Support Breeding Programs Research Articles

Reducing amylose content in wheat (Triticum aestivum L.) using a novel Wx-D1 null allele generated by chemical mutagenesis.

Amylose has a major influence over starch properties and end-use quality in wheat. The granule-bound starch synthase I, encoded by Wx-1, is the single enzyme responsible for amylose synthesis. Natural null mutants of Wx-1 appear at extremely low frequencies, particularly in the Wx-D1 locus, where only four spontaneous null variants have been identified, with different geographic origins. The current study identified an induced Wx-D1 null mutant (M4-9484) from the M4 generation of an ethyl methanesulfonate-mutagenized population of wheat cv. 'SM126'. The sequencing showed that the complete Wx-D1 ORF sequences of 'SM126' and M4-9484 were 2862 bp long and that there was one SNP mutation between them. The mutation was located at the RNA splice site within the junction of exon 8 and intron 8, which led to abnormal transcription of Wx-D1, with five different aberrant transcripts being identified in the mutant. The Wx-D1 null allele resulted in amylose and total starch content being decreased in M4-9484 in comparison with the wild-type 'SM126', with higher swelling capacity and being fully pasted at higher temperatures than the wild-type parent. The mutation of the Wx-D1 null gene affects the formation of amylose directly, resulting in significantly altered starch properties. This discovery offers valuable insights for enhancing wheat starch quality and contributes to the diversification of starch characteristics. It also deepens our understanding of the genetic and molecular mechanisms underlying amylose synthesis, thereby supporting breeding programs. © 2024 Society of Chemical Industry.

Genome-wide association for agro-morphological traits in a triploid banana population with large chromosome rearrangements

Abstract Banana breeding is hampered by the very low fertility of domesticated bananas and the lack of knowledge about the genetic determinism of agronomic traits. We analysed a breeding population of 2 723 triploid hybrids resulting from crosses between diploid and tetraploid M. acuminata parents, which was evaluated over three successive crop-cycles for 24 traits relating to yield components and plant, bunch and fruit architectures. A subset of 1 129 individuals was genotyped-by-sequencing revealing 205 612 single nucleotide polymorphisms. Most parents were heterozygous for one or several large reciprocal chromosomal translocations, which are known to impact recombination and chromosomal segregation. We applied two linear mixed models to detect associations between markers and traits: (i) a standard model with a kinship calculated using all SNPs and (ii) a model with chromosome-specific kinships that aims at recovering statistical power at alleles carried by long non-recombined haplotypic segments. For 23 of the 24 traits, we identified one to five significant quantitative trait loci (QTLs) for which the origin of favourable alleles could often be determined among the main ancestral contributors to banana cultivars. Several QTLs, located in the rearranged regions, were only detected using the second model. The resulting QTL landscape represents an important resource to support breeding programs. The proposed strategy for recovering power at SNPs carried by long non-recombined rearranged haplotypic segments is an important methodological advance for future association studies in banana and other species affected by chromosomal rearrangements.

Genetic Diversity Losses in Mantis Shrimp Oratosquilla oratoria Offspring Created for Supportive Releases Using an Ecological Breeding in Earthen Pond Method

ABSTRACTArtificial breeding of mantis shrimp Oratosquilla oratoria, using the ecological breeding in earthen pond (EBEP) method, has been carrying out from 2019, and the produced larvae have always been used for supportive breeding programs in Bohai Bay. To assess the degree of fidelity of enhancement programs used an EBEP method to native genetic pools, genetic diversity at 10 microsatellite loci was analyzed in three hatchery offspring populations, their wild parent stocks, and their wild contemporaneous offspring. Significant decrease in the almost genetic diversity parameters and highly significant differences in shannon's information index (decreasing by 22.54%–40.97%) and allelic richness (33.80%–46.87%) were observed between in hatchery populations. This further created relatively more genetic differentiation between the hatchery and wild population, as the pairwise Fst values and genetic distances showed. The mean pairwise relatedness coefficients showed higher values within hatchery populations and lower values within wild populations. Hatchery populations contained the fewest full‐sib families and offspring were extremely distributed in 10–11 full‐sib groups in each hatchery population. The relatively small number of actual spawning females and large variance in parental contribution to the next generation possibly causes allele reduction in the hatchery population, which in turn leads to a decrease in allelic diversity and an increase in genetic similarities among individuals. Promoting synchrony of ovarian development in females, providing good conditions for incubation and larvae culture and balancing the contributions of parents will be important in future breeding propagation.

