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Journal of Biotechnology

and Crop Science


4(5): 4-21, 2015

Molecular breeding approach for crop improvement of quality traits


GP Mishra, RK Singh

Received: 08 August 2015 Revised Accepted: 12 October 2015

ABSTRACT

Plant breeding and molecular maker assisted selection (MAS) approaches have been used to produce plants carrying the
desired traits. Molecular marker based breeding strategies have been used to accelerate the process of moving trait
genes into high-yielding germplasm for commercialization. These products are being tested for applications in food,
feed and industrial markets. Clearly, DNA based marker techniques are not a replacement for classical breeding and
selection techniques. Rather they have become a powerful accelerating tool to improve the rate of selection for quality
traits. The specificity of molecular monitoring provides the confidence in trait selection and overall cost-effectiveness
for improvement for these complex quality traits.

Key Words: Gene discovery, MAS, Quality traits, QTL

INTRODUCTION

There are many aspects of crop quality, which can However, to meet the challenges posed by severe
be defined differently according to, for example, crop damage by pests and diseases, the extensive
crop species, geographical region and intended use use of pesticides and chemical fertilizers, and a
of crop or crop product. Some attributes that define shortage of water and energy, more elite cultivars
crop quality include: nutritional value (amino acid are needed in different crops. In recent years, world
composition, protein content, micronutrients, has seen continued improvements in crop genetics,
vitamins, secondary metabolites, nutraceuticals, powered by functional genomics as a way forward
etc.), consumer preference (flavour, texture, colour, to safeguard its food production. Biotic and abiotic
grain size/shape), pre- and post-harvest and stresses have a negative impact on product quality.
industrial/technological characteristics (fibre traits, Indeed, in developing countries with low input
sucrose content, storage quality, sprouting, oil agricultural systems or reduced access to plant
content, starches, processing, bread-making). The protection compounds, such stresses can have
market value of most crops is determined by devastating effects on crop quality. Resistances to
various factors. Quality is a subjective, complex such quality-affecting stresses should be essential
trait, with many different components determined components of breeding programmes aimed at crop
by the growing environment and the target market. quality improvement. Therefore, quality traits are
Although HYV varieties in many crops have usually complex, controlled by the action of several
contributed greatly to world agriculture in the past genes, and are also subject to environmental
decades, its potential to improve grain quality influences. The complex genetics of quality traits
further is being questioned. has led to their being difficult to improve through
conventional plant breeding. Furthermore, the
GP Mishra ( )
DIHAR, DRDO, C/o 56 APO, Leh, 901205 complexity in assessing some quality characters
Email: gyangene@gmail.com aggravates the difficulties in improving crop
RK Singh quality. Breeding activities that rely on use of
Indian Institute of Sugarcane Research, Lucknow, UP, India genotypic rather than phenotypic selection have the
J of Biotech & Crop Sci (2015) 4(5): 4-21

potential to overcome these limitations. For those that have easily identifiable phenotypes (eg.
example, traits controlled by recessive alleles, waxy mutation in rice, barley and other crops).
environmentally-sensitive characters, traits that are Recent development of screening procedures for
expensive or difficult to score, or expressed late in quality traits in mutagenised populations will allow
development will benefit greatly from application the more efficient identification of novel and useful
of genotypic selection. The advent of molecular variants. Such screening procedures and the
marker techniques now makes it possible to tag development of markers linked to the induced
alleles conferring desirable quality traits. For many mutant alleles will facilitate their incorporation into
crop plants large numbers of molecular markers of breeding programmes (Shu 2004). Researches at
different types (RFLP, SSR, AFLP etc) are now different labs now use biotechnology to introduce
available. These vary widely in cost of various desired quality traits in different crops and
development and deployment and the choice of assure that new varieties have those components at
markers to be used will depend largely on the the DNA level. So far the technology has found the
breeders objectives and the available facilities. DNA markers for starch quality and for resistance
Development of markers tightly linked to quality to blast, a fungal plant disease that takes its toll on
traits or resistance to quality-affecting stresses rice yields throughout the growing regions of the
should enable breeders to select on a genotypic world. It's faster, cheaper and better to use this
basis. Marker assisted selection (MAS) offers great technology in breeding new varieties. And it is
promise for both the selection of individual quality being put to use in the field more quickly than
traits and the pyramiding of a number of important research findings often are with the DNA sequences
quality characters simultaneously into the same of every gene known, researchers now are trying to
improved genotype. Breeding programmes could delve further into the code to "mark" what each
benefit from the implementation of MAS for gene gene expresses in the plant (Phillips 2001).
pyramiding in terms of time saving and reduction
of cost as compared to conventional breeding. MAS Marker-assisted (or molecular-assisted) breeding
should be considered as complementary to provides a dramatic improvement in the efficiency
conventional breeding, in that it can be used to with which breeders can select plants with desirable
replace certain phenotypic assessments, rather than combinations of genes. A marker is a "genetic tags"
as an alternative to selection based on phenotype. that identifies a particular location within a plant's
Despite their great potential, DNA-based markers DNA sequences. Markers can be used in
have not yet been widely implemented in breeding transferring a single gene into a new cultivar or in
for quality, particularly in developing countries, testing plants for the inheritance of many genes at
due to economic constrain and cost effectiveness. once (Suslow et al 2001). Advanced breeding
technologies that meet these goals have resulted
Improvement of quality traits depends on the from recent research in plant biotechnology. The
availability of sufficient variability for the targeted techniques have been utilized for some time using a
traits. In the past the level of variability in some bar-code-like fingerprint of differentiating enzymes
quality traits has been increased using mutagenesis. and proteins (the products of the genes) for many
However, the full potential of induced mutations important quality traits to monitor or reveal
has not been realized in plant breeding for quality inheritance in the same way (Suslow and Bradford
traits because of the difficulty in screening large 1999). By providing quick and efficient tests for
mutagenised populations for infrequent mutations many different genes, DNA markers have become
generating desirable crop quality alleles. The valuable new tools for breeding crop varieties
exploitation of mutated genes has been restricted to having optimal combinations of desirable genes.
J of Biotech & Crop Sci (2015) 4(5): 4-21

