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

Jose J De Vega ,Dave Kudrna,Rod A Wing,Åshild Ergon,Michael T Abberton,Steven Yates,Leif Skøt,Chunting Lang,Stephan Rössner,Martin Swain,Sarah Ayling,Iain S Donnison,Giles Oldroyd ,René Geurts ,Klaus Mayer ,Odd-Arne Rognli ,W Powell ,Matthew J Hegarty ,José Luis Goicoechea ,Cerys Jones ,Mario Cáccamo ,K Judith Webb

doi:10.1038/srep17394

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.

Highlights

Red clover is one of the most important forage legume crops in temperate agriculture, and a key component of sustainable intensification of livestock farming systems
The anchoring of a significant number of scaffolds, that contained at least half of the genes, allowed the spatial comparison of features between M. truncatula and red clover
We estimated that the divergence of red clover and M. truncatula is comparable to the divergence of common bean and soybean

Summary

Introduction

Red clover is one of the most important forage legume crops in temperate agriculture, and a key component of sustainable intensification of livestock farming systems. We report a chromosome-scale reference draft genome for a red clover genotype of the variety Milvus (Milvus B) by integration of Whole Genome Sequencing (WGS) of short-length reads, Sanger-based bacterial artificial chromosome (BAC) end sequences, a physical and two genetic maps. This assembly is the first within the major Trifolium genus, one of the largest in the Fabaceae family with 255 species[16]. After the model species M. truncatula, it is the second genome assembly of a forage legume at pseudo-molecule level This will provide a great platform for advances in genomics studies of traits of biological and agronomic importance in forage crops

Methods

Results

Conclusion