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

Yan CJ et al.(2009) compare the nucleotide sequencesencoding the OsCKX2 enzyme on the
Gn1a locus, a gene for grain size revealed a 16-bp deletion in the 50-untranslated region and an
11-bp deletion in the coding region in the two high-yielding rice cultivars Habataki and 5150,
respectively, as compared to those in the Koshihikari cultivar. On the basis of sequence variation
among different alleles, two sequence-tagged site (STS) markers, Gn1a-M1 and Gn1a-M2, were
developed for genotyping Gn1a alleles.
In another study of Wang (2011)three polymorphic loci, namely SR17, RGS1, and RGS2,
were found on the second intron, the last intron and the final exon of GS3, respectively. The
mutation in the cysteine codon (TGC) in the small grain group was changed to a termination
codon (TGA) in the large-grain group. Numerous insertion/deletion and nucleotide
polymorphisms at these three loci were identified besides the C-A mutation at the locus SF28
within GS3 in a wide collection of rice germplasm.
4. QTL Fine Mapping
To narrow down the targated QTL region of interest a fine mapping strategy was used in
several studies. This will help to easy transfer the targated QTL into new cultivars of interest and
their identification into it. Based on sequence information the different types of molecular
markers like SSR, SNP, Indels had been designed in the targated QTL region using bioinformatics
tools. Onces the markers were identified their cosegression pattern used to identification of
flanking region which was associated with our trait of interest.
4.1 Approaches based on advanced populations
F2, DH or RIL populations are powerful and adequate to fine map qualitative genes if
there are plenty of polymorphism markers. To date, only a few genes have been identified and
isolated using F2 populations: e.g. SRS3, DEP2/EP2, DEP3, EP3, APO1 and GIF1. The mutation
of loss-of-function or gain-of-function versions of these genes causes a significant variation, in
which individuals of the target population can be easily classified into groups. However, it is
difficult to precisely estimate the genetic effect of a single QTL in a primary mapping population
due to the genetic background noise in a F2 population. Moreover, it is difficult to fine-map a
major QTL in a F2 population, let alone a minor QTL. In view of this point, NILs were proposed
by Tanksley and Nelson (1996) for isolating and cloning a candidate QTL/gene. The target QTL
region is segregated and the genetic background is fixed in the NILs. Compared with the primary
mapping population, NILs eliminate the genetic background noise. Thus, the related trait
controlled by a target QTL shows the characterization of a Mendelianfactor with a segregation
ratio of 3:1 in the NIL-F2 population. In addition, a QTL can explain more variation in the NIL
than in the primary population. Hence, NILs are widely used for QTL fine-mapping and isolation.
Many QTLs have been fine-mapped and cloned using consecutive backcrossing strategy, known
as CB-NILs populations (Ashikariet al., 2005; Fan et al.., 2006;Song et al., 2007; Xing et al., 2008;
Xueet al., 2008 and He et al., 2010). However,construction of CB-NILs is time consuming; usually
taking three years to develop NILs in rice after QTL information is obtained.
The RIL populations, such as F6 and F7, are obtained by single-seed descent method.
TheF6 plant and its F7 progeny show a nearly identical phenotype. However, if one unknown
gene/QTL for a trait is located in the heterozygous region, its progeny should segregate in the
target trait which is easily observed. Thus, the progeny of the heterozygous plant consists of the
NILs of the unknown gene/QTL. This type of NIL is known as trait performance based NILs (TP-
NILs) as they are obtained according to trait performance without any QTL information in
advance.The TP-NILs strategy depends completely on the variation in trait performance. Hence,
it is an efficient way to identify the major QTLs that cause large trait variations.

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