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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Dairy Forage Research » Research » Publications at this Location » Publication #336556
Title: Using variable importance measures to identify a small set of single nucleotide polymorphisms capable of predicting heading date in perennial ryegrass

Author
item BYRNE, STEPHEN - Teagasc (AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY)
item CONAGHAN, PATRICK - Teagasc (AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY)
item BARTH, SUSANNE - Teagasc (AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY)
item KRISHNA AROJJU, SAI - Teagasc (AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY)
item Casler, Michael
item MICHEL, THIBAULD - Teagasc (AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY)
item MILBOURNE, DAN - Teagasc (AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY)

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary: Perennial ryegrass is the most important forage grass for humid temperate regions. In ryegrass breeding programs, heading date is one of the most important traits to measure because all parents of a new variety must have similar heading dates to synchronize flowering and produce adequate amounts of seed. However, heading date is extremely time-consuming to measure in the field, so DNA marker systems that accurately predict heading date of seedlings would be extremely valuable and useful. Using a training population of 1600 individuals that represent the Irish national ryegrass breeding program, prediction accuracy for heading date was 0.73 to 0.86, based on DNA markers that represented the entire genome. Ryegrass seedlings can now be tested using a single, inexpensive DNA marker assay that consists of 50 markers that can then be used to accurately predict their heading date. Prediction of heading date on seedlings allows the seedlings to be grouped before flowering and arranged into field blocks with similar heading date, saving one or two years in the field phase of the breeding program.

Technical Abstract: Prior knowledge on heading date enables the selection of parents for synthetic cultivars that are well-matched with respect to heading date, which is necessary to ensure plants put together will successfully cross with each other. Heading date of individual plants can be determined directly, which has a time and labor cost. It can also be inferred from family means, although the spread in days to heading within families demands removing undesirable plants. Another option is to predict heading date from molecular markers. In this study, we used a large training population consisting of individual plants to develop equations to predict heading date from marker genotypes. Using permutation-based variable selection measures, we reduced the marker set from 217,563 to 50 without impacting the predictive ability. Furthermore, use of the smaller selected marker set resulted in higher predictive ability when predicting in unrelated material. Opportunities exist to develop cheap assays to sequence a small number of regions in linkage disequilibrium with heading date loci in thousands of samples. Simultaneous use of these markers in non-linkage based selection applications, such as paternity testing and diversity analysis, should enhance the utility of such an approach.