DNA markers have been used for transferring The use of cost-effective DNA markers derived
quality genes to cultivated varieties, assisting from the fine mapped position of the genes for
selection of complex multi-gene traits (such as important agronomic traits and MAS strategies will
flavor), aiding evaluation of regionally and provide opportunities for breeders to develop high-
seasonally optimized varieties (Suslow et al 2001). yielding, stress-resistant, and better-quality rice
cultivars (Jena and Mackill 2008). Phillips (2001)
Rice is the most important food crop and the found the first marker (after rice genome
challenge to produce enough rice for the future, sequencing) which regulates amylose, a component
however, remains daunting, as the current rate of of starch. In rice, high amylose means that the
population growth outpaces that of increases in rice grains are firm and separate and low starch means
production. Examining molecular, genetic and we can eat it with chopsticks because it sticks
cellular techniques, it considers recent advances in together. A problem in breeding new varieties is
four research approaches for increasing yields and that the air temperature while rice is growing
improving the nutritional quality of rice. influences the amount of amylose that the plant
1. Plant genomics: knowing the identity and produces. By diagnosing rice in breeding programs
location of each gene in the rice genome is of with DNA markers, however, scientists can
immense value in all aspects of rice science and accurately decide whether to keep working with
cultivar improvement. progeny from a cross, or to cease selection.
2. Molecular biological approaches to increase Breeders don't have to worry about unusual weather
yield: to produce more biomass by increasing giving false reads on a potentially good variety.
photosynthetic rate and duration and by improving
grain filling. Long-te-fu (LTF) and Zhan-shan 97 (ZS) are two
3. Enhancing tolerance to biotic and abiotic key female parents for the generation of indica
stresses: with new DNA array technologies, it is hybrid rice, which have greatly contributed to the
now possible to assess global genomic response to achievement of rice production in China. However,
stresses. Understanding the relationships among the high amylose content (AC) in the endosperm,
stress pathways may create new opportunities for controlled by the Waxy (Wx) gene encoded
gene manipulation to enhance tolerance to multiple granule-bound starch synthase I, of both lines
biotic and abiotic stresses. results in poor cooking and eating quality of the
4. Improving nutritional quality in the grain: milled rice. Previous studies have shown that AC
knowledge of the biosynthesis of micronutrients in was correlated with the ability to excise intron 1
plants permits genetic engineering of metabolic from the leader sequence of the Wx transcript, and
pathways to enhance the availability of which is responsible by a single nucleotide
micronutrients. Recent advances in rice genomics polymorphism (G or T) located at the first
research and completion of the rice genome nucleotide of the splice donor site of Wx intron 1.
sequence have made it possible to identify and map Thus, a CAPS marker was subsequently developed,
precisely a number of genes through linkage to and with this MAS, Qiao-Quan et al (2006)
DNA markers. Noteworthy examples of some of the successfully introgressed the Wx-TT locus of rice
genes tightly linked to markers are resistance to or cultivars with good quality intermediate AC into
tolerance of blast, bacterial blight, improved LTF-B and ZS-B. These were subsequently
agronomic and grain quality traits etc. MAS can be introduced into their relevant male-sterile lines
used for monitoring the presence or absence of (LTF-A and ZS-A) to generate improved indica
these genes in breeding populations and can be hybrids. In the selected lines LTF (tt)-B and ZS (tt)-
combined with conventional breeding approaches. B, the AC was reduced to a relatively low level
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(15%). Consequently, the hybrids crossed from the geranylgeranyl diphosphate formation occurs. The
selected lines had dramatically reduced amylose bacterial crt1 gene was an important inclusion to
levels. The ability to transfer cloned genes allows complete the pathway, since it can catalyze
plant breeders to use genes from essentially any multiple steps in the synthesis of carotenoids, while
source as tools for crop improvement. For example, these steps require more than one enzyme in plants
to enable rice grains to accumulate beta-carotene (Hirschberg 2001). The end product of the
(which is converted into vitamin A when consumed engineered pathway is lycopene, but if the plant
by animals) and create the so-called Golden rice, accumulated lycopene the rice would be red.
scientists used genes from daffodil, pea, a Recent analysis has shown that the plant's
bacterium and a virus. Transgenic plant methods endogenous enzymes process the lycopene to beta-
enable these four well characterized genes to be carotene in the endosperm, giving the rice the
inserted into a transgenic plant, producing a highly distinctive yellow colour for which it is named
specific change in only the trait of interest. Woody (Schaub et al 2005). The original Golden rice was
tree and vine crops are exceedingly difficult to called SGR1, and under greenhouse conditions it
improve by traditional breeding technology because produced 1.6 g/g of carotenoids.
it takes a number of years for a seedling to begin
flowering, and the unique traits of specific varieties Golden rice was developed as a fortified food to be
are hard to regain after sexual crosses (Suslow et al used in areas where there is a shortage of dietary
2001). Golden rice was created by Ingo Potrykus of vitamin A. In 2005 a new variety called Golden
the Institute of Plant Sciences at the Swiss Federal Rice 2 was announced which produces up to 23
Institute of Technology, working with Peter Beyer times more beta-carotene than the original variety
of the University of Freiburg. The project started in of golden rice (Paine et al 2005). Neither variety is
1992 and at the time of publication in 2000, golden currently available for human consumption.
rice was considered a significant breakthrough in
biotechnology as the researchers had engineered an Molecular marker technology is playing an
entire biosynthetic pathway. increasingly important role in the selection of wheat
Golden rice was created by transforming rice with lines with improved quality attributes. This is due
two beta-carotene biosynthesis genes: to the identification of molecular markers tightly
linked to chromosome regions involved in the
1. Psy (Phytoene synthase) from daffodil control of important quality characteristics such as
(Narcissus pseudonarcissus) dough properties, grain hardness, semolina and
2. Crt1 from the soil bacterium Erwinia uredovora flour colour, grain protein content and starch
composition, which strongly influence wheat end
(The insertion of a lyc (lycopene cyclase) gene was use, and its nutritional and market value. Moreover,
thought to be needed but further research showed the implementation of MAS allows the selection of
that it is already being produced in wild-type rice individuals carrying the favourable alleles at the
endosperm). target loci, and also the pyramiding of favourable
quantitative trait loci (QTL) alleles from different
The psy and crt1 genes were transformed into the sources and for different traits. This not
rice nuclear genome and placed under the control of withstanding, the progress obtained until now in
an endosperm specific promoter, so that they are applying MAS to quality characteristics has been
only expressed in the endosperm. The exogenous slow compared to other traits (Lafiandra et al 2007).
lyc gene has a transit peptide sequence attached so
that it is targeted to the plastid, where
