Trunk distortion weakens the tree productivity revealed by half-sib progeny determination of Pinus yunnanensis.

Twisted trunks are not uncommon in trees, but their effects on tree growth are still unclear. Among coniferous tree species, the phenomenon of trunk distortion is more prominent in Pinus yunnanensis. To expand the germplasm of genetic resources, we selected families with excellent phenotypic traits to provide material for advanced generation breeding. The progeny test containing 93 superior families (3240 trees) was used as the research material. Phenotypic measurements and estimated genetic parameters (family heritability, realistic gain and genetic gain) were performed at 9, 15, and 18 years of age, respectively. The genetic evaluation yielded the following results (1) The intra-family variance component of plant height (PH) was greater than that of the inter-family, while the inter-family variance components of other traits (diameter at breast height (DBH), crown diameter (CD), height under branches (HUB), degree of stem-straightness (DS)) were greater than that of the intra-family, indicating that there was abundant variation among families and potential for selection. (2) At half rotation period (18 years old), there was a significant correlation among the traits. The proportion of trees with twisted trunks (level 1-3 straightness) reached 48%. The DS significantly affected growth traits, among which PH and DBH were the most affected. The volume loss rate caused by twisted trunk was 18.06-56.75%, implying that trunk distortion could not be completely eliminated after an artificial selection. (3) The influence of tree shape, crown width, and trunk on volume increased, and the early-late correlation between PH, DBH and volume was extremely significant. The range of phenotypic coefficient of variation, genetic variation coefficient and family heritability of growth traits (PH, DBH, and volume) were 44.29-127.13%, 22.88-60.87%, and 0.79-0.83, respectively. (4) A total of 21 superior families were selected by the method of membership function combined with independent selection. Compared with the mid-term selection (18 years old), the accuracy of early selection (9 years old) reached 77.5%. The selected families' genetic gain and realistic gain range were 5.79-19.82% and 7.12-24.27%, respectively. This study can provide some useful reference for the breeding of coniferous species.

Accuracy of genomic within-family selection in aquaculture breeding programmes.

In aquaculture breeding programmes, selection within families cannot be applied for traits that cannot be recorded on the candidates (e.g., disease resistance or fillet quality). However, this problem can be overcome if genomic evaluation is used. Within-family genomic evaluation has been proposed for these programmes as large family sizes are available and substantial levels of linkage disequilibrium (LD) within families can be attained with a limited number of markers even in populations in global linkage equilibrium. Here, we compare by computer simulation: (i) within-family and population-wide LD; and (ii) the accuracy of within-family genomic selection when genomic evaluations are carried out either at the population level or within families. The population simulated was composed by a varying number of families of full-sibs (half for training and half for testing). The results indicate that, to practice within-family selection, performing the genomic evaluation separately for each family using only molecular information from the family could be recommended for populations either in linkage equilibrium or with a low level of disequilibrium.

Prediction of additive genetic variances of descendants for complex families based on Mendelian sampling variances.

The ability to predict the outcome of selection and mating decisions enables breeders to make strategically better selection decisions. To improve genetic progress, those individuals need to be selected whose offspring can be expected to show high genetic variance next to high breeding values. Previously published approaches enable to predict the variance of descendants of two future generations for up to 4 founding haplotypes, or 2 outbred individuals, based on phased genotypes, allele effects and recombination frequencies. The purpose of this study was to develop a general approach for the analytical calculation of the genetic variance in any future generation. The core development is an equation for the prediction of the variance of double haploid lines, under the assumption of no selection and negligible drift, stemming from an arbitrary number of founder haplotypes. This double haploid variance can be decomposed into gametic Mendelian sampling variances (MSV) of ancestors of the double haploid lines allowing usage for non-double haploid genotypes which enables application in animal breeding programs as well as in plant breeding programs. Together with the breeding values of the founders, the gametic MSV may be used in new selection criteria. We present our idea of such a criterion that describes the genetic level of selected individuals in four generations. Since breeding programs do select, the assumption made for predicting variances is clearly violated which decreases the accuracy of predicted gametic MSV caused by changes in allele frequency and linkage disequilibrium. Despite violating the assumption, we found high predictive correlations of our criterion to the true genetic level which was obtained by means of simulation for the "corn" and "cattle" genome models tested in this study (0.90 and 0.97). In practice, the genotype phases, genetic map and allele effects all need to be estimated meaning inaccuracies in their estimation will lead to inaccurate variance prediction. Investigation of variance prediction accuracy when input parameters are estimated was not part of this study.

Genomic prediction in family bulks using different traits and cross-validations in pine.

