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Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement.

De Vega JJ, Ayling S, Hegarty M, Kudrna D, Goicoechea JL, Ergon Å, Rognli OA, Jones C, Swain M, Geurts R, Lang C, Mayer KF, Rössner S, Yates S, Webb KJ, Donnison IS, Oldroyd GE, Wing RA, Caccamo M, Powell W, Abberton MT, Skøt L - Sci Rep (2015)

Bottom Line: Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems.Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition.Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.

View Article: PubMed Central - PubMed

Affiliation: The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.

ABSTRACT
Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.

No MeSH data available.


Related in: MedlinePlus

Divergence of red clover.Timeline in million years ago (MYA) for the divergence of red clover, M. truncatula, L. japonicus, soybean and common bean from each other, and from Arabidopsis thaliana.
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f3: Divergence of red clover.Timeline in million years ago (MYA) for the divergence of red clover, M. truncatula, L. japonicus, soybean and common bean from each other, and from Arabidopsis thaliana.

Mentions: There were 10,449 orthologous groups of genes common to red clover and four other Fabaceae species, and 2,730 groups common to all but L. japonicus (Fig. 2). The number of genes in each cluster was similar among these legumes, but differed from A. thaliana. Only 57 GO term clusters had more than twice the number of genes in red clover than in M. truncatula. This corresponded to 1,253 proteins mostly belonging to regulatory and transport families (Supplementary Fig. 7). We constructed a phylogenic tree on the basis of the alignment of the proteins of 818 single-copy clusters present in the five Fabaceae species and A. thaliana. We estimated that red clover and M. truncatula diverged around 23 million years ago (MYA) (Fig. 3), similar to that observed between common bean and soybean, which diverged ~19.4 MYA5. Furthermore, our analysis showed that the split of the papilionoid clades took place around 50 MYA, consistent with previous results21.


Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement.

De Vega JJ, Ayling S, Hegarty M, Kudrna D, Goicoechea JL, Ergon Å, Rognli OA, Jones C, Swain M, Geurts R, Lang C, Mayer KF, Rössner S, Yates S, Webb KJ, Donnison IS, Oldroyd GE, Wing RA, Caccamo M, Powell W, Abberton MT, Skøt L - Sci Rep (2015)

Divergence of red clover.Timeline in million years ago (MYA) for the divergence of red clover, M. truncatula, L. japonicus, soybean and common bean from each other, and from Arabidopsis thaliana.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4663792&req=5

f3: Divergence of red clover.Timeline in million years ago (MYA) for the divergence of red clover, M. truncatula, L. japonicus, soybean and common bean from each other, and from Arabidopsis thaliana.
Mentions: There were 10,449 orthologous groups of genes common to red clover and four other Fabaceae species, and 2,730 groups common to all but L. japonicus (Fig. 2). The number of genes in each cluster was similar among these legumes, but differed from A. thaliana. Only 57 GO term clusters had more than twice the number of genes in red clover than in M. truncatula. This corresponded to 1,253 proteins mostly belonging to regulatory and transport families (Supplementary Fig. 7). We constructed a phylogenic tree on the basis of the alignment of the proteins of 818 single-copy clusters present in the five Fabaceae species and A. thaliana. We estimated that red clover and M. truncatula diverged around 23 million years ago (MYA) (Fig. 3), similar to that observed between common bean and soybean, which diverged ~19.4 MYA5. Furthermore, our analysis showed that the split of the papilionoid clades took place around 50 MYA, consistent with previous results21.

Bottom Line: Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems.Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition.Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.

View Article: PubMed Central - PubMed

Affiliation: The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.

ABSTRACT
Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.

No MeSH data available.


Related in: MedlinePlus