Recent Advancements in Rice

Submitted To:
Dr. Abdul Rehman

Submitted By:
Muhammad Anas, Tauqeer Abbas, Shahzaib Asghar

B.Sc. (Hons.) Agriculture

Assignment submitted as partial fulfillment of the Requirement of the

course Breeding Cereal Crops (PBG-308)

College of Agriculture, BZU Bahadur Sub Campus

Layyah
 Recent Advancements in Rice

Introduction

Rice provides staple food for more than 50% of the world's population and is an important crop
in the world. In order to meet the growing food need and overcome malnutrition, rice varieties
with higher yield potential and multiple resistance to biotic and abiotic stresses with improved
nutritional quality are needed. During the last few decades, major progress has been made in
increasing rice productivity. World rice production has more than doubled from 257 million tons
in 1966 to 589 million tons in 2003. This has mainly been achieved through the application of
principles of Mendelian genetics and conventional plant breeding methods.
The present world population of 7.6 billion is likely to reach 8.5 billion by 2030. Recent
advances in genetics offer new opportunities to achieve these objectives to feed this increasing
population. With the new technologies such as high-throughput genome sequencing and genetic
engineering methods applied in rice researches, great advancements have been made. This
assignment is aimed to show a glance of new advancements in the international rice researches.

Rice Genetics

Cultivated rice is a diploid with 24 or 12 pairs of chromosomes which have been numbered
according to the decreasing order of length at the pachytene stage of sexual cell division. Thus,
the longest chromosome is number 1, the second longest, number 2 and the shortest, number 12.
Chromosomes of both the cultivated species and closely related wild species are similar and their
genomes are designated as AA. The chromosomes of other wild species, however, differ from
those of cultivated rice.

Advancements to improve Rice Characteristics

Marker genes and linkage groups

Nearly 400 mutant genes affecting morphological, physiological and biochemical characters,
disease and insect reaction, abiotic stresses and coloration of plant parts have been described.
These genes have been assigned to different groups through genetic analysis, and 12 linkage
groups corresponding to 12 chromosomes have been established.

Biochemical markers

The second category of markers are isozymes, which are more useful than morphological
markers. They are codominant and, thus, all genotypes can be distinguished in segregating
populations. They have no deleterious effect on plant phenotype and a large number of samples
can be scored in the laboratory at very early stages of growth. However, only a limited number
of isozyme loci are known and the number is not sufficient to saturate the genetic maps. In rice,
for example, only about 50 isozyme loci are known.

DNA markers

The third category of markers, which includes random fragment length polymorphism (RFLP),
random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP)
and microsatellites, have all the advantages of isozyme markers but are far more numerous,
making it possible to prepare saturated maps.

Molecular markers for gene tagging

Disease and insect resistance genes can be tagged by tight linkage with DNA or isozyme
markers, time and money can be saved when transferring them from one varietal background to
another. The presence or absence of the associated molecular marker would indicate, at a very
early stage, the presence or absence of the desired target gene.

Synteny among cereal genomes

In other cereals, such as sorghum, maize, oats, barley and wheat, high density molecular genetic
maps have been prepared. Molecular markers have been utilized to study genetic relationships
among the cereal species. In particular, cDNAs with coding regions of expressed genes are very
useful as common landmarks for comparative linkage mapping, because they are well conserved
between distantly related species. Rice is used as the base for comparative mapping simply
because it has the smallest genome among the cereals analyzed.

Comparative Genetics
Comparative genome research is an excellent tool for gene isolation. The similarity in gene
content and order allows the search for genes of interest using cloned genes of one species to
look for similar genes in other species. For example, used cloned barley gene Rpg 1 to search for
a similar gene in the syntenic region of rice.

QTL mapping

Yield, quality and tolerance to abiotic stresses are of a quantitative nature. Genetic differences
affecting such traits are controlled by a relatively large number of loci, each of which can make a
small positive or negative contribution to the final phenotypic value of the traits. These loci are
termed quantitative trait loci (QTLs). Molecular markers provide the opportunity to manipulate
QTLs as Mendelian or quasi-Mendelian entities. Several QTLs for traits of economic
importance, such as blast resistance, root length submergence tolerance and yield potential have
been tagged with molecular markers.