Genomic prediction integrates statistical, genomic, and computational tools to improve the estimation of breeding values and increase genetic gain. Due to the broad diversity in mating systems, breeding schemes, propagation methods, and unit of selection, no universal genomic prediction approach can be applied in all crops. In a genome-wide family prediction (GWFP) approach, the family is the basic unit of selection. We tested GWFP in two loblolly pine (Pinus taeda L.) datasets: a breeding population composed of 63 full-sib families (5-20 individuals per family), and a simulated population with the same pedigree structure. In both populations, phenotypic and genomic data was pooled at the family level in silico. Marker effects were estimated to compute genomic estimated breeding values (GEBV) at the individual and family (GWFP) levels. Less than six individuals per family produced inaccurate estimates of family phenotypic performance and allele frequency. Tested across different scenarios, GWFP predictive ability was higher than those for GEBV in both populations. Validation sets composed of families with similar phenotypic mean and variance as the training population yielded predictions consistently higher and more accurate than other validation sets. Results revealed potential for applying GWFP in breeding programs whose selection unit are family, and for systems where family can serve as training sets. The GWFP approach is well suited for crops that are routinely genotyped and phenotyped at the plot-level, but it can be extended to other breeding programs. Higher predictive ability obtained with GWFP would motivate the application of genomic prediction in these situations.

Favorable Conditions for Genomic Evaluation to Outperform Classical Pedigree Evaluation Highlighted by a Proof-of-Concept Study in Poplar.

Forest trees like poplar are particular in many ways compared to other domesticated species. They have long juvenile phases, ongoing crop-wild gene flow, extensive outcrossing, and slow growth. All these particularities tend to make the conduction of breeding programs and evaluation stages costly both in time and resources. Perennials like trees are therefore good candidates for the implementation of genomic selection (GS) which is a good way to accelerate the breeding process, by unchaining selection from phenotypic evaluation without affecting precision. In this study, we tried to compare GS to pedigree-based traditional evaluation, and evaluated under which conditions genomic evaluation outperforms classical pedigree evaluation. Several conditions were evaluated as the constitution of the training population by cross-validation, the implementation of multi-trait, single trait, additive and non-additive models with different estimation methods (G-BLUP or weighted G-BLUP). Finally, the impact of the marker densification was tested through four marker density sets. The population under study corresponds to a pedigree of 24 parents and 1,011 offspring, structured into 35 full-sib families. Four evaluation batches were planted in the same location and seven traits were evaluated on 1 and 2 years old trees. The quality of prediction was reported by the accuracy, the Spearman rank correlation and prediction bias and tested with a cross-validation and an independent individual test set. Our results show that genomic evaluation performance could be comparable to the already well-optimized pedigree-based evaluation under certain conditions. Genomic evaluation appeared to be advantageous when using an independent test set and a set of less precise phenotypes. Genome-based methods showed advantages over pedigree counterparts when ranking candidates at the within-family levels, for most of the families. Our study also showed that looking at ranking criteria as Spearman rank correlation can reveal benefits to genomic selection hidden by biased predictions.

Studying the Genetics of Resistance to CyHV-3 Disease Using Introgression from Feral to Cultured Common Carp Strains.

Sustainability and further development of aquaculture production are constantly challenged by outbreaks of fish diseases, which are difficult to prevent or control. Developing fish strains that are genetically resistant to a disease is a cost-effective and a sustainable solution to address this challenge. To do so, heritable genetic variation in disease resistance should be identified and combined together with other desirable production traits. Aquaculture of common carp has suffered substantial losses from the infectious disease caused by the cyprinid herpes virus type 3 (CyHV-3) virus and the global spread of outbreaks indicates that many cultured strains are susceptible. In this research, CyHV-3 resistance from the feral strain "Amur Sassan" was successfully introgressed into two susceptible cultured strains up to the first backcross (BC1) generation. Variation in resistance of families from F1 and BC1 generations was significantly greater compared to that among families of any of the susceptible parental lines, a good starting point for a family selection program. Considerable additive genetic variation was found for CyHV-3 resistance. This phenotype was transferable between generations with contributions to resistance from both the resistant feral and the susceptible cultured strains. Reduced scale coverage (mirror phenotype) is desirable and common in cultured strains, but so far, cultured mirror carp strains were found to be susceptible. Here, using BC1 families ranging from susceptible to resistant, no differences in resistance levels between fully scaled and mirror full-sib groups were found, indicating that CyHV-3 resistance was successfully combined with the desirable mirror phenotype. In addition, the CyHV-3 viral load in tissues throughout the infection of susceptible and resistant fish was followed. Although resistant fish get infected, viral loads in tissues of these fish are significantly lesser than in those of susceptible fish, allowing them to survive the disease. Taken together, in this study we have laid the foundation for breeding CyHV-3-resistant strains and started to address the mechanisms underlying the phenotypic differences in resistance to this disease.

