Progeny Testing Research Articles

Age trends in genetic parameters and genetic gains of growth traits in multiple progeny test sites of hinoki cypress (Chamaecyparis obtusa)

ABSTRACT Growth data obtained from Chamaecyparis obtusa growing at 28 progeny test sites in the Kanto breeding region of Japan were analyzed to estimate the genetic parameters and genetic gains. Specifically, the data were used to estimate stem diameter at breast height (DBH), tree height (TH), and stem volume in order to assess the feasibility of breeding, and differences in genetic parameters and genetic gains associated with growth traits based on age and climatic conditions were clarified. The median values of narrow-sense heritability for DBH and TH across all ages ranged from 0.229 to 0.263 and from 0.201 to 0.433, respectively. Based on the efficiency of improvement (genetic gain per year), it appears that the most efficient selection for DBH and stem volume would be at one-third of the improvement target age (set to 30 years in the present study). We analyzed the variation of narrow-sense heritability and age trends of those among three groups of test sites exposed to different climatic conditions. Age and group × age interaction were shown to have significant effects on the narrow-sense heritability of TH and volume and that of DBH and volume, respectively. However, no significant effects of group × age interaction were detected on the efficiencies for gain per year of all traits, implying that this parameter might not be affected by climate conditions. Therefore, it was suggested that early selection is possible with almost equal efficiency in all climate groups.

Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)

In dioecious crops such as Actinidia arguta (kiwiberries), some of the main challenges when breeding for fruit characteristics are the selection of potential male parents and the long juvenile period. Currently, breeding values of male parents are estimated through progeny tests, which makes the breeding of new kiwiberry cultivars time-consuming and costly. The application of best linear unbiased prediction (BLUP) would allow direct estimation of sex-related traits and speed up kiwiberry breeding. In this study, we used a linear mixed model approach to estimate narrow sense heritability for one vine-related trait and five fruit-related traits for two incomplete factorial crossing designs. We obtained BLUPs for all genotypes, taking into consideration whether the relationship was pedigree-based or marker-based. Owing to the high cost of genome sequencing, it is important to understand the effects of different sources of relationship matrices on estimating breeding values across a breeding population. Because of the increasing implementation of genomic selection in crop breeding, we compared the effects of incorporating different sources of information in building relationship matrices and ploidy levels on the accuracy of BLUPs’ heritability and predictive ability. As kiwiberries are autotetraploids, multivalent chromosome formation and occasionally double reduction can occur during meiosis, and this can affect the accuracy of prediction. This study innovates the breeding programme of autotetraploid kiwiberries. We demonstrate that the accuracy of BLUPs of male siblings, without phenotypic observations, strongly improved when a tetraploid marker-based relationship matrix was used rather than parental BLUPs and female siblings with phenotypic observations.

Estimation the genetic parameters and evaluating the correlation between the maternal linear type traits and the birth weight of the progeny in Hanwoo cows

This study aimed to investigate the correlation between the linear type traits of mother cows (dams) and the birth weight(BW) of the progeny. The study used data collected between 2002 and 2018 by the Korea Animal Improvement Association (KAIA). This study evaluated the data specifically with respect to 19 traits. A statistical model was established to estimate the correlation between the maternal linear classification traits and the progeny BW. The significance of each statistical variable was analyzed using the generalized linear model (GLM) method in the SAS package 9.1.3 software, while the genetic parameters were estimated using the BLUPF90 Family program. The BW of Hanwoo cows increased by approximately 0.4 kg each year; however, the BW heritability was moderate (0.23). The linear classification traits showed values of 0.34, 0.37, 0.11, 0.45, 0.31, and 0.40, for ST (Vertical distance from the apex of the rump to the ground), BL (Horizontal distance between anterior shoulder point to the posterior extremity of the pin bone), RA (The slope from the rump to the pin bone), RL (Horizontal distance from the anterior rump to the tip of the pin bone), PBW (Lateral width of pin bone), and FS (Final score), respectively, with moderate heritability for all traits, except RA. The BW of the progeny showed phenotypic correlations of 0.06, -0.01, 0.03, and 0.04, and genetic correlations of 0.09, 0.03, 0.02, and -0.04 with ST, BL, RL, and PBW, respectively. The average parity in Hanwoo cows increased from 2.5 in 2016 to 2.8 in June 2020. There is a low genetic correlation between the maternal linear classification traits and the BW of the progeny. An increase in the parity of dams and a greater accumulation of progeny BW data and test records could lead to the accurate evaluation of the BW as a breeding objective trait.

