Comparative Analyses between Functional Markers Concerning Yield-related Traits of Rapeseed and Sequences of Rice Genome Database

Brassica napus L. is an important oilseed and fodder crop grown throughout the world. Its yield is the important goal in B. napus breeding programs. In this study, comparative analyses were carried out between rapeseed and rice based on the functional markers linked to QTLs of important yield-related traits in rapeseed. The results showed that the level of rapeseed and rice on the sequence homology was extensive and some QTLs controlling the similar traits were found in the region of the homologous genes in rice and rapeseed, simultaneously. This study will be helpful to clone QTL in rapeseed using the information of rice.


INTRODUCTION
Comparative genomics is the study of the relationship of genome structure and function across different biological species or strains using kinds of classification methods and alignment techniques.Sequence alignment is one of the main techniques, which is widely used for researches on bioinformatics, such as database searching, evolutionary and development analysis and protein homology modeling.In higher plants, functional genes among different plants are highly conserved and genes controlling important traits may be located in the same or similar position and be linked with the same molecular markers.The sequence information and genomic resources of the extensively studied model organisms could be used for marker development, map-based gene cloning and candidate gene identification in other plants.Relying on synteny between radish and Arabidopsis, a single radish nuclear gene, Rfo, was cloned by a map-based cloning approach (Brown et al., 2003).In rapeseed (Brassica napus L.), the fine mapping of the blackleg R gene was also based on the conserved regions between Arabidopsis and rapeseed (Mayerhofer et al., 2005).Recently, Qin et al. (2011) saturated the powdery mildew resistance gene, Pm6, in wheat using the collinearity-based markers by extensively exploiting the genomic resources of rice, Brachypodium distachyon and the comprehensive Triticeae ESTs (Expressed Sequence Tags).
B. napus L. is an important oilseed and fodder crop grown throughout the world.Recently, attention has been given to its potential as a renewable resource for biofuel production.Yield is the important goal in B. napus breeding programs and it is difficult to accurately evaluate and select this trait in conventional breeding programs due to yield complexities arising from both the number of segregating loci of all the traits involved and the influence of genotype×environment interactions.Recent advances in marker technologies have made it possible to discover the Quantitative Trait Loci (QTLs) for the traits and detect the molecular markers linked to them, which will advance selection by marker-assisted methods and facilitate the development of high-yield cultivars (Koebner et al., 2001).
In a previous publication, we developed 177 functional markers corresponding to 111 differentially expressed genes in hybrid of B. napus in an F 2 population resulting from crossing "SI-1300 × Eagle" (Li et al., 2006).Furthermore, QTLs were detected for 12 yield-related traits based on the genetic map containing 177 functional markers.And, 45 functional markers involved in 39 Expressed Sequence Tags (ESTs) were found to be linked with the QTLs of 12 traits (Li et al., 2007).In this study, comparative analyses were carried out between rapeseed and rice based on the functional markers linked to QTLs of important yield-related traits in rapeseed in order to investigate the commonality between different crops on genes controlling the same traits.This study will lay a foundation for cloning the genes of rapeseed using rice genome resources.

MATERIALS AND METHODS
Functional markers linked to QTLs of agronomic traits in rapeseed: In total, 45 functional markers involved in 39 different ESTs or genes were found to be linked with the QTLs of agronomic traits (Table 1).

Databases used for comparative analyses: NCBI (National
Center Biotechnology Information, http:∥www.ncbi.nlm.nih.gov) and Gramene (http://www.gramene.org/).Software: Sequence alignment was done by BLASTx in NCBI.The threshold value was set to E≤10 -10 .The physical positions of the corresponding ricegenes were determined in silicon using the software provided by Gramene and the QTLs of related traits in rice were found in Gramene QTL Database.

RESULTS
The homologous sequences in rice: These 39 different ESTs or genes linked with the QTLs of agronomic traits in rapeseed were applied to search homogous sequences in rice by BLASTx in NCBI.As shown in Table 2, the majority of the sequences in rapeseed found homologous sequences in rice except two genes (AF229401 and CD820841), indicating that the level of rapeseed and rice on the sequence homology is extensive.
The physical positions of the rice homologous sequences: It was showed from Table 3 that the physical positions of the corresponding rice genes determined in silicon using the software provided by Gramene.These rice genes dispread in all of 12 chromosomes.Chromosome 1, 4, 7 and 8 had the most corresponding rice genes while Chromosome 6 had the least ones.
The QTLs for yield related traits around the homologous genes in rice: The QTLs for yield and related traits were searched in the region where the corresponding rice genes existed in rice genome according to the information provided by the Gramene (Table 4).In the region of homologue rice genes, the QTLs controlling the yield and related traits were found for rice.The similar QTLs controlling the similar traits were searched in the region of corresponding genes between rice and rapeseed.For example, RPSaA, encoding a 40S ribosomal protein SA, was found in the region of yield QTL in both rice and rapeseed.RabGAP, RabGAP/TBC domain-containing protein, was found in the region of 1000-seed weight in both rice and rapeseed.VHSD, related to the QTL for YP, PH, FB, SMI and SP in rapeseed.In rice, the homologous gene of VHSD was found also in the region of QTLs for YP, PNN, PH, SBN and SN.These results showed that some QTLs controlling the similar traits were found in the region of the homologous genes in rice and rapeseed and some have pleiotropy effects.

CONCLUSION
Rice is a model plant of monocotyledon.And, studies on agronomic traits in rice are carried out in full swing.A large number of information resources in rice are available.In this research, comparative analyses between rapeseed and rice were carried out based on the functional markers linked to QTLs of important yield-related traits in rapeseed.The results showed that the level of rapeseed and rice on the sequence homology is extensive and some QTLs controlling the similar traits were found in the region of the homologous genes in rice and rapeseed.This study will be helpful for us to understand the genome structure and evolution and clone QTL in rapeseed using the information of rice.

Table 1 :
Functional markers involved in QTLs for agronomic traits in rapeseed a: PH: Plant height; HPB: Height of primary effective branch; LMI: Length of main inflorescence; ELMI: Effective length of main inflorescence; SMI: Number of siliques per plant; SDMI: Siliques density on main inflorescence; FB: Number of first branches; SFB: Number of siliques on main first branche; SS: Number of seeds per silique; SW: 1000-seed weight; SP: Number of siliques per plant; YP: Yield per plant

Table 2 :
The homologous sequences in rice compared to the ones located in the QTLs regions of rapeseed