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Forni S.,Genus plc | Aguilar I.,Instituto Nacional Of Investigacian Agropecuaria | Aguilar I.,University of Georgia | Misztal I.,University of Georgia
Genetics Selection Evolution | Year: 2011

Background: The incorporation of genomic coefficients into the numerator relationship matrix allows estimation of breeding values using all phenotypic, pedigree and genomic information simultaneously. In such a single-step procedure, genomic and pedigree-based relationships have to be compatible. As there are many options to create genomic relationships, there is a question of which is optimal and what the effects of deviations from optimality are. Methods. Data of litter size (total number born per litter) for 338,346 sows were analyzed. Illumina PorcineSNP60 BeadChip genotypes were available for 1,989. Analyses were carried out with the complete data set and with a subset of genotyped animals and three generations pedigree (5,090 animals). A single-trait animal model was used to estimate variance components and breeding values. Genomic relationship matrices were constructed using allele frequencies equal to 0.5 (G05), equal to the average minor allele frequency (GMF), or equal to observed frequencies (GOF). A genomic matrix considering random ascertainment of allele frequencies was also used (GOF*). A normalized matrix (GN) was obtained to have average diagonal coefficients equal to 1. The genomic matrices were combined with the numerator relationship matrix creating H matrices. Results: In G05 and GMF, both diagonal and off-diagonal elements were on average greater than the pedigree-based coefficients. In GOF and GOF*, the average diagonal elements were smaller than pedigree-based coefficients. The mean of off-diagonal coefficients was zero in GOF and GOF*. Choices of G with average diagonal coefficients different from 1 led to greater estimates of additive variance in the smaller data set. The correlation between EBV and genomic EBV (n = 1,989) were: 0.79 using G05, 0.79 using GMF, 0.78 using GOF, 0.79 using GOF*, and 0.78 using GN. Accuracies calculated by inversion increased with all genomic matrices. The accuracies of genomic-assisted EBV were inflated in all cases except when GN was used. Conclusions: Parameter estimates may be biased if the genomic relationship coefficients are in a different scale than pedigree-based coefficients. A reasonable scaling may be obtained by using observed allele frequencies and re-scaling the genomic relationship matrix to obtain average diagonal elements of 1. © 2011 Forni et al; licensee BioMed Central Ltd. Source


Cabrera D.,Instituto Nacional Of Investigacian Agropecuaria | Rodriguez P.,Instituto Nacional Of Investigacian Agropecuaria | Zoppolo R.,Instituto Nacional Of Investigacian Agropecuaria
Acta Horticulturae | Year: 2015

'Williams B.C.' pear was grafted on two pear rootstocks: 'Farold®40' and 'Farold®69', and on three clonal quince rootstocks: 'BA 29', 'Adams' and 'EMC' with and without 'Beurré Hardy' as an interstem. To evaluate the performance of these combinations in the south of Uruguay, grafted trees were planted in 2003 at INIA Las Brujas, 'Wilson Ferreira Aldunate' Experimental Station (34°40 S- 56°20 W). Rows were 4.5 m apart and variable distance was used between plants according to rootstock: 1.70 m ('BA29', 'Farold®40' and 'Farold®69'), 1.50 m ('Adams'), and 1.30 m ('EMC'). Observations on phenological, vegetative, and productive behavior of the 'Williams B.C.' scions were carried out each year. From 2004 onwards, trunk cross-sectional areas (TCSA) showed differences allowing rootstocks to be ranked in order of decreasing vigor: > 'Farold®69' > 'Farold®40' > 'BA 29' > 'Adams' > 'EMC'. In 2014, trunk cross-sectional area on 'Farold®69' was 198.7 cm2 while a minimum of 53.8 cm2 was measured on 'EMC'. Different rate of plant death occurred, having higher losses among 'EMC' and 'Adams' with interstem and all quince rootstocks without interstem. Cumulative fruit yields per plant of nine harvests ranged between 149.8 ('BA29' with interstem) and 73.5 kg tree-1 ('EMC'). The best performances were recorded on 'BA29' with interstem, 'Farold®40' and 'Farold®69' pear rootstocks, with an average of cumulative production of 190 ton ha-1. The highest yield efficiency was obtained with 'Farold®40' rootstock (0.35 kg cm-2 TCSA) and with 'BA29' with interstem (0.30 kg cm-2 TCSA). Therefore, to achieve maximum pear production potential under Uruguayan conditions, rootstock quince 'BA29' with 'Beurré Hardy' as an interstem, 'Farold®40', and 'Farold®69' are the better options. Source

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