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

O'Rourke JA, Fu F, Bucciarelli B, Yang SS, Samac DA, Lamb JF, Monteros MJ, Graham MA, Gronwald JW, Krom N, Li J, Dai X, Zhao PX, Vance CP - BMC Genomics (2015)

Bottom Line: Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56.Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified.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.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA. Jamie.ORourke@ars.usda.gov.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

Phenotypes of Medicago sativa ssp. falcata and Medicago sativa ssp. sativa. a Recumbent stem architecture and (b) flower raceme of Medicago sativa ssp. falcata (F56). c Upright stem architecture and (d) flower raceme of Medicago sativa ssp. sativa (B47)
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Fig1: Phenotypes of Medicago sativa ssp. falcata and Medicago sativa ssp. sativa. a Recumbent stem architecture and (b) flower raceme of Medicago sativa ssp. falcata (F56). c Upright stem architecture and (d) flower raceme of Medicago sativa ssp. sativa (B47)

Mentions: Most modern alfalfa cultivars grown in the U.S. are a result of introgression of Medicago sativa ssp. falcata and M. sativa ssp. sativa. The two subspecies readily hybridize although they have distinct phenotypes and geographic origins [5]. M. sativa ssp. falcata originated in central Asia and is characterized by orange-yellow flowers (Fig. 1a and b), straight to sickle-shaped seedpods, broad crowns, creeping-root habit, and extreme winter hardiness. Both diploid and autotetraploid accessions occur naturally. M. sativa ssp. sativa is an autotetraploid that originated in the Near East, with Iran as the geographic center of origin. M. sativa ssp. sativa has violet or lavender colored flowers (Fig. 1c and d), coiled seed pods, and is adapted to temperate regions. Both subspecies suffer from severe inbreeding depression when self-pollinated and are therefore bred as cross-pollinated synthetic cultivars. For this study, clones of one individual from each subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56), were selected for analysis. These lines exhibited superior performance when used as female parents in experiments to evaluate M. sativa ssp. falcata x M. sativa ssp. sativa semi-hybrids for enhancing forage yield (Lamb, unpublished).Fig. 1


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

O'Rourke JA, Fu F, Bucciarelli B, Yang SS, Samac DA, Lamb JF, Monteros MJ, Graham MA, Gronwald JW, Krom N, Li J, Dai X, Zhao PX, Vance CP - BMC Genomics (2015)

Phenotypes of Medicago sativa ssp. falcata and Medicago sativa ssp. sativa. a Recumbent stem architecture and (b) flower raceme of Medicago sativa ssp. falcata (F56). c Upright stem architecture and (d) flower raceme of Medicago sativa ssp. sativa (B47)
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4492073&req=5

Fig1: Phenotypes of Medicago sativa ssp. falcata and Medicago sativa ssp. sativa. a Recumbent stem architecture and (b) flower raceme of Medicago sativa ssp. falcata (F56). c Upright stem architecture and (d) flower raceme of Medicago sativa ssp. sativa (B47)
Mentions: Most modern alfalfa cultivars grown in the U.S. are a result of introgression of Medicago sativa ssp. falcata and M. sativa ssp. sativa. The two subspecies readily hybridize although they have distinct phenotypes and geographic origins [5]. M. sativa ssp. falcata originated in central Asia and is characterized by orange-yellow flowers (Fig. 1a and b), straight to sickle-shaped seedpods, broad crowns, creeping-root habit, and extreme winter hardiness. Both diploid and autotetraploid accessions occur naturally. M. sativa ssp. sativa is an autotetraploid that originated in the Near East, with Iran as the geographic center of origin. M. sativa ssp. sativa has violet or lavender colored flowers (Fig. 1c and d), coiled seed pods, and is adapted to temperate regions. Both subspecies suffer from severe inbreeding depression when self-pollinated and are therefore bred as cross-pollinated synthetic cultivars. For this study, clones of one individual from each subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56), were selected for analysis. These lines exhibited superior performance when used as female parents in experiments to evaluate M. sativa ssp. falcata x M. sativa ssp. sativa semi-hybrids for enhancing forage yield (Lamb, unpublished).Fig. 1

Bottom Line: Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56.Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified.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.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA. Jamie.ORourke@ars.usda.gov.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus