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Title:	Fine mapping of a grain-weight quantitative trait locus in an advanced backcross population derived from Oryza rufipogon IRGC105491/Oryza sativa cv. MR219
Authors:	Mee Siing Ngu (P42607)
Supervisor:	Wickneswari Ratnam,Prof. Dr.
Keywords:	Universiti Kebangsaan Malaysia -- Dissertations Dissertations, Academic -- Malaysia Red rice Oryza
Issue Date:	21-Jun-2012
Description:	Grain weight is a major determinant of crop grain yield and is controlled by naturally occurring quantitative trait loci (QTLs). In an earlier study, a grain weight QTL (qGW-6) was detected near marker RM587 on chromosome 6 in a backcross population (BC2F2) derived from a cross between O. rufipogon IRGC105491 and O. sativa cv. MR219. A total of 45 pairs of new SSR primers were synthesized for the target region of qGW-6. Among them, 20 (44.4%) showed polymorphism between the parents. However, only 15 polymorphic primers which gave consistent and repeatable amplification after optimization were used for screening the progenies or mapping populations. Using 212 individuals from the BC2F5 population of family A20 (R2-10- 18-2), the 25cM target region of qGW-6 was refined to 4.8 cM (1.2 Mb) in the interval between RM508 and RM588 using single-marker regression (SMR) (LOD=6.0, R2 =12.2%). Fine mapping with 102 BC4F3 sub-near isogenic lines (NILs) using SMR (LOD=7.7, R2=29.4%) narrowed the interval containing qGW-6 to about 510 kb between marker RM435 and RM7399. Using 34 NILs and eight BC4F4 fixed lines, the interval containing qGW-6 was further refined to 248 kb between markers RM19266.1 and RM7399 using SMR (LOD=4.5, R2 =39.0%). According to Duncan's multiple range test, eight BC4F4 NILs had significantly higher 100 grain weight compared to recurrent parent, MR219 (P<0.05). Grain weight of the eight NILs was increased by 4.8 to 7.5% over MR219, with an average of 6.3% (P< 0.05). According to the rice genome automated annotation database, there are 50 predicted genes and transposons in the 248 kb target region (RM19266.1 - RM7399) with 19 being known functional annotations. In silico gene expression analysis showed that a total of 13 genes and transposons showed significant up-regulation (more than 2-fold change) in grain/seed or endosperm related experiments. Putative candidate genes underlying qGW-6 were gene encoding ATOZI1, acyl-CoA-binding protein, superoxide dismutase, high-affinity nickel-transport family protein and chaperone protein dnaJ. Background marker analysis using 96 SSR markers revealed a new grain weight QTL (qGW-1) contributed by O. rufipogon on chromosome 1. Analysis of grain weight using 13 SSR markers for 28 BC4F2 individuals (LOD =3.1, R2 = 39.3%) and six SSR markers for 99 BC4F3 individuals (LOD=14.7, R2 = 49.5%) had mapped the qGW-1 between RM428 and RM294 which corresponded to the size of 7.5 Mb. This new QTL region of qGW-1 was narrowed down to 4.8 Mb between RM3604 and RM572 using an additional 19 polymorphic SSR markers with LOD= 3.2 (R2 = 32.3%) using SMR,Certification of Master's/Doctoral Thesis" is not available
Pages:	88
Call Number:	SB191.R53N478
Publisher:	UKM, Bangi
Appears in Collections:	Faculty of Science and Technology / Fakulti Sains dan Teknologi

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