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The mechanisms underlying some quality traits in dough strength (Metakovsky et al 1997), and
wheat are now understood. Examples include the implementation of these markers in Australian
role of high and low molecular weight glutenins in breeding programmes will provide many benefits
contributing to strength and extensibility of wheat for growers.
doughs, puroindolines that affect grain texture, and
variation in granule-bound starch synthase that Wheat (Triticum aestivum) gluten contains both
produces starches with altered amylose content and high molecular weight (HMW-GS) and low
physical properties. This knowledge, coupled with molecular weight (LMW-GS) glutenin subunits.
the availability of the DNA sequences of various The high molecular weight glutenin subunits
alleles of the genes encoding these proteins and the (HMW-GS) are key factors in bread making quality
wide application of the polymerase chain reaction, since they are major contributors of glutenin
has enabled the design of diagnostic DNA markers elasticity and polymer formation of wheat dough.
for these quality traits. Such markers are now being The effects of (HMW-GS) on dough properties
used by wheat breeders to select lines with the (strength and elasticity) may be additive or
required quality attributes, without the need for the synergistic with significant interactions with
direct measurement of those traits in early (LMW-GS) subunits (Beasley et al 2002). The
generation screening. DNA markers may be HMW-GS are encoded by polymorphic genes at the
implemented on leaf tissue from individual plants, Glu 1 loci that are present on the long arm of group
for a number of independent traits, with results that 1 chromosome (Payne and Lawrence 1983). At
are independent of environmental variation. The each locus (Glu-A1, GluB1, GluD1) there are two
use of a common platform for all marker assays and tightly linked HMW-GS genes, one of them is x-
the potential for multiplexing or parallel analysis of type with higher molecular weight and the other is
many different markers will further increase the y-type. For instance, at the Glu-1 there are subunits
efficiency and speed of the development of 1, 2 and null (there is no y allele), at the Glu-B1
improved cultivars in the future (Gale 2005). locus there are Bx17+By18, Bx7+By8, Bx7+By9,
Bx6+By8 subunits, and at the Glu-D1 locus, there
Wheat quality is a subjective, complex trait, with are Dx5+Dy10, Dx2+Dy12, Dx3+Dy12,
many different components determined by the Dx4+Dy12 subunits.
growing environment and the target market. Using
Australian germplasm Schmidt et al (2004) have The presence of different allelic composition of the
identified molecular markers for milling yield, HMW-GS in one specific wheat variety is one of
water absorption, flour colour and specialised the most important genetic factors in determining
dough development properties required for the bread making quality (Payne et al 1987). For
expansion into markets where sponge and dough example, wheat varieties containing allelic
style baking dominates. Novel marker-trait compositions of (Dx5 paired with Dy10) at the Glu-
associations were identified for milling yield, D1 locus will form stronger dough than those
dough strength and dough development time. A containing (Dx2 paired with Dy12). Due to the
novel sponge and dough QTL has been located on large contribution of allelic interaction in bread
chromosome 4B and further characterization of this making quality, Bks et al (2006) suggested
locus is still underway. Previous studies have targeting different allelic combinations rather than
resulted in identification of molecular markers for individual glutenin allele in developing new lines
many general interest traits such as milling yield with certain quality attributes. Baking quality is a
(Parker et al 1999), flour colour (Parker et al 1998, major target in wheat breeding programs. However,
Mares and Campbell 2001), protein content and due to small population size of wheat that can be
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obtained in early generations of breeding programs, restriction fragment length polymorphisms (RFLP)
full-scale mill and bakery testing is not routinely and simple sequence repeats (SSR). These loci
feasible. Alternatively, DNA marker screening of were specifically selected for their complete or
these quality traits may be performed on leaf close linkage to storage protein gene families. No
materials at early stage and before grain setting (De significant differences in BMQ were detected at
Bustos et al 2000). XGlu-B1 and XGlu-A1 loci using RFLP markers.
Highly significant (P<0.01) differences in all BMQ
DNA markers for HMW-GS allelic composition parameters were detected for XGli-B1 and XGlu-
have proven to be superior to electrophoresis of B3 loci on chromosome arm 1 BS. The increase in
SDS-PAGE in some instances (D'Ovidio and the number of Klein 32 alleles at these loci
Anderson 1994). Moreover, this assay can be used determined a linear increase in sedimentation and
to select individual plants within populations and to mixogram values. It was not possible to
overcome the environmental variation originating differentiate the effect of XGli1 from that of XGlu3
from both field and laboratory. Data presented by because of the close linkage between these two loci.
Uthayakumaran et al (2006) showed that the MAS These two loci, considered together, explained from
for the HMW-GS are especially valuable tool for 11 to 15% of the variation in BMQ observed in this
breeding programs since the information about the cross.
bread making quality can be obtained at an earliest
stages of breeding program, thus poor-quality lines Similarly Gale (2005) reported that some diagnostic
are not propagated. Moreover, MAS for the HMW markers had been used by wheat breeders in
and LMW glutenin alleles is widely performed by identifying the BMQ of varieties without the need
breeding programs throughout the world to select for the direct measurement of those traits in early
for improved dough characters. Blechl et al (2007) generation screening. DNA markers applied on leaf
suggested that contribution of alleleallele tissue from individual plants will further increase
interactions, and different allelic combinations the efficiency and speed of the development of
should be targeted rather than the individual improved cultivars in the future. MAS could
glutenin alleles in breeding program to develop new increase the genetic gain and economic efficiency
lines with certain quality attributes, especially to of a specific breeding strategy.
improve extensibility. The main reason given was
the significant differences found among the values, Development of high-yielding wheat varieties with
which described the contribution of HMW- good end-use quality has always been a major
GSLMW-GS interactions on extensibility. concern for wheat breeders. To genetically dissect
QTLs for quality traits such as grain and flour
The association between molecular markers and protein content, gluten strength as evaluated by
bread-making quality (BMQ) was investigated by mixograph and SDS sedimentation volume, an F1-
Manifesto et al (1998) in a cross between two derived doubled haploid (DH) population of 185
wheat cultivars with the same high Mr-glutenin individuals was developed from a cross between a
subunits but significantly different BMQ. A Canadian wheat variety "AC Karma" and a
segregant F2 population was generated after breeding line 87E03-S2B1. A genetic map was
crossing Klein 32 and Chinese Spring, and the constructed based on 167 marker loci, consisting of
BMQ of each F2-derived F3 family was estimated 160 microsatellite loci, three HMW glutenin
using sodium dodecyl sulfate (SDS) sedimentation subunit loci: Glu-Al, Glu-B1 and Glu-D1, and four
and mixograms. The same families were STS-PCR markers. QTL analyses were performed