Antioxidant Profile, Amino Acids Composition, and Physicochemical Characteristics of Cherry Tomatoes Are Associated with Their Color.

This study was conducted to characterize different colored lines of cherry tomatoes and derive information regarding their metabolite accumulation. Different colored cherry tomato cultivars, namely 'Jocheong', 'BN Satnolang', 'Gold Chance', 'Black Q', and 'Snacktom', were assessed for their firmness, taste characteristics, and nutritional metabolites at the commercial ripening stage. The cultivars demonstrated firmness to withstand impacts during harvesting and postharvest operations. The significant variations in the Brix to acid ratio (BAR) and the contents of phenylalanine, glutamic acid, and aspartic acid highlight the distinct taste characteristics among the cultivars, and the nutritional metabolites are associated with the color of the cultivars. The cultivar choices would be the black-colored 'Black Q' for chlorophylls, β-carotene, total flavonoids, and anthocyanins; the red-colored 'Snacktom' for lycopene; the orange-colored 'Gold Chance' for total phenolics; and the green-colored 'Jocheong' for chlorophylls, vitamin C, GABA, glutamic acid, essential amino acids, and total free amino acids. The antioxidant capacity varied among the cultivars, with 'Gold Chance' consistently exhibiting the highest activity across the four assays, followed by 'Snacktom'. This study emphasizes the importance of screening cultivars to support breeding programs for improving the nutritional content and encourages the inclusion of a diverse mix of different colored cherry tomatoes in packaging to obtain the cumulative or synergistic effects of secondary metabolites.

Antioxidant activity, anthocyanin profile, and mineral compositions of colored wheats

The antioxidant activities (ABTS and CUPRAC) of 40 different colored wheat genotypes were investigated, and some of the diverse wheat genotypes were selected to investigate their anthocyanin profiles and mineral compositions. The ABTS values of free and bound fractions were in the range of 15.61-157.36 mg TE/100 g and 33.26-189.48 mg TE/100 g, respectively. For the free and bound fractions of the colored wheat samples, the CUPRAC values were determined between 25.73 and 229.20 mg TE/100 g, and between 82.00 and 348.93 mg TE/100 g, respectively. The anthocyanin profiles of the colored wheats varied depending on the genotypes. Cyanidin-3-O-glucoside chloride was abundant in the samples w3, w8, w17, w18 and w20 while malvidin-3-O-glucoside chloride was the major anthocyanin for the samples w13, w23, w14, w30 and w34. Cyanidin-3-O-glucoside chloride was significantly higher in w18 than others (p<0.05). Cyanidin-3,5-di-O-glucoside was only found in the free extracts of the two samples (w17 and w20). The best accessions with high antioxidant activity and anthocyanin profile were identified for their potential utilization in wheat breeding programs. According to the results, the w17 sample (line BW 49880–Dark colored P, F4) was chosen as the best sample due to its highest antioxidant activity (p<0.05) and the best anthocyanin profile. The macronutrients Ca, K, and Mg highly varied among the genotypes studied. The trace elements, Zn and Fe were significantly higher in purple-grained lines than that of the red-grained variety. The study’s outcomes are likely to support breeding programs to generate new wheat cultivars with greater nutritional benefits.

Non-foliar photosynthesis and nitrogen assimilation influence grain yield in durum wheat regardless of water conditions.

There is a need to generate improved crop varieties adapted to the ongoing changes in the climate. We studied durum wheat canopy and central metabolism of six different photosynthetic organs in two yield-contrasting varieties. The aim was to understand the mechanisms associated with the water stress response and yield performance. Water stress strongly reduced grain yield, plant biomass and leaf photosynthesis, and downregulated C/N-metabolism genes and key protein levels, which occurred mainly in leaf blades. By contrast, higher yield was associated with high ear dry weight and lower biomass and ears per area, highlighting the advantage of reduced tillering and its consequent improvement in sink strength that promoted C/N metabolism at the whole plant level. An improved C metabolism in blades and ear bracts and N assimilation in all photosynthetic organs facilitated C/N remobilisation to the grain and promoted yield. Therefore, we propose that further yield gains in Mediterranean conditions could be achieved by considering the source-sink dynamics and the contribution of non-foliar organs, particularly N assimilation and remobilisation during the late growth stages. We highlight the power of linking phenotyping with plant metabolism to identify novel traits at the whole plant level to support breeding programmes.

