Title: “ Subterranean Clover (Trifolium subterraneum L.) Genomic Resources: Building a Comprehensive Platform For Molecular Breeding”




Dr Parwinder Kaur



Research Scientist
Plant Molecular Genetics & Genomics
The University of Western Australia


Subterranean clover (Trifolium subterraneum L.) is the key forage pasture legume species in Australia and is also an ideal reference species for comparative mapping within the Leguminosae. It is a diploid (2n =16), predominantly inbreeding annual species that can be readily hybridised. It also has a wide range of diversity for both qualitative and quantitative agronomic and morphological characters. A draft genome sequence of size ~480-Mb has been described for subterranean clover (based on cv. Daliak). This represents 86% of the estimated 556.6 Mb subterranean clover genome. We used an Illumina next-generation sequencing platform to generate 277.1 Gb (HiSeq) + 23.6 Gb (MiSeq) of genome sequence, which along with sequences derived from a Roche 454 machine (2.72 Gb) enabled us to assemble a total of 7,788 scaffolds (N50 size of 0.332 Mb; the largest scaffold was 4.7 million base pairs). We further evaluated using genome mapping on nanochannel arrays and generation of a transcriptome atlas across tissues to advance the assembly and gene annotation. Using a BioNano-based assembly spanning 512 Mb (93% genome coverage), we validated the draft assembly, anchored unplaced contigs and resolved misassemblies. The advanced assembly was annotated using transcriptome atlas data to contain 31,272 protein-coding genes capturing >96% of the gene content. Functional characterisation and GO enrichment confirmed gene expression for response to water deprivation, flavonoid biosynthesis, and embryo development ending in seed dormancy, reflecting adaptation to the harsh Mediterranean environment. Comparative analyses across Papilionoideae identified 24,893 Trifolium-specific and 6,325 subterranean-clover-specific genes that could be mined further for traits such as geocarpy and grazing tolerance. Eight key traits, including persistence, improved livestock health by isoflavonoid production in addition to important agro-morphological traits, were fine-mapped on the high density SNP linkage map anchored to the assembly. This new genomic information is crucial to identify loci governing traits allowing marker-assisted breeding, comparative mapping and identification of tissue-specific gene promoters for biotechnological improvement of forage legumes. 

Qualification: PhD (Molecular Biology and Plant Pathology, The University of Western Australia (UWA) 2011

Current institution: Research Scientist | Plant Molecular Genetics & Genomics, Centre for Legumes in Mediterranean Agriculture at The University of Western Australia (since 2011) Previous positions: PhD student - The University of Western Australia (2007 - 2011), Senior Research Fellow at Dept. of Entomology, Punjab Agricultural University, Punjab, India (2006; June - December), MSC student - Punjab Agricultural University, Punjab, India (2004 – 2006)

: Expertise in Plant Biology, Plant Biotechnology, Molecular Biology, Transcriptomics, Proteomics, Genomics, Next Generation Sequencing, Bioinformatics and Computational Biology, Plant Genetics, Legumes, Plant Physiology, Plant Breeding, Biotechnology, Molecular Plant Breeding, Disease Resistance, Crop Improvement, Pathogens, Plant Phenotyping, Rumen, Forage, Biotic/Abiotic Stress, Transgenics, CRISPR and HiC 3D genomics. Parwinder Kaur is working as a Research Scientist with a focus on the Plant Molecular Genetics & Genomics at the Centre for Plant Genetics and Breeding (PGB) in UWA. Dr Kaur has been involved in the Sub-clover genomics project since 2011, received the Science and Innovation Award for young people in Agriculture, Fisheries and Forestry in 2013 and produced the world first genome scaffold for subterranean clover using the de-novo sequencing pipelines anchored to a high resolution genetic map and BioNano optical maps for trait mapping. She has been working with a team of researchers across various disciplines to develop methodologies to enable breeders to identify environmentally friendly pasture legume to tackle future challenges for Australian livestock industries.

Awards & Scholarships

2016: The AW Howard Memorial Trust Inc. Grant-in-Aid
2014: Australian Academy of Science Award for Japan bilateral exchange program
2013: Science and Innovation Award for young people in Agriculture, Fisheries and Forestry
2012: UWA Travel Award (STG)
2012: The AW Howard Memorial Trust Inc. Travel award
2012: CLIMA Major theme top-up funding & travel award.
2009: Scientific Endeavour Award (APPS Plant Health and Protection Research Symposium)
2009: Mike Carroll Travelling Fellowship (Institute of Agriculture, UWA)
2008: UWA Grant for Research Student Training (GRST)
2008: Convocation Postgraduate Research Travel Award (UWA)
2007-2010: International Postgraduate Research Scholarship (IPRS) for PhD at UWA
2004-2006: Novartis Crop Protection Fellowship in MSc. (Entomology)
2004-2005: Punjab Agricultural University Merit Scholarship holder in MSc. (Entomology)
2003-2004: Dr. H. S. Pruthi Memorial Scholarship