Selection In Breeding Programs Research Articles

Population structure and genetic relatedness of Sri Lankan Jaffna Local sheep with major South Indian breeds

Jaffna Local is an endangered indigenous sheep population in the island country of Sri Lanka. The present study was aimed at assessing genetic diversity of Jaffna Local sheep and its relationship with major South Indian breeds. A total of 320 sheep were genotyped at 19 short tandem repeat marker loci and sequenced for mitochondrial DNA (mtDNA) control region to assess population structure, genetic admixture and phylogeography. The results revealed Jaffna Local sheep having relatively low diversity and high estimated inbreeding coefficient as compared to major South Indian breeds. The results of genetic distance estimations, AMOVA and Bayesian analysis clearly indicated relatively closer genetic relationship of Jaffna Local sheep with Southern Tamil Nadu sheep breeds (Vembur, Kilakarisal) and Mandya as compared to other South Indian breeds. Analysis of mtDNA control region revealed 16 haplotypes in Jaffna Local sheep, of which four were observed to be singletons and specific to this breed. The maternal lineages of all the Jaffna Local and South Indian sheep belonged to haplogroup A (HPG-A). Sequence mismatch analysis revealed uni-modal distribution in Jaffna Local sheep indicating haplotype expansion. Considering Jaffna Local sheep is the only defined breed of Sri Lanka, it is imperative to implement selective breeding program in the native tract to prevent genetic dilution and foster conservation of this important indigenous genetic resource of Sri Lanka.

Developing Novel Rice Genotypes Harboring Specific QTL Alleles Associated with High Grain Yield under Water Shortage Stress.

Rice is considered a strategic crop for many countries around the world, being the main cash crop for farmers. Water shortage stress occurrence as a result of climate change is among the main threats challenging rice breeders in the last few decades. In the current study, 19 Fn-lines were developed from four populations by crossing a reverse thermo-responsive genic male sterile (rTGMS) line, M.J.5460S, with the three high-quality Egyptian commercial cultivars Giza177, Sakha105, Sakha106 and the promising line GZ7768 as male parents. These newly developed lines, along with their parents, and two water shortage stress-tolerant international genotypes (Azucena and IRAT170), were cultivated under water-shortage stress conditions and compared with their performance under well-watered conditions. Results indicated that the yielding ability of the 19 newly developed lines exceeded those for the two Egyptian parents (Giza177 and Sakha105) under well-watered conditions. The lines M.J5460S/GIZA177-3 and M.J5460S/GIZA177-12 were the best performing genotypes under water shortage stress conditions. The genetic and heritability in broad sense estimates indicated that direct selection for grain yield (GY) under water-shortage stress is highly effective in the current study. Molecular marker analysis revealed that M.J5460S/GIZA177-3 had accumulated the quantitative trait loci (QTL)s, on the chromosomes 2, 3, and 9, which contribute to GY under water-shortage stress from their high yielding tolerant ancestor, M.J5460S. It could be concluded that those lines are high yielding under both well-watered and water-stress conditions harboring several QTLs for yield enhancement under both conditions and that the markers RM555, RM14551, RM3199, RM257, RM242, and RM410 are among the markers that could be used in marker-assisted selection (MAS) breeding programs for such stress condition.

Heritable variation and lack of tradeoffs suggest adaptive capacity in Acropora cervicornis despite negative synergism under climate change scenarios.

Knowledge of multi-stressor interactions and the potential for tradeoffs among tolerance traits is essential for developing intervention strategies for the conservation and restoration of reef ecosystems in a changing climate. Thermal extremes and acidification are two major co-occurring stresses predicted to limit the recovery of vital Caribbean reef-building corals. Here, we conducted an aquarium-based experiment to quantify the effects of increased water temperatures and pCO2 individually and in concert on 12 genotypes of the endangered branching coral Acropora cervicornis, currently being reared and outplanted for large-scale coral restoration. Quantification of 12 host, symbiont and holobiont traits throughout the two-month-long experiment showed several synergistic negative effects, where the combined stress treatment often caused a greater reduction in physiological function than the individual stressors alone. However, we found significant genetic variation for most traits and positive trait correlations among treatments indicating an apparent lack of tradeoffs, suggesting that adaptive evolution will not be constrained. Our results suggest that it may be possible to incorporate climate-resistant coral genotypes into restoration and selective breeding programmes, potentially accelerating adaptation.

Commercial implementation of genomic selection in Tasmanian Atlantic salmon: Scheme evolution and validation.

Genomic information was included for the first time in the prediction of breeding values for Atlantic salmon within the Australian Salmon Enterprises of Tasmania Pty Ltd selective breeding program in 2016. The process to realize genomic selection in the breeding program begun in 2014 with the scheme finalized and fully implemented for the first time in 2018. The high potential of within family selection to accelerate genetic gain, something not possible using the traditional pedigree‐based approach, provided the impetus for implementation. Efficient and effective genotyping platforms are essential for genomic selection. Genotype data from high density arrays revealed extensive persistence of linkage disequilibrium in the Tasmania Atlantic salmon population, resulting in high accuracies of both imputation and genomic breeding values when using imputed data. Consequently, a low‐density novel genotype‐by‐sequence assay was designed and incorporated into the scheme. Through the use of a static high‐ and dynamic low‐density genotyping platforms, an optimized genotyping scheme was devised and implemented such that all individuals in every year class are genotyped efficiently while maximizing the genetic gains and minimizing costs. The increase in the rates of genetic gain attributed to the implementation of genomic selection is significant across both the breeding programs primary and secondary traits. Substantial improvement in the ability to select parents prior to progeny testing is observed across multiple years. The resultant economic impacts for the industry are considerable based on the increases in genetic gain for traits achieved within the breeding program and the use of genomic selection for commercial production.

Impact of a divergent selective breeding programme on individual feed conversion ratio in Nile tilapia Oreochromis niloticus measured in groups by video-recording

Feed conversion ratio (FCR) is an important trait to target in breeding programs in order to improve fish farming sustainability and increase environmental efficiency. Due to the complexity of accurately measuring the individual feed consumption of fish, developing a selective breeding programme to improve FCR is a challenge. Using video-recordings of several consecutive meals in tilapia groups, we selected two divergent lines of Nile tilapia for high (FCR+) and low (FCR-) FCR at juvenile stage (12.2 g) combining BLUP and within family selection. After two generations, we observed a 12% realized difference in FCR between both divergent lines, indicating that the inclusion of FCR in a selective breeding programme can be efficient in practice. This divergence was in line with a realized heritability of 0.19 for FCR. The divergence in estimated breeding values of FCR between the two lines was reduced (3%) but still present. Another important result was that the realized genetic correlation between FCR and Daily Weight Gain (DWG) was highly negative (rg = −0.69 ± 0.16), meaning that improving growth by selective breeding would also indirectly improve FCR in juvenile Nile tilapia, although direct selection for FCR would be more efficient than indirect selection through growth to improve FCR.

Genetic Analysis of the Fatty Acid Profile in Gilthead Seabream (Sparus aurata L.).

Simple SummaryHumans require essential fatty acids in their diet and marine fish are a source of them, especially omega3 fatty acids that present high benefits on diverse vascular diseases and the immune system. Breeding programs in gilthead seabream usually include growth as the first criterion in the selection process of the fish. However, that could lead to fish with a higher fillet fat content and a fatty acid profile with a lower polyunsaturated fatty acids percentage. Fillet fat content and its fatty acids profile have been revealed as heritable traits. Therefore, further studies to go deeper in the selection process are advisable.The gilthead seabream is one of the most valuable species in the Mediterranean basin both for fisheries and aquaculture. Marine fish, such as gilthead seabream, are a source of n3 polyunsaturated fatty acids, highly appreciated for human food owing to their benefits on the cardiovascular and immune systems. The aim of the present study was to estimate heritability for fatty acid (FA) profile in fillet gilthead seabream to be considered as a strategy of a selective breeding program. Total of 399 fish, from a broodstock Mediterranean Sea, were analysed for growth, flesh composition and FA profile. Heritabilities for growth traits, and flesh composition (fat, protein, and moisture content) were medium. Heritability was moderate for 14:0, 16:0 and 18:1n9 and for sum of monounsaturated FA and n6/n3 ratio, and it was low for 20:1n11 and 22:6n3 and the ratio unsaturated/saturated FA. Breeding programs in gilthead seabream usually include growth as the first criterion in the selection process of the fish. However, other quality traits, such as fillet fat content and its fatty acids profile should be considered, since they are very important traits for the consumer, from a nutritional point of view and the benefits for the health.

A high-density linkage map and sex-linked markers for the Amazon Tambaqui Colossoma macropomum

BackgroundTambaqui (Colossoma macropomum, Cuvier, 1818) is the most economically important native freshwater fish species in Brazil. It can reach a total length of over 1 m and a weight of over 40 kg. The species displays a clear sex dimorphism in growth performance, with females reaching larger sizes at harvest. In aquaculture, the production of monosex populations in selective breeding programmes has been therefore identified as a key priority.ResultsIn the present study, a genetic linkage map was generated by double digest restriction-site associated DNA (ddRAD) sequencing from 248 individuals sampled from two F1 families. The map was constructed using 14,805 informative SNPs and spanned 27 linkage groups. From this, the tambaqui draft genome was improved, by ordering the scaffolds into chromosomes, and sex-linked markers were identified. A total of 235 markers on linkage group 26 showed a significant association with the phenotypic sex, supporting an XX/XY sex determination system in the species. The four most informative sex-linked markers were validated on another 206 sexed individuals, demonstrating an accuracy in predicting sex ranging from 90.0 to 96.7%.ConclusionsThe genetic mapping and novel sex-linked DNA markers identified and validated offer new tools for rapid progeny sexing, thus supporting the development of monosex female production in the industry while also supporting breeding programmes of the species.

The Complete Mitochondrial Genome of One Breeding Strain of Asian Swamp Eel (Monopterus albus, Zuiew 1793) Using PacBio and Illumina Sequencing Technologies and Phylogenetic Analysis in Synbranchiformes.

Asian swamp eel (Monopterus albus, Zuiew 1793) is a commercially important fish due to its nutritional value in Eastern and Southeastern Asia. One local strain of M. albus distributed in the Jianghan Plain of China has been subjected to a selection breeding program because of its preferred body color and superiority of growth and fecundity. Some members of the genus Monopterus have been reclassified into other genera recently. These classifications require further phylogenetic analyses. In this study, the complete mitochondrial genomes of the breeds of M. albus were decoded using both PacBio and Illumina sequencing technologies, then phylogenetic analyses were carried out, including sampling of M. albus at five different sites and 14 species of Synbranchiformes with complete mitochondrial genomes. The total length of the mitogenome is 16,621 bp, which is one nucleotide shorter than that of four mitogenomes of M. albus sampled from four provinces in China, as well as one with an unknown sampling site. The gene content, gene order, and overall base compositions are almost identical to the five reported ones. The results of maximum likelihood (ML) and Bayesian inference analyses of the complete mitochondrial genome and 13 protein-coding genes (PCGs) were consistent. The phylogenetic trees indicated that the selecting breed formed the deepest branch in the clade of all Asian swamp eels, confirmed the phylogenetic relationships of four genera of the family Synbranchidae, also providing systematic phylogenetic relationships for the order Synbranchiformes. The divergence time analyses showed that all Asian swamp eels diverged about 0.49 million years ago (MYA) and their common ancestor split from other species about 45.96 MYA in the middle of the Miocene epoch. Altogether, the complete mitogenome of this breed of M. albus would serve as an important dataset for germplasm identification and breeding programs for this species, in addition to providing great help in identifying the phylogenetic relationships of the order Synbranchiformes.

Mapping of QTL for agronomic traits using high-density SNPs with an RIL population in maize.

Genome wide association studies (GWAS) have been widely used to identify QTLs underlying quantitative traits in humans and animals, and they have also become a popular method of mapping QTLs in many crops, including maize. Advances in high-throughput genotyping technologies enable construction of high-density linkage maps using SNP markers. High-density genetic mapping must precede to find molecular markers associated with a particular trait. The objectives of this study were to (1) construct a high-density linkage map using SNP markers and (2) detect the QTLs for grain yield and quality related traits of the Mo17/KW7 RIL population. In this study, two parental lines, Mo17 (normal maize inbred line) and KW7 (waxy inbred line) and 80 F7:8 lines in the Mo17/KW7 RIL population were genotyped using the MaizeSNP50 BeadChip, an Illumina BeadChip array of 56,110 maize SNPs. Marker integration and detection of QTLs was performed using the inclusive composite interval mapping (ICIM) method within the QTL IciMapping software. This study was genotyped using the Illumina MaizeSNP50 BeadChip for maize Mo17/KW7 recombinant inbred line (RIL) population. The 2904 SNP markers were distributed along all 10 maize chromosomes. The total length of the linkage map was 3553.7cm, with an average interval of 1.22cm between SNPs. A total of 18 QTLs controlling eight traits were detected in the Mo17/KW7 RIL population. Three QTLs for plant height (PH) were detected on chromosomes 4 and 8 and showed from 16.01% (qPH8) to 19.85% (qPH4a) of phenotypic variance. Five QTLs related to ear height (EH) were identified on chromosomes 3, 4, and 6 and accounted for 3.79% (qEH6) to 27.57% (qEH4b) of phenotypic variance. Five QTLs related to water content (WC) on chromosomes 1, 4, 8, and 9 accounted for 9.55% (qWC8b) to 23.30% (qWC4) of phenotypic variance. One QTL (qAC9) relating to amylose content (AC) on chromosome 9 showed 82.10% of phenotypic variance. The high-density linkage map and putative QTLs of the maize RIL population detected in this study can be effectively utilized in waxy and normal maize breeding programs to facilitate the selection process through marker-assisted selection (MAS) breeding programs.

The potential for mitigation of methane emissions in ruminants through the application of metagenomics, metabolomics, and other -OMICS technologies.

Ruminant supply chains contribute 5.7 gigatons of CO2-eq per annum, which represents approximately 80% of the livestock sector emissions. One of the largest sources of emission in the ruminant sector is methane (CH4), accounting for approximately 40% of the sectors total emissions. With climate change being a growing concern, emphasis is being put on reducing greenhouse gas emissions, including those from ruminant production. Various genetic and environmental factors influence cattle CH4 production, such as breed, genetic makeup, diet, management practices, and physiological status of the host. The influence of genetic variability on CH4 yield in ruminants indicates that genomic selection for reduced CH4 emissions is possible. Although the microbiology of CH4 production has been studied, further research is needed to identify key differences in the host and microbiome genomes and how they interact with one another. The advancement of “-omics” technologies, such as metabolomics and metagenomics, may provide valuable information in this regard. Improved understanding of genetic mechanisms associated with CH4 production and the interaction between the microbiome profile and host genetics will increase the rate of genetic progress for reduced CH4 emissions. Through a systems biology approach, various “-omics” technologies can be combined to unravel genomic regions and genetic markers associated with CH4 production, which can then be used in selective breeding programs. This comprehensive review discusses current challenges in applying genomic selection for reduced CH4 emissions, and the potential for “-omics” technologies, especially metabolomics and metagenomics, to minimize such challenges. The integration and evaluation of different levels of biological information using a systems biology approach is also discussed, which can assist in understanding the underlying genetic mechanisms and biology of CH4 production traits in ruminants and aid in reducing agriculture’s overall environmental footprint.

Spotted Wolffish Broodstock Management and Egg Production: Retrospective, Current Status, and Research Priorities.