Transcriptome and Metabolome Provide Insights into Fruit Ripening of Cherry Tomato (Solanum lycopersicum var. cerasiforme).

Insights into flavor formation during fruit ripening can guide the development of breeding strategies that balance consumer and producer needs. Cherry tomatoes possess a distinctive taste, yet research on quality formation is limited. Here, metabolomic and transcriptomic analyses were conducted on different ripening stages. The results revealed differentially accumulated metabolites during fruit ripening, providing candidate metabolites related to flavor. Interestingly, several key flavor-related metabolites already reached a steady level at the mature green stage. Transcriptomic analysis revealed that the expression levels of the majority of genes tended to stabilize after the pink stage. Enrichment analysis demonstrated that changes in metabolic and biosynthetic pathways were evident throughout the entire process of fruit ripening. Compared to disease resistance and fruit color genes, genes related to flavor and firmness may have a broader impact on the accumulation of metabolites. Furthermore, we discovered the interconversion patterns between glutamic acid and glutamine, as well as the biosynthesis patterns of flavonoids. These findings contribute to our understanding of fruit quality formation mechanisms and support breeding programs aimed at improving fruit quality traits.

Rapid detection and quantification of Aphanomyces cochlioides in sugar beet

Sugar beet (Beta vulgaris L.) is an economically important crop in temperate climates providing nearly 30% of sugar production worldwide. The oomycete Aphanomyces cochlioides is the causative agent of seedling damping-off and root rot disease in sugar beet. The pathogen is responsible for plant degeneration and drastic yield losses in all major sugar beet producing areas. The identification of resistant germplasm is essential to reduce the use of chemical treatments as well as the costs of protective measures and to effectively limit the damage caused by the pathogen. In this study we aimed to establish a qPCR-based method to quantify the pathogen DNA in infected plants and to predict the resistance levels of different sugar beet genotypes in response to A. cochlioides. The difference in the response to A. cochlioides isolates with different geographical origins was investigated. In addition, confocal microscopy was performed in order to observe the spatial and temporal colonization pattern in infected seedlings of susceptible and partially resistant breeding lines. The research presented in this article provides a tool to understand the progress of the infection in infected tissues and to identify the genetic background of resistance to A. cochlioides that can be used to support breeding programs.

Cryopreservation of local black rabbit spermatozoa in the Mekong delta region of Vietnam: Evaluating cryoprotectant effectiveness.

Rabbit production is well developed in the Mekong Delta and Vietnam, with increased consumption of rabbit meat in both urban and rural areas. Consequently, meat rabbit breeds have become popular in almost all provinces in Vietnam, resulting in a decline in the population of Local Black rabbits over the years. To support breeding programs, there is a crucial need to develop a cryopreservation method. The objective of this study was to develop sperm cryopreservation protocols and determine the optimal cryoprotectant for Local Black rabbit spermatozoa. Rabbit spermatozoa were obtained and diluted with TCG-EggYolk freezing medium containing 5%, 8%, and 10% glycerol or DMSO in a 1:1 ratio. Glycerol and DMSO-free mediums served as the controls. Samples were put into 0.5-mL straws, cooled to 15°C and 5°C, then placed on nitrogen vapour for 15 min and directly immersed in liquid nitrogen at -196°C. Samples were thawed at 37°C for 60 s after being frozen for 72 h Sperm quality measures, such as viability, motility, and membrane integrity, were assessed both before and after freezing. The results showed that the average viability, average motility, and average membrane integrity were 61.9%, 53.9%, and 42.9%, respectively, after thawing with 5% glycerol, which was higher than the two higher concentrations of glycerol (8% and 10%) (p < .05). Similarly, with 8% DMSO, the average viability, average motility, and membrane integrity were 59.2%, 51.0%, and 41.8%, respectively, which were higher than the two concentrations of DMSO (5% and 10%) (p < 0.05). Therefore, the cryopreservation of local black rabbit sperm with 5% glycerol or DMSO 8% resulted in high sperm quality, but considering the practical aspect of minimizing the volume of the preservative, a concentration of 5% glycerol may be the best option.

