Quantitative genetics theory for genomic selection and efficiency of breeding value prediction in open-pollinated populations

To date, the quantitative genetics theory for genomic selection has focused mainly on the relationship between marker and additive variances assuming one marker and one quantitative trait locus (QTL). This study extends the quantitative genetics theory to genomic selection in order to prove that prediction of breeding values based on thousands of single nucleotide polymorphisms (SNPs) depends on linkage disequilibrium (LD) between markers and QTLs, assuming dominance. We also assessed the efficiency of genomic selection in relation to phenotypic selection, assuming mass selection in an open-pollinated population, all QTLs of lower effect, and reduced sample size, based on simulated data. We show that the average effect of a SNP substitution is proportional to LD measure and to average effect of a gene substitution for each QTL that is in LD with the marker. Weighted (by SNP frequencies) and unweighted breeding value predictors have the same accuracy. Efficiency of genomic selection in relation to phenotypic selection is inversely proportional to heritability. Accuracy of breeding value prediction is not affected by the dominance degree and the method of analysis, however, it is influenced by LD extent and magnitude of additive variance. The increase in the number of markers asymptotically improved accuracy of breeding value prediction. The decrease in the sample size from 500 to 200 did not reduce considerably accuracy of breeding value prediction.

Quantitative genetics theory for genomic selection and efficiency of breeding value prediction in open-pollinated populations

To date, the quantitative genetics theory for genomic selection has focused mainly on the relationship between marker and additive variances assuming one marker and one quantitative trait locus (QTL). This study extends the quantitative genetics theory to genomic selection in order to prove that prediction of breeding values based on thousands of single nucleotide polymorphisms (SNPs) depends on linkage disequilibrium (LD) between markers and QTLs, assuming dominance. We also assessed the efficiency of genomic selection in relation to phenotypic selection, assuming mass selection in an open-pollinated population, all QTLs of lower effect, and reduced sample size, based on simulated data. We show that the average effect of a SNP substitution is proportional to LD measure and to average effect of a gene substitution for each QTL that is in LD with the marker. Weighted (by SNP frequencies) and unweighted breeding value predictors have the same accuracy. Efficiency of genomic selection in relation to phenotypic selection is inversely proportional to heritability. Accuracy of breeding value prediction is not affected by the dominance degree and the method of analysis, however, it is influenced by LD extent and magnitude of additive variance. The increase in the number of markers asymptotically improved accuracy of breeding value prediction. The decrease in the sample size from 500 to 200 did not reduce considerably accuracy of breeding value prediction.(AU)

Quantitative trait locus mapping associated with earliness and fruit weight in tomato

The flowering time is regarded as an important factor that affects yield in various crops. In order to understand how the molecular basis controlling main components of earliness in tomato (Solanum lycopersicum L.), and to deduce whether the correlation between fruit weight, days to flowering and seed weight, is caused by pleiotropic effects or genetic linkage, a QTLs analysis was carried out using an F2 interspecific population derived from the cross of S. lycopersicum and S. pimpinellifolium. The analysis revealed that most of the components related to earliness were independent due to the absence of phenotypic correlation and lack of co-localization of their QTLs. QTLs affecting the flowering time showed considerable variation over time in values of explained phenotypic variation and average effects, which suggested dominance becomes more evident over time. The path analysis showed that traits such as days to flowering, seed weight, and length of the first leaf had a significant effect on the expression of fruit weight, confirming that their correlations were due to linkage. This result was also confirmed in two genomic regions located on chromosomes 1 and 4, where despite showing high co-localization of QTLs associated to days to flowering, seed weight and fruit weight, the presence and absence of epistasis in dfft1.1 × dftt4.1 and fw1.1 × fw4.1, suggested that the linkage was the main cause of the co-localization.

Quantitative trait locus mapping associated with earliness and fruit weight in tomato

The flowering time is regarded as an important factor that affects yield in various crops. In order to understand how the molecular basis controlling main components of earliness in tomato (Solanum lycopersicum L.), and to deduce whether the correlation between fruit weight, days to flowering and seed weight, is caused by pleiotropic effects or genetic linkage, a QTLs analysis was carried out using an F2 interspecific population derived from the cross of S. lycopersicum and S. pimpinellifolium. The analysis revealed that most of the components related to earliness were independent due to the absence of phenotypic correlation and lack of co-localization of their QTLs. QTLs affecting the flowering time showed considerable variation over time in values of explained phenotypic variation and average effects, which suggested dominance becomes more evident over time. The path analysis showed that traits such as days to flowering, seed weight, and length of the first leaf had a significant effect on the expression of fruit weight, confirming that their correlations were due to linkage. This result was also confirmed in two genomic regions located on chromosomes 1 and 4, where despite showing high co-localization of QTLs associated to days to flowering, seed weight and fruit weight, the presence and absence of epistasis in dfft1.1 × dftt4.1 and fw1.1 × fw4.1, suggested that the linkage was the main cause of the co-localization.(AU)

Clonal study of avian Escherichia coli strains by fliC conserved-DNA-sequence regions analysis / Estudo clonal de Escherichia coli aviário por análise de seqüências de DNA conservadas do gene fliC

The clonal relationship among avian Escherichia coli strains and their genetic proximity with human pathogenic E. coli, Salmonela enterica, Yersinia enterocolitica and Proteus mirabilis, was determined by the DNA sequencing of the conserved 5' and 3'regions fliC gene (flagellin encoded gene). Among 30 commensal avian E. coli strains and 49 pathogenic avian E. coli strains (APEC), 24 commensal and 39 APEC strains harbored fliC gene with fragments size varying from 670bp to 1,900bp. The comparative analysis of these regions allowed the construction of a dendrogram of similarity possessing two main clusters: one compounded mainly by APEC strains and by H-antigens from human E. coli, and another one compounded by commensal avian E. coli strains, S. enterica, and by other H-antigens from human E. coli. Overall, this work demonstrated that fliC conserved regions may be associated with pathogenic clones of APEC strains, and also shows a great similarity among APEC and H-antigens of E. coli strains isolated from humans. These data, can add evidence that APEC strains can exhibit a zoonotic risk.(AU)

A relação clonal entre linhagens de Escherichia coli de origem aviária e sua proximidade genética com E. coli patogênica para humanos, Salmonella enterica, Yersinia enterocolitica e Proteus mirabilis foi determinada através da utilização das seqüências conservadas 5' e 3' do gene fliC (responsável pela codificação da flagelina). Entre as 30 linhagens comensais de E. coli aviária e as 49 linhagens patogênicas de E. coli para aves (APEC), 24 linhagens comensais e 39 APEC apresentaram o gene fliC, que foi encontrado em tamanhos que variam de 670pb a 1900pb. Um dendrograma representando similaridade genética foi obtido a partir do seqüenciamento das regiões 5' e 3' conservadas do gene fliC das linhagens de E. coli de origem aviária, das seqüências dos antígenos H de E. coli de origem humana, de S. enterica, Y. enterocolitica e de P. mirabilis. A análise do dendrograma demonstrou que este apresenta dois grupos principais: um composto principalmente por isolados APEC e por antígenos H de E. coli de origem humana e outro formado por isolados comensais de E. coli aviária, S. enterica e por antígenos H de E. coli. No geral, o presente trabalho demonstrou que as regiões conservadas do gene fliC podem estar associadas à diferenciação clonal de linhagens de E. coli aviária, e que existe uma grande similaridade genética entre estas linhagens e antígenos H de E. coli humana. Estes dados podem adicionar evidências de que linhagens APEC podem apresentar riscos zoonóticos.(AU)