Search

The interaction between genotype and environment (GEI) significantly influences plant performance, crucial for breeding programs and ultimately boosting crop productivity. Alongside GEI, breeders encounter another hurdle in their quest for yield improvement, notably adverse and negative correlations among pivotal traits. This study delved into the stability of white sugar yield (WSY), root yield (RY), sugar content (SC), extraction coefficient of sugar (ECS), and the interplay among essential traits including RY, SC, alpha amino nitrogen (N), sodium (Na+), and potassium (K+) across 15 sugar beet hybrids and three control varieties. The investigation spanned two locations over two consecutive years (2022–2023), employing a randomized complete block design with four replications to comprehensively analyze these factors. The analysis of variance highlighted the significant effects of environment, genotype, and GEI at the 1% probability level. Notably, the AMMI analysis of GEI revealed the significance of the first component for WSY, RY, and SC, with the first two components proving significant for ECS. Within the linear mixed model (LMM), WSY, RY, SC, and ECS demonstrated significant effects from both genotype and GEI. In the WAASB biplot, genotypes 10, 8, 17, 6, 13, 14, 15, 7, 12, and 16 exhibited stability in WSY, while genotypes 9, 10, 6, 14, 7, 8, 13, 12, 18, and 15 displayed stability in RY. Additionally, genotypes 10, 15, 12, 13, 16, 17, 6, and 14 were stable for SC, and genotypes 8, 10, 7, 6, 13, 12, 16, 17, 15, 14, and 18 showcased stability in ECS, boasting above-average yield values. In the genotype by yield × trait (GYT) biplot, genotypes 15, 18, and 16 emerged as top performers when combining RY with SC, Na+, N, and K+, suggesting their potential for inclusion in breeding programs. [ABSTRACT FROM AUTHOR]

Abstract The interaction between genotype and environment (GEI) significantly influences plant performance, crucial for breeding programs and ultimately boosting crop productivity. Alongside GEI, breeders encounter another hurdle in their quest for yield improvement, notably adverse and negative correlations among pivotal traits. This study delved into the stability of white sugar yield (WSY), root yield (RY), sugar content (SC), extraction coefficient of sugar (ECS), and the interplay among essential traits including RY, SC, alpha amino nitrogen (N), sodium (Na+), and potassium (K+) across 15 sugar beet hybrids and three control varieties. The investigation spanned two locations over two consecutive years (2022–2023), employing a randomized complete block design with four replications to comprehensively analyze these factors. The analysis of variance highlighted the significant effects of environment, genotype, and GEI at the 1% probability level. Notably, the AMMI analysis of GEI revealed the significance of the first component for WSY, RY, and SC, with the first two components proving significant for ECS. Within the linear mixed model (LMM), WSY, RY, SC, and ECS demonstrated significant effects from both genotype and GEI. In the WAASB biplot, genotypes 10, 8, 17, 6, 13, 14, 15, 7, 12, and 16 exhibited stability in WSY, while genotypes 9, 10, 6, 14, 7, 8, 13, 12, 18, and 15 displayed stability in RY. Additionally, genotypes 10, 15, 12, 13, 16, 17, 6, and 14 were stable for SC, and genotypes 8, 10, 7, 6, 13, 12, 16, 17, 15, 14, and 18 showcased stability in ECS, boasting above-average yield values. In the genotype by yield × trait (GYT) biplot, genotypes 15, 18, and 16 emerged as top performers when combining RY with SC, Na+, N, and K+, suggesting their potential for inclusion in breeding programs.

Poplar plantations cover 31.4 million ha around the world and supply timber for paper, sawn wood and other wood-based products. In each region where poplars are planted, it is possible to identify “model clones” which are massively adopted by foresters. Improving the rationale of clone selection in breeding programs requires a comprehensive understanding of the physiological traits that explain the differences in genotypes growth. Moreover, given that growth is related to the use of resources (water, light and nutrients) we also need to determine which morphological and physiological traits explain the model condition of most widespread clones. A controlled-condition study was carried out to evaluate eight Populus deltoides and two Populus × canadensis clones, including the model Populus deltoides €˜Australiano 129/60’. For each clone, physiological and morphological traits related to biomass partitioning (roots, stem and leaf dry mass), growth (height, diameter), light use (leaf area duration, leaf size, net photosynthetic rate), water use (stem hydraulic conductivity, water consumption) and nutrient use (nitrogen and phosphorus concentrations) were measured. High variability in the physiology and morphology was observed among clones, and similar and contrasting clones in relation to the model clone were identified. Similarities among clones varied depending on the characteristic being evaluated at the time-water use, light use or nutrient use. The results showed that variability not only relates to visible phenotype, but also to functionality. This information is significant since the breeding programs can evaluate non-traditional traits and select genotypes which are similar or complementary to the model clone. The characterization of model clones is key for breeding programs which seek new candidates taking into account the use of water, nutrients and light. It is also important because it helps explain why foresters prefer one clone over others. Knowledge about functional variability within clones of the same species enables foresters to conduct more intelligent and site-specific silviculture and to optimize the genotype selection in breeding programs.

Petroselinum crispum (Mill.) Nym. ex A.W. Hill (Parsley) is a culinary and medicinal vegetable of the family Apiaceae, which has been used by humans since ancient time. A molecular genetic diversity study was conducted on 10 Iranian populations of P. crispum using start codon targeted (SCoT) molecular markers to investigate infraspecific genetic diversity and population structure. The nuclear genomes extraction were performed using the cetyltrimethylammonium bromide (CTAB) protocol, then amplified using 10 SCoT primers. We found a large amount of population genetic differentiation index (GST) and total genetic difference in the pooled populations (HT) among the examined populations, which were supported by HS, NM. Additionally, we detected a significant genetic diversity (PhiPT = 0.755, P = 0.001) among the populations and their individuals by the analysis of molecular variance (AMOVA) test, in which its great proportion was assigned to among populations. We detected the largest amounts of genetic polymorphism in populations 1 and 5, while a reverse condition was observed for population 7. We found four genotype groups among the populations that was similar with phytogeographic mapping. The level of genetic divergence between populations (PhiPT) of each genotype was relatively low. This species produce protandrous florets and cross-pollination plays a significant role in seed production. Therefore, the genetic structure of genotypes must be heterogeneous. In Iran, the genetic structure of all genotypes was nearly homogenous which resulted from a flat rate of gene flow, which agreed with our estimated amount of NM (0.13). We supposed a range of isolation mechanisms including, isolation by distance, isolation by environment, isolation by ecology, and isolation by resistance act as driving forces to create high genetic differentiation among the parsley populations. These genotypes can be used for future genetic and breeding research to develop new cultivars can survive under biotic and abiotic stresses and yield high biomass. [ABSTRACT FROM AUTHOR]

The present study was carried out to evaluate the quality of different pear genotypes used in the breeding programs at Genetic and Breeding Department of Research Institute for Fruit Growing Pitești, Romania. Thirteen new pear genotypes harvested at the commercial maturity stage: 'Argessis', 'Carpica', 'Cristal', 'Daciana', 'Haydeea', 'Isadora', 'Paradox', 'Paramis', 'Romcor', 'P20R41P30', 'SP06C2P', 'Triumph' and 'Tudor' were compared with internationally recognized varieties: 'Monica' (Romanian cultivar), 'Xenia' and 'Williams'. In this study we analyzed the commercial parameters (weight, firmness, color) and the biochemical indicators (total dry mater content, soluble dry matter, titratable acidity, the soluble dry matter/titratable acidity ratio, vitamin C, and polyphenols). The obtained data leads to the conclusion that 'Isadora' and 'SP06C2P5P' fruits have the biggest chance to fulfill consumer expectations, due to their commercial qualities, then the reference variety 'Williams' cultivar. Also, the 'Isadora' variety had the content of polyphenols and the total dry substance superior to the three control cultivars. [ABSTRACT FROM AUTHOR]

Alpaca fibers are used to create luxury garments, and simultaneous selection for optimizing fiber density and the density of hair ducts in the skin of alpacas could result in a more profitable product for breeders. The objective of this study was i) to quantify fiber density (FibDen), density of hair ducts (DenDuc), and the relationship between No. of fibers/No. of ducts (Fib/Duc) by age and sex, and ii) to estimate heritability and genetic correlation between FibDen and DenDuc. This study was conducted in the CEDAT (Centro de Desarrollo Alpaquero de Toccra) in the Department of Arequipa, Peru. A total of 1,813 alpacas of different sex and age with pedigree information were analyzed from years 2004–2018. The quantification of FibDen, DenDuc and Fib/Duc was estimated using Fiber-Den equipment in an area of 1 mm2 in the middle rib region of the animal. The average FibDen, DenDuc and Fib/Duc was 24.75 ± 5.48, 7.83 ± 2.17 and 3.25 ± 0.55, respectively. The heritability for FibDen, DenDuc, and Fib/Duc was 0.48 ± 0.04, 0.53 ± 0.04, and 0.20 ± 0.03, respectively. The genetic correlation between FibDen and DenDuc was 0.87 ± 0.06. The estimated heritabilities of these traits in Peruvian alpaca population are moderate to high and indicate that these characteristics could be used as selection criteria in breeding programs.

Abstract Genetic improvement is crucial for ensuring food security globally. Indeed, plant breeding has contributed significantly to increasing the productivity of major crops, including rice, over the last century. Evaluating the efficiency of breeding strategies necessitates a quantification of this progress. One approach involves assessing the genetic gain achieved through breeding programs based on quantitative traits. This study aims to provide a theoretical understanding of genetic gain, summarize the major results of genetic gain studies in rice breeding, and suggest ways of improving breeding program strategies and future studies on genetic gain. To achieve this, we present the concept of genetic gain and the essential aspects of its estimation. We also provide an extensive literature review of genetic gain studies in rice (Oryza sativa L.) breeding programs to understand the advances made to date. We reviewed 29 studies conducted between 1999 and 2023, covering different regions, traits, periods, and estimation methods. The genetic gain for grain yield, in particular, showed significant variation, ranging from 1.5 to 167.6 kg/ha/year, with a mean value of 36.3 kg/ha/year. This translated into a rate of genetic gain for grain yield ranging from 0.1% to over 3.0%. The impact of multi-trait selection on grain yield was clarified by studies that reported genetic gains for other traits, such as plant height, days to flowering, and grain quality. These findings reveal that while breeding programs have achieved significant gains, further improvements are necessary to meet the growing demand for rice. We also highlight the limitations of these studies, which hinder accurate estimations of genetic gain. In conclusion, we offer suggestions for improving the estimation of genetic gain based on quantitative genetic principles and computer simulations to optimize rice breeding strategies.

Genetic improvement is crucial for ensuring food security globally. Indeed, plant breeding has contributed significantly to increasing the productivity of major crops, including rice, over the last century. Evaluating the efficiency of breeding strategies necessitates a quantification of this progress. One approach involves assessing the genetic gain achieved through breeding programs based on quantitative traits. This study aims to provide a theoretical understanding of genetic gain, summarize the major results of genetic gain studies in rice breeding, and suggest ways of improving breeding program strategies and future studies on genetic gain. To achieve this, we present the concept of genetic gain and the essential aspects of its estimation. We also provide an extensive literature review of genetic gain studies in rice (Oryza sativa L.) breeding programs to understand the advances made to date. We reviewed 29 studies conducted between 1999 and 2023, covering different regions, traits, periods, and estimation methods. The genetic gain for grain yield, in particular, showed significant variation, ranging from 1.5 to 167.6 kg/ha/year, with a mean value of 36.3 kg/ha/year. This translated into a rate of genetic gain for grain yield ranging from 0.1% to over 3.0%. The impact of multi-trait selection on grain yield was clarified by studies that reported genetic gains for other traits, such as plant height, days to flowering, and grain quality. These findings reveal that while breeding programs have achieved significant gains, further improvements are necessary to meet the growing demand for rice. We also highlight the limitations of these studies, which hinder accurate estimations of genetic gain. In conclusion, we offer suggestions for improving the estimation of genetic gain based on quantitative genetic principles and computer simulations to optimize rice breeding strategies. [ABSTRACT FROM AUTHOR]

Alpaca fibers are used to create luxury garments, and simultaneous selection for optimizing fiber density and the density of hair ducts in the skin of alpacas could result in a more profitable product for breeders. The objective of this study was i) to quantify fiber density (FibDen), density of hair ducts (DenDuc), and the relationship between No. of fibers/No. of ducts (Fib/Duc) by age and sex, and ii) to estimate heritability and genetic correlation between FibDen and DenDuc. This study was conducted in the CEDAT (Centro de Desarrollo Alpaquero de Toccra) in the Department of Arequipa, Peru. A total of 1,813 alpacas of different sex and age with pedigree information were analyzed from years 2004–2018. The quantification of FibDen, DenDuc and Fib/Duc was estimated using Fiber-Den equipment in an area of 1 mm2 in the middle rib region of the animal. The average FibDen, DenDuc and Fib/Duc was 24.75 ± 5.48, 7.83 ± 2.17 and 3.25 ± 0.55, respectively. The heritability for FibDen, DenDuc, and Fib/Duc was 0.48 ± 0.04, 0.53 ± 0.04, and 0.20 ± 0.03, respectively. The genetic correlation between FibDen and DenDuc was 0.87 ± 0.06. The estimated heritabilities of these traits in Peruvian alpaca population are moderate to high and indicate that these characteristics could be used as selection criteria in breeding programs. [ABSTRACT FROM AUTHOR]

Simple Summary: The development of reproductive technologies for amphibian species has accelerated over the last decade to the point that the industry implementation of these methodologies to assist breeding and genetic management is underway globally. A conservation breeding program was established at Taronga Conservation Society (Australia) in 2019 for the critically endangered Booroolong frog (Litoria booroolongensis) following an emergency extraction from the wild. Shortly thereafter, a trial was undertaken to compare the efficacy of two sperm cryopreservation protocols with a view to creating a "sperm bank" from these genetically important founder individuals. Spermic urine samples from L. booroolongensis were successfully cryopreserved using both methods tested; however, higher numbers of sperm retained motility post-thaw when using a faster cooling method for cryopreservation. Moreover, the two cryoprotectants tested were equally effective at supporting sperm survival and function post-thaw, regardless of cooling speed. We utilized the method outlined in this paper to collect and cryopreserve spermic urine samples across three breeding seasons from all (n = 28) L. booroolongensis founder males at Taronga and are now investigating the use of these samples to create offspring via assisted fertilization. The cryopreservation and storage of gametes (biobanking) can provide a long-term, low-cost option for the preservation of population genetic diversity and is particularly impactful when applied to manage selective breeding within conservation breeding programs (CBPs). This study aimed to develop a sperm cryopreservation protocol for the critically endangered Booroolong frog (Litoria booroolongensis) to capture founder genetics within the recently established (est. 2019) CBP for this species. Hormone-induced sperm release was achieved using established protocols, and spermic urine samples were collected over a 6-h period. Pooled spermic urine samples (n = 3 males) were divided equally between two cryoprotectant (CPA) treatments and diluted by 1:5 (sperm:CPA) with either 15% (v/v) dimethyl sulfoxide + 1% (w/v) sucrose in simplified amphibian Ringer's (SAR; CPAA) or 10% (v/v) dimethylformamide + 10% (w/v) trehalose dihydrate in SAR (CPAB). The samples were cryopreserved in 0.25 mL straws using either a programmable freezer (FrA) or an adapted dry shipper method (FrB). The thawed samples were activated via dilution in water and assessed for viability and motility using both manual assessment and computer-assisted sperm analysis (CASA; 0 h, 0.5 h post-thaw). Upon activation, the survival and recovery of motility (total motility, forward progression and velocity) of cryopreserved sperm suspensions were higher for sperm preserved using FrB than FrA, regardless of CPA composition. This work supports our long-term goal to pioneer the integration of biobanked cryopreserved sperm with population genetic management to maximize restoration program outcomes for Australian amphibian species. [ABSTRACT FROM AUTHOR]