Breeding full-sib families of sugar cane using selection index / Melhoramento em famílias de irmãos-completos de cana-de-açúcar usando índices de seleção

An experiment with families belonging to the first selection stage (T1) of the Sugar Cane Breeding Program (PMGCA) of the Universidade Federal Rural do Rio de Janeiro (UFRRJ)/RIDESA was carried out in the Plant Disa, located in the municipality of Conceição da Barra-ES, in 2006, aiming to evaluate families, for the selection of superior plants for the later stages of the breeding program of the culture. Sixty-eight full-sib families and three genotypes considered standards with potential recommendation for the area under study were evaluated. The experiment was arranged in a statistical randomized block design, in which the families were grouped into four sets. Each set had four replicates and one hundred seedlings per plot, with spacing of 0.5 meters between plants and 1.40 between rows. The evaluations were conducted during two growing seasons, corresponding to the first and second ratoon, 2008 and 2009, respectively. The traits stem diameter (DMC), total weight of the plot (P), number of stems (NC) Brix of the lower stem (Brix PE) and Brix of the upper stem (Brix PT) were assessed. All traits were significant for the genotypes, by the F test (P<0.01), in joint analyses of environments, which reveals significant differences between families. The values found in this study for the genetic variation coefficient (CVg) indicate great potential for success in breeding programs targeting at the selection of the traits evaluated. The highest gains were achieved when the indices of Smith and Hazel and Mulamba and Mock were used, which allowed simultaneous superior gains in all traits for the best families.

Foi instalado, em 2006, na Usina Disa, Município de Conceição da Barra-ES, um ensaio de famílias pertencentes a primeira fase de seleção (T1) do Programa de Melhoramento Genético da Cana-de-Açúcar (PMGCA) da Universidade Federal Rural do Rio de Janeiro (UFRRJ)/ RIDESA, com o objetivo de avaliar famílias, visando à seleção de plantas superiores para as fases posteriores do programa de melhoramento genético da cultura. Foram avaliadas 68 famílias de irmãos-completos e mais três genótipos considerados padrões, com potencial de recomendação para a região avaliada. O delineamento estatístico utilizado foi em blocos ao acaso, no qual as famílias foram agrupadas em quatro sets, cada qual com quatro repetições e cem seedlings por parcela, espaçadas a 0,5 metros entre plantas e 1,40 metros entre linhas. As avaliações foram efetuadas durante duas safras agrícolas, correspondentes a primeira e a segunda soca, 2008 e 2009, respectivamente, sendo avaliadas as características diâmetro médio do colmo (DMC), peso total da parcela (P), número de colmos (NC), Brix da parte inferior do colmo (Brix PE) e Brix da parte superior do colmo (Brix PT). Todas as características foram significativas para famílias avaliadas, pelo teste F (P<0,01) nas análises conjuntas dos ambientes, demonstrando haver diferenças significativas entre as famílias. Os valores encontrados, no presente estudo, para o parâmetro genético coeficiente de variação genético (CVg), indicam grandes possibilidades de sucesso neste programa de melhoramento visando à seleção para as características avaliadas, sendo atribuídos os maiores ganhos genéticos quando utilizados os índices de Smith e Hazel e Mulamba e Mock, os quais permitiram ganhos simultâneos superiores em todas as características avaliadas para as melhores famílias.

Effect of intrarow plant spacing on the effectiveness of family selection in sugarcane: Selection indices / Efecto de la distancia entre plantas en la eficiencia en la selección de familias de caña de azúcar: Indices de selección / Efeito do espaçamento entre touceiras na eficiência na seleção de familias de cana-de-açúcar: Indices de seleção

Cross prediction trials or progeny tests for family selection are commonly employed at the beginning of each breeding cycle in clonally propagated crops such as sugarcane (Saccharum spp. Hybrid). When selecting sugarcane families, the factors affecting variability between and within those families should be considered. This research examined the influence of family and intra-row plant spacing on the efficiency of the index selection procedure as a method of simultaneous improvement of a population for multiple traits at the first selection stage of the Louisiana Sugarcane Variety Development Program (LSVDP). Therefore, the main objective of this study was to develop a selection index for selecting sugarcane families within the LSVDP. Expected genetic advance values for plant weight were greater in the wide-spaced indices than in the narrow-spaced ones. Irrespective of plant spacing, selection indices revealed that an increase in efficiency was observed over direct selection for plant weight when all four plant weight contributing traits were included along with plant weight. The efficiency in selection tended to decrease when indices were based on fewer traits. Nevertheless, a few of the indices that included two traits had relative efficiencies comparable to the best indices and the majority certainly was as effective as direct selection for plant weight.

