Breeding Programs Research Articles

Investigating the Welfare of Zoo-Housed Cryptoprocta ferox: Behavioral Observations and Hormonal Profiling.

The global decline of species necessitates intensive conservation efforts, including ex-situ breeding programs to safeguard endangered populations. However, managing welfare and reproduction in zoological gardens can present several challenges. This study aims to explore behaviors and endocrinological responses of two specimens of fossa (Cryptoprocta ferox) under human care. One hundred and twenty hours of observation through focal animal sampling continuous recording and 67 fecal samples were collected. From fecal samples, cortisol (FCM), progesterone (FPM), and testosterone (FTM) metabolites' concentrations were analyzed using Radio Immuno Assay. According to our results, higher FTM (p < 0.05) and FPM levels at the beginning of the study, showing a potential alignment with the breeding season. When the male entered the female outdoor area, he recorded longer durations of seeking and marking behaviors (p ≤ 0.01), along with lower FCM levels (p < 0.05), suggesting an enriching effect. In the same period, the female's FCM level was higher (p ≤ 0.01), indicating potential stress. When both animals were in their respective outdoor areas, the FCM level of the female remained significantly higher (p < 0.05), and the male showed a peak in pacing duration (p < 0.01), implying a potential stress or frustration status. In her indoor area, the female exhibited significantly shorter durations of locomotion, marking, and seeking (p < 0.01) and did not show any abnormal behavior, likely due to the reduced complexity of the environment. However, we cannot exclude that her complete visual and olfactory separation from the male and visitors may also have contributed to a decrease in her overall stress levels. The findings highlight the interplay between hormonal fluctuations and behavioral responses in the two zoo-housed fossa, providing essential insights for fostering their well-being and facilitating conservation efforts.

Multiple Trait Bayesian Analysis of Partitioned Genetic Trends Accounting for Uncertainty in Genetic Parameters. An Example With the Pirenaica and Rubia Gallega Beef Cattle Breeds.

Genetic trends are a valuable tool for analysing the efficiency of breeding programs. They are calculated by averaging the predicted breeding values for all individuals born within a specific time period. Moreover, partitioned genetic trends allow dissecting the contributions of several selection paths to overall genetic progress. These trends are based on the linear relationship between breeding values and the Mendelian sampling terms of ancestors, enabling genetic trends to be split into contributions from different categories of individuals. However, (1) the use of predicted breeding values in calculating partitioned genetic trends depends on the variance components used and (2) a multiple trait analysis allows accounting for selection on correlated traits. These points are often not considered. To overcome these limitations, we present a software called "TM_TRENDS." This software performs a Bayesian analysis of partitioned genetic trends in a multiple trait model, accounting for uncertainty in the variance components. To illustrate the capabilities of this tool, we analysed the partitioned genetic trends for five traits (Birth Weight, Weight at 210 days, Cold Carcass Weight, Carcass Conformation, and Fatness Conformation) in two Spanish beef cattle breeds, Pirenaica and Rubia Gallega. The global genetic trends showed an increase in Carcass Conformation and a decrease in Birth Weight, Weight at 210 days, Cold Carcass Weight, and Fatness Conformation. These trends were partitioned into six categories: non-reproductive individuals, dams of females and non-reproductive individuals, dams of sires, sires with fewer than 20 progeny, sires between 20 and 50 progeny, and sires with more than 50 progeny. The results showed that the main source of genetic progress comes from sires with more than 50 progenies, followed by dams of males. Additionally, two additional features of the Bayesian analysis are presented: the calculation of the posterior probability of the global and partitioned genetic response between two time points, and the calculation of the posterior probability of positive (or negative) genetic progress.

Investigation of growth traits in Turkish Merino lambs using multi-locus GWAS approaches: Middle Anatolian Merino

This study explored the genetic basis of growth traits in Middle Anatolian Merino lambs using multi-locus genome-wide association study (GWAS) analyses. Descriptive statistics indicated moderate heritability (h² = 0.363) for birth weight (BW) and (h² = 0.309) for weaning weight (WW), both statistically significant (p < 0.001). Strong genetic correlations were observed between WW and BW (rG = 0.922) and WW and Kleiber ratio (KR, rG = 0.896), implying that simultaneous improvements may be possible through targeted selection. Five multi-locus methods (mrMLM, FASTmrMLM, pLARmEB, FASTmrEMMA, and ISIS EM-BLASSO) were used to identify the polygenic basis of the traits. For BW and WW, 20 and 18 significant SNPs (LOD ≥ 5) were detected, respectively, with some SNPs co-detected by multiple methods. In contrast, only 10 significant SNPs were identified for KR, all exclusively by the ISIS EM-BLASSO approach. Pathway analyses within ± 100 Kb of associated SNPs revealed genes and pathways influencing these traits, which could be leveraged in future breeding programs for enhanced growth performance. The identified SNPs, particularly those associated with BW and WW traits, could facilitate genomic selection if validated in larger and more diverse populations.