The study comparatively analyzed 15 maize genotypes, under the aspect of production potential and some quality indices. The experiment was organized within the ARSD Lovrin. Eight maize genotypes from Lovrin (L experimental code; L1 to L8) and seven genotypes represented by commercial hybrids (CH experimental code; CH9 to CH15) were considered. The production of maize ears, Y(ears), varied between 6,236.00±570.14 kg ha-1 in hybrid L4 and 12,839.33±570.14 kg ha-1 in hybrid CH15. The physical grains production, Y(pgp) varied between 5,371.00±524.39 kg ha-1 in hybrid L4 and 11,640.00±524.39 kg ha-1 in hybrid CH15. The recalculated production (STAS, 14% moisture), Y(STAS) varied between 5,371.00±507.36 kg ha-1 for hybrid L4 and 11,579.33±507.36 kg ha-1 for hybrid CH15. The protein content (Pro, %) varied between 7.20±0.33% in the CH14 hybrid and 10.60±0.33% in the L3 hybrid. The oil content (Oil, %) varied between 5.20±0.09% in the CH15 hybrid and 6.40±0.09% in the L1 and L2 hybrids. According to PCA (95% confidence), the hybrids from group L were placed associated with the content of protein (Pro) and oil (Oil) as biplot. Hybrids from the CH group were placed associated with the Y(STAS) parameter. PC1 explained 72.693% of variance and PC2 explained 17.704% of variance. For the selection process of genotypes in breeding programs, the genotypes from the CH group (commercial hybrids) are of interest for the production potential, and the genotypes from the L group (Lovrin) are of interest for the quality indices (Pro, Oil). [ABSTRACT FROM AUTHOR]

High genetic diversity is the guarantee of success in a breeding program. Therefore, it is important to study the genetic diversity in plant populations. Because Iran consider as one of the primary walnut origin centers, this study was conducted to evaluate the genetic diversity of the walnut population in the Bavanat region in the Southwestern Iran during the 2010-2015 growing season. For this purpose, 349 walnut seed-originated walnut trees from seven different regions of Bavanat were pre-selected based on local information. After primary evaluation, 92 walnut genotypes were selected to be further studied. The phenological and pomological characteristics of the genotypes were evaluated based on IPGRI descriptor. The results showed that high genetic diversity was observed in the studied germplasm in terms of important horticultural traits, especially nut and kernel weight, kernel percentage, nut size, shell thickness, lateral bearing, leafing date, and harvest date. The nut weight, kernel percentage, kernel weight, and shell thickness varied between 6.75-16.33 g, 40.15-67.22%, 3.30-8.15 g, and 0.58-2.30 mm, respectively. Cluster analysis classified the studied genotypes into six main groups. Furthermore, correlations among some horticultural traits indicated that kernel weight, nut weight, difficulty of removal of kernel halves, and shell thickness are main traits in determining kernel percentage. Also, lateral bearing, leafing date, nut weight, and nut size determine the final yield of walnut trees. In conclusion, high biodiversity in the walnut population of Bavanat region provides unique plant genetic resources for walnut genetic improvement programs to achieve desirable commercial cultivars and rootstocks.

Incarvillea sinensis var. przewalskii has attracted great attention because of the anticancer value of its alkaloids and the potential use of the species for ecological restoration. However, the scarcity of high-quality seeds has significantly hindered the cultivation and efficient utilization of this species. Understanding how seeds respond to maternal environmental conditions is crucial for developing high-yield and top-notch seed accessions, but the available knowledge in this area is limited. Here, we determined the effect of shading treatments on seed development, seed quality, and yield. Compared to the control, shade significantly increased the seed germination rate and 1000-seed weight by 29.2% and 25.6%, respectively. Regardless of light conditions, the seed germination rate and 1000-seed weight decreased by 7.13% and 37.5%, respectively, as the fruit positioned from base to apical. The seed yield per plant was 27.9% higher under shade than under the control treatment. The structural equation model showed that shade promoted seed yield through increasing flowers per reproductive branch and seed numbers per capsule. These findings suggest that adjusting shading conditions and optimizing inflorescence development can lead to high-yield and high-quality seeds. Additionally, prioritizing the number of flowers per reproductive branch and seeds per capsule in breeding programs can further enhance the seed yield of I. sinensis var. przewalskii. [ABSTRACT FROM AUTHOR]

The selection of superior genotypes considering several traits simultaneously allows the release of more adapted, productive, and nutritive cultivars. To select forage peanut genotypes for use as animal feed and for ornamental purposes, 67 genotypes were evaluated. Twelve agronomic and nutritive value traits were evaluated in three temporally separated trials: a randomized complete block design. The mixed model method (Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP)) was employed for estimating genetic parameters and predicting genotypic values, which were used in the selection indexes. The selection criteria considered vegetative and seed propagation traits corresponding to the use of forage peanut as animal feed and for ornamental purposes. Seed productivity was also evaluated and correlated with other traits. Genetic variability with high heritability in seed production was observed. Plant vigor, ground cover, and dry matter yield were negatively correlated with seed production. Among the genotypes evaluated, there is a possibility of selecting 14 and 16 genotypes corresponding to seed propagation for animal feed and ornamental purposes, respectively. For vegetative propagation, there are 16 and 14 promising genotypes for animal feed and ornamental purposes, respectively. Vegetatively propagated genotypes generally performed better in terms of agronomic traits related to feed production.

Durio zibethinus, known as durian in several Southeast Asian countries, is a prospective horticultural commodity to cultivate and develop. This study aimed to determine the phenotypic diversity and relationship of superior durian varieties from South Kalimantan in Indonesia based on morphological characteristics. Here, 20 varieties of durian (D. zibethinus), including an outgroup, were used. Meanwhile, 57 morphological characteristics, comprising 35 qualitative and 22 quantitative, were observed. The Shannon index (H’) method was applied for phenotypic diversity, and the relationships were by the UPGMA. The results show that durians of the region have low phenotypic diversity. However, some morphological characteristics show high ones, e.g., crown shape, fruit skin color and thickness, fruit flesh thickness, and fruit spine length, including tree age. In this case, the highest fruit skin and flesh thickness are present in Malutu and Bamban Birin, respectively. In addition, the fruit spine length and tree age are also in ‘Malutu’. The UPGMA revealed that the durians were separated into seven clusters and near-corresponding to geographic origin. In this case, ‘Gentarbumi Uya’ is the closest to ‘Taradak Uya’, whereas the farthest is ‘Malutu’ with ‘Tapai Idaman’. Thus, this information is essential in promoting the future durian-breeding program in local and global coverages. [ABSTRACT FROM AUTHOR]

The need for breeding research to obtain new cultivars of baking pumpkin results from the fact that in the Official Catalog of Cultivated Plant Cultivars in Romania, edition 2021, there are only 4 cultivars: 'Alb mare', 'Dorin', 'Baron' and 'Tudor'. As a result, at Dabuleni Research-Development Station for Plant Culture on Sands (RDSPCS), in the period 2020-2022, the 'D19' baking pumpkin genotype was studied as part of the creative breeding process. The results obtained showed that both the weight of the fruit and the thickness of the fruit flesh (determining characters for the agronomic value of a cultivar) recorded constant values from year to year, which constitute important arguments in support of the enrolment of the 'D19' genotype at State Institute for Cultivars Testing and Registration for testing in order to homologation. 'D19' pumpkin genotype also showed good stability for the characters fruit height, fruit diameter, seed cavity diameter and shape index. The statistical analysis of the characters analyzed during the 3 years of the study highlighted the fact that the 'D19' pumpkin genotype behaved well in the pedoclimatic conditions of Dabuleni and steps can be taken to test and approve it as a crop plant cultivar in Romania

