Full-sib Families Research Articles

Recurrent Interpopulation Selection in Popcorn: From Heterosis to Genetic Gains

In view of the need to develop new popcorn cultivars and considering the uncertainties in choosing the most appropriate breeding methods to ensure consistent genetic progress, simultaneously for both popping expansion and grain yield, this study addressed the efficiency of interpopulation recurrent selection regarding genetic gains, the study of the response in genetic parameters as well as heterotic effects on the control of the main agronomic traits of popcorn. Two populations were established, Pop1 and Pop2. A total of 324 treatments were evaluated, which consisted of 200 half-sib families (100 from Pop1 and 100 from Pop2), 100 full-sib families from the two populations and 24 controls. The field experiment was arranged in a lattice design with three replications in two environments, in the north and northwest regions of the State of Rio de Janeiro, Brazil. The genotype × environment interaction was partitioned and the genetic parameters, heterosis and predicted gains were estimated by the Mulamba and Mock index, based on selection results in both environments. The genetic parameters detected variability that can be explored in successive interpopulation recurrent selection cycles. Exploring heterosis for GY, PE and yield components is a promising option to increase grain yield and quality. The Mulamba and Mock index was efficient in predicting the genetic gains in GY and PE. Interpopulation recurrent selection proved effective to provide genetic gains for traits with predominantly additive and dominance inheritance.

Combined growth index determination and high-throughput sequencing provides new insights into wood formation in poplar

Wood is the raw material used in the production of paper and building materials. It also plays an important role in human productivity and survival. However, the regulatory mechanisms of wood formation remain unclear in woody plants. In this study, we selected two poplar clones with different growth rates from the same full-sib family and performed SMRT and Illumina sequencing. We obtained 218,439 consensus reads and 50.73 G Illumina clean reads for subsequent analysis. A total of 4032 novel genes, 6587 alternatively spliced (AS) genes, 34,895 AS events, and 3602 long noncoding RNAs (lncRNAs) were identified. Moreover, 2545 genes, 89 lncRNAs, and 554 AS events were found to be differentially expressed in the two clones. Furthermore, we found that 56 and 38 genes involved in wood formation could undergo alternative polyadenylation (APA) and AS, respectively. In addition, 377 lncRNAs have the potential to regulate wood formation. This study reveals potential factors that regulate wood formation at the transcriptional level and provides new insights into wood formation.

Estimation of genetic parameters for female reproduction traits in the Pacific oyster, Crassostrea gigas

The Pacific oyster (Crassostrea gigas) is one of the most important aquaculture species worldwide. Female reproduction traits are considered as the major factor for production efficiency. Estimating genetic parameters for female reproduction is a common method for formulating breeding program, which has not been evaluated in the Pacific oysters. Therefore, this study aimed to estimate the genetic parameters for female reproduction traits in Pacific oysters. Genetic parameters were performed on 44 full-sib Pacific oyster families, including 646 individuals from three cultured populations (“Haida No. 1” strain, South Korean population, and Japanese population) and a wild population. The heritability of female reproduction traits including relative brood amount and egg diameter ranged from 0.32 to 0.38, while the heritability of growth traits were in the range of 0.13–0.37, suggesting that both traits may benefit from successive selection breeding. The genetic and phenotypic correlations between female reproduction and growth traits were low at −0.44 to 0.33, indicating that these traits were relatively independent traits that could be improved respectively. The four populations showed significant growth differences, whereas no significant difference was observed in female reproduction traits. This study represents the first report of genetic parameters for female reproduction in Pacific oysters, which suggests that these traits may be improved through selection breeding.