Characteristics of meat production traits in the Hungarian Simmental herd selected for the simultaneous improvement of milk and meat production.

Phenotypic and genetic trends, population genetic parameters, and the heritability and breeding values of the fattening and slaughter traits - namely muscularity score (MUS), final fattening weight (FFW), weight gain per day of life (WGD), slaughter weight (SLW), carcass weight (CAR), dressing percentage (DRP), bone-meat production per day of life (BMP), SEUROP conformation and fat coverage score (EUR, FAT), and meat percentage (MEP) - of 1162 Hungarian Simmental bulls were evaluated with the progeny test database of the Association of Hungarian Simmental Breeders. Trends were calculated by weighted linear regression analysis, while the population genetic parameters and breeding values used the BLUP (best linear unbiased prediction) animal model and general linear model (GLM). According to the results, the lowest heritability value () was found in FAT. In the case of MUS, EUR and MEP, the values were moderate (, 0.26 and 0.32), and in the case of the other traits, high heritability values ( 0.42-0.52) were estimated. The phenotypic trends of the fattening and slaughter traits of bull progeny born between 2001 and 2019 showed a stagnant direction. Between the sires, the differences in the breeding values for some traits (WDG, CAR and BMP) were large, and with other traits (DRP, EUR and FAT), small differences were found. According to the data of the genetic-trend calculation, the steepness values of the evaluated traits were positive, and the genetic trends showed a slightly improving direction in the estimated period.

Integrating the Rate of Moisture Loss into Needle Retention Testing to Improve the Selection of Balsam Fir (Abies balsamea) for Use as Christmas Trees

A study was conducted to identify balsam fir (Abies balsamea) for use in Christmas tree breeding programs in Northeastern North America. A total of sixty-four phenotypically good trees were identified from a provincial clonal seed orchard in New Brunswick, a multi-aged natural seed production area in Nova Scotia, and an operational plantation in Quebec, Canada. Trees were selected for good growth and form, numbers, and vigour of internodal branches, acceptable crown taper, needle colour, age class, branch angle, needle configuration, and freedom from insects and diseases or deformities, all traits deemed desirable in a Christmas tree. Three branches from each tree were collected at two harvest dates each year, one early and one late during the normal harvesting season in 2020, 2021, and 2022. Qualitative assessments of colour and branch pliability were performed weekly in conjunction with needle loss rub tests. A quantitative assessment of moisture loss was conducted weekly by measuring branch weights. The combination of qualitative and quantitative assessments was used to identify 7 of the 64 trees for which one or more tested branches consistently remained green and pliable, retained the majority of their needles, and lost moisture at a significantly reduced rate in all six testing periods. Grafts of the seven ‘Select’ trees are currently being integrated into seed orchards in the three participating provinces. These second-generation seed orchards are part of breeding programs designed to develop Christmas trees that will perform well under warm fall conditions, an outcome of climate change. The results from this study combined with the progeny testing of the ‘Select’ trees will be used to test for the heritability of needle retention, a key trait for the next generation of Christmas trees in the Northeast.

A simulation study comparing advanced marker-assisted selection with genomic selection in tree breeding programs.

Advances in DNA sequencing technologies allow the sequencing of whole genomes of thousands of individuals and provide several million single nucleotide polymorphisms (SNPs) per individual. These data combined with precise and high-throughput phenotyping enable genome-wide association studies (GWAS) and the identification of SNPs underlying traits with complex genetic architectures. The identified causal SNPs and estimated allelic effects could then be used for advanced marker-assisted selection (MAS) in breeding programs. But could such MAS compete with the broadly used genomic selection (GS)? This question is of particular interest for the lengthy tree breeding strategies. Here, with our new software "SNPscan breeder," we simulated a simple tree breeding program and compared the impact of different selection criteria on genetic gain and inbreeding. Further, we assessed different genetic architectures and different levels of kinship among individuals of the breeding population. Interestingly, apart from progeny testing, GS using gBLUP performed best under almost all simulated scenarios. MAS based on GWAS results outperformed GS only if the allelic effects were estimated in large populations (ca. 10,000 individuals) of unrelated individuals. Notably, GWAS using 3,000 extreme phenotypes performed as good as the use of 10,000 phenotypes. GS increased inbreeding and thus reduced genetic diversity more strongly compared to progeny testing and GWAS-based selection. We discuss the practical implications for tree breeding programs. In conclusion, our analyses further support the potential of GS for forest tree breeding and improvement, although MAS may gain relevance with decreasing sequencing costs in the future.

