Genetics and genomics of key agronomic traits in field pea (Pisum sativum L.)

Submission note: A thesis submitted in total fulfilment of the requirements for the degree of Doctor of Philosophy by published work to the School of Applied Systems Biology, Faculty of Science, Technology and Engineering, La Trobe University, Bundoora.

Thesis with publications.

Field pea (Pisum sativum L.) is a self-pollinating, diploid, cool-season food legume. Crop production is constrained by multiple abiotic (including soil salinity and boron [B] toxicity) and biotic (powdery mildew and bacterial blight infection) stress factors, that cause reduced growth and yield. Development of varieties which are tolerant to these stresses is essential, and application of molecular genetic markers could greatly accelerate this process. Advances in genomic technology have permitted the development of 768 single nucleotide polymorphism (SNP) markers associated with expressed sequence tags (ESTs). Comprehensive genetic linkage maps were generated based on existing simple sequence repeat (SSR) markers and new SNP markers for four RIL-based mapping populations of field pea. By combining these four bi-parental maps with previously published consensus maps, a comprehensive integrated structure was obtained. Comparative genomic analysis of field pea with other legume species revealed high levels of conserved synteny between the genomes. Trait dissection of resistance to bacterial blight caused by Pseudomonas syringae pv. syringae and salinity tolerance identified multiple contributory genomic regions leading to quantitative inheritance. In contrast, B toxicity tolerance, powdery mildew resistance and bacterial blight (caused by P. syringae pv. pisi) resistance were predominantly controlled by a single genomic region. Resequencing of the PsMLO1 candidate gene from powdery mildew resistant and susceptible genotypes allowed the design and validation of a putative diagnostic marker. This study also generated a comprehensive transcriptome data sets from two genotypes of field pea through the use of RNA sequencing technology (RNA-Seq), and performed comparison to gene complements in related species, sequence annotation and assessment of tissue-specific expression. The resources generated in this study will support further development of genetic markers, map construction and enhancement, identification of marker-trait associations, genomics-assisted breeding, map-based gene cloning, comparative genetics as well to identify target genes for genetic modification approaches on the basis of annotation and expression analysis.