus

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4. TRANSGENIC APPROACHES this, coat protein mediated resistance (CPMR)


has been successfully applied to generate virus
Biotechnology is well known branch of science resistant fruits and vegetables such as papaya,
which deal with the use of living organisms and plum and squash. Recently, the United States
bioprocess to make or modify a product, to get Department of Agriculture allowed Monsanto
improve plants or animals or develop new Company to sell drought tolerant maize MON
products for specific uses. Biotechnology is 87460. Other than that, genetically engineered
widely being used for generation of genetically tomato and sweet pepper have been developed
modified (GM) crops, where one or several for longer shelf life that prevent them from rotting
genes coding for desirable traits have been and degrading. The crops have since been
inserted through the process of genetic released for commercial production by farmers in
engineering (GE). The gene to develop the USA and China. Introduction of provitamin A
transgene is originate from the same or other and β carotene genes have resulted in the
species and organisms unrelated to the recipient production of golden rice [11,12,13]. To add
organism. Transgenic technology is a gene value to agri-foods vitamin producing transgenic
transfer process from same or unrelated species plants have also been developed and emphasis
to desired crop plant species for genetic analysis is being laid on multigene engineering.
and direct manipulation of DNA. This gene
technology is also known as recombinant DNA 5. MOLECULAR BREEDING
technology or genetic engineering. During the
Depending on application and species involved,
past 15 years, the combined use of recombinant
ideal DNA markers for efficient use in marker-
DNA technology and tissue-culture techniques
assisted breeding should meet the following
has led to the efficient transformation and
criteria:
production of transgenic in a wide variety of crop
plants [10]. In fact, transgenesis has emerged as  High level of polymorphism
an additional tool to carry out single-gene  Even distribution across the whole genome
breeding or transgenic breeding of crops. Two (not clustered in certain regions)
methods are being used to transfer foreign genes  Co-dominance in expression (so that
into plants. The first method involves the use of a heterozygotes can be distinguished from
plant pathogen called Agrobacterium homozygotes)
tumefaciens, soil-borne, Gram-negative  Clear distinct allelic features (so that the
bacterium which causes crown gall disease in different alleles can be easily identified)
many species. This bacterium has a plasmid that  Single copy and no pleiotropic effect
contains tumor-inducing genes (T-DNA), along  Low cost to use (or cost-efficient marker
with additional genes that help the T-DNA development and genotyping)
integrate into the host genome. This is done by  Easy assay/detection and automation
removing most of the T-DNA while leaving the  High availability (un-restricted use) and
left and right border sequences (24 bp), which suitability to be duplicated/multiplexed (so
integrate a foreign gene into the genome of that the data can be accumulated and
cultured plant cells. The second delivery method shared between laboratories)
is a “gene gun,” which bombard gold particles  Genome-specific in nature (especially with
carrying the foreign DNA into plant cells. Some of polyploids)
these particles pass through the plant cell wall  No detrimental effect on phenotype
and enter the cell nucleus, where the transgene
integrates itself into the plant chromosome. Markers are small fragments of DNA which are
Rapid and remarkable achievements have been responsible for specific traits. They can broadly
made in the production, characterization, and be categorized into three types; morphological
field evaluation of transgenic plants in several (visible phenotypic traits), biochemical (protein,
field crop, and fruit and forest plant species. First phenolics, enzymes etc) and molecular markers
generation transgenic crops were insect resistant (Fig. 3). Molecular markers are piece of DNA
(IR) maize, cotton, canola and herbicide tolerant which code for specific traits and their inheritance
(HT) soybean, cotton, maize, sugar beet, alfalfa could be detected. They have been categorized
plants, expressing bacterial genes CRY and CP4 into hybridization based and PCR based [14].
EPSPS, respectively. These crops were later Since Botstein et al. [15] first used DNA
joined by those with a combination of the two restriction fragment length polymorphism (RFLP)
traits in the same plant (IR/HT), known as in human linkage mapping, substantial progress
stacked IR/HT cotton and maize. In addition to has been made in development and