Quantitative Genetics of a Hybrid Population of Eucalyptus nitens × Eucalyptus globulus: Estimation of Genetic Parameters and Implications for Breeding Strategies

In Chile, interspecific hybrids between Eucalyptus nitens × Eucalyptus globulus (GloNi) were developed by Arauco Forestry to capture specific traits from each parental species: growth rate and cold resistance from E. nitens (NIT) and wood properties from E. globulus (GLO). Field tests of E. nitens × E. globulus were distributed in two geographic zones: Arauco (12 tests) and Valdivia (15 tests), where growth and wood properties measurements were recorded at different ages. The hybrid population is composed of clones from 28 full-sib families, being the result of crossing 12 E. nitens females and 8 E. globulus males. Progeny from each of these families were vegetatively propagated and tested on each growth zone, with a total of 1214 clones developed. The quantitative genetic parameter estimates reveal high genetic variation in hybrid volume gain and wood properties, which make possible large genetic gain in all traits analyzed. Additionally, E. nitens has a considerable impact on the volume gain of the hybrid, making it important to test more parents in future interspecific crosses in both hybrid zones. In contrast, E. globulus demonstrated zero impact in volume. In wood traits, E. globulus in Arauco zone demonstrates a large effect on the genetic variability of these traits; meanwhile, in the Valdivia zone, E. nitens and E. globulus parents contributed roughly similar amounts of genetic variation. The high General Hybridizing Ability (GHA) and General Combining Ability (GCA) relationship between hybrid progeny and pure species progeny performance indicates that parents could be selected for interspecific crosses based on pure species test results for volume and wood properties.

Comparison on chromosome stability between inbred and outbred full-sib families of tetraploid Crassostrea gigas by cytogenetic technique

The building of the superior tetraploid strains is the key to the development of the oyster triploid industry. The tetraploids with abnormal chromosome number are often not conducive to the further breeding of its new strain. Inbreeding, which occurs frequently in artificially selected populations, is equally likely to occur in artificially induced tetraploid oysters. To explore the differences on chromosome stability between the inbred and outbred tetraploids of Crassostera gigas, 22 full-sib families with inbreeding coefficient of 0 (F0), 0.25 (F1) and 0.375 (F2) were built to compare the distribution and frequency of chromosome number of tetraploid cells. From the cellular level, the chromosome number of embryonic cells and somatic cells in all families mainly varied from 30 to 40, and with most cells containing 40. Of all the aneuploid cells observed, most of them contain 38 and 39 chromosomes. From the individual level, both the proportions of aneuploidy and mosaic individuals in inbred lines increased, maximally up to 13.89% and 27.78%, respectively. From the family level, the distributions of cell chromosome number in the inbred families were more dispersed than that in line F0. The aneuploidy rates of embryonic cells in inbred lines F1 and F2 were 6.3% and 19.5% higher than that in the outbred line F0, respectively. The rates of somatic cells were 11.3% and 15.5% higher than that in line F0. These results indicate that continuous inbreeding of tetraploid oysters may decrease their chromosome stability.

Computer vision system using deep learning to predict rib and loin yield in the fish Colossoma macropomum.

Computer vision system (CVSs) are effective tools that enable large-scale phenotyping with a low-cost and non-invasive method, which avoids animal stress. Economically important traits, such as rib and loin yield, are difficult to measure; therefore, the use of CVS is crucial to accurately predict several measures to allow their inclusion in breeding goals by indirect predictors. Therefore, this study aimed (1) to validate CVS by a deep learning approach and to automatically predict morphometric measurements in tambaqui and (2) to estimate genetic parameters for growth traits and body yield. Data from 365 individuals belonging to 11 full-sib families were evaluated. Seven growth traits were measured. After biometrics, each fish was processed in the following body regions: head, rib, loin, R + L (rib + loin). For deep learning image segmentation, we adopted a method based on the instance segmentation of the Mask R-CNN (Region-based Convolutional Neural Networks) model. Pearson's correlation values between measurements predicted manually and automatically by the CVS were high and positive. Regarding the classification performance, visible differences were detected in only about 3% of the images. Heritability estimates for growth and body yield traits ranged from low to high. The genetic correlations between the percentage of body parts and morphometric characteristics were favorable and highly correlated, except for percentage head, whose correlations were unfavorable. In conclusion, the CVS validated in this image dataset proved to be resilient and can be used for large-scale phenotyping in tambaqui. The weight of the rib and loin are traits under moderate genetic control and should respond to selection. In addition, standard length and pelvis length can be used as an efficient and indirect selection criterion for body yield in this tambaqui population.