Simple SummarySpotted wolffish, a cold-water fish species, is a high potential candidate marine fish species for the diversification of the aquaculture sector in Norway, Canada, and Iceland. A review of the state of advancement of all aspects of its reproduction is proposed. Species-specific life-history and reproduction traits are discussed in parallel with relevant information originating from past R&D activities and the current state of knowledge regarding rearing environmental conditions and practices possibly affecting broodstock performances.The first artificially fertilized spotted wolffish (Anarhichas minor) eggs hatched in Norway in the mid-1990s as this species was considered by Norwegian authorities to be a top candidate species for cold-water aquaculture in the North Atlantic regions. Previous research conducted in Norway (since 1992) and Canada (since 2000), focused on identifying key biological parameters for spotted wolffish cultivation which led, respectively, to the rapid establishment of a full commercial production line in northern Norway, while Québec (Canada) is witnessing its first privately driven initiative to establish commercial production of spotted wolffish on its territory. The control of reproduction can be viewed as a major requirement to achieve the development of performant strains using genetic selection tools and/or all-year-round production to bring about maximal productivity and synchronization among a given captive population. Although the basic reproduction aspects are more understood and controlled there are still some challenges remaining involving broodstock and upscaling of operations that limit the achievement of a standardized production at the commercial level. Quality of gametes is still considered a major constraint and it can be affected by multiple factors including nutrition, environmental conditions, handling practices, and welfare status. Internal insemination/fertilization and the protracted incubation period are challenging as well as the establishment of a health monitoring program to secure large-scale operations. The profound progress achieved in the control of reproduction, sperm handling, and cryopreservation methods for this species is presented and discussed. In this review, we also go into detail over the full range of up-to-date cultivation practices involving broodstock and identify areas that could benefit from additional research efforts (i.e., broodstock nutrition, health and welfare, scaling-up egg and larval production, genetics, and development of selective breeding programs).

JAYANTI” ROHU- A PROMISING FISH VARIETY FOR IMPROVING AQUACULTURE PRODUCTION

Selective breeding program was initiated at ICAR-Central Institute of Freshwater Aquaculture (ICAR-CIFA) in collaboration with Institute of Aquaculture Research (AKVAFORSK) in the year 1992 to improve growth of rohu through selective breeding following combined selection method. The base population was established from five riverine sources i.e. Ganga, Yamuna, Brahmaputra, Sutlej, Gomati and local farm stock of ICAR-CIFA. For each year class one control group was produced using 10-15 male and 10-15 female parents with average reeding value for harvest body weight and growth comparison was made with the progeny of selected group. The average realized selection response of harvest body weight after eight generations of selection was estimated to be 18.3% per generation. Multilocational field testing as well as on-farm trials in different parts of India showed significant growth improvement of genetically improved rohu for different generation of selectively bred rohu. The improved rohu popularly known as “Jayanti” has been disseminated to 16 states and different hatcheries of India from ICAR-CIFA. The improved rohu also proved to be feed neutral and effective under all culture practices which have enhanced the acceptance level. Impact assessment study further confirmed superiority of strain of rohu over the normal rohu. Disease resistance against Aeromonas hydrophila is added as second trait of selection to rohu breeding program. A wide range of variation in survival was observed among different families of rohu. Based on sire-dam model underlying heritability of survival at end of test was 0.15-0.19. After mass challenge, two lines of rohu have been produced i.e. resistant line and susceptible line. Resistant line rohu showed significantly higher survival over susceptible line. Estimated genetic correlation between growth and survival was observed to be 0.43. The estimation result showed positive correlation between both the traits in rohu breeding program. Key words: Selective breeding, base population, realized selection response, heritability, Jayanti rohu

Application of Genomics Approaches for the Improvement in Ascochyta Blight Resistance in Chickpea

Advancements in high-throughput genotyping and sequencing technologies are enabling the development of a vast range of genomic tools and resources for a new revolution in plant breeding. Several genotyping-by-sequencing (GBS) methods including capture-based, genome complexity reduction and sequencing of cDNA (GBS-t) are available for application in trait dissection, association mapping, and genomic selection (GS) in crop plants. The aims of this study were to identify genomic regions conferring resistance to Ascochyta blight (AB) introgressed from the wild Cicer echinospernum into the domesticated C. arietinum, through a conventional recombinant inbred population genotyped using a variety of GBS methods. Evaluation of GBS methods revealed that capture-based approaches are robust and reproducible while GBS-t is rapid and flexible. A genetic linkage map consisting of 5886 polymorphic loci spanning 717.26 cM was generated. Using field phenotyping data from two years, a single genomic region on LG4 was identified with quantitative trait loci (QTL) mapping. Both GBS methods reported in this study are well suited for applications in genomics assisted plant breeding. Linked markers for AB resistance, identified in the current study, provide an important resource for the deployment into chickpea breeding programs for marker-assisted selection (MAS).

