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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

Expression of transcripts conferring flower color in Medicago sativa ssp. sativa (B47) and Medicago sativa ssp. falcata (F56). Expression patterns comparing B47 and F56 are presented as heat map blocks. a Anthocyanin biosynthesis. Early in the pathway, transcripts are up-regulated 2-fold in B47 compared to F56 (blue blocks). This results in increased delphinidin, the anthocyanin that confers blue coloration to flowers. b Carotenoid biosynthesis. Transcripts involved in the conversions of trans-lycopene to δ-carotene and β-cryptoxinthin to zeantin, are up regulated 17- and 6-fold, respectively, in F56 (yellow blocks). The increased carotene synthesis is responsible for the orange and yellow flower color, characteristic of F56
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Fig4: Expression of transcripts conferring flower color in Medicago sativa ssp. sativa (B47) and Medicago sativa ssp. falcata (F56). Expression patterns comparing B47 and F56 are presented as heat map blocks. a Anthocyanin biosynthesis. Early in the pathway, transcripts are up-regulated 2-fold in B47 compared to F56 (blue blocks). This results in increased delphinidin, the anthocyanin that confers blue coloration to flowers. b Carotenoid biosynthesis. Transcripts involved in the conversions of trans-lycopene to δ-carotene and β-cryptoxinthin to zeantin, are up regulated 17- and 6-fold, respectively, in F56 (yellow blocks). The increased carotene synthesis is responsible for the orange and yellow flower color, characteristic of F56

Mentions: One of the most notable differences between M. sativa ssp. sativa and M. sativa ssp. falcata is flower color. M. sativa ssp. sativa has violet to lavender-colored flowers while M. sativa ssp. falcata has orange to yellow-colored flowers (Fig. 1). Alfalfa cultivars with mixtures of M. sativa ssp. sativa and M. sativa ssp. falcata express a range of flower colors including purple, yellow, cream, white and variegated (ranging from very dark blue to a green or yellow green). Anthocyanins are the primary pigments contributing to violet and blue flowers while orange and yellow flowers are a result of increased carotenoid synthesis. The biochemical pathways of both anthocyanin and carotenoid biosynthesis are well characterized [52–55] but the expression profiles of these sequences in alfalfa have not been previously investigated. Using the MSGI 1.2 assembly and RNA-seq profiles, we examined the expression patterns of transcripts involved in the biosynthesis of floral pigments in both subspecies. In floral tissues of M. sativa ssp. sativa (B47) the transcript encoding a flavone 3-dioxygenase converting dihydrotricetin to dihydromyricetin (contig_11784) was up-regulated two-fold compared to the floral tissues of F56 (Fig. 4a). Dihydromyricetin is a precursor to delphinidin, the anthocyanin responsible for blue/purple coloration. Conversely, in F56 the transcript for lycopene ε-cyclase, which converts trans-lycopene to δ-carotene and the transcript for ß-cryptoxanthin 3′-hydroxylase, which converts ß-cryptoxanthin to zeaxanthin (both imparting orange or yellow coloration to floral tissues) were 17- and 6-fold higher relative to B47 (Fig. 4b). The data from this study indicate both anthocyanin and carotenoid pathways are expressed in the floral tissues of both subspecies, suggesting that it is the relative expression of these genes and/or enzyme activities that are responsible for the flower colors exhibited by B47 and F56. These results lend genetic support to extend the earlier biochemical work that found evidence for activity of both pathways in yellow and purple flowers of diploid alfalfa [56]. That analysis found that yellow flower color in M. sativa ssp. falcata was largely due to carontenoid xanthophyll esters and that the quercetin pigments from the anthocyanin synthesis pathway had minor phenotypic effects. In contrast, purple alfalfa flowers contained a mixture of three anthocyanins (delphinidin, petunidin, and malvidin) and color variation was due to background effects of the xanthophyll pigments and their interactions with anthoxanthin pigments, rather than differences in the anthocyanin content [56].Fig. 4


