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United States Department of Agriculture

Agricultural Research Service

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Location: Plant, Soil and Nutrition Research

2013 Annual Report

1a. Objectives (from AD-416):
When specific marker alleles segregate together with alleles at loci that affect the phenotype, the marker can explain and predict phenotypic variation. It may also occur that combinations of alleles at different markers (that is haplotypes) co-segregate more reliably with causal alleles, so that haplotypes are more effective at prediction. In this context, we will determine the ranges of the effective population size, the age of the causal mutation, and the marker density parameters for which haplotype methods are superior to single marker methods. We will also assess whether different haplotype block identification methods differently affect the performance of QTL detection methods in real and simulated data. Beyond identifying QTL, these marker data can be used to predict a genotype’s performance. We will evaluate analysis methods that use haplotypes for this purpose. Finally, to perform these analyses in practice, large amounts of DNA marker data are needed. We will take advantage of Cornell expertise to develop lower cost methods of obtaining marker data using sequencing.

1b. Approach (from AD-416):
Populations under a Wright-Fisher neutral model will be simulated using a standard coalescent approach with a range of effective population sizes thought to correspond to the effective population sizes of elite small grain crops in North America (Ne = 25 to 400). A polymorphism of the appropriate age (g = 25 to 400 generations) will be selected and effects will be attributed to its alleles. Four hundred individuals will be simulated in this way. These data will then be subjected to single marker and haplotype block analyses. Since the methods use different test statistics, their power will be assessed on the basis of detection power at fixed false discovery rates. Whole chromosomes will also be simulated and populated with one to several causal polymorphisms simulating a locus bearing several mutations and generating an allelic series. Different haplotype block identification methods will be applied to the whole chromosome marker profile. Chromosomes will also be simulated in structured populations. Finally, these analyses will also be applied to real marker and phenotype data from the Barley Coordinated Agricultural Project. Similar approaches can be used to compare performance prediction models rather than QTL detection models. For marker development and scoring through sequencing, we will use subsets of lines from bi-parental populations in barley and wheat. These lines will be sequenced on Cornell machines and progeny sequence compared to parental sequence.

3. Progress Report:
To predict small grain field performance, we are working directly with the collaborator’s breeding program as a test case for the use of genomic selection in a small, public sector breeding program. The collaborator has had a long-standing recurrent selection program using male sterility. Use of male sterility could be advantageous for genomic selection in self-pollinating species because of the high frequency with which crossing occurs. This crossing is greatly facilitated by male sterility. The first project has therefore been to map the male sterility locus (region of genome where male sterility gene is located) or loci such that future male sterile or fertile plants can be easily tagged. Second, we are using the breeding program as a basis to explore genomic selection for nutritional quality in wheat, particularly with regard to inulin content. Initial population selection and crossing have been made in this empirical selection research.

4. Accomplishments

Last Modified: 05/24/2017
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