Parametric mapping of QTL for resistance to European canker in apple in ‘Aroma’ × ‘Discovery’

Resistance to European canker (Neonectria ditissima) in apple is currently one of the most important breeding targets for commercial production in Sweden. Previous research has identified significant genetic variation in susceptibility to the disease, with the local Swedish cultivar ‘Aroma’ considered as one of the most resistant cultivars. Identification of genetic regions underlying the resistance of this cultivar would be a valuable tool for future breeding. Thus, we performed Bayesian quantitative trait loci (QTL) mapping for resistance to European canker in a full-sib family of ‘Aroma’ × ‘Discovery’. Mapping was performed with the area under the disease progression curves (AUDPCs) from all seven (AUDPC_All7) and the first four assessments (AUDPC_First4), and three parameters of a sigmoid growth model for lesion length. As a scale for the effect of the different parameters, historic phenotypic data from screenings of a genetically diverse germplasm was compiled and re-analyzed. The parametrization of the data on lesion growth increased the number of QTL that could be identified with high statistical power, and provided some insight into their roles during different stages of disease development in the current experimental setup. Five QTL regions with strong or decisive evidence were identified on linkage groups 1, 8, 15, and 16. The QTL regions could be assigned to either of the parameters lesion length at the first assessment (‘LL_A1’), the maximal lesion growth rate (lesion length doubling time, ‘t_gen’), and the lesion length at girdling (‘LL_G’). Three of these QTL were traced along the pedigrees of some known relatives of the FS family, and discussed in relation to future crosses for breeding and genetic research.

Effects of sexual polyploidization on reproductive development in a full-sib poplar family

Populus is an important source of woody biomass in the Northern Hemisphere. Sexual polyploidization plays a valuable role in the genetic improvement of Populus, resulting in tremendous variation in phenotypic traits. Most studies have focused on the variations in the vegetative growth of allopolyploid Populus; however, variations in the reproductive development of different polyploid genotypes of the progeny remain unclear. In this study, catkin traits, pollen size and viability, meiotic development, and reproductive ability were analyzed based on a full-sib family including diploid and triploid hybrids of (Populus pseudo-simonii × P. nigra ‘Zheyin3#’) × (P. × beijingensis) to understand the effects of sexual polyploidization on reproductive development in Populus hybrids. Catkin traits varied among the genotypes in the full-sib family. A ploidy change resulted in significant variation in male catkin length and male flower number per catkin but not in female catkin traits, suggesting that Populus catkin development may be more sensitive to respond to a change in ploidy level in male plants than in female plants. The male diploid hybrids had significantly smaller pollen grains, but higher pollen germination rates than the triploid hybrids. Giant pollen grains with large diameters were recorded in all-male diploid and triploid hybrids, which were speculated to be unreduced gametes. Premature cytokinesis, misorientation of the spindles, and aberrant cytokinesis were observed in a cytological analysis, which explained the production of unreduced pollen. Premature cytokinesis was only detected in triploid hybrids, which might be attributed to a ploidy change. The frequencies of meiotic abnormalities, such as precocious chromosomal migration, chromosome bridges, and micronuclei in the triploid hybrids were higher than those in diploid hybrids, suggesting that the unbalanced chromosomes in the triploid hybrids caused more complex meiotic chromosome behaviors. Backcrosses with the triploid hybrids resulted in low seed sets and seed germination rates, suggesting that polyploidization reduced pollen viability. Our findings provide new insight into the effect of sexual polyploidization on reproductive development in Populus and could be used to guide a Populus polyploid breeding program.