characterized for 11 polymorphic loci using using composite interval mapping. A total of 26
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QTLs for quality-related traits were identified. The confirmed a previously tagged major QTL on
largest QTL clusters, consisting of up to nine chromosome 5DS, and two additional minor QTLs
QTLs, were found on chromosomes 1D and 4D. were found on chromosome 1A and 6D,
HMW glutenin subunits at Glu-1 loci had the respectively. For protein content two main QTLs
largest effect on BMQ. However, other genomic were identified on chromosomes 1B and 6A,
regions also contributed genetically to bread respectively. For W, three consistent QTLs were
making quality (Huang et al 2006). detected: two at the same location as those for
hardness, on chromosomes 1A and 5D; the third
Breseghello et al (2005) conducted a study to one on chromosome 3B.
identify genomic regions related to differences in
milling and baking quality between a soft and a Gene discovery to improve quality related traits
hard cultivar of hexaploid wheat. A population of Maize is clearly a diverse crop with many specialty
101 double-haploid lines was generated from a uses and types. These types have evolved from a
cross between Grandin, a hard spring wheat variety, rich past of selection based on recognition of
and AC Reed, a soft spring wheat variety. The unique properties associated with various genetic
genetic map included 320 markers in 43 linkage variants. The continued analysis of genetic
groups and spanned 3555 cM. The effect of variation has provided additional resources for the
qualitative variation for kernel texture, caused by refinement and development of specialty corn. The
the segregation of the Hardness gene, was ability of the geneticists to discover new genes and
controlled by regression on texture class. The to manipulate genetic variation at the level of
residual variance was used for composite interval specific genes offers the potential to tailor genetic
mapping, and QTLs on 1A, 1B, 1A/D, 2A, 2B, 2D, variation for the production of precisely designed
3A/B, 4B, 5B and 6B were detected. The effect of specialty maize in the future.
some QTLs was opposite to the direction expected
on the basis of parental phenotypes. The hard wheat By utilizing genetic variation, the composition of
parent contributed alleles favorable for soft wheat the kernel can be altered for both the quantity and
varieties at QTLs on 1AS,L, 1BL-2, and 6B, quality (structure and chemical diversity) of starch,
whereas the soft parent contributed alleles for protein and oil throughout kernel development. The
higher protein content at QTLs on 2BL-1, 4B-1, ability of future generations of plant breeders/plant
and 6B and higher flour yield on 2BL-2 and 4B-2. scientists to use existing genetic variation and to
Their results indicated that hard x soft wheat identify and manipulate commercially important
crosses have considerable potential for improving genes will open new avenues for designing novel
milling and baking quality of either class. variation in grain composition. This will provide
the basis for the development of the next generation
A set of 187 doubled haploid lines derived from the of specialty maize and of new products to meet
cross between cvs. Courtot and Chinese Spring was future needs. Developing plants with improved
explored for QTLs for three bread-making quality grain quality traits involves overcoming a variety of
tests: hardness, protein content and strength of the technical challenges inherent in metabolic
dough (W of alveograph) by Perretant et al (2000). engineering programs. Advances in plant genetics
About 350 molecular and biochemical markers and in technologies for genome-wide studies and
were used to establish the genetic map, and for large-scale gene expression analysis are
technological criteria were evaluated in 1 to 3 contributing to the acceleration of gene discovery
years. QTL detection was performed by the for product development (Motto et al 2003).
marker regression method. For hardness, they
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Developing plants with improved grain quality microarray technology (Brown and Botstein 1999)
traits involves overcoming a variety of technical represents a collection of promising tools for the
challenges inherent in metabolic engineering discovery of mRNA level controls of complex
programs. Advances in plant genetics and genomic pathways and may shed light on pathway
technologies are contributing to the acceleration of interactions, the understanding of which is essential
gene discovery for product development. The for successful metabolic engineering of crop plants.
complexity of the maize genome, particularly the
abundance of repetitive sequences, makes direct DNA microarray analysis has been used to study
genome sequencing for gene discovery difficult; the gene expression in a wide range of organisms
segmental allotetraploid origin of maize suggests including yeast (Spellman et al 1998), humans
that this species may contain more genes than a true (Schena et al 1996) and Arabidopsis seed (Girke et
diploid. Estimates of gene number for maize range al 2000). Progress in these four areas will permit
from 50,000 to 80,000 distributed in a 2.3 x 109 the isolation of many new genes and regulatory
base pairs present in ten chromosomes (Gai et al control points that will have a major impact on the
2000). improvement of the maize grain cell factory.
Hunter et al (2002) assayed the pattern of gene
In the past few years there has been much progress expression in normal and opaque endosperm
in the development of strategies to discover new patterns by profiling endosperm mRNA transcripts
plant genes. In large part, these developments with an Affinetrix GeneChip containing
derive from four experimental approaches: approximately 1,400 selected maize gene
sequences. The results revealed distinct, as well as
1. Genetic and physical mapping in plants and the shared, gene expression pattern in these mutants,
associated ability to use map-based gene isolation and they provide a framework for investigating a
strategies (Coe et al 2002), common mechanism that underlines the opaque
kernel phenotype.
2. Transposon tagging which allows the direct
isolation of a gene via forward and reserve genetic
The project "A Functional Blueprint of the Zea
strategies (Walbot 2000),
mays Endosperm Cell Factory" funded by the EU
3. Protein-protein interaction cloning that permits examines in considerable detail the transcriptome
the isolation of multiple genes contributing to a and proteome of the developing maize endosperm.
single pathway or metabolic process (Pelletier and This information will be used to target distinctive,
Sidhu 2001) and previously uncharacterized endosperm specific
4. Through bioinformatics/genomics, the genes which will be knocked out via Mutator
development and use of large expressed sequence transposon tagging. Characterization of the normal
tags (ESTs) databases, which are easier to generate and modified endosperm will provide further
than long tracts of genomic sequences and provide research material for the academic laboratories
large-scale information on the gene complement of involved, including this laboratory, as well as
maize (Fernandes et al 2002). material for the plant breeders and food processors
While extensive collections of maize ESTs have to include in their respective research or product
been assembled by the commercial sector, development pipelines.
approximately 154,500 ESTs derived from 20
cDNA libraries have been deposited in the ZMDB Breeding for improved protein quality in maize
database http://www.zmdb.iastate.edu/zmdb/EST/) began in the mid-1960s with the discovery of
of the NSF Maize Gene Discovery Project. DNA mutants, such as opaque-2, that produce enhanced
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levels of lysine and tryptophan, the two amino acids altered flavor and brewing procedures. Selection for