Genetic control and early selection of three Corymbia species

The main objective of this study was to investigate genetic control for individual volume and genetic and phenotypic correlation between trait measured at two different ages. We also assessed three different selection intensities ( i = 1%, i = 5% and i = 10%) to understand the effects on genetic gain and effective size. Eight progeny tests were evaluated which included three tests of Corymbia citriodora subsp. citriodora (CCT), two tests of C. citriodora subsp. variegata (CCV), and three tests of C. torelliana (CTO). Narrow-sense heritability [Formula: see text] ranged from 0.26 to 0.62 for the CCT tests, from 0.07 to 0.21 for the CCV tests, and from 0.14 to 0.69 for CTO. The coefficients of individual genetic variation ([Formula: see text]) ranged from 22.5% to 63.9% for CCT, from 19.3% to 28.3% for CCV, and from 22.8% to 41.3% for CTO. Considering a selection intensity of 10%, the Ne after selection would range from 31 to 98 for CCT, 36 to 47 for CCV, and 45 to 62 for CTO. For the TP8 CTO test, a selection intensity greater than 10% is recommended. With a selection intensity of 10%, genetic gains ranged from 25 to 107% for CCT, from 14 to 27% for CCV, and from 19 to 64% for CTO.

Partitioning of the genetic trends of French dairy sheep in Mendelian samplings and long-term contributions

The genetic trend of milk yield for 4 French dairy sheep breeds (Lacaune, Basco-Béarnaise, Manech Tête Noire, and Manech Tête Rousse) was partitioned in Mendelian sampling trends by categories of animals defined by sex and by selection pathways. Five categories were defined, as follows: (1) artificial insemination (AI) males (after progeny testing), (2) males discarded after progeny testing, (3) natural mating males, (4) dams of males, and (5) dams of females. Dams of males and AI males were the most important sources of genetic progress, as observed in the decomposition in Mendelian sampling trends. The yearly contributions were more erratic for AI males than for dams of males, as AI males are averaged across a smaller number of individuals. Natural mating males and discarded males did not contribute to the trend in terms of Mendelian sampling, as their estimated Mendelian sampling term is either null (natural mating males) or negative (discarded males). Overall, in terms of Mendelian sampling, females contributed more than males to the total genetic gain, and we interpret that this is because females constitute a larger pool of genetic diversity. In addition, we computed long-term contributions from each individual to the following pseudo-generations (one pseudo-generation spanning 4 years). With this information, we studied the selection decisions (selected or not selected) for females, and the contributions to the following generations. Mendelian sampling was more important than parent average to determine the selection of individuals and their long-term contributions. Long-term contributions were greater for AI males (with larger progeny sizes than females) and in Basco-Béarnaise than in Lacaune (with the latter being a larger population).

Phenotyping of architecture traits of loblolly pine trees using stereo machine vision and deep learning: Stem diameter, branch angle, and branch diameter

Loblolly pine is one of the most planted forest tree species in the Southern United States for sawtimber production. The sawtimber yield potential of a pine tree is significantly impacted by its stem and branch architecture, which is of important focus in tree improvement programs. However, phenotyping these traits in the upper crown of pine trees is currently based on subjective visual assessments. This study investigated the feasibility of quantifying stem diameter, branch angle, and branch diameter of six-year-old loblolly pine trees in a progeny test using stereo 3D imaging, deep learning-based instance segmentation, and image and point cloud processing techniques. Instance segmentation of branches and stems was performed as well as principal component analysis (PCA) in 2D images, followed by 3D reconstruction of the segmented organs. The resulting 3D point clouds were further processed using random sample consensus (RANSAC) and statistical outlier removal to extract stem diameter, branch angle, and branch diameter. When compared to the manual ground-truth measurements, the three system-derived parameters achieved RMSEs of 0.055 m, 5.0˚, and 5.6 mm, respectively. In addition, Bland-Altman analyses showed that the stem diameter and branch angle estimations were found with limits of agreement of±0.098 m and±9.8˚, respectively, with nonsignificant biases. On the other hand, branch diameter estimation showed −12.1 mm and 9.3 mm for lower and upper limits of agreement with a bias. The proposed system demonstrates promising potential as a high-throughput low-cost precision phenotyping tool for the characterization of loblolly pine tree architecture under field conditions, facilitating the selection of superior genotypes with improved sawtimber properties.

