Development of R&D plans for phala ris/cocksfoot

Summary

Phalaris (Phalaris aquatica) is an important perennial grass sown for meat production in temperate Australia.  The species has a reputation for being persistent and able to support high levels of animal production. In contrast to species such as perennial ryegrass where major efforts have been undertaken to develop genetic and genomic technologies to increase the rate of genetic gain in the species, genetic research in phalaris has focussed on the development of new cultivars to address requirements of farming systems such as winter-activity, aluminium tolerance and grazing tolerance. Further gains in various traits in phalaris will be possible by continued selection based on quantitative genetics principles but the new field of genomic selection enabled by advances in rapid genome sequencing offer clear prospects of increased rate of genetic gain and is attracting interest worldwide not only in crop species and major pasture species like perennial ryegrasss (Lolium perenne L.), but also in species such as switchgrass (Panicum virgatum L.) which commercially on a world scale can be considered a minor species like phalaris.
This latest project B.PBE.0038 was initiated with the objective that it would develop the tools to enable genomics assisted breeding in phalaris through the provision of publicly available genomic sequence data, the assessment of the practicality of genomic selection in phalaris and the development of a model to value genetic gain in phalaris.
Background 
During the development of the MLA Feedbase Investment Plan there was agreement on the need for investment in perennial grass genetics and breeding with an emphasis on the following attributes (Smith 2012):
Greatly increased rates of genetic gain for traits of importance to red meat producers
Description of the value of this gain in economic terms
Investment aligned with a public:private partnership model whereby the majority of science and development activities were in the public sector and cultivar development activities in the private sector
That the germplasm and tools developed with MLA co-investment would be utilised in cultivars that would be broadly available to and widely adopted by red meat producers
Prior MLA reviews had demonstrated that progress in pasture plant breeding programs was limited by the low usage of quantitative genetics and economics to develop breeding objectives and that programs generally had a 'trait' emphasis that ignored the need for concurrent selection of a range of traits and the relative importance of traits within the breeding objective.
As a result MLA contracted the delivery of an investment plan for pre-breeding in phalaris following guidelines set out in the Terms of Reference (B.PBE.0029).
Based on these recommendations and further industry consultation the project team considers that the best approach is to develop a pre-breeding program that embraces quantitative genetics, molecular genetics and genomics to develop genomics assisted breeding values for key target traits in phalaris. Because the key traits are quantitative it is most unlikely that they will be improved greatly with simple marker-assisted breeding strategies and the use of quantitative genetics to develop breeding values is facilitated greatly through the use of genomics to reduce generation intervals and to determine the relationships between individuals. By developing these technologies in phalaris, the breeding systems in this cross-pollinated grass species will align with those used in modern animal breeding programs.
The project to develop a genomics-assisted selection strategy for phalaris will by 2017:
Describe genetic diversity in Australian-bred phalaris germplasm to guide the design of future commercial breeding programs with an emphasis on winter-active germplasm pools
Develop a methodology of genomic selection in phalaris for Australian commercial breeding programs, in collaboration with private seed companies, to more efficiently select for the quantitative traits which dominate the economic value of phalaris
Develop genetic markers for the seed retention trait as a tool to increase the rate of genetic gain in commercial phalaris breeding programs.
Use economic analyses to develop robust estimates of the economic importance of genetic gain in phalaris in red meat production systems that can be used to
a. assess of the genetic merit of individual plants and cultivars
b. assess the value of individual sub-traits (such as pest and disease tolerance) that contribute to pasture characteristics such as seasonal yield and persistence
c. calculate the economic benefit of new sowings to producers
These analsyes will address a major deficiency in most forage plant breeding programs, which includes the limited use of quantitative genetics and other tools to develop and implement robust economically-based breeding objectives similar to those which have been used to highly accelerate the rate of genetic gain in sheep and beef cattle breeding, and to prioritise between individual traits in a breeding program.
Due to cost constraints, the project will not address the important areas of livestock toxicity and herbage quality. Both areas are acknowledged to be important, and the technologies developed here will be suitable for application to these traits in future work.