Genomewide predictions from maize single-cross data

Title 
Genomewide predictions from maize single-cross data 
Publication Type 
Journal Article 
Authors 
Massman JM, Gordillo A, Lorenzana RE, Bernardo R 
Year of Publication 
2013 
Volume 
126 
Journal 
Theoretical and Applied Genetics 
Issue 
Pagination 
13 - 22 
Date Published 
1/2013 
ISSN 
1432-2242 
Keywords 
., best linear unbiased prediction, best untested single crosses, biparental cross, BLUP, genomewide marker effects, genomewide predictions, Maize, marker-based relatedness, ridge-regression BLUP, RR-BLUP, single-cross hybrids 
URL 
http://link.springer.com/article/10.1007/s00122-012-1955-y 
DOI 
10.1007/s00122-012-1955-y 
Abstract 

Maize (Zea mays L.) breeders evaluate many single-cross hybrids each year in multiple environments. Our objective was to determine the usefulness of genomewide predictions, based on marker effects from maize single-cross data, for identifying the best untested single crosses and the best inbreds within a biparental cross. We considered 479 experimental maize single crosses between 59 Iowa Stiff Stalk Synthetic (BSSS) inbreds and 44 non-BSSS inbreds. The single crosses were evaluated in multilocation experiments from 2001 to 2009 and the BSSS and non-BSSS inbreds had genotypic data for 669 single nucleotide polymorphism (SNP) markers. Single-cross performance was predicted by a previous best linear unbiased prediction (BLUP) approach that utilized marker-based relatedness and information on relatives, and from genomewide marker effects calculated by ridge-regression BLUP (RR-BLUP). With BLUP, the mean prediction accuracy (r MG) of single-cross performance was 0.87 for grain yield, 0.90 for grain moisture, 0.69 for stalk lodging, and 0.84 for root lodging. The BLUP and RR-BLUP models did not lead to r MG values that differed significantly. We then used the RR-BLUP model, developed from single-cross data, to predict the performance of testcrosses within 14 biparental populations. The r MG values within each testcross population were generally low and were often negative. These results were obtained despite the above-average level of linkage disequilibrium, i.e., r 2 between adjacent markers of 0.35 in the BSSS inbreds and 0.26 in the non-BSSS inbreds. Overall, our results suggested that genomewide marker effects estimated from maize single crosses are not advantageous (compared with BLUP) for predicting single-cross performance and have erratic usefulness for predicting testcross performance within a biparental cross.

 
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