Phenotyping wood properties of Corymbia torelliana x Corymbia citriodora and Eucalyptus dunnii based on NIR spectra

ABSTRACT Selecting individuals in breeding programs for pulp production, the physical and chemical wood traits must be considered in the genotype selection. In this study, trees from hybrid progeny tests of Corymbia torelliana x Corymbia citriodora (CTOxCCT) and progenies of Eucalyptus dunnii (EDU) were investigated. Sawdust of genetically selected standing trees was collected, classified and prepared for near infrared (NIR) spectra readings. The chemical properties of the selected trees were determined through kraft pulping. Predictive models for each property were developed based on the reference data and NIR spectra. Two approaches for models were developed. The first approach, models were fitted with 25 samples of CTOxCCT, and in the second approach, models were fitted using 61 samples (25 of CTOxCCT and 36 of EDU). The estimated R²cv values were 0.60 and 0.73 for basic chip density, 0.37 and 0.65 for extractive contents, 0.56 and 0.53 for total lignin contents, 0.63 and 0.66 for S/G ratio, and 0.52 and 0.77 for screened pulp yield for the first and second approaches, respectively. All developed models have potential for ranking trees in breeding programs. NIR spectroscopy can potentially be applied as a high-throughput field phenotyping tool where thousands of varieties need to be evaluated.

Whole blood transcriptome analysis of lactating Murrah buffaloes divergent to contrasting genetic merits for milk yield

Functional genome profiling of Murrah buffaloes (Bubalus bubalis) was performed for milk-production trait by whole blood transcriptome analysis comparing RNA-seq data assembled from high and low milk producing multiparous (5 -6 parity) animals. These buffaloes reflected the genetic merit inherited as daughters born to extremely high- and low-end bulls evaluated under a progeny testing scheme and ranked by the estimated breeding value. The average standard milk yield (SMY) over the 305 d during the parity was recorded as 2909.50L ± 492.63 and 1869.57 ± 189.36L in high- and low-performance buffaloes, respectively. The “reference” assembly data was assembled from transcriptome libraries of a group of buffaloes (n=16), comprising of animals in different physiological states. Replicates selected within each category of the high and low genetic merit animals showed a correlation coefficient of high order (R2=0.98) while comparing with the `reference' assembly. The sequence data of selected buffaloes, mapped over the Mediterranean water buffalo genome, revealed differentially expressed genes (DEGs) distinctly depicted via heat maps and volcano plots obtained for two categories of animals, determining more than 25,000 genes via the Cufflink analysis. DEGs included 83 down-regulating and 142 up-regulating genes (p<0.05, FDR<0.05). Functional classification of the DEGs revealed a fine networking of biological processes, primarily cell signaling, cell proliferation, cell differentiation, RNA splicing, fat metabolism, and inflammasome generation. These processes are regulated by transcription factors and binding proteins covered under the network of TNF alpha signaling, NF-kappa B signaling and MAPK PI3K-AKT signaling pathways/ cascade emerged as main biological pathways. Emerged pathways revealed remarkably intricate tuning of metabolic and cell development processes converging into milk production in buffaloes. Segregated patterns of gene expression obtained for high and low milk producing buffaloes using the non-invasive method of whole blood transcriptome analysis has emerged as a promising resource comprising gene network and protein -protein interactions, primarily involved in lactation. Synergism of transcription factors and binding proteins promoting epigenetic regulation at all development stages of mammary tissue induce mammogenic and lactogenic responses for subsequent milk secretion under optimum feeding management. These findings may help improve breeding strategies to achieve the desired milk yield in Murrah buffaloes.