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improvement of molecular techniques that help to improvement for successful breeding


easily find markers of interest on a largescale, applications. Gene based markers are being
resulting in extensive and successful uses of used widely in basic molecular biology labs, as
DNA markers in human genetics, animal they are specific to particular gene and fewer in
genetics and breeding, plant genetics and number for screening of biotic and abiotic stress
breeding, and germplasm characterization and resistance. Most advance molecular markers are
management. Selection of desirable plant SNPs, but due to requirement of technical
species is the basic principle of plant breeding; expertise and costly machines and reagents,
which involves evaluation of agronomic traits, they are limited to well-developed laboratories
biotic and abiotic stress resistance / tolerance only. Molecular markers are being rapidly applied
and response towards chemicals. Marker for marker assisted foreground and background
assisted selection a new discipline of molecular selection, gene pyramiding, QTL mapping, fine
breeding helps to evaluation traits using mapping, gene tagging, association mapping,
molecular marker that are based on banding TILLING and Eco-TILLING etc. The markers
pattern of linked DNA marker. Several types of have made selection independent of the
DNA markers that have been developed and are phenotype, the desirable plants can be selected
being used in plants include: restriction fragment- in the seedling stage, and the selected plants
length polymorphism (RFLP), amplified fragment- can be used for hybridization in the same season.
length polymorphism (AFLP), randomly amplified In addition, MAS allows easy pyramiding of
polymorphic DNA (RAPD), sequence-tagged oligogenic resistance and combining of horizontal
sites (STS), expressed sequence tags (ESTs), resistance with vertical resistance which is
and simple sequence repeats (SSRs) or considerably difficult on the basis of disease
microsatellites, sequence-characterized amplified tests. Closely linked molecular markers have
regions (SCARs), and single nucleotide been used for positional cloning of a number of
polymorphisms (SNPs) [16,17]. Table 2 is clearly plant genes. Molecular markers have stimulated
highlighting comparative study of some of the the development of novel breeding schemes like
molecular markers, which are being used in Genomic selection (GS) and Genomics Assisted
broad spectrum in molecular breeding Breeding (GAB) Scheme to develop varieties
approaches. Day to day advances in molecular with superior adaptation.
marker technology is being applied in crop

Fig. 3. Different types of molecular markers

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Table 2. Comparative of different types of molecular markers

Characteristics Restriction Randomly Amplified Simple Cleaved Amplified Inter Simple Expressed Single Nucleotide
Fragment Length Polymorphic DNA Sequence Polymorphic Sequence Repeats Sequence Tags Polymorphism
Polymorphism (RAPD) Repeats (SSR) Sequence (CAPS) (ISSR) (EST) (SNP)
(RFLP)
Level of Medium Very high High Moderate High High High
polymorphism
Cost Expensive Cheap Expensive Cheap Cheap Costly then SSR Variable
Allelism Co-dominant Dominant Co-dominant Mostly co-dominant Dominant Co-dominant Co-dominant
Time Time consuming Quick working Quick working Quick quick Time Consuming quick
Banding pattern Locus specific Multi locus Locus specific Locus specific Multi locus Locus specific Locus specific
Probe / primer Probe Primer primer Primer Primer primer Primer
DNA required (ng) 10000 20 10-20 30-100 20-50 20-50 5-20
Advantage They are first DNA Less DNA require, Less DNA Versatile, easily Highly polymorphic, Rapid and Widely distributed in
marker discovered. easy to use and required, high scored and no need of prior inexpensive genome, co-
Co-dominant and no polymorpic reproductive interpreted sequencing dominant, highly
need of prior reproductive
sequencing
Disadvantage Use of radioactive Low reproducibility. High developing Restriction Non-homology of Lack of prime High developing cost
probe & southern dominant ,highly cost, presence of enzymes must be similar sized specificity, labour
blotting step involve purified DNA is more null allele tested for fragments, low oriented
required polymorphisms reproducibility
References Botstein et al. [15] Willians et al., Welsh Tautz et al. [20] Konieczny et al. Gupta et al. , Adams et al., [24, Michaels et al. Batley
et al. [18, 19] [21] Godwin et al. 25] et al. Wiltshire et al.
[22, 23] [26, 27, 28]

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6. GENOMICS ASSISTED BREEDING its own shortcomings, it required prior genomic