Marker-assisted breeding

DNA markers have several potential applications in the genetic improvement of rice, including
characterization and protection of germplasm, assessment of genetic diversity, tracing of gene
flow and marker-assisted selection (MAS). Compared with traditional backcrossing by
phenotypic selection, gene transfer by marker-assisted backcrossing is more accurate and faster,
particularly when the trait is difficult to assess. In marker-assisted backcrossing or gene
pyramiding, individuals carrying the target gene are selected by segregating populations based
on tightly linked markers rather than on their phenotype. Thus, the populations can be screened
at early seedling stage and under various environmental conditions. MAS can overcome
interference from interactions between alleles of one locus or of different loci. MAS was
successfully employed in pyramiding four different genes (Xa-4, Xa-5, Xa-13 and Xa-21) for
bacterial blight resistance. These pyramided lines are being used as donors for transferring
resistance genes into elite rice varieties developed at IRRI and by the national rice improvement
programs through MAS.

Low-cost DNA markers

MAS protocol that is based on the polymerase chain reaction (PCR). This protocol is one-tenth
the cost of RFLP protocols and more than ten times faster.

Gene cloning

Cloning rice genes based on map position have been greatly enhanced with the development of
bacterial artificial chromosome (BAC) libraries. Using BAC libraries scientists identified clones
carrying Xa-21 gene for bacterial blight resistance and isolated Xa-21 by positioning cloning.
The isolated gene has been introduced into several elite rice cultivars through transformation.

Genetic engineering

Direct DNA transfer methods, including protoplast-based, biolistic-based and Agrobacterium-

mediated are being used for rice transformation. Major targets for rice improvement through
transformation are: disease and insect resistance, abiotic stress tolerance, and enhancement of
yield potential.

Gene silencing

The widespread occurrence of transgene inactivation in plants has been explained in terms of the
triggering of defense systems that monitor and manipulate intrusive or aberrant DNA Studies on
the events underlying transgene silencing are defining ways of minimizing the problem and,
thus, increasing the likelihood of achieving stable expression in the field. One approach is to
select transformants that contain very few copies (between one and three) of the introduced
genes, because multiple copies often lead to events that trigger silencing. A related precaution is
to avoid using transgenes that so closely resemble endogenous genes that either one gene or both
are switched off in a phenomenon termed co-suppression. A third strategy is related to DNA
methylation, which is common in plants. Methylation of promoter sequences can prevent the
binding of regulatory proteins and lead directly to gene silencing. Foreign genes should,
therefore, be introduced into rice under the control of promoters that will function appropriately,
even when the gene is methylated. Suitable promoters will most likely be found in rice or other
cereals in association with genes that show regulatory behavior similar to that desired for the
transgene.
Wide hybridization

The genus Oryza, to which cultivated rice belongs, has 22 wild species and two cultivated
species. The wild species are a reservoir of useful genes for rice improvement. Wild species with
AA genome can be crossed routinely with cultivated species and useful genes can easily be
transferred to cultivated rice. However, special techniques such as embryo rescue and hormone
treatment are necessary to produce hybrids between cultivated rice and more distantly related
species. Hybrids have been produced through an embryo rescue technique between elite breeding
lines and cultivars and several accessions of 11 wild species representing BBCC, CC, CCDD,
EE, FF, GG and HHJJ genomes. A number of useful genes have been transferred from wild to
cultivated species.

Characteristics for which these technologies may be used

 Good grain quality (especially cooking characteristics, color, shape, taste and aroma,
and head rice recovery)
 High market price
 Optimum yield potential and stability over seasons
 Maximum tillering capacity for weed competition
 Resistance or tolerance to major diseases, insects, and other stresses (i.e. drought and
flood) of the area
 The right growth duration (maturity length) to match the season
o Avoid varieties that need to be planted or harvested earlier or later than
surrounding rice fields to minimize pest damage (e.g., birds during maturation),
and growth problems during times of harmful environmental conditions (e.g.,
late-maturing varieties running out of water)
 Resistance to lodging under normal farmer management

Achieved Goals

Abiotic stress tolerance

Recently reported some success in using a Hva1 gene, producing late embryogenesis abundant
(LEA) proteins controlling water and salinity stress in rice plants. It is believed that LEA
proteins may play a protective role in plant cells under water stress conditions.

