Prospects for advancing defense to cereal rusts through genetical genomics

Abstract

Rusts are one of the most severe threats to cereal crops because new pathogen races emerge regularly, resulting in infestations that lead to large yield losses. In 1999, a new race of stem rust, Puccinia graminis f. sp. tritici (Pgt TTKSK or Ug99), was discovered in Uganda. Most of the wheat and barley cultivars grown currently worldwide are susceptible to this new race. Pgt TTKSK has already spread northward into Iran and will likely spread eastward throughout the Indian subcontinent in the near future. This scenario is not unique to stem rust; new races of leaf rust (Puccinia triticina) and stripe rust (Puccinia striiformis) have also emerged recently. One strategy for countering the persistent adaptability of these pathogens is to stack complete- and partial-resistance genes, which requires significant breeding efforts in order to reduce deleterious effects of linkage drag. These varied resistance combinations are typically more difficult for the pathogen to defeat, since they would be predicted to apply lower selection pressure. Genetical genomics or expression Quantitative Trait Locus (eQTL) analysis enables the identification of regulatory loci that control the expression of many to hundreds of genes. Integrated deployment of these technologies coupled with efficient phenotyping offers significant potential to elucidate the regulatory nodes in genetic networks that orchestrate host defense responses. The focus of this review will be to present advances in genetical genomic experimental designs and analysis, particularly as they apply to the prospects for discovering partial disease resistance alleles in cereals.

Genetical and Comparative Genomics of Brassica under Altered Ca Supply Identifies Arabidopsis Ca-Transporter Orthologs

“…Recent developments in genetical genomics, also known as expression quantitative trait locus (eQTL) analysis, can now measure variation in global gene expression among individuals within mapping populations (Kliebenstein, 2009;Druka et al, 2010;Hammond et al, 2011;Holloway et al, 2011;Moscou et al, 2011;Cubillos et al, 2012;Ballini et al, 2013;Huang et al, 2013). Variation in gene expression can be linked to sequence polymorphisms in target genes or, perhaps more interestingly, inherited differences in cis-regulatory (proximal) or trans-regulatory (distal) regions.…”

Advances in metabolomic applications in plant genetics and breeding.

“…a metabolic trait). This often results in more molecular trait variation being directly explained by genetic effects as compared with a case involving a morphological trait [48]. As a result, mQTLs typically localize to narrower genomic intervals than QTLs associated with morphological variation.…”

Induced plant responses to microbes and insects

“…Cereal pathogens have major impacts on future food security. Ballini et al (2013) and Balmer et al (2013) describe how modern technology such as genetical genomics and metabolomics can help to investigate these scientifically and societally challenging host-pathogen interactions. On a more applied note, Abdul Latif et al (2013) and Reglinski et al (2013) describe how modeling approaches and fundamental knowledge on induced resistance can be used to develop control strategies in practice, such as to fight bacterial canker of kiwifruit.…”