In the last century broiler chicken lines have undergone an extensive breeding regime aimed primarily at growth and high meat yield. It is not known if breeding has also resulted in a change to the broiler breeder’s associated gut microbiota. Here we compared the gut microbiota of 37-week-old commercial Cobb breeding dams with dams from a broiler Legacy line which has not undergone selection since 1986. The dams from both lines were kept together in the same shed under the same management protocol from day of hatch to avoid additional confounders. We chose this age to allow significant bacterial exchange, thus avoiding exposure dependent artifacts and so that we could compare dams at the same developmental state of adulthood and peak laying performance. Significant differences in the composition of the cecum bacterial communities were found. Bacteria of the genus Akkermansia, implicated in mucin degradation and associated with host metabolic health, accounted for 4.98% ± 5.04% of the Cobb cecum community, but were mostly absent from the ceca of the Legacy line dams. Inversely, Legacy dams had higher levels of Clostridiales, Lactobacillales and Aeromonadales. These results show that breeding has resulted in a change in the gut microbiota composition, likely by changing the physiological conditions in the mucosa. It remains unclear if changes in gut microbiota composition are a part of the mechanism affecting growth or are a secondary result of other physiological changes accelerating growth. Therefore, the identification of these changes opens the door to further targeted research. [ABSTRACT FROM AUTHOR]

Through repeated cycles of selection and recombination, tree breeding programs deliver genetically improved varieties for a range of target characteristics such as biomass production, stem form, resistance to biotic stresses, wood properties, etc. However, in the context of increased drought and heat waves, it is not yet known whether growth performance will impede drought resistance. To address this question, we compared the hydraulic properties, such as hydraulic efficiency and hydraulic safety, in four varieties over successive varieties of genetically improved maritime pines (i.e. Pinus pinaster Aït.) for growth and stem form. We measured 22 functional traits related to hydraulic efficiency, hydraulic safety, xylem anatomy and wood density. We found that improved varieties presented higher hydraulic conductivity with larger tracheid lumen size and tracheid lumen fraction, and smaller wall thickness reinforcement and tracheid density, but not at the cost of reduced embolism resistance. The reported absence of trade-off between hydraulic conductivity and embolism resistance is a strong asset to improve biomass productivity, through increased hydraulic efficiency, without impacting drought resistance, and should enable new maritime pine varieties to cope with a drier climate. Our study is one of the first to reveal the hydraulic mechanisms over successive varieties of genetic improvement for tree growth. It provides guidelines for sustainable forest management through breeding for other forest tree species. [ABSTRACT FROM AUTHOR]

Fusarium wilt on melons is the most harmful fungal disease, both in Bulgaria and in countries along the entire Mediterranean coast. The strong development of the disease leads to a significant reduction in yield and quality of production. The genetic resistance to this pathogen is the best sustainable strategy to control the disease. In 2019, a study on the immune responses of ten new created melon lines to the causative agent of Fusarium wilt - Fusarium oxysporum (Schlecht.) Snyder et Hansen f.sp. melonis (L et C) Snyder et Hansen was conducted. The study was done under controlled conditions and artificial infectious in the vegetation house of IPGR - Sadovo. All melon lines were provided by the Company “Agrotop” - Gorna Oryahovitsa. The results of the study showed differences in the resistance of the materials to the fungus Fusarium oxysporum f. sp. melonis. Depending on their response, the tested lines were separated by cluster analysis of resistance and sensitivity. The resistant lines can be successfully used as a potential initial material in future breeding programs to create pathogen-resistant melon varieties. [ABSTRACT FROM AUTHOR]

Intramuscular fat (IMF) content and fatty acids (FA) profile determine important sensory and technological characteristics of the meat, being interesting traits to be included in breeding programs for Iberian pig. In a previous study, we analyzed the longissimus dorsi transcriptome of Iberian pigs with divergent breeding values for IMF identifying 63 and 12 functional candidate genes and long non-coding RNA being differentially expressed. The first objective of this work was to use the RNA-seq data generated in that study in order to design a low-density panel with 50 single-nucleotide polymorphisms (SNP). The second aim was to evaluate the effects of this SNP panel on IMF content and backfat FA profile in a closed commercial population of Iberian pigs. The IMF content and backfat FA composition were determined in 940 Iberian pigs. A total of 837 SNPs were identified in the selection of genes and lncRNA. Out of the 50 selected SNP, 11 were monomorphic in the population and 2 failed in their genotyping. Association analyses were carried out for the 37 SNP segregating in the population (minor allele frequency, MAF > 0.05). Regarding IMF content, a significant additive effect (q-value < 0.05) was observed for ADIPOQ:g.124646194T > G SNP, in which the G allele was linked to an increase of 7.59% (additive effect expressed as a percentage of the mean of the trait). For the backfat FA composition, we observed 24 SNP with significant associations. The strongest effects were detected for the ELOVL6:g.112186423A > G and FASN_rs331694510G > A SNP. The A allele of both SNPs were associated to a lower percentage of palmitic (C16:0) and palmitoleic (C16:1) acids and an increase in oleic acid (C18:1). In addition, the AMPD3:g.49043886C > G SNP had significant effects on C16:0, stearic (C18:0), C18:1 and on the sum of saturated and monounsaturated fatty acids. Finally, significant effects of the EGR2:66286345G >T SNP on C18:0 and C18:1 and other minor FA were observed. Our findings reveal ADIPOQ:g.124646194T > G, ELOVL6:g.112186423A > G, and FASN_rs331694510G > A may be useful in breeding programs for Iberian pigs including FA profile and IMF content as selection goals, provided that their potential effects on other traits of interest are controlled. [ABSTRACT FROM AUTHOR]

The selection of superior genotypes considering several traits simultaneously allows the release of more adapted, productive, and nutritive cultivars. To select forage peanut genotypes for use as animal feed and for ornamental purposes, 67 genotypes were evaluated. Twelve agronomic and nutritive value traits were evaluated in three temporally separated trials: a randomized complete block design. The mixed model method (Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP)) was employed for estimating genetic parameters and predicting genotypic values, which were used in the selection indexes. The selection criteria considered vegetative and seed propagation traits corresponding to the use of forage peanut as animal feed and for ornamental purposes. Seed productivity was also evaluated and correlated with other traits. Genetic variability with high heritability in seed production was observed. Plant vigor, ground cover, and dry matter yield were negatively correlated with seed production. Among the genotypes evaluated, there is a possibility of selecting 14 and 16 genotypes corresponding to seed propagation for animal feed and ornamental purposes, respectively. For vegetative propagation, there are 16 and 14 promising genotypes for animal feed and ornamental purposes, respectively. Vegetatively propagated genotypes generally performed better in terms of agronomic traits related to feed production. [ABSTRACT FROM AUTHOR]

Koi herpesvirus disease (KHVD), caused by Cyprinid herpesvirus-3 (CyHV-3), is one of the most serious threats to carp farming. In the present study, we investigated the efficiency of a low-density (LD) SNP panel for estimating genetic parameters and breeding values to KHVD resistance in the Amur mirror carp (AMC). Two populations (Pop 1 and Pop 2) of AMC generated from unrelated parents were created using a partial factorial design. One-year old fish (Pop 1 = 1500 individuals.; Pop 2 = 1200 individuals) were challenged with CyHV-3 and phenotyped to KHVD resistance. 218 SNPs originating from a medium genotyping platform previously applied to Pop 1 (15615 SNPs; denoted as MD panel) with the highest association to KHVD resistance were used as a LD panel to genotype individuals of Pop 2. Genetic parameters and estimated pedigree-based BLUP (EBV) and genomic-based GBLUP (GEBV_MD and GEBV_LD) breeding values were calculated and obtained for Pop 1 using either pedigree, MD or LD panel and for Pop 2 using either pedigree or the LD panel. The heritability estimates of KHVD resistance were very high for both populations ranging from 0.42 to 0.96. Selection for KHVD resistance in Pop 2 using the LD panel would have led to a relative increase of ∼7% in prediction accuracy compared to the pedigree-based selection. Pearson correlation coefficients between pedigree-based and genomic-based estimated breeding values (EBV vs. GEBV_MD; EBV vs. GEBV_LD; GEBV_MD vs. GEBV_LD) showed a strong association for both populations (0.79 – 0.91). In addition, the concordance rate of individuals selected by pedigree-based (EBV) and genomic-based breeding values (GEBV_MD and GEBV_LD) within selection pressures of 5%, 10% and 20% were not statistically different in most cases. In conclusion, the low-density SNP panel could be useful for a selection program focused on the genetic improvement of KHVD resistance.