deficient in maize endosperm proteins. However, malting quality in breeding programs by micro-
adverse pleiotropic effects imposed severe malting and micro-mashing is time consuming, and
constraints on successful exploitation of these resource-intensive and is a major breeding
mutants. Interdisciplinary and concerted research objective for any breeding programs. Characters
efforts led to amelioration of the negative features that affect malting quality (i.e. malt extract content,
of the opaque phenotype, and the rebirth of Quality - and -amylase activity, diastatic power, malt -
Protein Maize (QPM). QPM holds superior glucan content, malt -glucanase activity, grain
nutritional and biological value and is essentially protein content, kernel plumpness, and dormancy)
interchangeable with normal maize in cultivation are quantitatively inherited and variously
and kernel phenotype (Prasanna et al 2001). influenced by the environment (E) (Zale et al
2000). With the advent of molecular markers, it is
A set of 23 Quality Protein Maize (QPM) lines, possible to map and tag the loci affecting malting
including 13 lines developed in India and 10 lines quality.
at CIMMYT (International Maize and Wheat
Improvement Center), Mexico, was analyzed by Considerable QTL analyses have been performed in
Kassahun and Prassana (2003) using microsatellite recent years on a number of crosses. A minimum
or simple sequence repeat (SSR) markers. of 168 malting quality QTLs representing 19
Polymorphic profiles for 36 SSR loci have aided in malting quality traits have been mapped in nine
differentiating the QPM inbred lines. The study mapping populations. QTL regions are spread
resulted in identification of SSR markers, such as across each of the seven barley chromosomes with
bnlg439, phi037, bnlg125, dupssr34 and bnlg105, concentrations especially within chromosomes 1, 2,
with high polymorphism information content in the 4, 5 and 7. Whereas, there is remarkable QTL
selected QPM genotypes. Detection of 30 conservation in some chromosome regions among
unique/rare SSR alleles could contribute to crosses, some regions hold unique QTLs as well. It
effective differentiation of 14 of the 23 QPM is also noteworthy that there are many overlapping
inbreds. An opaque-2 specific microsatellite QTLs, especially but not surprisingly, of related
marker, phi057, also facilitated differentiation of traits. Malt extract QTLs are almost always
opaque-2 carrying QPM inbreds from the non- coincident with component traits such as
opaque genotypes. Analysis using SSR markers carbohydrate hydrolytic enzyme activities.
indicated high levels of heterozygosity in majority Diastatic power QTLs are often associated with -
of the Indian QPM lines and in one CIMMYT QPM and/or -amylase activity QTLs. In some cases
inbred, CML188. Cluster analysis using SSR data, widely conserved QTL chromosome regions may
followed by canonical discriminant analysis, clearly be targets for selection to maintain malting quality,
distinguished the Indian QPM inbreds from those but selection for unique regions may lead to new
developed at CIMMYT. The cluster patterns were improvements (Zale et al 2000). Two major QTL
largely in congruence with the available pedigree regions in six-row barley for malt extract
information of the QPM inbreds studied. The study percentage, -amylase activity, diastatic power, and
demonstrates the effectiveness of SSR markers in malt -glucan content on chromosomes 1 (QTL1)
QPM genotype discrimination and analysis of and 4 (QTL2) have been previously identified. The
genetic relationships. flanking markers, Brz and Amy2, and WG622 and
BCD402B, for these two major QTL regions were
Brewers are reluctant to change malting barley used in MAS (Han et al 1997). Schmierer et al
(Hordeum vulgare L.) cultivars due to concerns of (2005) wanted to develop high yielding near
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isogenic lines that maintain traditional malting breeding methodology and the development of a
quality characteristics by transferring QTL fiber selection index that includes more measurable
associated with yield, via molecular marker- fiber properties. Future approaches to fiber quality
assisted backcrossing, from the high yielding cv. improvement will also include plant biotechnology
Baronesse to the North American two-row malting beyond recombinant DNA techniques, molecular
barley industry standard cv. Harrington. For breeding and plant-based biotechnology solutions
transfer, they targeted Baronesse chromosome 2HL beyond input traits.
and 3HL fragments presumed to contain QTL that
affect yield. Analysis of genotype and yield data Currently, there is a disparity compared to some
suggests that QTL reside at two regions, one on other agronomic crops in terms of availability of
2HL (ABG461C-MWG699) and one on 3HL effective molecular tools for use in a targeted
(MWG571A-MWG961). Based on yield trials molecular breeding approach. Cotton is behind in
conducted over 22 environments and malting molecular breeding approaches because of its
analyses from 6 environments, they selected one complex and large genome, its low genetic
isogenic line (00-170) that has consistently variability and the complexity of priority traits such
produced yields equal to Baronesse while as fiber properties. It is expected that cotton
maintaining a Harrington-like malting quality breeding will evolve along the same lines as
profile. breeding has evolved in other crops over the past
ten years. Looking further into the future, the
QTLs associated with malting quality traits were ultimate breeding approach is design based. In this
mapped in 2 populations derived from parents with view, accumulated genomic information will allow
elite malting quality by Panozzo et al (2007). assembly of an ideal genotype from available allelic
Progenies were tested for grain protein percentage, variants for all known genes. However, as a guiding
-amylase activity, diastatic power, hot water principle for the development and implementation
extract, wort viscosity, wort -glucan, -glucanase, of a molecular breeding technology platform, it is a
and free -amino acids. QTLs for malting quality very valuable concept.
traits were detected on all chromosomes and for
both populations. There were many coincident Until very recently, little was known about the
QTLs for traits that are expected to be related such molecular aspects leading to specific cotton fiber
as diastatic power and -amylase activity, wort - properties and few research tools were available to
glucan and wort viscosity and for some traits that probe cotton fiber quality. The initial focus is on
are not expected to be related such as hot water improving fiber characteristics such as fiber length,
extract and malt viscosity (Panozzo et al 2007). uniformity and strength that are important in
spinning. Approaches are also being explored to
Germplasm improvement in cotton has been improve properties of cotton fiber that would add
practiced since ancient spinners selected plants that value to the overall fiber processing industry and be
produced fiber with improved properties for cloth of real benefit to consumers (Dever and Hamill
production. More recently, breeding approaches for 2005).
traditional pedigree breeding and biotechnology Although potential genetic diversity exists in
have been employed in cotton to address the quality Gossypium genus, it is largely underutilized due
of output fiber quality. Traditional approaches to photoperiodism and the lack of innovative tools
include germplasm access with a focus on fiber to overcome such challenges. The application of
quality, intense selection pressure throughout the linkage disequilibrium (LD) based association
breeding process, modifications to pedigree mapping is an alternative powerful molecular tool
J of Biotech & Crop Sci (2015) 4(5):
): 4-21

