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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

Structure of the red clover genome and synteny with the M. truncatula genome.(a) Lines connect duplicated genes between different chromosomes, and (b) concentric histograms of the density of genes (grey) and repetitive elements Copia (purple), Gypsy (orange) and total DNA transposons (hAT in red, TcMar in green, and MULE in blue) in sliding windows of 1 Mb at 100 Kb intervals, only values in the top quartile are coloured.
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f1: Structure of the red clover genome and synteny with the M. truncatula genome.(a) Lines connect duplicated genes between different chromosomes, and (b) concentric histograms of the density of genes (grey) and repetitive elements Copia (purple), Gypsy (orange) and total DNA transposons (hAT in red, TcMar in green, and MULE in blue) in sliding windows of 1 Mb at 100 Kb intervals, only values in the top quartile are coloured.

Mentions: We annotated 40,868 genes and 42,223 transcripts. Fig. 1 illustrates the spatial density of the 22,042 genes in the chromosomes (see Supplementary Fig. 5 for the individual chromosomes). A homologous protein in the UniprotKB database was found for 39,516 transcripts (93.6%), and 1,580 of the remaining transcripts (3.7%) had a novel ORF. A total of 31,576 transcripts (74.8%) was annotated with at least one GO term (Supplementary Table 3). The number of genes in red clover is lower than in M. truncatula (50,894) and soybean (56,044), but higher than in common bean (27,197). Red clover and M. truncatula have similar gene density, around 1.3 genes per 10 Kb (40,868 genes in 309 Mb and 50,894 genes in 389 Mb, respectively). However, the genes are not equally distributed in the genome. The mean value of the gene density in 10 Kb windows is similar in red clover, common bean and soybean (approximately 0.75 ± 0.96 genes per 10Kb), but lower than in M. truncatula (1.51 ± 1.13 genes per 10 Kb), because the latter has more intervals with many genes as observed in Fig. 1, and Supplementary Fig. 5. The CDS and exon lengths were similar in the four legumes, but the intron lengths were significantly longer in the legumes than in Arabidopsis thaliana (Supplementary Fig. 6).


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)

Structure of the red clover genome and synteny with the M. truncatula genome.(a) Lines connect duplicated genes between different chromosomes, and (b) concentric histograms of the density of genes (grey) and repetitive elements Copia (purple), Gypsy (orange) and total DNA transposons (hAT in red, TcMar in green, and MULE in blue) in sliding windows of 1 Mb at 100 Kb intervals, only values in the top quartile are coloured.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Structure of the red clover genome and synteny with the M. truncatula genome.(a) Lines connect duplicated genes between different chromosomes, and (b) concentric histograms of the density of genes (grey) and repetitive elements Copia (purple), Gypsy (orange) and total DNA transposons (hAT in red, TcMar in green, and MULE in blue) in sliding windows of 1 Mb at 100 Kb intervals, only values in the top quartile are coloured.
Mentions: We annotated 40,868 genes and 42,223 transcripts. Fig. 1 illustrates the spatial density of the 22,042 genes in the chromosomes (see Supplementary Fig. 5 for the individual chromosomes). A homologous protein in the UniprotKB database was found for 39,516 transcripts (93.6%), and 1,580 of the remaining transcripts (3.7%) had a novel ORF. A total of 31,576 transcripts (74.8%) was annotated with at least one GO term (Supplementary Table 3). The number of genes in red clover is lower than in M. truncatula (50,894) and soybean (56,044), but higher than in common bean (27,197). Red clover and M. truncatula have similar gene density, around 1.3 genes per 10 Kb (40,868 genes in 309 Mb and 50,894 genes in 389 Mb, respectively). However, the genes are not equally distributed in the genome. The mean value of the gene density in 10 Kb windows is similar in red clover, common bean and soybean (approximately 0.75 ± 0.96 genes per 10Kb), but lower than in M. truncatula (1.51 ± 1.13 genes per 10 Kb), because the latter has more intervals with many genes as observed in Fig. 1, and Supplementary Fig. 5. The CDS and exon lengths were similar in the four legumes, but the intron lengths were significantly longer in the legumes than in Arabidopsis thaliana (Supplementary Fig. 6).

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