The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies

BMC Genomics

Carroll P. Vance²  Patrick X. Zhao⁴  Xinbin Dai⁴  Jun Li⁴  Nick Krom⁴  John W. Gronwald²  Michelle A. Graham³  Maria J. Monteros⁴  JoAnn F. S. Lamb²  Deborah A. Samac²  S. Sam Yang¹  Bruna Bucciarelli²  Fengli Fu⁵  Jamie A. O’Rourke³ 

[1] Present Address: Monsanto Company, Molecular Breeding Technology, Chesterfield 63167, MO, USA;USDA-ARS-Plant Science Research Unit, St. Paul 55108, MN, USA;USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames 50011, IA, USA;Samuel Roberts Noble Foundation, Ardmore 73401, OK, USA;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108, MN, USA

关键词: Nodule-specific cysteine-rich peptide;    Cysteine cluster protein;    Gene expression atlas;    RNA-seq;    Illumina;    Medicago sativa;   

Others  :  1219160
DOI  :  10.1186/s12864-015-1718-7

 received in 2015-03-05, accepted in 2015-06-24,  发布年份 2015

【 摘 要 】

Background

Alfalfa (Medicago sativa L.) is the primary forage legume crop species in the United States and plays essential economic and ecological roles in agricultural systems across the country. Modern alfalfa is the result of hybridization between tetraploid M. sativa ssp. sativa and M. sativa ssp. falcata. Due to its large and complex genome, there are few genomic resources available for alfalfa improvement.

Results

A de novo transcriptome assembly from two alfalfa subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56) was developed using Illumina RNA-seq technology. Transcripts from roots, nitrogen-fixing root nodules, leaves, flowers, elongating stem internodes, and post-elongation stem internodes were assembled into the Medicago sativa Gene Index 1.2 (MSGI 1.2) representing 112,626 unique transcript sequences. Nodule-specific and transcripts involved in cell wall biosynthesis were identified. Statistical analyses identified 20,447 transcripts differentially expressed between the two subspecies. Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56. Comparing transcript abundance in floral tissues of B47 and F56 identified expression differences in sequences involved in anthocyanin and carotenoid synthesis, which determine flower pigmentation. Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified.

Conclusions

The Medicago sativa Gene Index 1.2 increases the expressed sequence data available for alfalfa by ninefold and can be expanded as additional experiments are performed. The MSGI 1.2 transcriptome sequences, annotations, expression profiles, and SNPs were assembled into the Alfalfa Gene Index and Expression Database (AGED) at http://plantgrn.noble.org/AGED/, a publicly available genomic resource for alfalfa improvement and legume research.

【 授权许可】

   
2015 O’Rourke et al.

【 图 表 】

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