Morphological Crown Attributes Contributing to Differential Height and Diameter Growth among Families in a Coastal Douglas-Fir Progeny Test: Crown Structural Evidence for Crop Ideotypes

Theoretical tree crop ideotypes have long and narrow live crowns with a high total leaf area. This crown form allows more efficient exploitation of site resources, in part by physically occupying less growing space per unit leaf area and by packing a greater number of trees into a given area. Genetic selection for crop ideotypes has been proposed as a strategy for maximizing productivity per unit area in stands managed under intensive silviculture. The primary objective of this study was to test the relationship between the relative growth performance of different families in a Douglas-fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco) progeny test and morphological crown attributes that conform to a theoretical crop ideotype. The overarching goal was to identify attributes conferring superior height and diameter growth on families and to facilitate the incorporation of these attributes and associated growth mechanisms into hybrid growth models for intensively managed plantations. Crown structural attributes were measured on destructively sampled trees and averaged for the entire crown and each third of live crown length among families. Multivariate analysis revealed that crown attributes averaged over the entire crown performed best for identifying families with different height and diameter growth, followed successively by the bottom, middle, and top crown third. Trees with relatively short branch lengths and steep branch angles tended to have higher total leaf area per unit crown length (TLACL), and this structural attribute showed a strong positive correlation with cumulative diameter growth. The ratio of crown width to crown length (CWL) was moderately and negatively correlated with cumulative height growth. The families displaying the most rapid diameter growth in this progeny test conformed to a theoretical crop ideotype, while those with the most rapid height growth displayed crown attributes with a less obvious relationship to the crop ideotype concept. TLACL implied one possible mechanism driving genetic gain in Douglas-fir families, given its high heritability and strongly positive correlation with growth performance. Incorporating TLACL as an explanatory variable in diameter growth models could at least partly represent different genetic levels. TLACL is less strongly correlated with height growth rate, so incorporating CWL may better represent genetic effects on height growth models.

Микросателлитные локусы в генетической оценке плюсовых деревьев Pinus sylvestris L.

In this study, a comparative analysis was performed to estimate the genetic diversity levels of Pinus sylvestris L. in 49 seed orchards of I generation and progeny test plantings using 4-nucleus microsatellite loci. The seed orchards are located in the Petrozavodsk and Zaonezhye regions of the Republic of Karelia. The progeny trials were created by half-sibling seed progenies of the clones in the Petrozavodsk seed orchard. Micro-Checker software was used to identify null alleles and exclude genotyping errors. Coefficients of genetic originality were determined by examining the genetic structure of breeding objects in relation to the proportion between the rare and the dominant alleles for each selected tree. A major part of the rarest alleles (27.3–37.0 %) and a small fraction of the most common alleles (3.3–14.8 %) were detected for the distinct range of the pine trees in both seed orchards and test cultures. The largest number (40) of all identified alleles (51) was found in the Petrozavodsk seed orchard. The Hardy-Weinberg test comparing allele rates to expectational values showed a lack of heterozygotes in each category of the empirical substances. The selected material also had high levels of allelic and genetic diversity. The average number of alleles per locus ranged from 7.75 to 10.50. The average effective number was from 5.00 to 6.54. The observed heterozygosity varied from 0.60 to 0.70. The expected heterozygosity was 0.63–0.71. The numerical deviations were statistically insignificant. The AMOVA molecular dispersion result was 5 %, indicating the absence of significant genetic differentiation between the breeding objects. The heterozygote deficiency was caused not only by the presence of null alleles, but also by the selection. Namely, the set of alleles in the experimental material, randomly selected from a limited number of genotypes (clones), may differ from the natural population. The high level of the rarest alleles in the given range of the pine trees can also be explained as a selection effect. The results obtained in this study are important for creating breeding objects with higher genetic value. For citation: Ilinov A.A., Raevsky B.V. Genetic Evaluation by Microsatellite Loci of Pinus sylvestris L. Plus Trees. Lesnoy Zhurnal = Russian Forestry Journal, 2023, no. 3, pp. 48–68. (In Russ.). https://doi.org/10.37482/0536-1036-2023-3-48-68

RELATIONSHIP BETWEEN FRESH FRUIT BUNCH PRODUCTION AND OIL IN THE BUNCH OF TWO DESCENDANTS OF BM119 AVROS FROM IOI PISIFERA BREEDING PROGRAMME

This short paper analyses the performance of two AVROS descendants of BM119 oil palm. Two progeny testing DxP trials using pisifera descendant of BM119 from PORIM Kluang (PK754) and Ulu Dusun (UD33) laid out in 2009 in similar soil and adjacent to each other had performed differently for fresh fruit bunch (FFB) production and oil in the bunch (OB). Progenies of AVROS of PK754 crossed with Deli dura yielded significantly high FFB. However, UD33 yielded significantly higher OB when compared to PK754. There is a quadratic expression for families of progenies showing high FFB production, but relatively low OB and reverse was the situation for families exhibiting low FFB production and high OB. However, the mean total oil (kg) per palm per year in DxP crossed with both pisifera progenies were not significantly different. This indicates that some of the AVROS selected could have high FFB production, while others were high for OB. Somehow, the high FFB compensates the low OB in total oil production and vice versa in the two AVROS pisiferas studied. Keywords: Oil palm breeding, BM119, AVROS, pisifera.