to dissect and exploit the natural genetic diversity


diversit selection is difficult. Five chromosome regions
conserved within cotton germplasm collections, strongly involved in organoleptic quality attributes
attribute
greatly accelerating still lagging
lagging cotton MAS were then chosen to be introgressed into three
programs. different recipient lines through MAS. A marker-
marker
assisted backcross (MABC) strategy was performed
per
Abdurakhmonov et al (2008) reported the extent of by Lecomte et al (2004), as all the favorable alleles
genome-wide
wide LD and association mapping of fiber for quality traits were provided by the same
quality traits by using a 95 core set of microsatellite
microsatel parental tomato line, whose fruit weight (FW) and
markers in a total of 285 exotic Gossypium firmness were much lower than those of the lines
hirsutum accessions, comprising of 208 landrace commonly used to develop fresh market varieties.
stocks and 77 photoperiodic va variety accessions. Three
ree improved lines were obtained after three
They demonstrated the existence of useful genetic backcrossing and two selfing generations. Breeding
diversity within exotic cotton germplasm. In their efficiency strongly varied according to the recipie
recipient
germplasm set, 1112%12% of SSR loci pairs revealed parent, and significant interactions between QTLs
a significant LD. At the significance threshold and genetic backgrounds were shown for all of the
(r2 0.1), a genome-widewide average of LD declines traits studied.
within the genetic distance at < 10 cM in the
landrace stocks germplasm and > 30 cM in variety Improving organoleptic quality of fresh market
germplasm. Genome wide LD at r2 0.2 was tomato fruit has become an important objective for
reduced on average to 12 cM in the landrace tomato breeders. Several QTLs controlling the
stock germplasm and 68 cM in variety germplasm, variation of tomato quality traits have been detected
detect
providing evidence of the potential for association using a recombinant inbred line population derderived
mapping of agronomically important traits in cotton.
cotton from a cross between a cherry tomato chosen for its
They observed significant population structure and good flavor and a line with bigger fruits but poor
relatedness in assayed germplasm. Consequently, taste. A MAS scheme was then set in order to
the application of the mixed liner model (MLM), transfer the five most important QTLs involved in
considering both th kinship (K) and population fruit quality into three recurrent lines. The
structure (Q) detected between 6% and 13% of SSR backcross
ss optimisation (population size, number
markers associated with the main fiber quality traits
trai and position of markers) is used, taking into
in cotton. Their results highlight for the first time
ti account both theoretical and practical aspects
the feasibility and potential of association mappin
mapping, (Causse et al 2004).
with consideration
ion of the population structure and
stratification existing in cotton germplasm Color is among the most important attributes of
resources. The number of SSR markers associated tomato for processing into whole and diced
with fiber quality traits in diverse cotton germpla
germplasm, products. Both color and color uniformity are
which broadly covered many historical meiotic greatly affected by Yellow Shoulder Disorder
events, should be useful to effectively exploit (YSD), a ripening disorder that results in
potentially new genetic variation by using MAS discoloration of the proximal end tissue
tissues of the
programs. fruit. Darrigues et al (2008) show that lycopene and
beta-carotene
carotene concentrations are reduced by 18%
The evaluation of organoleptic quality of tomato and 22%, respectively, in fruits affected by YSD.
fruit requires physical, chemical and sensory Variance partitioning suggests that YSD incidence
analyses, which are expensive and difficult to and severity is affected by both genetics and
assess. Therefore, their practical use in phenotypic environment. In order to elucidate
elucid the genetic basis
J of Biotech & Crop Sci (2015) 4(5): 4-21