Purebred-crossbred genetic parameters for reproductive traits in swine

For swine breeding programs, testing and selection programs are usually within purebred (PB) populations located in nucleus units that are generally managed differently and tend to have a higher health level than the commercial herds in which the crossbred (CB) descendants of these nucleus animals are expected to perform. This approach assumes that PB animals selected in the nucleus herd will have CB progeny that have superior performance at the commercial level. There is clear evidence that this may not be the case for all traits of economic importance and, thus, including data collected at the commercial herd level may increase the accuracy of selection for commercial CB performance at the nucleus level. The goal for this study was to estimate genetic parameters for five maternal reproductive traits between two PB maternal nucleus populations (Landrace and Yorkshire) and their CB offspring: Total Number Born (TNB), Number Born Alive (NBA), Number Born Alive > 1 kg (NBA > 1 kg), Total Number Weaned (TNW), and Litter Weight at Weaning (LWW). Estimates were based on single-step GBLUP by analyzing any two combinations of a PB and the CB population, and by analyzing all three populations jointly. The genomic relationship matrix between the three populations was generated by using within-population allele frequencies for relationships within a population, and across-population allele frequencies for relationships of the CB with the PB animals. Utilization of metafounders for the two PB populations had no effect on parameter estimates, so the two PB populations were assumed to be genetically unrelated. Joint analysis of two (one PB plus CB) vs. three (both PB and CB) populations did not impact estimates of heritability, additive genetic variance, and genetic correlations. Heritabilities were generally similar between the PB and CB populations, except for LWW and TNW, for which PB populations had about four times larger estimates than CB. Purebred-crossbred genetic correlations () were larger for Landrace than for Yorkshire, except for NBA > 1 kg. These estimates of indicate that there is potential to improve selection of PB animals for CB performance by including CB information for all traits in the Yorkshire population, but that noticeable additional gains may only occur for NBA > 1 kg and TNW in the Landrace population.

Animal as the Solution: Searching for Environmentally Friendly Dairy Cows

There is increasing societal concern surrounding the environmental externalities generated from ruminant production systems. Traditional responses to address these externalities have often been system-based. While these approaches have had promising results, they have served to view the animal as a problem that needs solving, rather than as a potential solution. This review attempts to answer the question: can we breed animals that are more environmentally friendly to address environmental outcomes and satisfy consumer demand? This was done by exploring the literature of examples where animals have been specifically bred to reduce their environmental impact. The use of milk urea nitrogen breeding values has been demonstrated as a tool allowing for selective breeding of dairy cows to reduce nitrogen losses. Low milk urea nitrogen breeding values have been documented to result in reduced urinary nitrogen concentrations per urination event, which ultimately reduces the level of nitrogen that will be lost from the system. The ability to breed for low methane emissions has also shown positive results, with several studies demonstrating the heritability and subsequent reductions in methane emissions via selective breeding programs. Several avenues also exist where animals can be selectively bred to increase the nutrient density of their final product, and thus help to address the growing demand for nutrient-dense food for a growing human population. Animal-based solutions are permanent, cumulative, and often more cost-effective than system-based approaches. With continuing research and interest in breeding for more positive environmental outcomes, the animal can now start to be viewed as a potential solution to many of the issues faced by ruminant production systems, rather than simply being seen as a problem.

