Yield is a complex trait and many genes are involved. Yet, it is emerging that single genes have profound effects in increasing yield (Ashikari et al 2005). Such genes are good targets for functional genomic studies. Molecular mapping studies have shown that wild species can contribute genes for high yield. Many yield enhancing QTLs have been mapped using populations derived from crosses with O. rufipogon. We hypothesized that genes that are indispensable for high yield are likely to be present in all significant yield enhancing QTLs mapped from O. rufipogon. Genes which are common across such QTLs mapped on different chromosomes in different accessions and in independent studies would be high priority candidate genes for functional genomic analysis of yield.

Ten yield enhancing QTLs (9 from Oryza rufipogon and 1from O sativa, Table 1) on chromosomes 2, 3, 8, 9 and 11 reported in 3 studies were analysed (Moncada et al. 2001, Thomson et al. 2003, Marri et al. 2005) .These included both indica and tropical japonica as recipients. Only those yield enhancing QTLs reported using interval mapping were selected. Gene content was noted based on annotated data of homologous regions in Nipponbare using TIGR, Release 4 (http://www.tigr.org/tdb/e2k1/osa1/).The main objective was to gain insight into genes underlying yield- enhancing QTLs by identifying the gene(s) that are common in 10 such QTLs, assuming the genes identified in Nipponbare regions are homologous and colinear to those underlying the yield enhancing QTLs mapped in the two O. rufipogon accessions.

There were 1299 genes or gene families with a total of 6126 genes (including hypothetical and expressed proteins) in 372 BAC/PAC clones in the 10 QTL regions of the pseudomolecules. The interval between flanking markers ranged from 6.2 to 27.3 cM and the number of clones ranged from 17 to 74 per QTL. Details of genes/gene families common to all 10 QTLs and those common to only 9 QTLs are given in Table 2. These can be considered as positional candidate genes determining high yield.

Cytochrome P450 genes underlying the selected regions are high priority genes associated with yield.This is supported by recent report of a rice brassinosteroid deficient mutant osdwarf 4-1 associated with increased biomass and grain yield under dense planting. The affected gene OsDWARF4 encodes a cytochrome P450, CYP90B1 (Sakamoto et al. 2005). Cytochrome P450 has a role in homeostasis of cytokinin in Arabidopsis and increased cytokinin has a role in regulating rice yield (Ashikari et al. 2005). HLH and NAM which have a role in axillary meristem development were present in 9 of the 10 QTLs. Some of the other genes common to 10 yield enhancing QTLs were genes related to seed set and those involved in stress response. Pentatricopeptide repeats are present in promoter region of Rf genes which restore fertility. Yield and adaptability to stress are important correlated traits and QTLs for these are often collocated. Genes involved in signal transduction or response to stress eg Leucine rich repeats, Zinc- finger family and protein kinase domain containing proteins were also present in atleast 9 QTLs. Hypothetical and expressed poteins, the details of which are not known accounted for 40% of the genes, about 6 % of the genes were transposons and about 15% retrotransposons. There were 2 kinds of transposons (Mutator, En/Spm,) and 2 kinds of retrotransposons (Ty1-copia, Ty3-gypsy) along with unclassified ones. The presence of specific kinds of transposons and retrotransposons may have some functional significance.

In addition, there were 18 genes common to atleast 5 yield enhancing QTLs. These were 14-3-3, C2 domain containing protein, NB-ARC domain containing protein, Exo70 exocyst complex subunit protein, hAT family dimerisation domain containing protein, AP2 domain containing protein, DnaJ domain containing protein, family of O-methyltransferase, UDP-glucoronosyl and UDP-glucosyl transferase, EF hand, NAD dependent epimerase/dehydratase, Zinc knuckle, zinc finger, Transposable element protein putative MuDR, putative transposon protein of Pong sub-class and Mariner sub-class, and putative retrotransposon protein of LINE subclass and centromere-specific sub class. Fine mapping of significant QTLs and a combination of loss of function and gain of function genetic approaches would help define functions of the important yield enhancing genes underlying several QTLs in rice.

References

Ashikari M., H. Sakakibara, S. Lin, T. Yamamoto, T. Takashi, A. Nishimura, E. R. Angeles, Q. Qian, H. Kitano and M. Matsuoka, 2005. Cytokinin oxidase regulates rice grain production. Sci. 309: 741-745.

Marri P. R., N. Sarla, V. L. N. Reddy and E. A .Siddiq, 2005. Identification and mapping of yield and related QTLs from an Indian accession of Oryza rufipogon. BMC Genet. 6: 33.

Moncada P., C. P. Martinez, J. Borrero, M. Chatel, H. Gouch Jr., E. Guimaraes, J. Tohme and S. R. McCouch, 2001. Quantitative trait loci for yield and yield components in an Oryza sativa x O. rufipogon BC2F2 population evaluated in an upland environment. Theor. Appl. Genet. 102: 41-52.

Sakamoto T., Y. Morinaka, T. Ohnishi, H. Sunohara, S. Fujioka, M. Ueguchi-Tanaka, M. Mizutani, K. Sakata, S. Takatsuto, S. Yoshida, H. Tanaka, H. Kitano and M. Matsuoka, 2005. Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice. Nature Biotech. 24(1): 105-109.

Thomson M. J., T. H. Tai, A. M. McClung, X-H. Lai, M. E. Hinga, K. B. Lobos, Y. Xu, C. P. Martinez and S. R. McCouch, 2003. Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor. Appl. Genet. 107: 479-493.