of YSD, they developed single nucleotide to amylopectin ratio, and potatoes with a higher
polymorphisms (SNPs) as molecular markers for nutritional value (Carputo et al 2005).
application in three inbred backcross populations
derived from either Solanum lycopersicum S. As PCR techniques have developed over the last
lycopersicum or S. lycopersicum S. 15 years, a wealth of new DNA marker
pimpinellifolium crosses. SNP discovery for technologies have arisen which have enabled the
application in these populations is based on both generation of high-density molecular maps for all
analyses of large public EST databases and on the major Brassica crop species. For numerous
hybridization to a custom oligonucleotide array. qualitative traits, traditional mapping approaches
The array was hybridized with target cDNA from S. have led to the development of MAS strategies in
lycopersicum (Ohio 7814) and S. pimpinellifolium oilseed Brassica breeding, and in some cases to
(LA1589). They developed algorithms to detect map-based cloning of the responsible genes.
outliers and identified 1,296 potential SNPs. These Because Brassica species represent the closest crop
putative SNPs are being verified by sequencing, plant relatives to the model plant Arabidopsis
screened for utility as markers on a collection of 99 thaliana, significant progress will be achieved in
S. lycopersicum lines and wild relatives and applied the coming years through integration of candidate
to the genetic dissection of YSD. Implementing gene approaches in crop brassicas, using the
SNP-based marker technology has the potential to detailed information now available for the
dramatically alter our approach to genetic Arabidopsis genome. Integration of information
characterization. This study will facilitate the use of from the model plant with the increasing supply of
population structures that favor simultaneous data from physical mapping and sequencing of the
genetic analysis and crop improvement. diploid Brassica genomes will undoubtedly give
great insight into the genetics underlying both
As one of the most versatile food crops, the potato simple and complex traits in oilseed rape (Snowdon
(Solanum tuberosum) is used worldwide for human and Friedt 2004).
and animal consumption, and as raw material for
starch and alcohol production. Nowadays, one of Cheung et al (1998) used a genetic map of B.
the most important aspects of potato production is juncea to localize genes and QTLs for a number of
tuber quality, that includes biological traits (e.g. seed quality traits in this species. The map was
proteins, carbohydrates, and minerals), sensorial constructed using a segregating population of 119
traits (e.g. flavour, texture); and industrial traits F1 microspore derived doubled haploid (DH) lines
(e.g. tuber shape, cold sweetening, starch quality). from a cross between a high oil B. juncea breeding
Since most quality traits are genetically controlled, line of AAFC Saskatoon (derived from a high oil
breeding work can successfully meet the needs of a Russian line) and an adapted canola quality B.
changing and demanding world. Exploitation of juncea line. The map consists of 343 RFLP markers
tuber bearing Solanum species as source of distributed in 18 linkage groups and five short
valuable quality traits/allelic diversity is favored by unassigned segments covering a distance of 2073
the possibility to manipulate whole chromosome cM. The seed quality traits concerning contents of
sets through sexual hybridization. Genetic oil, erucic acid, linolenic acid, total alkenyl
engineering is an additional tool to produce new glucosinolates and individual classes of alkenyl
genetic variability and to study important metabolic glucosinolates of the mapping population were
pathways. Examples are there on the use of this evaluated by field trials. The data were analyzed
strategy to produce starches with modified amylose using a QTL-interval mapping approach.
J of Biotech & Crop Sci (2015) 4(5): 4-21

Rines et al (2006) reported the development of sequencing strategy (http://soybeangenome.siu.edu,


PCR-based Sequence Characterized Amplified http://www.agbionetwork.orgsoybeangenome/GSA.
Region (SCAR) and Cleaved Amplified php). For the genetic and genomic analyses of the
Polymorphic Sequence (CAPS) molecular markers soybean genome, precise genetic and physical maps
in oat for application in genetic studies and marker are important. Indeed, various types of physical
assisted breeding. There are 8 marker sets known maps have so far been reported using RFLP, RAPD,
for oil content (Orr and Molnar 2007) and 15 sets SSR and AFLP markers. Sequencing of the
of markers for beta-glucan and protein content (Orr soybean genome and the model legume species will
and Molnar 2008). The more robust markers were provide us with a large amount of information for
developed from Random Amplified Polymorphic useful genes. Recently, a soybean genome sequence
DNA (RAPD) markers mapped in the Kanota x project was also started in Japan using a Japanese
Ogle (Wight et al 2003) or the Terra x Marion (De cultivar Enrei. More than 10,000 independent full-
Koeyer et al 2004) recombinant inbred populations length cDNAs have been collected from various
and associated with QTLs for the traits of interest. organs and stress-treated soybean. The reports in
While many of the new markers map to the same this issue will be useful for future functional
loci as the original RAPD markers, others map to analysis of genes involved in soybean productivity.
homologous or homoeologous genomic regions and
still others to regions not known to be orthologous Seed calcium content is an important quality
to the original RAPD regions. These markers have attribute of specialty soybean [Glycine max (L.)
potential to define homologous and homoeologous Merr] for soyfoods. However, analyzing seed for
relationships in oat, to investigate the complex calcium content is time consuming and labor
genetics of these grain quality traits, and for marker intensive. Knowing QTL for seed calcium will
assisted oat breeding. facilitate the development of elite cultivars with
proper calcium content through MAS. Calcium
Soybean is undoubtedly the most important legume content was tested in 178 F2:3 and 157 F2:4 lines
crop in the world. In the past decade, plant genome derived from the cross of SS-516 (low calcium) x
analyses using model organisms have provided a Camp (high calcium) by Zhang et al (2008). Four
large amount of genomic information and various QTL designated as Ca1, Ca2, Ca3, and Ca4 on
categories of knowledge for gene functions: linkage groups (LGs) A2, I and M were identified
genome sequence, collection of expressed sequence by both single-marker analysis and composite-
tags (ESTs) and DNA markers are widely exploited interval mapping, and the QTL accounted for
for the discovery of genes. Soybean has a large 10.7%, 16.3%, 14.9%, and 9.7% of calcium content
genome of 1,115 Mbp with 2n = 40 that contains variation, respectively. In addition, multiple-
complex regional duplications. Several types of interval mapping analysis revealed a significant
genome projects including linkage map production dominant-by-dominant interaction effect between
have been initiated to uncover its complex genomic Ca1 and Ca3, which accounted for 4.3% calcium
structure and to help gene discovery. As for the content variation. These QTL will facilitate the
EST collection, soybean has the sixth largest implementation of MAS for calcium content in
collection of more than 390,000 sequences soybean breeding programs.
(http://www.ncbi.nlm.gov/dbEST). Transcriptional
maps with single nucleotide polymorphism (SNP) Forage quality depends on the digestibility of
markers have been published using EST fodder, and can be directly measured by the intake
information. Recently, whole genome sequencing and metabolic conversion in animal trials. It is not
of soybean has started in the USA, using a shotgun
J of Biotech & Crop Sci (2015) 4(5): 4-21