Penerapan Teknologi Pakan Flushing pada Pembiakan Sapi di Desa Pangkal Jaya, Kecamatan Nanggung, Kabupaten Bogor

The Daarusa'adah farmer group had a cattle breeding program using 20 local heifers. The limited knowledge and skills in managing the farm made the breeding program did not run optimally. The community service program, therefore, aimed to conduct training of cattle production and flushing feed technology application to support breeding program at farmer. This activity was carried out in Pangkal Jaya Village, Nanggung District, Bogor Regency, West Java, through three stages: 1). Training on beef cattle production and breeding program, 2). Assessment of the reproductive organs and health status and 3). Application of flushing feed in beef cattle at farmer level. There were 15 farmers who participated in this program. The data of training questionnaire were analyzed using the Wilcoxon signed-rank test to determine statistic significant differences of their knowledge between before and after the training program. The cattle performance data due to flushing feed application were analyzed descriptively. The results of showed that farmers were increase their knowledge and skills significantly in all production aspects of production and breeding cattle (P&lt;0.05) due to the training program. Application of flushing feed increase the body condition score (BCS) and body weight of the heifers. However, 50% of heifers have ovarian hypofunction based on rectal palpation. Therefore, it can be concluded that the training program of community service activities have succeeded increase the knowledge and skill of farmers. Furthermore, application of flushing feed increases the performance of heifers to support the cattle breeding program.

Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits in Urochloa ruziziensis.

Tropical forage grasses, particularly those belonging to the Urochloa genus, play a crucial role in cattle production and serve as the main food source for animals in tropical and subtropical regions. The majority of these species are apomictic and tetraploid, highlighting the significance of U. ruziziensis, a sexual diploid species that can be tetraploidized for use in interspecific crosses with apomictic species. As a means to support breeding programs, our study investigates the feasibility of genome-wide family prediction in U. ruziziensis families to predict agronomic traits. Fifty half-sibling families were assessed for green matter yield, dry matter yield, regrowth capacity, leaf dry matter, and stem dry matter across different clippings established in contrasting seasons with varying available water capacity. Genotyping was performed using a genotyping-by-sequencing approach based on DNA samples from family pools. In addition to conventional genomic prediction methods, machine learning and feature selection algorithms were employed to reduce the necessary number of markers for prediction and enhance predictive accuracy across phenotypes. To explore the regulation of agronomic traits, our study evaluated the significance of selected markers for prediction using a tree-based approach, potentially linking these regions to quantitative trait loci (QTLs). In a multiomic approach, genes from the species transcriptome were mapped and correlated to those markers. A gene coexpression network was modeled with gene expression estimates from a diverse set of U. ruziziensis genotypes, enabling a comprehensive investigation of molecular mechanisms associated with these regions. The heritabilities of the evaluated traits ranged from 0.44 to 0.92. A total of 28,106 filtered SNPs were used to predict phenotypic measurements, achieving a mean predictive ability of 0.762. By employing feature selection techniques, we could reduce the dimensionality of SNP datasets, revealing potential genotype-phenotype associations. The functional annotation of genes near these markers revealed associations with auxin transport and biosynthesis of lignin, flavonol, and folic acid. Further exploration with the gene coexpression network uncovered associations with DNA metabolism, stress response, and circadian rhythm. These genes and regions represent important targets for expanding our understanding of the metabolic regulation of agronomic traits and offer valuable insights applicable to species breeding. Our work represents an innovative contribution to molecular breeding techniques for tropical forages, presenting a viable marker-assisted breeding approach and identifying target regions for future molecular studies on these agronomic traits.