The goal of this paper is to estimate the genetic parameters for production traits in a pattern pig line. The estimation of the variance-covariance components is a very important step in animal breeding because these components are necessary for: (1) estimation of the genetic parameters, (2) prediction of the breeding value and (3) the design of animal breeding programs. The estimation of the selection parameters (h2, rG, rF, rE) is the first step in the development of a Duroc line breeding program, using artificial insemination.

ABSTRACT: Butana is one of the local dairy cattle breeds of Sudan commonly kept by smallholder producers. This breed has been strongly promoted to advance the dairy production sector in the country. The main problem, however, is the lack of a systematic breeding program that involves smallholder producers. The aim of the current study was to identify the most promising design for a breeding program to improve the milk yield performance of Butana cattle under smallholder production conditions. In total, 3 breeding scenarios, including (1) the use of farm bulls, (2) the use of village bulls, and (3) the rotational use of village bulls within village groups, were simulated using a stochastic simulation approach. For each breeding scenario, 3 selection methods for bulls were considered, namely random mating, phenotypic selection, and selection based on estimated breeding value (EBV). The results showed that no genetic gain was realized with random mating in all breeding scenarios. In the farm bull breeding scenario, annual genetic gain (standard deviation units) ranged from 0.01 to 0.19 (phenotypic selection) and from 0.01 to 0.39 (selection based on EBV). In the village bull breeding scenarios, the annual genetic gain ranged from 0.01 to 0.21 (phenotypic selection) and 0.01 to 0.45 (selection based on EBV). The lowest genetic gain was realized for the rotational use of village bulls among villages within groups. Through the rotational use of village bulls, however, a higher genetic variance was maintained than in the farm and village bull breeding scenarios. We concluded that a village bull breeding program with selection based on EBV of young bulls was the most promising breeding design for achieving the breeding goal. Further studies are needed to assess the organizational feasibility of such a breeding program to ensure the participation of smallholder producers and its sustainability.

In the last century broiler chicken lines have undergone an extensive breeding regime aimed primarily at growth and high meat yield. It is not known if breeding has also resulted in a change to the broiler breeder’s associated gut microbiota. Here we compared the gut microbiota of 37-week-old commercial Cobb breeding dams with dams from a broiler Legacy line which has not undergone selection since 1986. The dams from both lines were kept together in the same shed under the same management protocol from day of hatch to avoid additional confounders. We chose this age to allow significant bacterial exchange, thus avoiding exposure dependent artifacts and so that we could compare dams at the same developmental state of adulthood and peak laying performance. Significant differences in the composition of the cecum bacterial communities were found. Bacteria of the genus Akkermansia, implicated in mucin degradation and associated with host metabolic health, accounted for 4.98% ± 5.04% of the Cobb cecum community, but were mostly absent from the ceca of the Legacy line dams. Inversely, Legacy dams had higher levels of Clostridiales, Lactobacillales and Aeromonadales. These results show that breeding has resulted in a change in the gut microbiota composition, likely by changing the physiological conditions in the mucosa. It remains unclear if changes in gut microbiota composition are a part of the mechanism affecting growth or are a secondary result of other physiological changes accelerating growth. Therefore, the identification of these changes opens the door to further targeted research.

Olive trees are the most cultivated evergreen trees in the Mediterranean Basin, where they have deep historical and socioeconomic roots. The fungus Verticillium dahliae develops inside the vascular bundles of the host, and there are no effective applicable treatments, making it difficult to control the disease. In this sense, the use of integrated disease management, specifically the use of resistant cultivars, is the most effective means to alleviate the serious damage that these diseases are causing and reduce the expansion of this pathogen. In 2008, the University of Cordoba started a project under the UCO Olive Breeding Program whose main objective has been to develop new olive cultivars with high resistance to Verticillium wilt. Since 2008, more than 18,000 genotypes from 154 progenies have been evaluated. Only 19.9% have shown some resistance to the disease in controlled conditions and only 28 have been preselected due to their resistance in field condition and remarkable agronomic characteristics. The results of this study represent an important advancement in the generation of resistant olive genotypes that will become commercial cultivars currently demanded by the olive growing sector. Our breeding program has proven successful, allowing the selection of several new genotypes with high resistance to the disease and agronomical performance. It also highlights the need for long-term field evaluations for the evaluation of resistance and characterization of olive genotypes.

Napier grass is a perennial tropical forage that is used in beef and dairy production systems. Despite its significance in animal nutrition, molecular information available, such as microsatellite or simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers, is limited. Using an assembled transcriptome, 50 novel SSR markers were developed, of which 21 were found to be polymorphic. These polymorphic markers were tested for DNA fingerprinting of Embrapa cultivars, five of which revealed distinct allele patterns for cultivar identification. SSR markers 05, 17, and 44 identified a unique pattern in the BRS Kurumi cultivar. The BRS Capiaçu cultivar was identified using SSR markers 17, 43, and 44. The Pioneiro cultivar exhibited a rare fragment amplification pattern using SSR marker 46, while SSR marker 44 revealed a distinct allele in the BRS Canará cultivar. SSR marker panels could be utilized as DNA fingerprinting tools to assist in cultivar identification [ABSTRACT FROM AUTHOR]

Incarvillea sinensis var. przewalskii has attracted great attention because of the anticancer value of its alkaloids and the potential use of the species for ecological restoration. However, the scarcity of high-quality seeds has significantly hindered the cultivation and efficient utilization of this species. Understanding how seeds respond to maternal environmental conditions is crucial for developing high-yield and top-notch seed accessions, but the available knowledge in this area is limited. Here, we determined the effect of shading treatments on seed development, seed quality, and yield. Compared to the control, shade significantly increased the seed germination rate and 1000-seed weight by 29.2% and 25.6%, respectively. Regardless of light conditions, the seed germination rate and 1000-seed weight decreased by 7.13% and 37.5%, respectively, as the fruit positioned from base to apical. The seed yield per plant was 27.9% higher under shade than under the control treatment. The structural equation model showed that shade promoted seed yield through increasing flowers per reproductive branch and seed numbers per capsule. These findings suggest that adjusting shading conditions and optimizing inflorescence development can lead to high-yield and high-quality seeds. Additionally, prioritizing the number of flowers per reproductive branch and seeds per capsule in breeding programs can further enhance the seed yield of I. sinensis var. przewalskii.

