Pea (Pisum sativum L.) in the genomics era

Authors: SMYKAL, PETR - Palacky University; AUBERT, GREGORIE - Institut National De La Recherche Agronomique (INRA); BUSTIN, JUSTIN - Institut National De La Recherche Agronomique (INRA); Coyne, Clarice - Clare; ELLIS, NOEL - Aberystwyth University; FLAVELL, ANDY - University Of Dundee; FORD, REBECCA - University Of Melbourne; HYBL, MIROSTAV - Agritec Plant Research Ltd; MACAS, JIRI - Academy Of Sciences Of The Czech Republic (ASCR); MCPHEE, KEVIN - North Dakota State University; REDDEN, ROBERT - Australian Tropical Field Crops Genetic Resource Center; RUBIALES, DIEGO - Ministry Of Science And Innovation, Csic; WELLER, JIM - University Of Tasmania; WARKENTIN, TOM - University Of Saskatchewan

Submitted to: Agronomy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2012
Publication Date: 4/4/2012
Citation: Smykal, P., Aubert, G., Bustin, J., Coyne, C.J., Ellis, N., Flavell, A., Ford, R., Hybl, M., Macas, J., Mcphee, K., Redden, R., Rubiales, D., Weller, J., Warkentin, T. 2012. Pea (Pisum sativum L.) in the genomics era. Agronomy. 2(2), 74-115.

Interpretive Summary: Pea (Pisum sativum L.) was the original model organism for Mendel´s discovery (1866) of the laws of inheritance, making it the foundation of modern plant genetics. Progress in pea genomics has lagged behind many other plant species, largely due to its low multiplication rate and because of its large genome size. Now with three legume crop genome sequences available, genome comparison techniques have leveraged this knowledge to identify the genes of important economic traits in pea, including four traits Mendel used to discover the laws of inheritance. Further, genomic resources of pea are increasing including BAC libraries with good coverage, co-dominant molecular marker sets, both transcriptome and proteome datasets and mutant populations for reverse genetics. The new strategy for gene discovery using association studies is being deployed by the major pea breeding and genetic groups around the world. These tools and approach hold great promise for the development of novel, highly accurate selective breeding tools for improved pea genotypes that are sustainable under current and future climates and farming systems.

Technical Abstract: Pea (Pisum sativum L.) was the original model organism for Mendel´s discovery of the laws of inheritance, making it the foundation of modern plant genetics. However, subsequent progress in pea genomics has lagged behind many other plant species, largely as a consequence of its low multiplication rate and more recently because of its large genome size and relative recalcitrance to transformation. The availability of the full genome sequences of three legume species has offered significant opportunities for genome wide comparison revealing synteny and colinearity to cultivated species. Syntenic blocks and signatures of ancient whole genome duplication have been uncovered to have occurred about 59 mya ago. To date four of seven Mendel´s original characters have been characterised at a molecular level. A combination of a candidate gene and colinearity approach has successfully led to the identification of these and other genes underlying agronomically important traits including virus resistances and plant architecture. Some of this knowledge has already been applied to marker assisted selection programs, increasing the precision and shortening the breeding cycle. Although the size and repetitive/redundant nature of the pea genome has so far restricted sequencing of the entire pea genome, comprehensive genomic and post genomic resources already exist. These include BAC libraries with good coverage, several types of co-dominant molecular marker sets, both transcriptome and proteome datasets and mutant populations for reverse genetics. Repetitive DNA elements have been efficiently used for molecular marker development, and subsequent genetic diversity and mapping of agronomically important quantitative trait loci. In line with progress in the understanding of genes and functional association to traits in model legume species, a switch has occurred in the world of pea marker development from a focus on repetitive sequences to those that encompass single nucleotide polymorphisms (SNP) within exonic regions. Also, with the access to substantial and diverse germplasm collections, association mapping is becoming more common to identify genetic variation related to desirable agronomic traits. This effort highlights novel sources of variation for traits that are largely quantitatively inherited and historically difficult to breed for in a traditional manner. Molecular analysis of major international pea collections has shown that substantial variation is present within cultivated material that has potential to be exploited outside specific the geographical regions of their origin. Wild relative material offers the possibility to reincorporate traits into the cultivated germplasm that had been previously excluded due to bottlenecks introduced by domestication. Reverse genetics tools include fast neutron and TILLING mutant populations for reverse genetics approaches, BAC libraries for positional gene cloning, as well as transgenics and in vitro regeneration for proof of function through gene silencing or over-expression. Put together with the availability of high throughput sequencing, genotyping and the omics methodologies, these hold great promise for the development of novel, highly accurate selective breeding tools for improved pea genotypes that are sustainable under current and future climates and farming systems.