Agronomic, nutritive value, reproductive, cytogenetic, and molecular aspects of Paspalum accessions: Contribution to the development of new forage cultivars

AbstractThis study investigated the agronomic, nutritive value, cytogenetic, molecular, and reproductive aspects of twenty‐five Paspalum accessions to support breeding programs. The agronomic aspects and the nutritive value were evaluated in a randomized block experimental design with four replications, and with monthly repeated measures for 2 years. For the molecular characterization 16 microsatellite markers developed for different Paspalum species in previous works were used. The number of chromosomes was determined by visualizing the meiotic cells and the DNA content was determined by flow cytometry. The embryo sac clarification technique was used to characterize the reproductive system. The results indicated genetic variability for all the variables related to yield and nutritive value. For almost all variables, the values of Paspalum accessions were higher than those of the commercial cultivars Megathyrsus maximus cv. Tanzania and Urochloa brizantha cv. Marandu, used as references. However, the accessions showed in vitro dry matter digestibility values lower than the mean value presented by the references. The groups formed in the molecular analysis showed correspondence to the groups observed in the principal components analysis, considering the variables related to yield and nutritive value. Most accessions were revealed to be tetraploid with 40 chromosomes and most accessions belonging to the Virgata group displayed a sexual embryo sac structure. Some crosses can be indicated for genetic breeding, due to a superior genomic affinity between the accessions and the higher probability of heterosis in the progeny. These results provide subsidies to genetic plant breeding programs that use these accessions.

Persistent high hatchery recruitment despite advanced reoligotrophication and significant natural spawning in a whitefish

Many lakes of the pre-Alpine region suffered from severe eutrophication that affected the natural reproduction of whitefish (Coregonus spp.) and necessitated large-scale supportive breeding programs. With the advanced reoligotrophication, it is now important to evaluate the relevance of continued artificial breeding for population dynamics. We focused on a whitefish population of a lake that has reached phase III of the reoligotrophication, i.e., lake biomass production is declining since 2012 in response to low phosphorus concentrations. We show that most eggs are naturally spawned, the observed oxygen concentrations would again support embryo development at all depths, and ready-to-hatch embryos can indeed be found on spawning grounds. We marked all hatchery-produced eggs of the 2014 cohort with Alizarin red, stocked them as usual (at larval or early juvenile stages), and recaptured them over a period of five years. Fish were aged from yearly growth rings on scales, and otoliths were checked for marks. We found 90.3 % of the 2014 cohort to be hatchery-born. This ratio did not decline with fish age. We also determined juvenile growth of the cohorts 2012–2020 (based on the first annual ring on scales) and found that stocking intensity predicted juvenile growth (r2 = 0.67). This strong density dependence of individual growth suggests that stocking has largely determined cohort size over the first nine years of reoligotrophication phase III. We conclude that large areas of spawning grounds allow again for successful embryogenesis, that large quantities of eggs are naturally spawned, but that natural recruitment is significantly reduced by ecological or evolutionary factors, e.g., competition with hatchery-born fish, desynchronization of trophic interactions, or long-term effects of fishing- or hatchery-induced evolution.

Reproductive biology of Butia capitata (Arecaceae) under cultivation - indicators for the domestication of a threatened fruit tree

Butia capitata is a netropical palm that has ecological and economic importance but is threatened by deforestation. The domestication of the species would contribute to its conservation and to income generation. However, there are gaps in knowledge about the phenology, floral biology and pollination of B. capitata and information on these topics is crucial to support breeding programs. We describe here the phenology and reproductive biology of B. capitata under cultivation and evaluated the storage potential of its pollen. Phenological and morphological evaluations of inflorescence and fruit development were carried out during both the rainy and dry seasons, the dynamics of anthesis and stigmatic receptivity were monitored and the reproductive system was experimentally evaluated. Pollen grain storage under different conditions was investigated for six months. Inflorescence emission were more rapid in the rainy season, with greater numbers of infructescences as well as fruit weight. Cross-pollination was predominant due to protandry, with a sterile period from one to six days. Cross- and open- pollination are the most efficient reproductive systems (46 and 47% fruting, respectively). Fruit fixation does not occur under spontaneous self-pollination or apomixis, while artificial self-pollination induces only a small fruiting rate. Pollen grain viability was maintained for 180 days under both refrigeration (4 °C) and freezing (-20 °C) conditions, but was less than 30 days under natural environmental conditions. The cultivation allows the production in the off-season of natural populations and pollen grain storage and artificial cross-pollination are promising possibilities for increasing the productivity of B. capitata orchards.

Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats.