Statistical models play a significant role in designing competent breeding programs related to complex traits. Recently; the holo-omics framework has been productively utilized in trait prediction; but it contains many complexities. Therefore; it is desirable to establish prediction accuracy while combining the host's genome and microbiome data. Several methods can be used to combine the two data in the model and study their effectiveness by estimating the prediction accuracy. We validate our holo-omics interaction models with analysis from two publicly available datasets and compare them with genomic and microbiome prediction models. We illustrate that the holo-omics interactive models achieved the highest prediction accuracy in ten out of eleven traits. In particular; the holo-omics interaction matrix estimated using the Hadamard product displayed the highest accuracy in nine out of eleven traits, with the direct holo-omics model and microbiome model showing the highest prediction accuracy in the remaining two traits. We conclude that comparing prediction accuracy in different traits using real data showed important intuitions into the holo-omics architecture of complex traits. [ABSTRACT FROM AUTHOR]

Simple Summary: The Caballo de Deporte Español (CDE) is a sport horse breed, which originated from crosses between different sport horse breeds in the search for a good sport aptitude for Dressage, Eventing and Show Jumping disciplines. The main aim of this study was to determine the effects of 15 years of selection on this breed and find out whether it has been effective and adequate regarding the CDE main breeding objectives. The whole known pedigree was used, comprising 47,884 animals (18,799 males and 29,085 females). Pedigree analyses were performed in order to check the population structure, origins and evolution over the years. For the analyses, animals were divided into fourteen breed groups. Performance data used in the analyses were the estimated breeding values (EBV) of the Show Jumping, Dressage and Eventing sport disciplines from the routine genetic evaluations of the CDE breeding programme. Results showed some degree of subdivision within the population and, therefore, inbred matings. Regarding the evolution of breeding values, we found that EBVs of offspring were higher than the EBVs of parents showing that genetic gain has actually occurred. Moreover, selection decisions seem to be taken by breeders based, to certain extent, on the genetic evaluations. The equine breeding industry for sport's performance has evolved into a fairly profitable economic activity. In particular, the Caballo de Deporte Español (CDE) is bred for different disciplines with a special focus on Show Jumping. The main aim of this study was to determine the effects of 15 years of selection and to find out whether it has been effective and adequate regarding the CDE main breeding objectives. The whole pedigree of 19,045 horses registered as CDE was used, comprising 47,884 animals (18,799 males and 29,085 females). An analysis performed to check for the pedigree completeness level yielded a number of equivalent complete generations (t) equal to 1.95, an average generation interval (GI) of 10.87 years, mean inbreeding coefficient (F) of 0.32%, an average relatedness coefficient (AR) of 0.09% and an effective population size (Ne) of 204. For the analyses, animals were divided into fourteen breed groups. Additionally, in order to study the evolution of these breeds over time and their influence on CDE pedigree, five different periods were considered according to the year of birth of the animals. Performance data used in the analyses were the estimated breeding values (EBV) of the Show Jumping sport discipline of 12,197 horses in the CDE pedigree, available from the 2020 routine genetic evaluations of the CDE breeding program (starting in 2004). Dressage and Eventing EBV values were also assessed. Results showed values of F higher than expected under random mating; this pointed to some degree of inbred matings. With regard to the evolution of breeding values, we found that, in general, EBVs of offspring were higher than the EBVs of parents. Notwithstanding, there is still a need for improvement in population management and the coordination of the breeders to get higher responses but controlling the loss of genetic diversity in the CDE breed. [ABSTRACT FROM AUTHOR]

Durian, especially Durio zibethinus, is an agricultural commodity with high economic value, both in local and global markets. This study aimed to determine the genetic diversity, relationships and correlation of superior cultivars of D. zibethinus(‘Likol’, ‘Sahang’ and ‘Si Japang’)native to South Kalimantan, Indonesia, using the rbcL marker, and compare them with other 48 cultivars from the GenBank database. All durian rbcL markers were analyzed using the MEGA-X software and phylogenetically reconstructed using two approaches: maximum likelihood (ML) and neighbor-joining (NJ). The durian phylogenetic tree was assessed by bootstrap analysis, and their relationships by Pearson’s correlation and principal component analysis. The durian showed a low genetic diversity (π% = 0.056); however, unique relationships were revealed. Following the rbcL region, this germplasm was grouped into five clades using ML and NJ. In this case, ‘Si Japang’ and ‘Sahang’ showed to be closely related to ‘T16’ from Malaysia, whereas ‘Likol’ was related to ‘Monthong’ from Thailand. However, based on the genetic divergence analysis, ‘Sahang’ had the farthest relationship with three durians from Thailand (‘MetnaiKanyao’,‘Chok Loi’and ‘Malet Ar-Ri’).

Butana is one of the local dairy cattle breeds of Sudan commonly kept by smallholder producers. This breed has been strongly promoted to advance the dairy production sector in the country. The main problem, however, is the lack of a systematic breeding program that involves smallholder producers. The aim of the current study was to identify the most promising design for a breeding program to improve the milk yield performance of Butana cattle under smallholder production conditions. In total, 3 breeding scenarios, including (1) the use of farm bulls, (2) the use of village bulls, and (3) the rotational use of village bulls within village groups, were simulated using a stochastic simulation approach. For each breeding scenario, 3 selection methods for bulls were considered, namely random mating, phenotypic selection, and selection based on estimated breeding value (EBV). The results showed that no genetic gain was realized with random mating in all breeding scenarios. In the farm bull breeding scenario, annual genetic gain (standard deviation units) ranged from 0.01 to 0.19 (phenotypic selection) and from 0.01 to 0.39 (selection based on EBV). In the village bull breeding scenarios, the annual genetic gain ranged from 0.01 to 0.21 (phenotypic selection) and 0.01 to 0.45 (selection based on EBV). The lowest genetic gain was realized for the rotational use of village bulls among villages within groups. Through the rotational use of village bulls, however, a higher genetic variance was maintained than in the farm and village bull breeding scenarios. We concluded that a village bull breeding program with selection based on EBV of young bulls was the most promising breeding design for achieving the breeding goal. Further studies are needed to assess the organizational feasibility of such a breeding program to ensure the participation of smallholder producers and its sustainability. [ABSTRACT FROM AUTHOR]

This study proposes a selection strategy to be applied to a large number of coffee accessions, which can be useful when exploring many genotypes in breeding programs for beverage quality. Over three consecutive years, 270 Arabica coffee accessions from the germplasm collection of Minas Gerais, Brazil, were sensorially characterized. At the end of this period, the 20 genotypes with the greatest potential for specialty coffee production were selected, which were subjected to a second sensory characterization. Additionally, we determined the genetic correlations between the attributes that make up the final beverage score. We did not identify an attribute that was more important than the others in the organoleptic performance of the studied accessions. Through the proposed method, we identified genetic variation in our original population and selected five accessions with beverage quality considered excellent according to the SCA classification. These accessions were planted in field conditions of highly specialized farms to study their interaction with the cultivation environment and to promote the increase in production of such coffees. Additionally, the five selected accessions are being used in crosses with elite cultivars in order to create new segregation. We conclude that estimation of the heritability of each accession, the use over the years of common check cultivars with known performance, and extreme careful of experimental precision in the entire processes allow adequate comparisons. [ABSTRACT FROM AUTHOR]

Studies on genetic diversity and relationships are necessary for breeders and scientists to increase the effectiveness of future breeding programs. The tidal swamp rice (Oryza sativa L.) is one of the potential germplasms which has a prominent opportunity to be incorporated in the rice breeding program. This study aimed to investigate and reveal the genetic diversity and relationship of tidal swamp rice germplasms indigenously from South Kalimantan, Indonesia, using Random Amplified Polymorphic DNA (RAPD) markers. A total of ten rice samples, consisting of nine from this region and one from South Sumatera (an outgroup), and five selected RAPD markers, i.e., OPB-06, OPAJ-01, OPAB-17, OPAL-09, and OPAL-08, were used in this study. DNA amplifications were performed and programmed for one cycle of initial denaturation (5 min, 94°C), 45 cycles of denaturation (30 sec, 94ºC), annealing (30 sec, 37ºC), and extension (1.5 min, 72ºC), as well as one cycle of final extension (7 min, 72°C). The genetic similarity was analyzed using Dice's coefficient method, whereas their relationship (dendrogram) by the UPGMA. The results showed that these germplasms have a moderate genetic diversity level, indicated by the polymorphism degree of 75.64%. The clustering analysis revealed that they are grouped into three main groups at a similarity coefficient of 0.70. In this case, Siam Unus is distantly related to the other cultivars and forms a solitaire group. Siam Unus also shows the farthest relationship with Sardani, an outgroup. It is a new finding for the genetic insight of tidal swamp rice of South Kalimantan, Indonesia, including their diversity and relationship. Thus, the results obtained from this study is useful in supporting future rice conservation and breeding programs. [ABSTRACT FROM AUTHOR]