Identification of quantitative trait loci for growth traits in red swamp crayfish (Procambarus clarkii)

Genetic breeding is an important approach to improve the economic traits of aquaculture animals. Unfortunately, the genetic basis for important economic traits of red swamp crayfish, including growth-related traits, has not yet been reported. In the present study, two full-sib families and two natural populations were employed to identify quantitative trait loci (QTLs) for growth-related traits of red swamp crayfish. In total, 28 QTLs for five growth-related traits, including body weight, body length, carapace length, carapace width, and abdomen length, were repeatedly identified in more than two families/populations, by means of association analysis; nine of these displayed a heterosis effect. The phenotypic variations of the five investigated traits explained by the 28 QTLs ranged from 4.2% to 19.0%. Eight additive and three heterosis QTLs were further successfully validated using comparative analysis of favoured alleles between the small and big size crayfish groups in the natural population. In conclusion, this study investigated the genetic basis of growth-related traits in red swamp crayfish, which is of great significance for their application in the future molecular breeding of the species.

Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus.

Common full-sib families (c 2 ) make up a substantial proportion of total phenotypic variation in traits of commercial importance in aquaculture species and omission or inclusion of the c 2 resulted in possible changes in genetic parameter estimates and re-ranking of estimated breeding values. However, the impacts of common full-sib families on accuracy of genomic prediction for commercial traits of economic importance are not well known in many species, including aquatic animals. This research explored the impacts of common full-sib families on accuracy of genomic prediction for tagging weight in a population of striped catfish comprising 11,918 fish traced back to the base population (four generations), in which 560 individuals had genotype records of 14,154 SNPs. Our single step genomic best linear unbiased prediction (ssGLBUP) showed that the accuracy of genomic prediction for tagging weight was reduced by 96.5%-130.3% when the common full-sib families were included in statistical models. The reduction in the prediction accuracy was to a smaller extent in multivariate analysis than in univariate models. Imputation of missing genotypes somewhat reduced the upward biases in the prediction accuracy for tagging weight. It is therefore suggested that genomic evaluation models for traits recorded during the early phase of growth development should account for the common full-sib families to minimise possible biases in the accuracy of genomic prediction and hence, selection response.

Inheritance of wood properties and their radial variations in full-sib families of 36-year-old Japanese larch (Larix kaempferi (Lamb.) Carr.)

Key messageLarger differences of maximum load among families were found in mature wood compared to juvenile wood, suggesting the possibility of improving mature wood with higher resistance to rupture and maintaining characteristics of material in Larix kaempferi (Lamb.) Carr. by selecting specific mating parents.ContextBecause the wood from L. kaempferi trees is used for construction lumber, wood properties and bending properties should be focused on as targeted traits of tree breeding programs.AimsWe clarified the radial variation of inheritance for wood properties and bending properties and classified the features of bending properties among families in L. kaempferi.MethodsAnnual ring width, latewood percentage, air-dry density, microfibril angle, modulus of elasticity, modulus of rupture, and bending work at five radial positions were investigated for 15 full-sib families of 36-year-old L. kaempferi grown in two progeny test sites in Japan.ResultsHigher heritability at almost all radial positions was found in air-dry density. Phenotypic and genetic correlations between air-dry density and bending properties showed relatively higher values at almost all radial positions. Load-deflection curves in 15 families could be divided into three groups in juvenile and mature wood. Variation among groups for load-deflection curves in mature wood was relatively larger than that in juvenile wood.ConclusionAir-dry density can be used as a criterion to select trees with superior bending properties. Mature wood in L. kaempferi could be effectively improved by selecting individuals.