Improvement of starch biosynthesis

Adenosine diphosphate-glucose phyrophosphorylase (ADPGPP) is a critical enzyme in

regulating starch biosynthesis in plant tissues. Starch levels and dry matter accumulation were
enhanced in potato tubers of plants transformed with glgc16 gene from Escherichia coli encoding
ADPGPP. The glgc16 gene has been introduced into rice at IRRI and its expression is being
investigated.

Insect resistance

As early as 1987, genes coding for toxins from Bacillus thuringiensis (Bt) were transferred to
tomato, tobacco and potato, where they provided protection against Lepidopteran insects. A
major target for Bt deployment in transgenic rice is the yellow stem borer. This pest is
widespread in Asia and causes substantial crop losses. As well as Bt genes, other genes for insect
resistance, such as those for proteinase inhibitors, a-amylase inhibitors and lectins are also
beginning to receive more attention. Transgenic rice carrying cowpea trypsin inhibitor (CpTi)
gene that had enhanced resistance against striped stem borer and pink stem borer.

Disease resistance

A highly successful strategy termed coat protein (CP) mediated protection has been employed
against certain viral diseases such as tobacco mosaic virus in tobacco and tomato. A CP gene for
rice stripe virus was introduced into two japonica varieties by electroporation of protoplasts. The
resultant transgenic plants expressed a high level of CP and exhibited a significant level of
resistance to virus infection, and this resistance was inherited by the progenies.

Salt stress tolerance in Rice

Excess salinity in soil is one of the major environmental factors that limit plant growth and yield
of a wide variety of crops including rice. On the basis of tolerance ability toward salinity, rice is
considered as salt-sensitive crop, and growth and yield of rice are greatly affected by salinity. In
general, rice can tolerate a small amount of saltwater without compromising the growth and
yield. However, it greatly depends on the types and species of rice and their growth stage.
Salinity-induced ionic and osmotic stresses reduce rate of photosynthesis and consequently cause
oxidative stress, which is also responsible for growth reduction. The negative effects of salt
stress that mentioned ultimately reduced yield of most crops including rice, except some
halophytes. In recent decades, researchers have developed various approaches toward making
salt-tolerant rice varieties. Using phytoprotectants is found to be effective in conferring salt
tolerance to rice plants. 

Golden rice 

Golden rice is a variety of rice (Oryza sativa) produced through genetic engineering to

biosynthesize beta-carotene, a precursor of vitamin Ain the edible parts of rice.

Golden rice was created by transforming rice with two beta-carotene biosynthesis genes:

1. psy (phytoene synthase) from daffodil (Narcissus pseudonarcissus)

2. crtI (carotene desaturase) from the soil bacterium Erwinia uredovora

(The insertion of a lcy (lycopene cyclase) gene was thought to be needed, but further research
showed it is already produced in wild-type rice endosperm.)

The psy and crtI genes were transferred into the rice nuclear genome and placed under the
control of an endosperm-specific promoter, so that they are only expressed in the endosperm.
The exogenous lcy gene has a transit peptide sequence attached, so it is targeted to the plastid,
where geranylgeranyl diphosphateis formed. The bacterial crtI gene was an important inclusion
to complete the pathway, since it can catalyze multiple steps in the synthesis of carotenoids up to
lycopene, while these steps require more than one enzyme in plants. The end product of the
engineered pathway is lycopene, but if the plant accumulated lycopene, the rice would be red.
Recent analysis has shown the plant's endogenous enzymes process the lycopene to beta-carotene
in the endosperm, giving the rice the distinctive yellow color for which it is named. The original
golden rice was called SGR1, and under greenhouse conditions it produced 1.6 µg/g of
carotenoids.