Novel interpretation of sperm stress test and morphology for maturity assessment of young Norwegian Red bulls

The use of genomic selection significantly reduces the age of dairy bulls entering semen production compared to progeny testing. The study aimed to identify early indicators that could be used for screening bulls during their performance testing period and could give us insight into their future semen production performance, acceptance for the AI station, and prediction of their future fertility. The study population consisted of 142 young Norwegian Red bulls enrolled at the performance test station, followed until we received semen production data, semen doses, and, subsequently, non-return rates (NR56) from the AI station. A range of semen quality parameters were measured with computer-assisted sperm analysis and flow cytometry from ejaculates collected from 65 bulls (9–13 months). The population morphometry of normal spermatozoa was examined, showing that Norwegian Red bulls at 10 months of age have homogenous sperm morphometry. Norwegian Red bulls could be separated into 3 clusters according to their sperm's reaction patterns to stress test and cryopreservation. Results of semi-automated morphology assessment of young Norwegian Red bulls showed that 42% of bulls rejected for the AI station and 18% of bulls accepted had ejaculates with abnormal morphology scores. For the youngest age group at 10 months, the mean (SD) proportion of spermatozoa with normal morphology was 77.5% (10.6). Using novel interpretation of sperm stress test combined with sperm morphology analysis and consecutive cryopreservation at a young age allowed identification of the candidate's sperm quality status. This could help breeding companies introduce young bulls earlier to the AI stations.

Extractives Content of White Jabon (Neolamarckia cadamba) and Red Jabon (Neolamarckia macrophyllus) Stemwood from Wonogiri, Central Java

Jabon is a fast-growing tree species with two types, white and red. The families or the origin of the mother tree are sources of variation that influence the chemical composition, particularly the extractive properties. This research aimed to determine the chemical properties of the wood and bark of 10-year-old white Jabon (families 23, 11, and 6) and 5-year-old red Jabon (families 75, 85, and 2) planted in a progeny test plot in Wonogiri, Central Java. In the wood portion of white Jabon, family 23 had the highest n-hexane (HEC), methanol (MEC), and hot water (HWEC) soluble extractive contents, as well as total extractive content (TEC) and total flavonoid content (TFC), while family 6 had the highest total phenolic content (TPC). Meanwhile, in red Jabon, family 75 had the highest HEC, HWEC, and TFC, family 2 had the highest MEC and TEC, and family 85 had the highest TPC. In the bark portion, family 11 had the highest HEC, MEC, TEC, and TPC, while family 6 had the highest HWEC and TFC for white Jabon. In red Jabon, family 2 had the highest HEC, family 85 had the highest MEC, HWEC, and TEC, while family 75 had the highest TPC and TFC.

Evaluating a short vs. long-term progeny test and investigating physiology associated with survival in extreme low salinity for the eastern oyster Crassostrea virginica

Low salinity negatively affects growth and survival in the eastern oyster, which decreases productivity of aquaculture operations along the mid-Atlantic and Gulf Coasts of the United States. With heavy rainfall events predicted to become more frequent, coastal aquaculture operations face increased risk of prolonged exposure to extreme low salinity conditions. While recent experimental work has determined that survival in extreme low salinity (< 3) is a moderately heritable trait in the eastern oyster, further experimental challenges were conducted to investigate the importance of challenge duration and temperature on the survival phenotype and estimation of its genetic parameters to hone the experimental challenge for potential incorporation into a breeding program. Growth (shell height) and algal removal were also assessed to investigate physiological phenotypes associated with differential survival in extreme low salinity. A subset of individuals from 51 half-sibling families were exposed to one of two experimental challenges: a short-term low salinity (2.5) challenge at constant temperature (27 °C) for 2 months, or a long-term low salinity (2.5) challenge where temperature was adjusted daily to match local ambient conditions for 6-months. Differential mortality was observed across families for both the short-term and long-term low salinity challenges, and narrow-sense heritability estimates were similar for both challenges (short-term h2 = 0.35, long-term h2 = 0.4). Strong phenotypic (rS = 0.89) and genetic (rG = 0.81) correlations for family mortality were found between challenges. Algal clearance metrics over a 24-h clearance experiment differed among families (p < 0.001), but were only weakly associated with family survival in the long-term low salinity exposure (range p = 0.08–0.23, R2 = 5–10%). Growth was negligible during the long-term challenge. However, after being returned to ambient salinities (13), there was no difference in growth rate, wet weight gain, or mortality between oysters from families with low or high survival in the long-term exposure (p > 0.05), indicating that low salinity tolerant oysters can recover following low salinity events. This work shows that a short-term (2 month) low salinity (2.5) challenge at a constant temperature captures the same patterns of family mortality as a 6-month, temperature fluctuating challenge. Additionally, measuring individual oyster clearance rate and the parameters derived from the algal removal curves provide additional insight into the physiological status of oysters under extreme low salinity stress.

