Grain yield of rice is increasing at a faster rate in sub-Saharan Africa than the world’s average; between 2007 to 2012, average grain rice yields in sub-Saharan Africa increased about 30% or 108 kg.ha^-1.year^-1 (AfricaRice, 2011), Despite this grain yield increase, rice productivity continues to be affected by a series of pests blast, bacterial blight, rice yellow mottle virus and stem borers, and abiotic factors drought, flood, salinity, cold and iron toxicity, in this continent. Soil salinity in reclaimed paddy fields is one of the important constraints limiting rice growth and yield. Salt-tolerant cultivars have been seldom selected in Africa. Furthermore, there are not many advanced salt-tolerant breeding lines with useful agronomic characteristics due to the difficulty of transferring tolerant traits into popular rice cultivars. Likewise, Munns and Tester 2008, indicated that the effect of salinity is caused by multigenic traits with complex genetics and mechanisms.

It has also been documented that multi-genes control various salt-tolerant associated traits such as shoot fresh weight, shoot dry weight, shoot length, root length, and shoot Na+/K+ ratio in rice (Akbar et al., 1986; Jones, 1986; Yeo and Flowers, 1986; Flowers et al., 2000; Ashraf, 2004; Masood et al., 2004; Munns and Tester, 2008). In spite of this difficulty, efforts have been made by International Rice Research Institute IRRI, in the Philippines in collaboration with many national institutes to develop and improve rice varieties tolerant to salinity. This has led to the release of varieties such as FL478, IR4630-22-2-5-1-3 (SAL 002), PSBRc 88, IR77644-B-9-3-3-21-15-2-AJY4 and IR83415-B-SDO3-3-AJY3. However most of these varieties were developed with limited number of resistant such as Nona Bokra or Pokkali or varieties derived from these parents such as CSR27 (Negrao et al., 2011), There is the need to broaden the genepool of rice for salinity tolerance. Hasawi is a landrace from eastern Saudi Arabia and characterized by its strong adaptability to soil salinity and drought making it a plausible donor to be used in salinity research.

Research on quantitative trait loci QTL, mapping for salt tolerance in rice has advanced significantly in the last 2 decades (Zhang et al., 1995; Lin et al., 1998; Gong et al., 1999; Flowers et al., 2000; Prasad et al., 2000; Tuan et al., 2000; Koyama et al., 2001; Lang et al., 2001; Masood et al., 2004; Yao et al., 2005; Sabouri and Sabouri, 2009; Ahmadi and Fotokian, 2011; Islam et al., 2011); but only few studies of heterogeneous quality have been conducted (Negrao et al., 2011), Several QTLs have been identified for salinity tolerance in rice using different mapping populations such as RIL, DH or F_2:3, ranging from indicaxjaponica originally developed for other purposes, such as IR64×Azucena or Co39×Moroberekan. Most of these QTLs compute indices for plant developments under normal and stress conditions www.Gramene, Some QTLs have been detected repeatedly on chromosomes 1, 4, 6, and 7, whilst none have been found on chromosomes 8 and 11 and very few on chromosomes 2, 3, 5, 9, 10 and 12 (Negrao et al., 2011), QTL studies have led to the conclusion that different loci are involved in the different plant responses under salt stress (Haq et al., 2010).

A large number of QTLs have been detected to concentrate on the segment of short arm on chromosome 1 (Bonilla et al., 2002, Gregorio et al., 2002, Lin et al., 2004; Ren et al., 2005).

More recently, the use of single nucleotide polymorphisms (SNPs), due to their high level of informative content, has led to identifying various QTL in rice.

The advantages of using recombinant inbred lines RILs, for a QTL analysis are well documented. First, multiple selfing processes can increase the number of recombination events (Soller and Beckmann, 1990), which results in a finer mapping of QTLs. More importantly, once RILs are established, in which the genotypes of all lines are fixed as homozygotes, these lines can be repeatedly used for investigating QTLs of various phenotypes under different environments. Thus, the establishment of a comprehensive set of RILs will be a substantial contribution to QTL mapping for salinity tolerance in rice.

The RILs population used in the current study consists of 300 lines using single seed descent until the F₅ generation developed at IRRI. This RIL population was derived from a cross between IR29 and Hasawi. IR29 is an IRRI-bred indica line and it is used as a susceptible check in salinity experiments. SNP-facilitated allelic diversity analysis have revealed that Hasawi is an Aus cultivar; suggesting that there may be a possibility of high level of polymorphism in offspring derived by crossing Hasawi with indica cultivars (Thomson et al., 2010a; Platten et al., 2013).

The objectives of our research were to identify and map QTL controlling salt tolerance at early seedling stage in IR29×Hasawi F₅ RIL population using 384 SNP chip under hydroponic conditions, and also to select best performing RILs for their further use as breeding materials or for cultivar development.

1 Results
1.1 Trait Analysis and Performance of F₅–derived RILs
The descriptive statistics of the qualitative and quantitative traits measured in the F₅ derived–RILs are given in Table 1. There was a significant variation for all traits in these RILs; besides we also observed transgressive for all traits (Figure 1~Figure 4).

Table 1 Descriptive statistics for salt-tolerant associated traits evaluated in 300 F5–derived recombinant inbred lines and their parents IR29 susceptible, and Hawasi tolerant, under salines stress S, and non-stress N

Figure 1 Distribution of salt tolerance score (SES), in 300 F5–derived recombinant inbred lines from IR29×Hasawi

Figure 2 Distribution of plant height under saline stress in 300 F5–derived recombinant inbred lines from IR29×Hasawi

Figure 3 Distribution of root length under saline stress in 300 F5–derived recombinant inbred lines from IR29×Hasawi

Figure 4 Distribution of fresh weight under saline stress in 300 F5–derived recombinant inbred lines from IR29×Hasawi

Ranking of F5:6 RILs for salinity damage using SES. Salinity tolerance was rated as any entry having an SES score of equal to that of the tolerant parent, Hasawi or better than it. The tolerant parent Hasawi had a score of 4 and IR29 had 7, confirming its susceptibility to salinity. Salinity damage scores were given to each RIL according to their plant vigor, leaf chlorosis, necrosis and general physical health. The mean SES score for the RILs was 6 but with a wide range of variation SES score of 3~9 (Table 1; Figure 1), Thirty-o