Candidate gene-based association genetics analysis of herbage quality traits in perennial ryegrass (Lolium perenne L.)
L. W. Pembleton A D E F , J. Wang B C D F , N. O. I. Cogan A C D , J. E. Pryce A D , G. Ye A C , C. K. Bandaranayake B C , M. L. Hand A C D , R. C. Baillie A C D , M. C. Drayton A C D , K. Lawless A C , S. Erb B C , M. P. Dobrowolski B C , T. I. Sawbridge A C D E , G. C. Spangenberg A C D E , K. F. Smith B C E and J. W. Forster A C D E G
+ Author Affiliations
- Author Affiliations
A Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, The Centre for AgriBioscience, 5 Ring Road, Bundoora, Vic. 3083, Australia.
B Department of Environment and Primary Industries, Biosciences Research Division, Hamilton Centre, Mount Napier Road, Hamilton, Vic. 3300, Australia.
C Molecular Plant Breeding Cooperative Research Centre, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, Bundoora, Vic. 3083, Australia.
D Dairy Futures Cooperative Research Centre, AgriBio, The Centre for AgriBioscience, 5 Ring Road, Bundoora, Vic. 3083, Australia.
E La Trobe University, Bundoora, Vic. 3086, Australia.
F Contributed equally to this work.
G Corresponding author. Email: john.forster@depi.vic.gov.au
Crop and Pasture Science 64(3) 244-253 https://doi.org/10.1071/CP12392
Submitted: 21 November 2012 Accepted: 7 June 2013 Published: 24 July 2013
Abstract
Due to the complex genetic architecture of perennial ryegrass, based on an obligate outbreeding reproductive habit, association-mapping approaches to genetic dissection offer the potential for effective identification of genetic marker–trait linkages. Associations with genes for agronomic characters, such as components of herbage nutritive quality, may then be utilised for accelerated cultivar improvement using advanced molecular breeding practices. The objective of the present study was to evaluate the presence of such associations for a broad range of candidate genes involved in pathways of cell wall biosynthesis and carbohydrate metabolism. An association-mapping panel composed from a broad range of non-domesticated and varietal sources was assembled and assessed for genome-wide sequence polymorphism. Removal of significant population structure obtained a diverse meta-population (220 genotypes) suitable for association studies. The meta-population was established with replication as a spaced-plant field trial. All plants were genotyped with a cohort of candidate gene-derived single nucleotide polymorphism (SNP) markers. Herbage samples were harvested at both vegetative and reproductive stages and were measured for a range of herbage quality traits using near infrared reflectance spectroscopy. Significant associations were identified for ~50% of the genes, accounting for small but significant components of phenotypic variance. The identities of genes with associated SNPs were largely consistent with detailed knowledge of ryegrass biology, and they are interpreted in terms of known biochemical and physiological processes. Magnitudes of effect of observed marker–trait gene association were small, indicating that future activities should focus on genome-wide association studies in order to identify the majority of causal mutations for complex traits such as forage quality.
Additional keywords: cultivar, digestibility, fructan, lignin, NIRS, single nucleotide polymorphism.
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