Rapid and precise genotyping of transgene zygosity in mice using an allele-specific method.

Precise determination of transgene zygosity is essential for use of transgenic mice in research. Because integration loci of transgenes are usually unknown due to their random insertion, assessment of transgene zygosity remains a challenge. Current zygosity genotyping methods (progeny testing, qPCR, and NGS-computational biology analysis) are time consuming, prone to error or technically challenging. Here, we developed a novel method to determine transgene zygosity requiring no knowledge of transgene insertion loci. This method applies allele-specific restriction enzyme digestion of PCR products (RE/PCR) to rapidly and reliably quantify transgene zygosity. We demonstrate the applicability of this method to three transgenic strains of mice (Atm TgC3001L, Nes-Cre, and Syn1-Cre) harboring a unique restriction enzyme site on either the transgene or its homologous sequence in the mouse genome. This method is as accurate as the gold standard of progeny testing but requires 2 d instead of a month or more. It is also exceedingly more accurate than the most commonly used approach of qPCR quantification. Our novel method represents a significant technical advance in determining transgene zygosities in mice.

Spatial heterogeneity analysis for estimating breeding values of tree height in a hybrid larch progeny test plantation

ABSTRACT Microenvironmental heterogeneity in forest stands results in spatial variations in growth traits. Especially in progeny tests in tree breeding, this spatial variation can prevent the accurate estimation of genetic parameters, including breeding values. To quantify spatial heterogeneity, genetic models incorporating spatial coordinate information have been effectively used to accurately estimate breeding values of individuals. In this study, we measured the height of all Japanese larch and hybrid larch individuals in a progeny trial at 1, 2, 5, 10, and 15 years after planting and calculated genetic parameters, including breeding values, using genetic models. According to the fittings of the candidate models, a genetic model incorporating spatial coordinate information is more suitable for estimating genetic parameters. Overall, a genetic model incorporating spatial coordinate information could be effective in explaining the genetic effects of tree height, which will be useful for estimating more accurate breeding values in hybrid larch breeding programs.

Genetic variability and &lt;i&gt;ex situ&lt;/i&gt; conservation strategies for the neotropical tree &lt;i&gt;Parkia platycephala&lt;/i&gt; Benth.

Parkia platycephala, known commonly as faveira, is a native species that occurs widely throughout Brazil and has high nutritional value and ecological potential. The objective of this study was to estimate the genetic variability in a P. platycephala provenance and progeny test. The test was established using a randomized block design, with 45 progenies from three provenances. The evaluated quantitative traits included height (HEI), diameter at ground level (DGL), and diameter below the first bifurcation (DFB). The data were submitted to Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP) analysis, from which estimates of genetic parameters, genetic correlations, BLUPs, genetic gains, and effective population size were obtained. Estimates of individual narrow sense heritability (h2a) and within progeny heritability (h2w) ranged from low to moderate (0.01 a 0.39), with the highest values observed for DGL (0.32 and 0.39, respectively). The coefficient of individual variation (CVgi(%)) and between progeny genetic variation (CVgp(%)) indicate the existence of genetic variability between and within provenances. The FST vaues demonstrate low to moderate genetic differentiation among the three populations, and genetic correlations between traits were all positive and significant. The results obtained show that there is genetic variability between the studied provenances and progenies. This ensures not only the ex situ conservation of the species, but it can also be exploited in breeding programs.