Flood Tolerant Rice

dies within days of complete submergence, resulting in total crop loss. These losses affect rice
farmers in rainfed and flood-affected areas where alternative livelihoods are limited. Therefore,
the incidences and severity of poverty in these areas are high.

In Asia, where most of the world’s rice is grown, about 20 million hectares of rice land is prone
to flooding. In India and Bangladesh alone, more than 5 million hectares of rice field are flooded
during most of the planting seasons.

The erratic floods experienced in rainfed and flood-affected areas are usually caused by heavy
rainfall, overflow of nearby rivers and canals or sometimes tidal movements as in coastal areas.
These floods cause serious problems for rice and other crops because of the poor or non-existent
drainage and, in some cases, the topography of the land prevents fast water movement to drain
flooded fields. Flooding is therefore considered a major challenge for rice production in South
and Southeast Asia, where the majority of the world’s rice farmers live.

A rice variety that can withstand being submerged under water for two weeks has been
developed by IRRI. Through conventional breeding, scientists scoured rice’s rich diversity for a
gene that gives flood-tolerance. After the gene (called SUB1 gene) was found, it was infused into
popularly grown rice varieties in rice-growing countries in Asia.

Several varieties with the “scuba” gene were released

to India, Bangladesh, Philippines, Indonesia, Myanmar and Nepal. The gene is also being
transferred into popular varieties in Africa.

Drought Tolerant Varieties

Drought is the most widespread and damaging of all environmental stresses, affecting 23 million
hectares of rainfed rice in South and Southeast Asia. In some states in India, severe drought can
cause as much as 40% yield loss, amounting to $800 million. IRRI has developed drought-
tolerant varieties which have been released in several countries and are now being planted by
farmers. These include Sahbhagi dhan in India, the 5411 variety in the Philippines, and
the Sookha dhan varieties in Nepal, and the BRRI dhan varieties in Bangladesh. Across these
varieties, the average yield advantage of drought-tolerant varieties over drought-susceptible ones
is 0.8-1.2 tons per hectare under drought.

IRRI scientists have identified several key regions of the rice genome that give the rice drought
tolerance and improve rice grain yield under drought. IRRI is working towards introducing
drought tolerance into popular high-yielding rice varieties including IR64, Swarna,
and Vandana.

By using drought-tolerant rice, farmers can enjoy a 0.8 to 1.2 ton per hectare yield advantage
than non-drought-tolerant varieties. This yield advantage will make the 23 million hectare-
drought prone area to be much more productive, contributing to food security in poor rural
communities.

Conclusion

In order to meet the growing food need and overcome malnutrition, rice varieties with higher
yield potential and multiple resistance to biotic and abiotic stresses with improved nutritional
quality are needed. Recent advances in genetics would offer new opportunities to achieve these
objectives.

References

 G.S. Khush, J. Bennet, S.K. Datta, D.S. Brar and Z. Li (Advances in Rice Genetics and
biotechnology) International Rice Research Institute (IRRI), Manila, the Philippines.
 Hirschberg, J. "Carotenoid biosynthesis in flowering plants". Current Opinion in Plant
Biology. 4 (3): 210–218.
 Schaub, P.; Al-Babili, S; Drake, R; Beyer, P. "Why Is Golden Rice Golden (Yellow)
Instead of Red?". Plant Physiology. 138 (1): 441–450.
  (Advances in International Rice Research) Edited by Jinquan Li, ISBN 978-953-51-3010-
9, Print ISBN 978-953-51-3009-3, 322 pages, Publisher: InTech, Chapters published
March 15, 2017 under CC BY 3.0 license.

Contents
  [hide] 

 1History
 2Overview
 3Steps
o Choice of host organism and cloning vector
o Preparation of vector DNA
o Preparation of DNA to be cloned
o Creation of recombinant DNA with DNA ligase
o Introduction of recombinant DNA into host organism
o Selection of organisms containing vector sequences
o Screening for clones with desired DNA inserts and biological properties