Las pruebas de progenie son comúnmente utilizadas para la selección de familias en cultivos de reproducción asexual como la caña de azúcar (Saccharum spp. Híbrido). En la selección de familias de caña es importante considerar los factores que afectan la variabilidad existente, no solo entre familias, sino también dentro de cada familia. Se examinó la influencia de familias y del espacio entre plántulas de caña de azúcar en la eficiencia del índice de selección como una metodología para mejorar simultáneamente una población por múltiples características. El trabajo se llevó a cabo en la etapa inicial del Programa de Desarrollo de Variedades de Caña de Azúcar de Louisiana, EEUU (LSVDP, por sus siglas en inglés). El objetivo principal fue desarrollar un índice para selección de familias de caña de azúcar dentro del LSVDP. El avance genético esperado para el peso de planta fue mayor en los índices obtenidos usando datos provenientes de familias donde la distancia entre individuos fue mayor. Independientemente de la distancia entre plántulas dentro de la hilera, los índices de selección donde intervinieron los cuatro componentes del carácter peso de planta, incluyendo a éste, resultaron ser más eficientes que la selección directa para ese mismo carácter. La eficiencia en la selección tendió a disminuir en la medida en que los índices contenían menos caracteres. Sin embargo, algunos de los índices que incluían solo dos caracteres mostraron eficiencias comparables a los mejores índices y la mayoría de ellos fueron más efectivos que la selección directa por peso de planta.

Ensaios de predição de cruzamentos o testes de progênie são comumente utilizados no início de cada ciclo de melhoramento genético das culturas de reprodução vegetativa como a cana-de-açúcar (Saccharum spp. Híbrido). Na seleção de famílias de cana-de-açúcar é importante considerar os fatores que afetam a variabilidade, não só entre as famílias, mais também dentro de cada família. Analisou-se a influência das famílias e do espaçamento entre plantas na eficiência do índice de seleção como uma metodologia para melhorar simultaneamente mais de uma característica em uma população. O trabalho foi feito na fase inicial do Programa de Desenvolvimento de Variedades de Cana-de-Açúcar de Louisiana, EEUU (LSVDP, por sua sigla em Inglês). Portanto, o principal objetivo foi desenvolver um índice para a seleção de famílias de cana-de-açúcar dentro do LSVDP. O ganho genético esperado para o peso da touceira foi maior nos índices obtidos a partir de dados de famílias onde a distancia entre indivíduos foi maior. Os resultados indicaram que, quando os quatro caracteres que contribuem para o peso da touceira foram incluídos, independentemente do espaçamento entre touceiras, os índices de seleção apresentaram aumento na eficiência na seleção, em comparação com a seleção direta para o peso da touceira. Á medida que os índices de seleção foram baseados em menos caracteres, a eficiência na seleção tendeu a diminuir. No entanto, alguns dos índices que incluía dois caracteres tiveran eficiências comparáveis a os melhores índices e certamente a maioria deles foram tão eficazes como a seleção direta para peso da touceira.

Artificial family selection based on growth rate in cultivated lines of Litopenaeus vannamei (Decapoda, Penaeidae) from Venezuela

We investigated the effects of family selection on the growth rates of four genetic lines of Litopenaeus vannamei, the Pacific white shrimp, from Venezuela. The mean family weight at selection was 16.79 g and the mean growth rate was 0.169 g d-1 at a mean age of 138 days. The mean growth rates per generation were 0.141 g d-1 for the parental generation (P0), 0.173 g d-1 for the F1 and 0.191 g d-1 for the F2. Survival varied from 83.3 percent to 94.4%. There were statistically significant differences between lines, with lines B and C, growing at higher temperatures and lower salinities, showing the fastest growth. Regression analysis between growth rate and age for each genetic line showed high r² values, but smaller than those shown between growth rate and generation. The mean heritability (h²) estimated for growth rate was 0.25 ± 0.04, with line per generation values ranging from 0.18 to 0.38. The mean heritability for growth rate per line showed some variation but there was no correlation between heritability and growth rate. Females showed a greater gain in growth rate per generation than males due to their faster growth when they were older. This study shows the high potential of these L. vannamei populations for the future of shrimp culture in the Americas.