Morphological growth performance and genetic parameters on Korean pine in Northeastern China

Abstract Korean pine (Pinus koraiensis) is an economically valuable species owing to its excellent timber quality and nuts useful for various purposes. But few studies have been made on growth performance, and aspects combining the genetic gain and classification method on phenotypic similarity in the selection process of superior families. Thus, the present study aimed at analyzing the genetic variation and highlight suitable morphological traits for family selection; establishing trait correlations and families’ ordination based on similarities in phenotypic characters, and selecting elite families and suitable parent trees. Full-sib families from 28 crosses established in randomized complete block design from Naozhi orchard in Northeast China were used, and 11 morphological traits were investigated. Significant differences were observed among families for all traits. The traits coefficients of variation ranged from 6.07 to 56.25 % and from 0.029 to 15.213 % in phenotype and genotypic variation, respectively. A moderate level of inherited genetic control was observed (broad sense heritability H2, varied from 0.155 to 0.438). Traits related to stem growth were highly positively correlated to each other whereas crown traits showed a weak correlation with stem traits (Pearson correlation r, ranged from -0.161 to 0.956). Based on multi-trait comprehensive analysis, we selected six elite families and six parents, which resulted in a genetic gain of 5.6 %, 16.9 %, and 36.4 % in tree height, diameter at breast height, and volume, respectively. These results make a theoretical basis for selecting excellent families and establish orchards of Korean pine from improved seeds.

Genetic gain in Passiflora seed traits from recurrent selection among full-sib families

Genetic gain in Passiflora seed traits from recurrent selection among full-sib families

Genetic divergence for seed traits in Passiflora full-sib families under recurrent selection for resistance to the cowpea aphid-borne mosaic virus

Genetic divergence for seed traits in Passiflora full-sib families under recurrent selection for resistance to the cowpea aphid-borne mosaic virus

Estimativa da diversidade genética em famílias de irmãos completos de capim-elefante Cenchrus purpureus (Schumach.) Morrone

ABSTRACT One of the challenges of the energy sector is the identification of renewable resources with less impact on the environment and that are economically viable. This study aimed to estimate the genetic diversity of eleven full-sib families of elephant grass, using quantitative traits associated with bioenergy production. The trial followed a randomized blocks design, with four replications and each plot (family) consisting of five plants, totaling 220 genotypes. Five quantitative traits were measured: dry matter yield, dry matter percentage, plant height, stem diameter and number of tillers. The genetic diversity was estimated using multivariate methods (principal component analysis and hierarchical clustering). The analysis revealed a significant genetic diversity among the full-sib of elephant grass, with a greater variability observed for dry matter yield and number of tillers. The families 1, 2, 5, 7 and 8 exhibited superior genotypes for bioenergy production-related traits. The grouping analysis generated twenty clusters, enabling the differentiation of genotypes. Eight clusters comprised genotypes with a high dry matter yield and plant height, simultaneously, surpassing the overall mean for number of tillers.

Repeatability estimates in longitudinal data on guava trees

The use of longitudinal measurements is an essential practice both in Psidium guajava L. breeding and in other perennial crops in which covariance structures can be introduced to explain the form of dependence between measurements. Hence, this study aimed to analyze six covariance structures to identify one that best described the correlation between the repeated measurements in time in traits of guava full-sib families. The repeatability coefficient for each trait was estimated and the minimum number of evaluations required for estimates representing the population was determined. The work was performed based on average data of three yield-related variables from nine harvests of a guava tree population evaluated from 2011 to 2018. The best model was chosen based on the Akaike and Schwarz Bayesian information criterion. The autoregressive covariance structure best represented the dependencies among families between crops for all traits. The number of variables of fruits and total yield per plant presented repeatability estimates higher than 0.5 and may be essential traits for indirect selection of others, such as fruit mass, which had an estimated repeatability of 0.24, proving low regularity in the repetition of the character from one cycle to another. It was also possible to define four harvests as the minimum acceptable number of observations necessary on the same individual for these traits; therefore, the repetitions represented the individuals.

