Page 14 - Molecular Plant Breeding

Molecular Plant Breeding 2013, Vol.5, No.9, 47-63
http://mpb.biopublisher.ca
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genes (Akbar et al., 1985; Jones, 1986; Yeo and
flowers, 1986; Ashraf, 2004; Masood et al., 2004).
We observed in this study that shoot growth in rice
under salt stress might be controlled by multiple genes
which are located on different chromosomes. All the
5 QTLs identified for both shoot fresh weight (1 QTL)
and shoot dry weight (4 QTL) are located on 3
different chromosomes namely 1, 2 and 6. Similar
findings were made by Haq et al (2010), where all
the 7 QTLs identified in their studies were located
on different chromosomes namely 1, 2 and 6. Two
of their identified QTLs controls shoot fresh weight,
one QTL for shoot dry weight and 4 QTLs for shoot
fresh/dry weight ratio. Different chromosomal regions
carrying one or more QTLs for various growth and
physiological traits under salt stress have also been
detected on chromosomes 1, 4 and 8 respectively
(Gong et al., 2001).
Seedling vigor remains as an important factor for
comparing ion concentration in plants; Akhtar (2002),
identified QTL for shoot fresh weight under salt stress
on chromosome 1 and suggested that high
concentration of Na+ might be important for rice
growth and could be responsible for the reduction in
shoot fresh weight. This is to some extent, supported
by our results.
Flowers et al. (1985) and Aslam et al. (1993) found
an inverse relationship between rice growth and Na+
concentration under salinity. Two QTL responsible for
Na+ concentration in shoots were found on
chromosomes 1 and 6 using genome-wide association
analysis (Zhou et al., 2013). These QTL accounted
for 14.5% and 53.3% of the variation for this trait.
Many QTL for salinity tolerance including Saltol,
which is a major QTL responsible for salinity
tolerance at early seedling stage, are on the short arm
of chromosome 1 in rice (Claes et al., 1990; Gregorio,
1997; Flowers et al., 2000; Lang et al., 2001, Koyoma
et al., 2001; Bonilla et al., 2002; Niones et al., 2004;
Takehisa et al., 2004; Lin et al., 2004; Ren et al., 2005;
Yao et al., 2005; Lee et al., 2007; Zang et al., 2008;
Sabouri and Biabani, 2009; Sabouri et al., 2009;
Ammar et al., 2009). We compared all the 7 QTLs
identified with the report by Negrão et al (2011) and
Gramene Web site (www.gramene.org/) and observed
that both qPH1.1, qPH1.2 share similar position with
a QTL controlling days from seedling to death (DSD)
on chromosome 1.The other QTL (qDW1.1) was
different thereby suggesting new genome regions
contributing to tolerance to salinity in rice. The 2 of
the 3 QTLs identified on chromosome 2 (qDW2.1 and
qDW2.2) shares similar positions with a QTL
controlling relative tiller number; whilst the other
QTL (qF2.1) was different, as the other QTL
(qDW6.1) on chromosome 6. Our research supports
the notion that chromosome 1 bears QTLs cluster for
salinity tolerance. It will be worth pursuing further
research to verify if the sequences of the QTL
detected in our study are similar to those already
known and located in the other chromosome arm.
2.3 Significance of SNPs in QTL identification
The importance of sequence-based SNP genotyping
for QTL analysis in rice has been demonstrated
(Konishi et al., 2006, McNally et al., 2009, Yu et al.,
2011, and Thomson et al., 2012). SNP map has been
used to validate the positions of several cloned genes
including GS3 and GW5/qSW5, two major QTLs for
grain length and grain width respectively, and OsC1,
a QTL for pigmentation (Yu et al., 2011) and for low
shattering traits (Konishi et al., 2006). In this report,
we identified 7 QTLs by using 384-SNP chips under
salinity stress in hydroponics conditions; these are
qDW1.1, qDW2.1, qDW2.2 and qDW6.1, the rests are
qPH1.1, qPH1.2 and qF2.1 and were classified as
major QTLs with very large effect ranging from
10.6% to 42.3% of the total phenotypic variation. The
SNP map used in the study had a total length of
1441.96 cM with an average interval of 7.88 cM
across all 12 chromosomes
The QTL we detected using SNP markers for shoot
fresh weight and shoot dry weight were in other
genome regions than those already found by earlier
workers (Koyama et al., 2001, Prasad et al., 2000,
Lin et al., 2004; Haq et al., 2010); thereby suggesting
their novelty as sources for breeding tolerance to
salinity in rice. Likewise, we used an ultra-high
density genetic map based on high quality SNP chip
from low-coverage sequences of RIL population of
rice, generated using new sequencing technology to
identify all the QTL. Previous research was based on
linkage maps ensuing from the use of low-throughput
DNA markers, such as restriction fragment
polymorphisms and microsatellites. Such DNA