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Increased genomic prediction accuracy in wheat breeding through spatial adjustment of field trial data.

Lado B, Matus I, Rodríguez A, Inostroza L, Poland J, Belzile F, del Pozo A, Quincke M, Castro M, von Zitzewitz J - G3 (Bethesda) (2013)

Bottom Line: A mixed-model using moving-means as a covariate was found to best fit the data.The best predictions between environments were obtained when data from different years were used to train the model.Our results confirm that genotyping-by-sequencing is an effective tool to obtain genome-wide information for crops with complex genomes, that these data are efficient for predicting traits, and that correction of spatial variation is a crucial ingredient to increase prediction accuracy in genomic selection models.

View Article: PubMed Central - PubMed

Affiliation: Programa Nacional de Investigación Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria, Est. Exp. La Estanzuela, Colonia 70000, Uruguay.

ABSTRACT
In crop breeding, the interest of predicting the performance of candidate cultivars in the field has increased due to recent advances in molecular breeding technologies. However, the complexity of the wheat genome presents some challenges for applying new technologies in molecular marker identification with next-generation sequencing. We applied genotyping-by-sequencing, a recently developed method to identify single-nucleotide polymorphisms, in the genomes of 384 wheat (Triticum aestivum) genotypes that were field tested under three different water regimes in Mediterranean climatic conditions: rain-fed only, mild water stress, and fully irrigated. We identified 102,324 single-nucleotide polymorphisms in these genotypes, and the phenotypic data were used to train and test genomic selection models intended to predict yield, thousand-kernel weight, number of kernels per spike, and heading date. Phenotypic data showed marked spatial variation. Therefore, different models were tested to correct the trends observed in the field. A mixed-model using moving-means as a covariate was found to best fit the data. When we applied the genomic selection models, the accuracy of predicted traits increased with spatial adjustment. Multiple genomic selection models were tested, and a Gaussian kernel model was determined to give the highest accuracy. The best predictions between environments were obtained when data from different years were used to train the model. Our results confirm that genotyping-by-sequencing is an effective tool to obtain genome-wide information for crops with complex genomes, that these data are efficient for predicting traits, and that correction of spatial variation is a crucial ingredient to increase prediction accuracy in genomic selection models.

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Related in: MedlinePlus

GBS-based SNP distribution along different wheat chromosomes.
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fig3: GBS-based SNP distribution along different wheat chromosomes.

Mentions: When comparing sequences using BLAST against the Poland et al. (2012a) GBS-based SNP database, we found that the sequences in common showed a good coverage throughout all 21wheat linkage groups. Of all the SNPs, 13% (13,357) found high-quality matches. Although a good coverage was observed, the D genome presented fewer SNPs than the A and B genomes (Figure 3). As expected, LD analysis between mapped SNPs indicated high LD between closely linked SNPs along all chromosomes (File S1).


Increased genomic prediction accuracy in wheat breeding through spatial adjustment of field trial data.

Lado B, Matus I, Rodríguez A, Inostroza L, Poland J, Belzile F, del Pozo A, Quincke M, Castro M, von Zitzewitz J - G3 (Bethesda) (2013)

GBS-based SNP distribution along different wheat chromosomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852373&req=5

fig3: GBS-based SNP distribution along different wheat chromosomes.
Mentions: When comparing sequences using BLAST against the Poland et al. (2012a) GBS-based SNP database, we found that the sequences in common showed a good coverage throughout all 21wheat linkage groups. Of all the SNPs, 13% (13,357) found high-quality matches. Although a good coverage was observed, the D genome presented fewer SNPs than the A and B genomes (Figure 3). As expected, LD analysis between mapped SNPs indicated high LD between closely linked SNPs along all chromosomes (File S1).

Bottom Line: A mixed-model using moving-means as a covariate was found to best fit the data.The best predictions between environments were obtained when data from different years were used to train the model.Our results confirm that genotyping-by-sequencing is an effective tool to obtain genome-wide information for crops with complex genomes, that these data are efficient for predicting traits, and that correction of spatial variation is a crucial ingredient to increase prediction accuracy in genomic selection models.

View Article: PubMed Central - PubMed

Affiliation: Programa Nacional de Investigación Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria, Est. Exp. La Estanzuela, Colonia 70000, Uruguay.

ABSTRACT
In crop breeding, the interest of predicting the performance of candidate cultivars in the field has increased due to recent advances in molecular breeding technologies. However, the complexity of the wheat genome presents some challenges for applying new technologies in molecular marker identification with next-generation sequencing. We applied genotyping-by-sequencing, a recently developed method to identify single-nucleotide polymorphisms, in the genomes of 384 wheat (Triticum aestivum) genotypes that were field tested under three different water regimes in Mediterranean climatic conditions: rain-fed only, mild water stress, and fully irrigated. We identified 102,324 single-nucleotide polymorphisms in these genotypes, and the phenotypic data were used to train and test genomic selection models intended to predict yield, thousand-kernel weight, number of kernels per spike, and heading date. Phenotypic data showed marked spatial variation. Therefore, different models were tested to correct the trends observed in the field. A mixed-model using moving-means as a covariate was found to best fit the data. When we applied the genomic selection models, the accuracy of predicted traits increased with spatial adjustment. Multiple genomic selection models were tested, and a Gaussian kernel model was determined to give the highest accuracy. The best predictions between environments were obtained when data from different years were used to train the model. Our results confirm that genotyping-by-sequencing is an effective tool to obtain genome-wide information for crops with complex genomes, that these data are efficient for predicting traits, and that correction of spatial variation is a crucial ingredient to increase prediction accuracy in genomic selection models.

Show MeSH
Related in: MedlinePlus