Coconut (Cocos nucifera L.) is one of the most important tree crops in the world, especially in the tropics. This study aimed to determine the genetic diversity of coconut germplasm native to South Kalimantan, Indonesia, using the rbcL marker. Nine coconut samples, being eight natively collected from this region and one as an outgroup (obtained from the GenBank database), were used in the study. According to the rbcL marker, the coconut germplasm native to South Kalimantan has a relatively high diversity, with a nucleotide diversity (π) of 0.51. The level of diversity is strongly correlated with the mutation present in the observed region, rbcL. The phylogenetic analysis showed that the coconut germplasm has a unique relationship, where the ‘Dalam’ cultivar is the closest to three other dwarf coconuts, i.e., ‘Genjah Kuning 1’, ‘Genjah Kuning 3’ and ‘Wulung’.

Preserving and maximizing genetic diversity in conservation programs, including for restocking, are of high importance. The threatened European flat oyster (Ostrea edulis) is currently the subject of several applied conservation and restocking programs, but concerns have been raised over potential negative side effects of these programs, for example due to our limited knowledge about the genetic effects in natural populations of releasing offspring of hatchery origin. Here, we developed an effective, easily applicable and highly reliable method to assess the genetic diversity and parental contributions in flat oyster hatchery production based on analyses of 17 microsatellite loci. We analysed four broodstocks and their hatchery-reared spat (total n = 354) and compared diversity to that in wild samples of adults and spat from the broodstock source in the Limfjorden (total n = 138). Based on four hatchery tank experiments with fully resolved parentage assignments, we found that five swarming events (larval releases) were characterized by a single maternal and multiple paternal contributions, and that the number of contributing parents varied greatly both among individual tanks, and between swarming events within tank. On average, the effective number of breeders was only one third of the actual broodstock size. Although the broodstock exhibited high genetic variation, the high reproductive skew resulted in produced offspring representing only a relatively small subset of this variation. The work demonstrates potential impact of hatchery reared offspring on decreasing genetic diversity in wild populations, but also that genetic monitoring can be integrated in conservation programs to minimize negative effects on restoration and supplementary restocking programs that utilize hatchery reared spats to support natural populations. [ABSTRACT FROM AUTHOR]

Copyright of Agricultural Research in the Tropics / Pesquisa Agropecuária Tropical is the property of Pesquisa Agropecuaria Tropical and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Agricultural Research in the Tropics / Pesquisa Agropecuária Tropical is the property of Pesquisa Agropecuaria Tropical and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Background Approximately every fifth Dachshund is affected by disc herniation - a painful, hereditary condition which is typically preceded by disc calcification. Therefore, the selection of dogs suitable for breeding can be based on radiographic examination of calcification status. Recently, an insertion of an FGF4 retrogene on CFA12 has been identified and associated with the risk of developing disc herniation in chondrodystrophic breeds and a DNA test is now offered. In this study we investigate the incidence of disc herniation in the smooth-haired, long-haired and wire- haired Dachshund populations. We also evaluate and compare the accuracy of the two breeding schemes predicting the risk of disc herniation: the DNA test and the radiography based scheme. Results The overall incidence of disc herniation in Danish Dachshunds was 18% and no significant difference was found between the long-haired (17%), smooth-haired (22%) and wire-haired (16%) populations (p > 0.05). We found a significant association (p 0.05) and here the insertion allele was almost fixed. Conclusion Our results show that the FGF4 retrogene insertion on CFA12 is not a valid risk indicator on its own. Relying on the DNA test will have an irreversible effect on the Dachshund breed excluding almost all dogs from breeding. Thus, using calcification status remains the most reliable breeding scheme for disc herniation in Dachshunds.

Genotype by environment interaction (G×E) may exist for traits that are expressed in different environments. The G×E is often ignored in the genetic evaluation of selection candidates. We hypothesized that genetic gain in 2 environments is always higher when the true value of the genetic correlation (r g) between traits expressed in different environments is considered in the genetic evaluation. We tested this hypothesis by stochastic simulation of dairy cattle breeding programs in a mainstream and a niche environment. The r g was varied from 0 to 1 in steps of 0.1. We simulated the following 3 scenarios: 1Trait_1Index, 2Traits_1Index, and 2Traits_2Indices. The G×E was ignored in the genetic evaluation in the scenario with 1Trait and included in scenarios with 2Traits. Selection was based on the mainstream selection index in both environments in scenarios with 1Index. Selection in the mainstream environment was based on the mainstream selection index and selection in the niche environment was based on the niche selection index in the scenario with 2Indices. With moderate G×E (r g between 0.6 and 0.9), the highest genetic gain was achieved in the niche environment by selecting for the mainstream selection index and ignoring G×E. At lower r g, the highest genetic gain was achieved when considering G×E and selecting for the niche selection index. For the mainstream environment, it was never an advantage to ignore G×E. Therefore, although our hypothesis was confirmed in most cases, there were cases where ignoring G×E was the better option, and using the correct evaluation led to inferior genetic gain. The results of the current study can be used in animal breeding programs that encompass multiple environments. [ABSTRACT FROM AUTHOR]

Climate change and global warming are leading to a change in weather patterns toward hot and cold waves. Citrus fruits are a tropical or subtropical crop whose growth is altered by changes in weather patterns. Thus, in the present work, two experiments are evaluated to obtain a screening method to select citrus rootstocks that help us to select new low-temperature-tolerant plant materials. One cold experiment was carried out with the Poncirus trifoliata and Citrus macrophylla rootstocks at 4 °C for 4, 8, 24 and 56 h. A second experiment was performed at 4 °C for 5 days with subsequent acclimatization lasting 0, 5, 10 and 24 h. The expression of the cold response genes CAMTA1, CAMTA3, CAMTA5, CBF1, ICE1 and COR413 IM1 was quantified. The results showed that the best rootstock selection strategy was the second experiment, as a higher expression of the genes CAMTA3, CAMTA5, CBF1 and COR413 IM1 was seen in the tolerant genotype P. trifoliata. We quantified the gene expression of proline biosynthesis P5CS1, dOAT and the proline transporters PROT1 and PROT2; the concentration of the amino acid proline in leaves was also quantified. These results once again showed that the best experiment to differentiate between tolerant and sensitive rootstocks was the second experiment with acclimation time. [ABSTRACT FROM AUTHOR]

Establishment of a core collection, of limited size and better representation of the whole germplasm phenotypic diversity, is fundamental for fruit tree breeding programs from an economic and management points of view. To achieve this goal with pomegranate fruit trees, 221 genotypes were evaluated for 25 morphological and pomological traits during two successive years. Using the maximization strategy in Power Core software, 12 out of 221 pomegranate genotypes were selected for the new core collection, reducing the population size to 5.42% of the entire collection. Variance difference (VD%) and mean difference (MD%) were calculated as 42.68% and 7.03% in core collection, respectively. This indicates an excellent diversity amongst genotypes within the core collection. The Shannon’s diversity index (H0) in the formed collection suggested that 19 out of 25 phenotypic variables were of high diversity. Results showed that core collection genotypes are equally presented in all three population groups formed by cluster analysis through the original collection. The current research is the first in using phenotypic data to establish a core collection of Iranian pomegranate germplasm. The formation of this core collection will be an effective step towards examining the diversity of the original population and breeding prospects. [ABSTRACT FROM AUTHOR]

