Mapping in the era of sequencing: high density genotyping and its application for mapping TYLCV resistance in Solanum pimpinellifolium

BMC Genomics

Sjaak van Heusden²  Yuling Bai³  Richard GF Visser²  Arnaud Bovy²  Yury Tikunov²  Richard Finkers²  Myluska Caro¹  Marcela Víquez-Zamora¹ 

[1] Graduate School Experimental Plant Sciences, Wageningen 6708 PB, the Netherlands;Centre for Biosystems Genomics, P.O. Box 98, Wageningen, AB 6700, the Netherlands;Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, Wageningen, AJ 6700, the Netherlands

关键词: Genotype by sequencing (GBS);    Hexose;    Flavonoids;    TYLCV;    In silico;    S. pimpinellifolium;    SNPs;   

Others  :  1122621
DOI  :  10.1186/1471-2164-15-1152

 received in 2014-08-18, accepted in 2014-12-12,  发布年份 2014

【 摘 要 】

Background

A RIL population between Solanum lycopersicum cv. Moneymaker and S. pimpinellifolium G1.1554 was genotyped with a custom made SNP array. Additionally, a subset of the lines was genotyped by sequencing (GBS).

Results

A total of 1974 polymorphic SNPs were selected to develop a linkage map of 715 unique genetic loci. We generated plots for visualizing the recombination patterns of the population relating physical and genetic positions along the genome.

This linkage map was used to identify two QTLs for TYLCV resistance which contained favourable alleles derived from S. pimpinellifolium. Further GBS was used to saturate regions of interest, and the mapping resolution of the two QTLs was improved. The analysis showed highest significance on Chromosome 11 close to the region of 51.3 Mb (qTy-p11) and another on Chromosome 3 near 46.5 Mb (qTy-p3). Furthermore, we explored the population using untargeted metabolic profiling, and the most significant differences between susceptible and resistant plants were mainly associated with sucrose and flavonoid glycosides.

Conclusions

The SNP information obtained from an array allowed a first QTL screening of our RIL population. With additional SNP data of a RILs subset, obtained through GBS, we were able to perform an in silico mapping improvement to further confirm regions associated with our trait of interest. With the combination of different ~ omics platforms we provide valuable insight into the genetics of S. pimpinellifolium-derived TYLCV resistance.

【 授权许可】

   
2014 Víquez-Zamora et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

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