Preferences for rohu fish (L. rohita) traits of women and men from farming households in Bangladesh and India

As selective breeding programs are time-consuming and expensive, it is critical that clients preferred traits are accurately identified. This is important to achieve value for money and adoption of selectively improved fish, and an essential foundation for effective contributions of genetic improvements to farming system. Data on fish trait preferences of smallholder farmers are rare; when these do exist, there is no information on whether the preferences of men and women are similar or not. The present work reports the first gender-disaggregated study of trait preferences of men and women from farming households for rohu carp (L. rohita) in Bangladesh (288 respondents) and India (270 respondents), addressing a major segment of aquaculture production in south Asia. The paper generates a nuanced, novel, and comparative understanding of the preferred characteristics through a survey of smallholder farmers that: 1) uses open-ended questions relating to producer and consumer perspectives; and, 2) applies a stated choice experiment using 1000minds software to address trade-offs in choices between traits for a subset of (58–38) respondents. General preferences derived from expressed likes or dislikes emphasized the importance of good taste, characteristics indicating freshness and safety such as aspects of appearance and color, as expected for a perishable product, and of value for money, including size of fish or relative flesh quantity. The overall pattern of preferences were similar for men and women, but there were differences in that men focused more on economic-related characteristics and women more on characteristics associated with nutritional value and food safety. When producers identified what to improve, they focused on larger size fish, reduced culture period, fry survival and disease resistance. When choosing between traits in pair-wise comparison exercises, ranking of traits was similar for both men and women in both Bangladesh and India. Significant differences were only observed between genders for the lower ranked traits in Bangladesh. Larger size fish as a charateristic ranked first in all groups, but there were marked differences between the importance of price and taste in the two countries. Methodologically, the study demonstrated that general preferences, do not automatically translate into characteristics for improvement by breeding programs, and the latter were not necessarily an accurate guide to the preferences expressed when specific tradeoffs were considered. These findings emphasize the need for well-designed and targeted surveys to be able to accurately define trait preferences, in particular to identify the relative values of heritable traits for practical application in breeding programs.

Selective Breeding for Disease-Resistant PRNP Variants to Manage Chronic Wasting Disease in Farmed Whitetail Deer.

Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy (TSE) of cervids caused by a misfolded variant of the normal cellular prion protein, and it is closely related to sheep scrapie. Variations in a host’s prion gene, PRNP, and its primary protein structure dramatically affect susceptibility to specific prion disorders, and breeding for PRNP variants that prevent scrapie infection has led to steep declines in the disease in North American and European sheep. While resistant alleles have been identified in cervids, a PRNP variant that completely prevents CWD has not yet been identified. Thus, control of the disease in farmed herds traditionally relies on quarantine and depopulation. In CWD-endemic areas, depopulation of private herds becomes challenging to justify, leading to opportunities to manage the disease in situ. We developed a selective breeding program for farmed white-tailed deer in a high-prevalence CWD-endemic area which focused on reducing frequencies of highly susceptible PRNP variants and introducing animals with less susceptible variants. With the use of newly developed primers, we found that breeding followed predictable Mendelian inheritance, and early data support our project’s utility in reducing CWD prevalence. This project represents a novel approach to CWD management, with future efforts building on these findings.

Genomic signatures of artificial selection in the Pacific oyster, Crassostrea gigas.

The Pacific oyster, Crassostrea gigas, is an important aquaculture shellfish around the world with great economic and ecological value. Selective breeding programs have been carried out globally to improve production and performance traits, while genomic signatures of artificial selection remain largely unexplored. In China, we performed selective breeding of C. gigas for over a decade, leading to production of several fast‐growing strains. In the present study, we conducted whole‐genome resequencing of 20 oysters from two fast‐growing strains that have been successively selected for 10 generations, and 20 oysters from the two corresponding wild populations. Sequencing depth of >10× was achieved for each sample, leading to identification of over 12.20 million SNPs. The population structures investigated with three independent methods (principal component analysis, phylogenetic tree, and structure) suggested distinct patterns among selected and wild oyster populations. Assessment of the linkage disequilibrium (LD) decay clearly indicated the changes in genetic diversity during selection. Fixation index (F st) combined with cross‐population composite likelihood ratio (XP‐CLR) allowed for identification of 768 and 664 selective sweeps (encompassing 1042 and 872 genes) tightly linked to selection in the two fast‐growing strains. KEGG enrichment and functional analyses revealed that 33 genes are important for growth regulation, which act as key components of various signaling pathways with close connection and further take part in regulating the process of cell cycle. This work provides valuable information for the understanding of genomic signatures for long‐term selective breeding and will also be important for growth study and genome‐assisted breeding of the Pacific oyster in the future.

