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Researchers Sequence Red Clover Genome, Providing Tool for Improvements

Red clover

NEW YORK (GenomeWeb) – Researchers from the Genome Analysis Center and elsewhere have sequenced the genome of the red clover, a forage legume crop used in sustainable agriculture.

Having the red clover (Trifolium pratense L.) genome in hand, the researchers said, will enable improvements in the crop's persistency, resistance to disease, and tolerance to grazing. As they reported today in Scientific Reports, researchers led by Jose de Vega at TGAC annotated nearly 41,000 genes in the red clover genome and identified gene clusters involved in biochemical pathways that are key for forage quality and livestock nutrition.

"The availability of the genome assembly will pave the way towards genomics­-assisted breeding methods for forage legumes, and provide a platform for deeper understanding of the genetics of forage crop domestication," de Vega said in a statement.

De Vega and his colleagues sequenced the Milvus variety of red clover and, using Platanus, assembled 309 megabase pairs in 39,904 scaffolds. They then integrated their whole-genome sequencing with Sanger-based bacterial artificial chromosomes.

They further annotated 40,868 genes and 42,223 transcripts, and noted that 22,042 genes were anchored onto the seven chromosomes. The number of genes in red clover, the researchers noted, is lower than that in Medicago truncatula and soybean, but higher than that in the common bean.

Nearly 10,450 orthologous groups of genes were common to red clover and four other Fabaceae, or legume, species, the researchers reported. In addition, they noted that 57 GO term clusters — mostly related to regulatory and transport families — had more than twice the number of genes in red clover than in M. truncatula.

De Vega and his colleagues constructed a phylogenic tree based on the alignment of the proteins of 818 single-copy clusters found in five Fabaceae species and Arabidopsis thaliana. This tree indicated that red clover and M. truncatula diverged around 23 million years ago, similar to when the common bean and soybean diverged.

The red clover genome also houses a number of gene clusters, the researchers found.

They reported most of the the enzymes involved in formononetin biosynthesis — isoflavone-synthase (IFS1), 2-hydroxyisoflavanone dehydratase (HIDH), isoflavone-O-methyltransferase (IOMT), and 2, 7, 4'-trihydroxyisoflavanone 4'-O-methyltransferase (HI4OMT) — could be found in clusters.

Formononetins, the researchers noted, have been linked to increased weight gain in lambs that munch on red clover.

All of these, except HIDH, the researchers reported, are distributed in five clusters in the red clover and M. truncatula genomes, and each cluster is dominated by one enzyme.

For instance, five IOMT genes clustered on M. truncatula chromosome 5, while three IOMT genes clustered on red clover scaffold 1068 and two genes on scaffold 29975. In both species, this IOMT cluster included two copies of tRNA pseudouridine synthase.

Similarly, the researchers reported that genes encoding the enzyme polyphenol oxidase appeared in clusters with three to seven members. The researchers uncovered five PPO genes in the red clover genome assembly, and four of these genes are highly similar to one another, but not to those in related species.

This PPO enzyme has been linked to both red clover's ability to transfer omega-3 fatty acids from ruminant feed to milk and have reduced levels of proteolysis during wilting and ensiling, they noted.

"[W]e are using our genomic tools to assist in improving the precision and speed of breeding better red clover varieties," added senior author Leif Skøt from Aberystwyth University in a statement. "This is very timely as the importance of legumes in sustainable agriculture is 'rediscovered.'"