Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis

BMC Genomics

Research Article

Foo Cheung¹  Yuanhong Han²  Maria J Monteros²  Ivone Torres-Jerez³  Michael K Udvardi³  Yun Kang³  Patrick X Zhao³  Christopher D Town⁴ 

[1] Center for Human Immunology, Autoimmunity and Inflammation, National Institute of Health, 9000 Rockville Pike, 20892, Bethesda, MD, USA;The J. Craig Venter Institute, 9704 Medical Center Drive, 20850, Rockville, MD, USA;Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, 73401, Ardmore, OK, USA;Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, 73401, Ardmore, OK, USA;The J. Craig Venter Institute, 9704 Medical Center Drive, 20850, Rockville, MD, USA;

关键词: Single Nucleotide Polymorphism;    Genomic Selection;    High Resolution Melting;    Candidate SNPs;    Single Nucleotide Polymorphism Marker;   

DOI  :  10.1186/1471-2164-12-350

 received in 2011-03-22, accepted in 2011-07-06,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundSingle nucleotide polymorphisms (SNPs) are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analysis (HRM) for high throughput SNP discovery in tetraploid alfalfa (Medicago sativa L.), a species with high economic value but limited genomic resources.ResultsThe alfalfa genotypes selected from M. sativa subsp. sativa var. 'Chilean' and M. sativa subsp. falcata var. 'Wisfal', which differ in water stress sensitivity, were used to prepare cDNA from tissue of clonally-propagated plants grown under either well-watered or water-stressed conditions, and then pooled for 454 sequencing. Based on 125.2 Mb of raw sequence, a total of 54,216 unique sequences were obtained including 24,144 tentative consensus (TCs) sequences and 30,072 singletons, ranging from 100 bp to 6,662 bp in length, with an average length of 541 bp. We identified 40,661 candidate SNPs distributed throughout the genome. A sample of candidate SNPs were evaluated and validated using high resolution melting (HRM) analysis. A total of 3,491 TCs harboring 20,270 candidate SNPs were located on the M. truncatula (MT 3.5.1) chromosomes. Gene Ontology assignments indicate that sequences obtained cover a broad range of GO categories.ConclusionsWe describe an efficient method to identify thousands of SNPs distributed throughout the alfalfa genome covering a broad range of GO categories. Validated SNPs represent valuable molecular marker resources that can be used to enhance marker density in linkage maps, identify potential factors involved in heterosis and genetic variation, and as tools for association mapping and genomic selection in alfalfa.

【 授权许可】

Unknown   
© Han et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.