Genetic parameters and response to selection for thermal tolerance, summer survival and growth in hybrid oyster (Crassostrea gigas ♀ × C. angulata ♂)

The Pacific oyster Crassostrea gigas is the most commonly farmed mollusks worldwide, while its production has been hindered by massive mortalities linked to high temperatures. Selective breeding focusing on thermal tolerance is an attractive option for reducing the impact of massive mortalities, but the genetic basis underlying this trait is currently unknown. Hybridization between C. gigas and C. angulata was conducted and followed by one generation of family selection for thermal tolerance. The genetic parameters for thermal resistance, summer survival and growth and selection response were investigated by using 50 full-sibling families. The mean survival of all families ranged from 30.2 to 69.5%, reflecting the large variation of thermal tolerance in the hybrid population. The estimates of heritability for thermal tolerance were low to moderate, ranging from 0.19 ± 0.03 to 0.27 ± 0.05, confirmed that there is genetic basis for thermal tolerance. The phenotypic (r = 0.537, P < 0.01) and genetic correlations (r = 0.546, P < 0.01) between thermal tolerance and summer survival were positive and significant, while the phenotypic and genetic correlations between growth and survival (including thermal tolerance and summer survival) were positive but low (P > 0.05). High response to selection (ΔG = 36.33%) was observed after one generation of selection for thermal tolerance, and there was also corresponding response (ΔG = 14.46%) for summer survival. These results demonstrated that genetic selection to improve summer survival of oyster may be facilitated by selecting highly heat-tolerant lines.

Estimated of Genomic Estimated Breeding Value and Accuracy Analysis according to the Amount of Genotypes in the Full-Sib Family

Estimated of Genomic Estimated Breeding Value and Accuracy Analysis according to the Amount of Genotypes in the Full-Sib Family

GENETIC PARAMETERS OF FIELD SURVIVAL IN STRIPED CATFISH (Pangasianodon hypophthalmus)

Grow-out or field survival (GS) is one of the most important traits of striped catfish. Genetic parameters of GS in generation 4 of the growth selected population of this species were estimated based on the data of 8,004 tagged and stocked and 6,410 harvested fish representing 152 full-sib and half-sib families. The heritability and estimated and realized correlated responses for GS, its phenotypic or genetic correlations with harvest weight (HW) and other growth traits, and direct realized response for HW were calculated. The low and significantly different from zero heritability for GS (0.12±0.05) was estimated. The medium positive and no significant difference from zero genetic correlation between GS and HW was found, 0.41±0.24. The estimated selection responses with the proposed selection proportion of 13.0% for GS was 8.5% in trait unit. Current and accumulated correlated selection responses for GS were -7.8% and -1.6%, and 25.5% and 47.6%, respectively, by Estimated Breeding Value and Least Square Means estimation methods. In addition to these results, the high heritability and direct estimated and realized responses for HW pose a great potential for applying multi-trait selection, including both GS and HW in G4 and in the long run.

Estimation of Genetic Parameters and Optimum Breeding Programme Design in Korean Flatfish Breeding Population

Olive flounder (Paralichthys olivaceus) is a vital aquaculture species in East Asia. However, few studies that estimate the genetic parameters of this species have been conducted. We estimated the genetic parameters of growth traits and designed an optimum breeding programme for this species. Heritability, genetic and phenotypic correlations, and breeding values were estimated for growth traits: body weight (BW), total length (TL), and condition factor (CF). A linear mixed animal model using the restricted maximum likelihood (REML) algorithm was applied to the statistical analysis of 9 traits (BW, TL, and CF at 11, 18, and 22 months of age) for a total of 54,159 animals from 7 generations. Increases of 13%, 8%, and 6.5% in BW, TL, and CF at the harvest stage were observed, respectively, after 7 generations of selection. The heritabilities of all growth traits were moderate, ranging from 0.35 to 0.46. The phenotypic and genetic correlations between BW and TL were high and positive in all three stages (0.91 and 0.92, 0.91 and 0.93, and 0.88 and 0.91). The estimated breeding values of BW and TL increased over the generations; however, the estimated breeding value of CF fluctuated. The optimum progeny number within full-sib families for an accuracy of 0.632 is suggested to be between 10 and 25. Findings indicated that a considerable response to selection and single-trait selection based on BW would be effective in olive flounder.