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Life Science Research and Sustainable Development ISBN: 978-98-84663-33-9

thatassociation mapping will detect more genes/QTLs with higherresolution compared to
linkage analysis. Some major QTLs cloned by linkage analysis have been fine-mapped to 100
kb(Huang et al., 2010). Huang et al. (2010) used ~3.6 million SNPs with 517 rice landraces. Lakewet
al.(2010) demonstrated association mapping of drought-related traits in barley using SSR and
SNP markers. Yanet al. (2011) reported that SSR markers provided more information on genetic
diversity and performed better at clustering all lines into groups than SNPs. Since both the DNA
markers are efficient at association mapping and population studies. Zhao et al.(2011) reported
GWAS using 44,100 SNPs with 413 rice accessions. In another experiment byZhao et al. (2010)
studied 130 rice accessions with 170 SSR markers to identify marker–trait associations by MLM
for grain quality. There are numerous reports on genomewide association studies (GWAS) in rice
using SNPs.
A major QTL for grain length, qGRL-1.1 has been mapped to a 108-kb region between
markers RM431 and CHR1.1 on chromosome 1 (Singh et al., 2012). GW3 and GW6 are major grain
weight QTLs that have been fine mapped on chromosome 3 and 6, respectively. GW3 has been
narrowed down to a 122-kb physical distance containing 16 open reading frames. The cloned GS3
gene is located in this region and it remains to be determined whether they represent the same
locus.
Notably, several QTLs that affect the vascularbundle system in rice have been further
cloned by positionalcloning. For instance, genes such asAPO1andNAL1have beenshown to
involve in enhanced translocation capacity ofvascular bundles (Fujita et al., 2013).Fujita et al.
(2013) identified the major QTL for number of spikelet per panicle i.e.NAL1 indirectly involved
in translocation capacity of photosynthats had been fine map to 18kb between markers Ind4 and
Ind 12. Recently another QTL for spikelet per panicle, qSPP6 map to a 429kb and cosegregate with
markers RM20521 and Ind1.LSCHL4 a QTL for flag leaf shape and chlorophyll content has been
mapped on chromosome 4 to a 18.97kb within T2957-2 and RM348 marker.qFLW7.2, a new major
QTL for flag leaf width, was fine mapped within 27.1 kb region on chromosome 7. Both qFLW7.2
and qPY7 were located in the interval of 45.30 ~ 53.34 cM on chromosome 7, which coincided
with the relationship between yield per plant (PY) and flag leaf width (FLW)( Zhang et al., 2015).
5.Cloning and functional characterization of Yield related traits
Higher yields of rice have always been apredominant goal in rice breeding techniques.
However,the inheritances of rice yield and its componentsare still unknown, and no information
regardingsuitable alleles can be directly provided for improvingthe rice yield level. Over the past
20 years, the development of DNA markers and genomic sequencing technology have led to rapid
progress in the mapping and cloning of genes underlying grain shape and grain weight in rice
(Ashikariet al., 2006). To date, ~40 QTL/genes associated yield and its contributing traits have
been isolated by map-based cloning strategies. Most of them are still poorly understood,
particularly with regard to their functions at the biochemical and cell biological levels.
Dwarf1 (D1), also known as the rice heterotrimeric G protein alpha subunit (RGA1), D2,
D11, and D61. Mutations in these genes result in dwarf plants and have detrimental pleiotropic
effects on organ growth, including a reduction in seed size. D1/RGA1 was the first gene to be
cloned that had substantial effects on seed-size regulation (Ashikariet al., 1999 and Fujisawa et al.,
1999). An 833-base pair (bp) deletion of D1 disrupts the coding region of the heterotrimeric G
protein alpha subunit and results in dwarf plant phenotypes with smaller grain. Genes affecting
brassinosteroid (BR) biosynthesis and signal transduction have also been shown to regulate grain
size in rice. D2 and D11 encode two cytochrome P450 oxidoreductase enzymes involved in BR
biosynthesis (Hong et al., 2003) and D61 encodes a BR receptor, an ortholog of BRI1 in Arabidopsis

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