In the largest DNA-based study of domestic cats to date, 11,036 individuals (10,419 pedigreed cats and 617 non-pedigreed cats) were genotyped via commercial panel testing elucidating the distribution and frequency of known disease, blood type, and physical trait associated genetic variants across cat breeds. This study provides allele frequencies for many disease-associated variants for the first time and provides updates on previously reported information with evidence suggesting that DNA testing has been effectively used to reduce disease associated variants within certain pedigreed cat populations over time. We identified 13 disease-associated variants in 47 breeds or breed types in which the variant had not previously been documented, highlighting the relevance of comprehensive genetic screening across breeds. Three disease-associated variants were discovered in non-pedigreed cats only. To investigate the causality of nine disease-associated variants in cats of different breed backgrounds our veterinarians conducted owner interviews, reviewed clinical records, and invited cats to have follow-up clinical examinations. Additionally, genetic variants determining blood types A, B and AB, which are relevant clinically and in cat breeding, were genotyped. Appearance-associated genetic variation in all cats is also discussed. Lastly, genome-wide SNP heterozygosity levels were calculated to obtain a comparable measure of the genetic diversity in different cat breeds. This study represents the first comprehensive exploration of informative Mendelian variants in felines by screening over 10,000 pedigreed cats. The results qualitatively contribute to the understanding of feline variant heritage and genetic diversity and demonstrate the clinical utility and importance of such information in supporting breeding programs and the research community. The work also highlights the crucial commitment of pedigreed cat breeders and registries in supporting the establishment of large genomic databases, that when combined with phenotype information can advance scientific understanding and provide insights that can be applied to improve the health and welfare of cats.

A trait-based model ensemble approach to design rice plant types for future climate.

Crop models are powerful tools to support breeding because of their capability to explore genotype×environment×management interactions that can help design promising plant types under climate change. However, relationships between plant traits and model parameters are often model specific and not necessarily direct, depending on how models formulate plant morphological and physiological features. This hinders model application in plant breeding. We developed a novel trait-based multi-model ensemble approach to improve the design of rice plant types for future climate projections. We conducted multi-model simulations targeting enhanced productivity, and aggregated results into model-ensemble sets of phenotypic traits as defined by breeders rather than by model parameters. This allowed to overcome the limitations due to ambiguities in trait-parameter mapping from single modelling approaches. Breeders' knowledge and perspective were integrated to provide clear mapping from designed plant types to breeding traits. Nine crop models from the AgMIP-Rice Project and sensitivity analysis techniques were used to explore trait responses under different climate and management scenarios at four sites. The method demonstrated the potential of yield improvement that ranged from 15.8% to 41.5% compared to the current cultivars under mid-century climate projections. These results highlight the primary role of phenological traits to improve crop adaptation to climate change, as well as traits involved with canopy development and structure. The variability of plant types derived with different models supported model ensembles to handle related uncertainty. Nevertheless, the models agreed in capturing the effect of the heterogeneity in climate conditions across sites on key traits, highlighting the need for context-specific breeding programmes to improve crop adaptation to climate change. Although further improvement is needed for crop models to fully support breeding programmes, a trait-based ensemble approach represents a major step towards the integration of crop modelling and breeding to address climate change challenges and develop adaptation options.

Diversity and population structure of indigenous chicken in Congo, using MHC-linked microsatellite LEI0258

Context Chickens are the most important livestock in the Democratic Republic of Congo in particular and in Africa in general; they are kept for their meat and eggs for nutrition and economic status. The availability of chicken diversity information is very important in selection of breeds and in conservation of genetic resources. Aims This study aimed to determine allelic variability, genetic diversity, and genetic relationships of the indigenous chicken populations from the South Kivu region to support breeding programs and genetic resource conservations. Methods The LEI0258 microsatellite marker within the major histocompatibility complex gene region was used for genotyping. The LEI0258 locus amplicon sequences of 163 indigenous chickens were analysed. Key results The number of R13 and R12 repeats varied from 1 to 21 and from 3 to 21 respectively, whereas several combinations of indels and single-nucleotide polymorphisms were observed in the microsatellite flanking regions. In total, 45 different LEI0258 alleles ranging from 193 to 473 bp were determined, including 14 private alleles (Np). Expected heterozygosity (He) varied from 0.864 (Mwenga) to 0.938 (Bukavu), with a mean of 0.911, and observed heterozygosity (Ho) ranged from 0.417 (Uvira) to 0.667 (Mwenga), with a mean of 0.519. The analysis of molecular variance (AMOVA) showed higher genetic variation within individuals (56%) than among individuals (43%) and among chicken populations (1%). Clustering into three admixed gene pools (K = 3) showed the relationships among the chicken populations. Conclusion The present study showed the existence of high genetic diversity in chicken populations from South Kivu. Implications This study provides information useful for better conservation and breeding strategies of indigenous chicken populations in South Kivu.