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)

Expression of transcripts conferring flower color in Medicago sativa ssp. sativa (B47) and Medicago sativa ssp. falcata (F56). Expression patterns comparing B47 and F56 are presented as heat map blocks. a Anthocyanin biosynthesis. Early in the pathway, transcripts are up-regulated 2-fold in B47 compared to F56 (blue blocks). This results in increased delphinidin, the anthocyanin that confers blue coloration to flowers. b Carotenoid biosynthesis. Transcripts involved in the conversions of trans-lycopene to δ-carotene and β-cryptoxinthin to zeantin, are up regulated 17- and 6-fold, respectively, in F56 (yellow blocks). The increased carotene synthesis is responsible for the orange and yellow flower color, characteristic of F56
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Expression of transcripts conferring flower color in Medicago sativa ssp. sativa (B47) and Medicago sativa ssp. falcata (F56). Expression patterns comparing B47 and F56 are presented as heat map blocks. a Anthocyanin biosynthesis. Early in the pathway, transcripts are up-regulated 2-fold in B47 compared to F56 (blue blocks). This results in increased delphinidin, the anthocyanin that confers blue coloration to flowers. b Carotenoid biosynthesis. Transcripts involved in the conversions of trans-lycopene to δ-carotene and β-cryptoxinthin to zeantin, are up regulated 17- and 6-fold, respectively, in F56 (yellow blocks). The increased carotene synthesis is responsible for the orange and yellow flower color, characteristic of F56
Mentions: One of the most notable differences between M. sativa ssp. sativa and M. sativa ssp. falcata is flower color. M. sativa ssp. sativa has violet to lavender-colored flowers while M. sativa ssp. falcata has orange to yellow-colored flowers (Fig. 1). Alfalfa cultivars with mixtures of M. sativa ssp. sativa and M. sativa ssp. falcata express a range of flower colors including purple, yellow, cream, white and variegated (ranging from very dark blue to a green or yellow green). Anthocyanins are the primary pigments contributing to violet and blue flowers while orange and yellow flowers are a result of increased carotenoid synthesis. The biochemical pathways of both anthocyanin and carotenoid biosynthesis are well characterized [52–55] but the expression profiles of these sequences in alfalfa have not been previously investigated. Using the MSGI 1.2 assembly and RNA-seq profiles, we examined the expression patterns of transcripts involved in the biosynthesis of floral pigments in both subspecies. In floral tissues of M. sativa ssp. sativa (B47) the transcript encoding a flavone 3-dioxygenase converting dihydrotricetin to dihydromyricetin (contig_11784) was up-regulated two-fold compared to the floral tissues of F56 (Fig. 4a). Dihydromyricetin is a precursor to delphinidin, the anthocyanin responsible for blue/purple coloration. Conversely, in F56 the transcript for lycopene ε-cyclase, which converts trans-lycopene to δ-carotene and the transcript for ß-cryptoxanthin 3′-hydroxylase, which converts ß-cryptoxanthin to zeaxanthin (both imparting orange or yellow coloration to floral tissues) were 17- and 6-fold higher relative to B47 (Fig. 4b). The data from this study indicate both anthocyanin and carotenoid pathways are expressed in the floral tissues of both subspecies, suggesting that it is the relative expression of these genes and/or enzyme activities that are responsible for the flower colors exhibited by B47 and F56. These results lend genetic support to extend the earlier biochemical work that found evidence for activity of both pathways in yellow and purple flowers of diploid alfalfa [56]. That analysis found that yellow flower color in M. sativa ssp. falcata was largely due to carontenoid xanthophyll esters and that the quercetin pigments from the anthocyanin synthesis pathway had minor phenotypic effects. In contrast, purple alfalfa flowers contained a mixture of three anthocyanins (delphinidin, petunidin, and malvidin) and color variation was due to background effects of the xanthophyll pigments and their interactions with anthoxanthin pigments, rather than differences in the anthocyanin content [56].Fig. 4

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