Investigadores responsables: Federico Iñiguez Luy y Maria Laura Federico, UBP CGNA-INIA Carillanca.

Duración: 3 años.

Fuente de financiamiento: Conicyt

 

PROPOSAL ABSTRACT:
The advent of next generation sequencing (NGS) technologies has facilitated the access to genomic sequence information due to their fast, systematic and cost-effective way of operation. However, a limiting step at applying these technologies resides in the specific enrichment of genomic DNA. Recently, a microarray-based genomic selection (MGS) method, also known as sequence capture, has addressed this limitation allowing for the isolation of user-defined genomic sequences in one simple step. This innovative technology has already revolutionized the field of human genetics and will soon impact other disciplines including plant genetics and breeding.

Targeted enrichment of specific genomic regions allows for large-scale resequencing and characterization of natural genetic variation in species with large and complex genomes, a characteristic shared by most important crops. The assessment of this genetic variation among individuals or cultivars can result in the identification of polymorphisms leading to the development of molecular markers. The main goal of this proposal is to combine Roche NimbleGen sequence capture microarray technologies with NGS to discover single nucleotide polymorphisms (SNPs) in specific captured areas of the rapeseed canola (Brassica napus L.) genome associated to traits of agronomical and nutritional importance, with an emphasis on oil quality and content.
These traits are particularly relevant for Chile where an increasing demand for vegetable oil driven primarily by the aquaculture industry cannot solely be met by increasing the cultivated area of rapeseed canola.

We plan to design 385K custom Roche NimbleGen arrays containing target sequences of interest (previously identified in quantitative trait loci ?QTL- studies) and sequence capture 6 winter (2 CGNA advanced breeding lines, Tapidor, Ningyou7, Express and V8) and 4 spring (DH12075, PSA12, YN-429 and Rainbow) rapeseed cultivars. Sequence data obtained from these 10 genotypes will be analyzed to identify sequence variation and to discover SNPs. These SNPs will be characterized and mapped to an existing linkage map and a newly developed recombinant inbred line (RIL) population. The SNP markers will also be used to screen a diverse B. napus germplasm collection in order to discover SNP-phenotype associations.

The generation of molecular tools for Brassica crops has been mainly conducted by the private sector hindering its availability for the entire Brassica research community. In addition, these tools have targeted specific genotypes or lines that may not be representative of the entire core Brassica germplasm. Such impairment calls for the generation of molecular tools that will be pertinent to the needs of rapeseed canola in Chile. In this context, our project proposes to target B. napus genomic regions previously associated to QTL explaining seed oil quality and content, seedling vigor, and black leg resistance, obtain cultivar-specific sequence information, assess sequence variation, discover single nucleotide polymorphisms (SNPs) and establish haplotype maps. This will contribute to further dissect the genetic nature and possible molecular functions of candidate genes located in these target genomic regions. In addition, it offers the opportunity to readily apply these SNP markers in our rapeseed canola breeding program and to help developing a high-throughput SNP genotyping platform for the species.

The proposed project reinforces the international research collaborations between Chile and Canada being conceived as a joint effort between INIA-CGNA, Dr. Andrew Sharpe from the National Research Council of Canada Plant Biotechnology Institute (NRC-PBI) and Dr. Isobel Parkin from the Agriculture and Agri-Food Canada Saskatoon Research Centre (AAFC-SRC). Our collaboration contemplates not only the exchange of scientific information and genomic resources but also the training of young Chilean scientists working in the area of plant genomics and bioinformatics.

 

GOALS

GENERAL GOAL:
To discover single nucleotide polymorphisms (SNPs) in targeted genomic regions underlying traits of agronomical and nutritional importance in Brassica napus L.

 

SPECIFIC GOALS:
1-To design 385K NimbleGen arrays containing target sequences of interest and sequence capture 10 genotypes.
2-To analyze the sequencing data and identify sequence variation among studied genotypes to discover SNPs.
3-To validate the discovered SNPs in two segregating populations.

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