Comparative proteomics of Pinus-Fusarium circinatum interactions reveal metabolic clues to biotic stress resistance.

Fusarium circinatum, causing pine pitch canker (PPC), affects conifers productivity and health worldwide. Selection and breeding for resistance arises as the most promising approach to fight PPC. Therefore, it is crucial to explore the response of hosts with varying levels of susceptibility to PPC to unveil the genes/pathways behind these phenotypes. We evaluated the dynamics of the needle proteome of a susceptible (Pinus radiata) and a relatively resistant (Pinus pinea) species upon F.circinatum inoculation by GeLC-MS/MS. Integration with physiological data and validation of key genes by qPCR allowed to identify core pathways regulating these contrasting responses. In P. radiata, the pathogen may target both the secondary metabolism to negatively regulate immune response and chloroplast redox proteins to increase energy-producing pathways for amino acid production in its favour. In contrast, chloroplast redox regulation may assure redox homeostasis in P. pinea, as well as nonenzymatic antioxidants. The presence of membrane trafficking-related proteins exclusively in P. pinea likely explains its defence response against F. circinatum. A crosstalk between abscisic acid and epigenetic regulation of gene expression is also proposed in PPC response. These results are useful to support breeding programs aiming to achieve PPC resistance.

Artificial Rearing of Atlantic Salmon Juveniles for Supportive Breeding Programs Induces Long-Term Effects on Gut Microbiota after Stocking.

In supportive breeding programs for wild salmon populations, stocked parr experience higher mortality rates than wild ones. Among other aspects of phenotype, the gut microbiota of artificially raised parr differs from that of wild parr before stocking. Early steps of microbiota ontogeny are tightly dependent upon environmental conditions, both of which exert long-term effects on host physiology. Therefore, our objective was to assess to what extent the resilience capacity of the microbiota of stocked salmon may prevent taxonomic convergence with that of their wild congeners after two months in the same natural environment. Using the 16S SSU rRNA marker gene, we tested the general hypothesis that environmental conditions during the very first steps of microbiota ontogeny imprint a permanent effect on later stages of microbiota recruitment. Our results first showed that gut microbiota composition of stocked and wild parr from the same genetic population, and sharing the same environment, was dependent on the early rearing environment. In contrast, skin microbiota in stocked individuals converged to that of wild individuals. Taxonomic composition and co-occurrence network analyses suggest an impairment of wild bacteria recruitment and a higher instability for the gut microbiota of stocked parr. This study is the first to demonstrate the long-term effect of early microbiota ontogeny in artificial rearing for natural population conservation programs, raising the need to implement microbial ecology.

Effect of cryoprotectant on the motility, viability, fertilization, and DNA integrity of naleh fish Barbonymus sp. (Cyprinidae) sperm

Naleh fish Barbonymus sp. is a commercial freshwater fish, which is indigenous to Aceh, Indonesia. The population of this species has declined over the years as a result of habitat perturbations and overfishing. Hence, the crucial need to develop a cryopreservation method to support breeding programs. This involved the use of a cryoprotectant as an important component. The objective of this study, therefore, was to explore the best cryoprotectant for naleh fish spermatozoa, and a total of five types were tested. These include the DMSO, Methanol, Ethanol, Glycerol, and Ethylene Glycol at a similar concentration of 10%, which were individually combined with 15% egg yolk, and every treatment was performed in three replications. Conversely, Ringer’s solution was adopted as an extender, and the sperm was cryopreserved in liquid nitrogen for 15 days. The results showed significant influence on sperm motility and viability, as well as egg fertility of naleh fish (P &lt;0.05), although the DMSO provided the best outcome, compared to others at 47.17%, 50.13%, and 45.67%, respectively. Furthermore, DNA fragmentation had not occurred in the fresh and cryopreserved sperm samples, indicating the protective effect of tested cryoprotectants. It is concluded that the 10% DMSO and 15% egg yolk is the best cryoprotectant for naleh fish spermatozoa.