possible to study thousands of plant genotypes, as establishment and comparatively lower quality
required in breeding programs. Therefore, several characteristics. Lolium and Festuca species
indirect methods including near-infrared reflectance hybridize naturally and exhibit high frequencies of
spectroscopy (NIRS) have been established to gene exchange in the hybrid condition. Intergeneric
overcome this limitation. However, the ideal hybrids (Festulolium) between Lolium and Festuca
indirect system for the prediction of forage species are being used to broaden the gene pool and
performance would be based on gene-derived to provide the plant breeder with options to
functional DNA markers, allowing early combine high quality traits with broad adaptations
selection ultimately without need of field trials, and to a range of environmental constraints.
being environment independent. In addition, once Festulolium varieties have promise as novel grasses
identified relevant genes controlling forage quality with high forage quality and resistance to
are targets for transgenic approaches. Substantial environmental stress and can thereby improve
progress has recently been achieved in the grassland productivity, persistency and benefit
development and application of genomic tools both incomes.
in model species and major forage crops such as
ryegrass and alfalfa. Key genes involved in Conventional forage grass breeding programs rely
developmental and biochemical pathways affecting on basis observable phenotypes using the natural
forage quality such as cell-wall, lignin, fructan, and genetic variation found between and within
tannin biosynthesis have been isolated and varieties or ecotypes. Genetic improvement of
characterized. For some of these genes, allelic forage grasses by conventional breeding programs
variation has been studied in detail and sequence is very slow due to the obligate outbreeding and
motifs with likely effect on forage quality have perennial nature of grasses. Advances in genomics
been identified by association studies. Moreover, and gene manipulation can complement and
transgenic approaches substantiated the effect of enhance conventional plant breeding programs.
several of these genes on forage quality. Many studies concerning the implementation of
Perspectives and limitations of findings for forage DNA markers, high-throughout gene discovery,
crop breeding needs to be discussed given expected genome-wide gene expression analysis and gene
further progress in forage crop genomics, but also manipulation are currently being conducted for
the complexity of the trait complex forage quality, forage grasses (Yamada et al 2005).
since typically species mixtures of heterogeneous
and heterozygous genotypes are grown in the field Molecular and biochemical studies were undertaken
(Lbberstedt 2007). to elucidate gene/product relationships which
influence key fruit quality traits in cultivated
Perennial ryegrass (Lolium perenne) and Italian strawberry (Fragaria ananassa Duch.).
ryegrass (L. multiflorum) are regarded as ideal grass Comparative transcription profiling experiments in
species for use as animal forage in temperate selected genotypes pointed out a number of
grassland agriculture. However, their use is differentially-expressed genes, possibly related to
restricted as they lack persistency, especially in important fruit quality traits as aroma and fruit
marginal areas and locations that are subject to firmness. Some of the altered cDNAs encode
summer and winter stresses and drought stress. putative cinnamyl alcohol dehydrogenase,
Close relative species from within genus Festuca cinnamoyl CoA reductase, cellulase and expansin
are much better adapted to such abiotic stresses but, genes, involved in the early steps of lignin
by contrast, do not compare well in animal forage biosynthesis and in cell wall structure, respectively.
provision to Lolium species as they show poor Parallel biochemical analyses studied the spectra of
J of Biotech & Crop Sci (2015) 4(5): 4-21

volatile compounds by Proton Transfer Reaction- enzyme including (a) a carotenoid-forming enzyme
Mass Spectrometry (PTR-MS) and alcohol acyl that is at least a ketolase. That gene is operatively
transferase (AAT) specific activity in red fruits. A linked to (b) a plastid-directed transit peptide. Some
correlation between the expression of an aat gene, higher plants to be transformed produce at least
total AAT activity and the presence of related esters zeaxanthin or beta-carotene in their flowers prior to
in fruit headspace was found by Fabrizio et al transformation, whereas other plants produce little
(2006). if any coloured carotenoid pigments prior to
transformation and are transformed with a cassette
The seed industry is beginning to use DNA based of carotenoids-forming genes (Hauptmann et al
markers to develop fingerprint patterns for 2003).
grouping or clustering complex beneficial traits.
This cluster analysis will allow breeders to The present invention provides a new method for
predict regional performance or environmental promoting the synthesis of fatty acid in a plant. The
adaptation based on shared marker patterns. For amount of protein of carboxyl transferase and beta
example, processing tomatoes adapted for subunit encoded by accD gene is increased by
California conditions cluster separately from introducing a promoter sequence of a gene highly
varieties that perform best in Ohio. The efficiency expressed in chloroplast at the upstream of an
and outcome of selection strategies can be greatly E.coli type acetyl CoA carboxylase accD gene by
enhanced by optimizing breeding crosses to a chloroplast transformation technique. The amount
targeted DNA marker cluster. Another practical of protein of other subunit constituting acetyl CoA
application is to identify seed lot purity in carboxylase is also increased by this process. Since
asparagus or in any seed lot. Molecular markers acetyl CoA carboxylase is the key enzyme of the
were used to show that some seed lots used for first stage of fatty acid synthesis, the synthesis of
crown production contained over 70% poor fatty acid can be promoted by the method of the
yielding types and types with low postharvest present invention. The transformed vegetable
quality. This can be critical information for a produced by the method exhibits remarkable
perennial crop that is expected to be productive promotion of fatty acid synthesis, prolonged life of
over a 10-12 year span (Suslow and Bradford the leaf, increased yield of seeds and improved
1999). productivity of the plant body (Sasaki et al 2002).
Preparing Transgenic Leguminous Plants with
4-Ketocarotenoids in Flower Petals (Patent # Increased Protein Content (Patent # WO0175128).
WO03080849). The invention relates to a method for the
production of leguminous plants with increased
The formation of a carotenoid compound protein content in the seeds and longer seed filling
containing a 4-keto-beta-ionene ring such as duration, by means of introduction of recombinant
astaxanthin or canthaxanthin in flowers, and DNA molecules. Said recombinant DNA molecules
particularly in the corolla and reproductive parts of are introduced into the plant, by means of a
a flower of a higher plant whose flowers produce a transformation system and comprise a DNA
carotenoid compound containing a beta-ionene ring sequence from the plant, expressed in plants, the
such as beta-carotene or zeaxanthin, but otherwise genetic product of which inhibits a protein in the
do not produce astaxanthin or canthaxanthin is seed with the enzymatic activity of an ADP glucose
disclosed. One or more genes controlled by a pyrophosphorylase (AGP) and/or a plastid
promoter are inserted (transformed) into a higher phosphoglucomutase (pPGM) and, optionally, the
plant. The inserted gene encodes a chimeric regulatory sequence of a seed-specific promoter in
J of Biotech & Crop Sci (2015) 4(5): 4-21

leguminous plants. Furthermore, at least one A, Sanchez-Villeda H, Soderlund C, Wing R


selection marker gene is separately transferred, (2002) Access to the maize genome: an
which is subsequently removed again. The plants integrated physical and genetic map. Plant
which display increased protein content and a Physiol 128: 9-12.
lengthier seed-filling duration are chosen (Weber et DOvidio R, Anderson OD (1994) PCR analysis to
al 2001). distinguish between alleles of a member of a
multigene family correlated with wheat
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caused by poverty and malnutrition through both Burrows VD, Odonoughue LS, Lybaert A,
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