An Overview of Omics for Wheat Grain Quality Improvement - Crop Improvement: New Approaches and Modern Techniques - page 321

developed for quality traits by cloning of 62 alleles at 16 loci. Functional markers
that have application for wheat quality improvement are presented in Table 10.2 .
Isolation and characterization of functional motifs within genes controlling phe-
notypic variability is critical to develop allele specific markers. These motifs are
usually characterized by single nucleotide polymorphisms (SNPs) or insertions/de-
letions (InDels) within the nucleotide sequences of different alleles. Using the map-
based cloning approach, several genes have been isolated in plants; however, the
very large genome is the main problem in common wheat which makes map-based
cloning difficult as compared to rice and maize. Rice-wheat micro-colinerarity and
different comparative genomics tools provides an alternate and efficient way to
dissect target genes in wheat. This is due to the fact that rthologs descended from a
common ancestor often have conserved functions and are expected to produce simi-
lar phenotypes across species (Devos 2005 ). The whole genome sequence is avail-
able for several grasses including rice, maize and Brachypodium which provided
powerful tools for gene discovery in wheat (Vogel et al. 2010 ). The in silico technol-
ogy is now widely used for discovery of genes of interest in wheat (Ma et al. 2012 ).
A major breakthrough is the availability of expressed sequence tags (EST) database,
from where the sequences of putative wheat genes can be obtained by aligning and
joining of orthologous genes with the same function in the grass.
DescriptionofQualityTraitsandTheirFunctionalMarkers
Significance of HMW-GS and LMW-GS ingrain quality has been described ear-
lier. There are several reports on the nucleotide sequences of the cloned genes for
HMW-GS and LMW-GS. The nucleotide sequence of these cloned genes provided
the basis for marker development for their further use in breeding. Zhang et al.
(2004) developed markers for Glu-A3 alleles based on DNA polymorphisms identi-
fied between the LMW glutenin genes. However markers developed by Wang et al.
(2009b, 2010) for Glu-A3 and Glu-B3 are more efficient and easier to use. However,
due to limited variation among Glu-D3 haplotypes, no allele specific marker was
developed (Liu et al. 2010 ), and comparatively their impact is also very small com-
pared to Glu-A3 and Glu-B3 loci (Gupta et al. 1989 ). Zhao et al. ( 2007b ) attempted
to develop markers for Glu-D3 haplotypes and later Appelbee et al. ( 2009 ) tried to
use those haplotype specific marker combinations for diagnosis of some specific al-
leles like Glu-D3a , b , c and f . A total of seven allele specific markers for Glu-A3 and
ten markers for Glu-B3 loci have been reported. Additionally, Wang et al. (2009b,
2010) also established multiplex PCR strategies to reduce the cost of technique in
practical breeding programs. The practical usage of functional markers for HMW-
GS and LMW-GS to test wheat cultivars and lines has been established and reported
(Liang et al. 2010 ; Jin et al. 2011 ; Ram et al. 2011 ; Khalid et al. 2013 ).
The GBSS I (granule-bound starch synthase) is defined as Waxy ( Wx ) protein,
and it is a primary enzyme involved in synthesis of amylose in wheat endosperm.
The amylose contents play an important role in determining noodle quality. The