The backfat thickness (BFT) was used to forecast the onset of ovarian activity and predict the calf growth. Eighty Brahman cows with their calves were allocated in two groups of 40 distributed in 4 months according to the month of calving, starting in March and finishing in June. One was synchronized and inseminated at fixed time following by natural mating (TAI+NM); whilst the other only by natural mating (NM). The programs started at 60 ± 5 days postpartum and ended 60 days later. From day 30 postpartum, serial ultrasound examinations and progesterone samples were used to monitor the onset of ovarian activity. The BFT in the rump area was measured by ultrasound from 30 days postpartum and every 15 days thereafter. The weight of the calves was recorded at birth and at weaning on 160 days. The adjusted effect of BFT on ovarian activity and the calves' development was assessed by binomial logistic regression at 30, 60, 75, and 120 days postpartum. The cycling cows averaged higher BFT irrespective of breeding program (P < 0.001). Also, slower changes in BFT were recorded during the follow-up at each time for all cows. However, the former had the higher BFT values from calving to the end of the study (P < 0.001). At 60, 75, and 120 days, the BFT measured, at the preceding time, was the only factor predicting the commencement of cyclicity (P < 0.001). The accumulative pregnancy through time was higher in TAI+NM (P = 0.003). Daily weight gain and weaning weight of the calves born in March was significantly heavier (P < 0.001) than peers born in April, May, or June. The most critical element to forecast the onset of ovarian activity is the monitoring of BFT around calving regardless of the breeding program. BFT to estimate the development of the calves until weaning was unpredictable.

Breeding for disease resistance has been one of the most important research objectives in melon for the last few decades. Fusarium wilt caused by Fusarium oxysporum f. sp. melonis (Fom) is among the most threatening melon fungal diseases along the Mediterranean coast, affecting yield and quality. Since genetic resistance is one of the best sustainable strategies that can be used to control this pathogen, 27 Tunisian melon accessions collected from local farmers have been tested using phenotypic and molecular approaches to identify new sources of resistance to be used directly as cultivars in affected areas or as resistance donors in breeding programs. The phenotypic evaluations, using artificial inoculations, showed several resistant accessions to the pathogenic races of Fom. Additionally, molecular analysis revealed that 13 out of 27 accessions carried the resistance Fom-1 gene (7 in homozygous state and 6 in heterozygous state), confirming their resistance to races 0 and 2. Two of them were also identified as heterozygous for the Fom-2 gene, being resistant to races 0 and 1. Furthermore, two accessions with a high level of resistance to the most virulent race 1.2 have been also reported. This melon germplasm should be explored as a potential source of resistance genes in breeding programs to develop new resistant melon cultivars. [ABSTRACT FROM AUTHOR]

The present study is a transversal analysis of the interest in genomic selection for plant and animal species. It focuses on the arguments that may convince breeders to switch to genomic selection. The arguments are classified into three different "bricks." The first brick considers the addition of genotyping to improve the accuracy of the prediction of breeding values. The second consists of saving costs and/or shortening the breeding cycle by replacing all or a portion of the phenotyping effort with genotyping. The third concerns population management to improve the choice of parents to either optimize crossbreeding or maintain genetic diversity. We analyse the relevance of these different bricks for a wide range of animal and plant species and sought to explain the differences between species according to their biological specificities and the organization of breeding programs. [ABSTRACT FROM AUTHOR]

The silver-lipped pearl oyster, Pinctada maxima, is an important aquaculture species extensively farmed in tropical Australia and Southeast Asia to produce “South Sea” pearls. The pearling industry in Australia is in the process of implementing breeding programs targeting improved disease resistance, growth and pearl quality, and as a result genetic tools that can be readily implemented into breeding programs have been developed. However, to date there is no routine single nucleotide polymorphism (SNP) pedigree reconstruction tool publicly available.In this study, we isolated and assessed a panel of 934 genome-wide DArTcap™ SNPs for their utility and discriminatory power in resolving pedigree relationships in P. maxima. The panel was assessed for its power to assign parentage through in silico simulations of 1,000 progeny in a mass-spawning scenario, based on genotypes of 100 broodstock (1:1 sex ratio) and allowing for random missing genotypes in individuals (0–40%). Assignment success was then assessed across various pedigree panel sizes (25–934 SNPs ranked from the highest minor allele frequency). Simulations showed that a SNP panel comprising 50 or more SNPs had high pedigree resolution and the power to correctly assign progeny to a parent-progeny trio with 95 % confidence. In the simulation examining the effect of missing genotypes on assignment success, even where 40 % of alleles were missing in individuals only 150 SNPs were required in the panel to accurately assign parentage. Progeny from a commercial hatchery mass spawn involving 184 candidate parents were also assigned to their parents using the SNP panel and identified 79 full-sib families and genetic contributions from 33 sires and 11 dams. A highly skewed representation of family distributions in the cohort was observed which highlights the challenge of using a mass-spawning approach to the capture and identification of genetic diversity in P. maxima breeding programs.

The present study is a transversal analysis of the interest in genomic selection for plant and animal species. It focuses on the arguments that may convince breeders to switch to genomic selection. The arguments are classified into three different “bricks.” The first brick considers the addition of genotyping to improve the accuracy of the prediction of breeding values. The second consists of saving costs and/or shortening the breeding cycle by replacing all or a portion of the phenotyping effort with genotyping. The third concerns population management to improve the choice of parents to either optimize crossbreeding or maintain genetic diversity. We analyse the relevance of these different bricks for a wide range of animal and plant species and sought to explain the differences between species according to their biological specificities and the organization of breeding programs.

Statistical models play a significant role in designing competent breeding programs related to complex traits. Recently; the holo-omics framework has been productively utilized in trait prediction; but it contains many complexities. Therefore; it is desirable to establish prediction accuracy while combining the host’s genome and microbiome data. Several methods can be used to combine the two data in the model and study their effectiveness by estimating the prediction accuracy. We validate our holo-omics interaction models with analysis from two publicly available datasets and compare them with genomic and microbiome prediction models. We illustrate that the holo-omics interactive models achieved the highest prediction accuracy in ten out of eleven traits. In particular; the holo-omics interaction matrix estimated using the Hadamard product displayed the highest accuracy in nine out of eleven traits, with the direct holo-omics model and microbiome model showing the highest prediction accuracy in the remaining two traits. We conclude that comparing prediction accuracy in different traits using real data showed important intuitions into the holo-omics architecture of complex traits.

Evaluating the effectiveness of captive breeding programs is central to improving conservation outcomes in released animals. However, few studies have assessed the impact of the strategies and trade-offs involved in husbandry decisions and the selection of traits on the success of breeding programs. This study evaluated a range of husbandry features including an animal's environment, health, and traits of the released individual and its parents involved in the zoo-based Regent Honeyeater breed for release program to optimise individual reproductive success and survivability, leading to improved conservation outcomes in the wild. We analysed 285 birds using a penalised Cox proportional hazard model to assess survival and an ordinal logistic model to evaluate the reproductive success of zoo bred birds released to the wild. Key features identified by the study highlight the importance of having parents that are successful breeders and parents that have an overall higher lifetime reproductive output. However, there were associated quantity-quality trade-offs, as the success of young (i.e., released birds) produced by parents was negatively associated to the number of clutches per year (where one clutch per year was found optimal). The study demonstrated the importance of considering the parental effects on the traits of its offspring beyond its pedigree information and found there was an associated decline in fitness of its offspring with older fathers. Song tutoring using wild Regent Honeyeaters was also important for increased survival post-release. Other important factors are discussed within the review. In general, the study recommended that a multi-faceted approach in the assessment and evaluation of the captive breeding program, to identify markers that will improve conservation outcomes of future releases.