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United States Department of Agriculture

Agricultural Research Service

Research Project: Sunflower Genetic Improvement with Genes from Wild Crop Relatives and Domesticated Sunflower

Location: Sunflower Research

Title: A high-density SNP map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12

Authors
item Talukder, Zahirul -
item Gong, Li -
item Hulke, Brent
item Pegadaraju, Venkatramana -
item Song, Qijian
item Schultz, Quentin -
item Qi, Lili

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 6, 2014
Publication Date: July 11, 2014
Citation: Talukder, Z., Gong, L., Hulke, B.S., Pegadaraju, V., Song, Q., Schultz, Q., Qi, L. 2014. A high-density SNP map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12. PLoS One. 9(7): e98628. Available http://dx.plos.org/10.1371/journal.pone.0098628.

Interpretive Summary: Cultivated sunflower is a diploid species with a large genome size of ~3.5 Gb. Molecular markers and high density genetic linkage maps are important tools for understanding genome organization, and can facilitate comparative genomics, marker-assisted selection breeding, and isolation of genes by map-based cloning. Single nucleotide polymorphisms (SNP) are the most common type of genetic variation. Through advances in sequencing technologies and high-throughput genotyping facilities, SNP markers have gained much interest in the scientific and breeding community because of their efficiency, repeatability, and low cost. Here we reported to construct a high-resolution genetic map of sunflower by integrating SNP data from three F2 mapping populations (HA 89/ RHA 464, B-line/ RHA 464, and CR 29/ RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers and 118 publicly available simple sequence repeat (SSR) markers distributed in 17 chromosomes of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity with individual maps across the genome. Three individual and consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.

Technical Abstract: A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/ RHA 464, B-line/ RHA 464, and CR 29/ RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity with individual maps with an average Spearman's rank correlation coefficient value of 0.972 across the genome. The order of the SSR markers was also in agreement with the order of the individual maps and with previously published sunflower maps. Three individual and consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.

Last Modified: 10/30/2014
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