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Molecular Plant Breeding Provisional publishing
Molecular Plant Breeding 2012, Vol.3, No.10, 103
-
114
http://mpb.sophiapublisher.com
103
Research Report Open Access
Validation of
SalTol
Linked Markers and Haplotype Diversity on Chromosome
1 of Rice
Mohammad Rafiqul Islam
1,2
, Glenn Borja Gregorio
1
, Md. Abdus Salam
2
, Bertrand C. Y. Collard
1
, Rakesh
Kumar Singh
1
, Lutful Hassan
3
1. Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
2. Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
3. Genetics and Plant Breeding Department, Bangladesh Agricultural University, Mymensingh, Bangladesh
Corresponding authors email:
g.gregorio@cgiar.org;
Authors
Molecular Plant Breeding, 2012, Vol.3, No.10 doi: 10.5376/mpb.2012.03.0010
Received: 15 Jun., 2012
Accepted: 25 Jun., 2012
Published: 29 Jun., 2012
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Islam et al., 2012, Validation of
SalTol
Linked Markers and Haplotype Diversity on Chromosome 1 of Rice, Molecular Plant Breeding, Vol.3, No.10 103
-
114
(doi: 10.5376/mpb.2012.03.0010)
Abstract
To determine the usefulness of SSR markers associated with a major QTL for salinity tolerance designated as ‘
SalTol
’, a
collection of 115 diverse rice genotypes was phenotyped and genotyped using tightly linked DNA markers. These markers include
five SSRs, RM1287, RM8094, RM3412, RM493 and RM140, and two EST markers, CP6224 and CP03970, on chromosome 1.
Among the seven markers, the highest number of alleles (15) was found in RM8094, followed by 10 in RM187, RM3412 and
RM493. The polymorphic information content (PIC) values ranged from 0.54 to 0.89. The highest PIC value (0.89) was found for
RM8094, followed by RM493 and RM3412 (0.81) and RM1287 and RM140 (0.77). The marker RM8094 was useful for
discriminating between tolerant and susceptible genotypes and therefore may be useful for marker-assisted selection. Seven
haplotypes were identified among the 115 genotypes using the haplotype of IR66946-3R-178-1-1 (FL478) – the most widely used
tolerant parent – which was used as a reference haplotype. Four genotypes had the same haplotype as FL478 and Pokkali-1. Of the
seven different Pokkali seed sources tested, Pokkali-1 (IRGC 8948) contributed the
SalTol
region on the chromosome 1 segment of
FL478. Genotypes from the haplotypes (in comparison with FL478) 1, 2 and 5 may be important for selecting alternative tolerant
parents.
Keywords
Haplotype; Rice; Salinity tolerance; Chromosome 1
Background
Rice (
Oryza sativa
L.) is a cereal plant of the grass
family whose seeds are among the most important
foods of the world and the most consumed staple in
Asia. Recently, because of land scarcity and high food
demand, to attain food security, marginal lands such as
saline-prone areas must be put into use.
Salinity is an important abiotic problem in the
rice-growing areas of the world. Salinity-affected
areas have increased day by day because of the
intrusion of brackish water during the dry season and
at the start of the wet season and also because of the
excessive use of irrigation water with improper
drainage coupled with the use of poor-quality
irrigation water (Ismail et al., 2010). Millions of
hectares in the tropics and arid and semi-arid regions
are technically suitable for rice cultivation. However,
they are left idle or they grow very low yielding
varieties due to the lack of suitable tolerant
high-yielding modern varieties. Some 400-950 million
hectares of global land are affected by different
concentrations of salinity (Lin et al., 1998). The rice
plant is one of the most suitable crops for saline soils,
although it is considered moderately sensitive to
salinity (Mori and Kinoshita, 1987).
Salt tolerance is a complex quantitative genetic
character controlled by many genes (Shannon, 1985;
Yeo and Flowers, 1986). Using conventional breeding
methods, plant selection for salt tolerance is not easy
because of the large effect of environment and low
heritability of salt tolerance (Gregorio and Senadhira,
1993; Gregorio, 1997). Because of the complexity of