AND HIGH THROUGHPUT GENO- information, and in some case manual dosage
TYPING scoring. Efforts have been taken to reduce these
limitations such as adopting whole genome
Functional molecular markers and advances in sequencing with high coverage and updating the
bioinformatics is generating new tools gradually markers on the SNP array. For SNP marker
in genomics research that could increase the selection in development of the array, Illumina
efficiency and precision of crop improvement. and Affymetrix platform are being applied widely.
Eventually, relative values of targeted alleles at SNP Array selection should include some of the
specific locus in a segregating population could general and important features as SNP depth,
allow the breeder to improve any genotype for SNP types, SNP frequency, additional variations
particular trait in silico and to do whole genome within probe sequence of target SNPs, and probe
selection. Genomics is most powerful tool for sequence parameters. Specifically, (1) accuracy
deciphering the stress responsiveness of crop of SNPs called can be relate with the average
species with adaptation traits or to identify SNP read depth, or single genotype SNP depth.
underlying genes, alleles or quantitative trait loci. If the depth is too low, sequence errors could be
Molecular breeding approaches are most considered for SNP call. If the depth is too high,
efficient in enhancing the biotic and abiotic stress the SNPs may be called from repetitive
adaptation of crop plants, and recent advances in sequences. (2) There are two types of SNPs:
high throughput genotyping, sequencing and transition SNPs (purine/purine or
phenotyping platforms (phenomics) have pyramidine/pyramidine i.e., A/G, T/C) and
transformed molecular breeding to genomics transversion SNPs (purine/pyramidine or
assisted breeding (GAB). Most commonly used pyramidine/purine i.e., A/T, C/G, A/C, and T/G).
approaches for genomics assisted breeding are For SNP array development, the transition SNP
marker assisted selection (MAS) and genomic type is preferred and transversion SNPs, multiple
selection (GS). High throughput genotyping is allelic SNPs and INDELs, are excluded to make
being applied by using SNP array, which is a array more reproducible [31]. The availability of
relatively cost-efficient, and automatically high-density SNP markers has opened a way for
genotyping assay. It has been widely used in genome wide association study (GWAS), an
genetic studies of crops, including genome-wide approach using natural populations. GWAS could
association studies (GWAS), linkage map overcome several constraints of conventional
construction, genomic selection, population linkage mapping and provide a powerful
structure analysis and gene mapping. Currently, complementary strategy for dissecting complex
the most popular high throughput genotyping traits. Genomic selection (GS) predicts genomic
platforms are the hybridization based SNP array estimated breeding values of lines by analyzing
and various NGS enabled genotyping such as traits and high-density marker scores within an
GBS and GS [29,30]. SNP array is a type of DNA artificially created population at the whole-
microarray containing designed probes focusing genome level [6]. GS is another promising
on the SNP positions, which is hybridized with breeding strategy for rapid improvement of
fragmented DNA or cDNA to determine the complex traits. Although still costly, GS has been
specific alleles of all SNPs on the array for the proved to be superior to marker assisted
hybridized DNA sample of targeted trait. Many recurrent selection for improving complex traits in
SNP arrays have been successfully applied in crops, as it can effectively avoid issues
diploid species genotyping, such as the Apple associated with the number of QTL that control a
480K SNP array, the Maize 600K SNP array, trait.
58K in tetraploids (peanut), 820K in hexaploids
(wheat), 90K in octoploids (strawberry), 345K in 7. FUTURE PROSPECTS
dodecaploids (sugarcane) and the Rice 700K
SNP array). For high-throughput genotyping of The genome sequences of organisms are
crops, SNP array has several advantages over fundamentally important for understanding the
traditional marker based genotyping and NGS functions of individual genes and defining
approaches. Some of the points includes, SNP evolutionary relationships. The identification of
array data is relatively easy to analyze compared genes and molecular markers underlying
to data generated using NGS-based methods, agronomic traits will help to accelerate the
labor intensive NGS library preparation and breeding process and lead to improved varieties
bioinformatics data analysis investment for with improved yield and quality, tolerance to
accurate SNP calling. However, SNP array has unfavourable environmental conditions and

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© 2019 Adlak et al.; This is an Open Access article distributed under the terms of the Creative Commons Attribution License
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