Effect of Soy Leaf Flavonoids on Pea Aphid Probing Behavior.

Simple SummaryFlavonoids are plant phenolic compounds whose biological activities include participation in plant responses to various stresses of biological and environmental origins, including protection against insect herbivore attack. We were interested in whether the specific flavonoids detected in soybean leaves have the potential to discourage the pea aphid from infesting other leguminous plants, peas in particular. We immersed the pea leaves in ethanolic solutions of the flavonoids apigenin, daidzein, genistein and kaempferol, offered them to the pea aphids and observed their behavior when they probed plant tissues with their piercing–sucking mouthparts. We discovered that aphids readily probed the pea leaves whether they were treated with flavonoids or not. However, later on, the behavior of the aphids changed depending on the flavonoid applied. Apigenin, daidzein and kaempferol caused a decrease in the intensity of plant sap ingestion. In addition, daidzein and kaempferol made the finding of sap-transporting vessels more difficult for aphids. In contrast, genistein did not affect the pea aphids’ feeding activity. Our findings provide the plant breeders and plant protection services with information on what direction their efforts should take to protect leguminous plants against aphids in a sustainable and environmentally friendly way.Flavonoids detected in soybean Glycine max (L.) Merr. (Fabaceae) cause various alterations in the metabolism, behavior, and development of insect herbivores. The pea aphid Acyrthosiphon pisum (Harris) (Hemiptera: Aphididae) poses potential threat to soybeans, but the effect of individual flavonoids on its feeding-associated behavior is relatively unknown. We monitored probing behavior (stylet penetration activities) of A. pisum on its preferred host plant, Pisum sativum L. untreated (control) and treated with 0.1% ethanolic solutions of flavonoids apigenin, daidzein, genistein, and kaempferol. We applied the electrical penetration graph (electropenetrography, EPG) technique, which visualizes the movements of aphid stylets within plant tissues. None of the applied flavonoids affected the propensity to probe the plants by A. pisum. However, apigenin enhanced the duration of probes in non-phloem tissues, which caused an increase in the frequency and duration of stylet mechanics derailment and xylem sap ingestion but limited the ingestion of phloem sap. Daidzein caused a delay in reaching phloem vessels and limited sap ingestion. Kaempferol caused a reduction in the frequency and duration of the phloem phase. Genistein did not affect aphid probing behavior. Our findings provide information for selective breeding programs of resistant plant cultivars to A. pisum.

Body-shape trajectories and their genetic variance component in Gilthead seabream (Sparus aurata L.)

The phenotype of juvenile fish is closely associated with the adult phenotype, thus consisting an important quality trait for reared fish stocks. In this study, we estimated the correlation between the juvenile and adult body-shape in Gilthead seabream, and examined the genetic basis of the ontogenetic trajectories. The body shape of 959 pit-tagged fish was periodically examined during the juvenile-to-adult period. Individual shape ontogenetic trajectories were studied in respect to the initial (juvenile) and final (adult) phenotypes, as well as to the rate that adult phenotype is attained (phenotypic integration rate). We found that the juvenile body-shape presented a rapid change up to 192.7 ± 1.9 mm standard length, followed by a phenotypically stable period (plateau). Depending on the shape component considered, body-shape correlations between juvenile and adult stages ranged from 0.22 to 0.76. Heritability estimates (h2) of the final phenotype ranged from 0.370 ± 0.077 to 0.511 ± 0.089, whereas h2 for the phenotypic integration rate was 0.173 ± 0.062. To our knowledge, this is the first study demonstrating that the variance of the ontogenetic trajectories has a substantial additive genetic component. Results are discussed in respect to their potential use in selective breeding programs of Gilthead seabream.