Deciphering genetic characteristics of South China and North China indigenous pigs through selection signatures

BackgroundIndigenous pig breeds in China have accumulated significant genetic diversity due to regional selection pressures. Investigating the selection signatures of these populations helps to understand their adaptive evolution and contributes to genetic improvement programs.ResultsWe collected whole-genome sequencing data from 133 individuals, including South China and North China indigenous pigs and Asian wild boars. After data filtering, we retained 31,521,978 high-quality SNPs. Population structure analysis using PCA revealed distinct genetic clustering among these populations. Selection signature detection identified 5,227 loci under selection in South China indigenous pigs and 5,800 in North China indigenous pigs compared to Asian wild boars. Candidate genes were enriched in immune response pathways, reproductive traits, and pigmentation pathways. South China indigenous pigs exhibited selection signals for fat deposition and immune responses, while North China indigenous pigs showed stronger signals related to growth, blood physiology, and reproductive performance. Additionally, key genes such as MC1R and KIT were associated with coat color variation, and IGF1R and IGF2R were linked to growth regulation.ConclusionOur results demonstrate that indigenous pigs in China have undergone selection for distinct traits aligned with their regional environments and farming systems. South China indigenous pigs have been selected for traits related to fat deposition and immunity, while North China indigenous pigs have been selected for growth and reproductive traits. The findings offer crucial insights into the genetic architecture of indigenous pig breeds, providing a valuable foundation for future genetic breeding programs.

Genomic regions associated with flag leaf and panicle architecture in rice (Oryza sativa L.)

BackgroundFlag leaf (FL) and panicle architecture (PA) are critical for increasing rice grain yield as well as production. A genome-wide association study (GWAS) can better understand the genetic pathways behind complex traits like FL and PA.ResultsIn this study, 208 diverse rice germplasms were grown in the field at the Texas A&M AgriLife Research Center at Beaumont, TX, during 2022 and 2023 following Augmented Randomized Complete Block Design. After heading, eight different flag leaf and panicle architecture (FLPA) related traits were measured. GWAS analyses were performed to identify potential genomic regions associated with FLPA traits. A total of 97 quantitative trait loci (QTLs) (48 in 2022 and 49 in 2023) were distributed across all 12 chromosomes. GWAS revealed four QTLs (qSBPP4-2, qFLW6-2, qGNPP9, and qGWPP2-3) with phenotypic variation ranging from 11.7 to 22.3%. Two genetic loci were identified as multi-trait QTLs, i.e., S04_32100268 (qFLL4-1 and qFLA4-1) and S04_11552936 (qFLW4 and qFLA4-2) during 2022 and 2023, respectively. Additionally, these loci were further utilized to analyze candidate genes, and 65 genes were predicted in the 100-kb genomic region upstream and downstream. In silico expression analysis revealed 15 genes were expressed during the reproductive stage. These genes were associated with protein kinase, heat shock transcription factor family, sugar transporter conserved site and transcription factor bHLH95- like basic helix-loop-helix domain protein, as well as those that regulate the FLPA-related traits. Os04g0631100 was identified as a potential candidate gene that is highly expressed during the endosperm development stage, and it is associated with an important sugar transporter protein that will be helpful in grain improvement.ConclusionGWAS results revealed four major and two multi-trait QTLs. Expanding their candidate genes, and expression analysis provide the genetic information for molecular improvement of the FLPA-related trait in rice breeding programs.

Chromosome-level genome assembly and annotation of the camouflage grouper (Epinephelus polyphekadion)

The camouflage grouper (Epinephelus polyphekadion) is an economically carnivorous fish widely distributed in the Indo-Pacific. However, no valid reference genome of E. polyphekadion severely hinders further research on biology and genomic breeding programs. Here, we presented a high-quality chromosome-level genome assembly of E. polyphekadion using PacBio sequencing and Hi-C technologies. The chromosome-level genome has a total length of 1.1 Gb with a contig N50 of 40.8 Mb. Approximately 99.4% of the assembly lengths were anchored to 24 pseudochromosomes. In total, 25,165 protein-coding genes were predicted, among which 24,634 genes (97.9%) were functionally annotated. The completeness of the assembly was estimated to be 99.1% using BUSCO. In summary, the first reference genome of E. polyphekadion in this study will not only provide pivotal genetic resources for further biological and evolutionary studies of groupers, but also benefit the development of genomic hybridization breeding in the artificial grouper industry.

PtrA, Piz-t, and a novel minor-effect QTL (qBR12_3.3–4.4) collectively contribute to the durable blast-resistance of rice cultivar Tainung 84

BackgroundRice blast caused by Pyricularia oryzae is a major threat to rice production worldwide. Tainung 84 (TNG84) is an elite japonica rice cultivar developed through the traditional pedigree method. It has maintained superior blast resistance since its release in 2010. This study aimed to investigate the genetic factors underlying the durable resistance of TNG84 in Taiwan.ResultsQuantitative trait locus (QTL) mapping was conducted using 122 F2 individuals and F2:3 families derived from the cross of TNG84 and a susceptible japonica cultivar Tainan 11 (TN11). Using 733 single nucleotide polymorphisms (SNPs) obtained through genotyping-by-sequencing and three P. oryzae isolates (D41-2, 12CY-MS1-2, and 12YL-TT4-1) belonging to different physiological races and Pot2 lineages, a major QTL was identified in the region of 52–54 cM (9.54–15.16 Mb) on chromosome 12. Fine-mapping using 21 F5:6 recombinants delimited the QTL to a 140.4-kb region (10.78 to 10.93 Mb) containing the known resistance gene Ptr. Sequencing analysis indicated that TNG84 carries the resistant PtrA allele and TN11 carries the susceptible PtrD allele. Investigation of the Ptr haplotypes in 41 local japonica rice cultivars revealed that eight PtrA-containing cultivars (19.5%) consistently exhibited good field resistance in Taiwan from 2008 to 2024. Subsequently, a few F5:6 lines (P026, P044, P092, and P167) lacking the resistant Ptr allele were observed to exhibit a resistant phenotype against P. oryzae 12YL-TT4-1-lab. Trait-marker association analyses using eight F6:7 homozygous recombinants, 378 BC1F2 from P044 backcrossed to TN11, and 180 BC1F2 from P092 backcrossed to TN11, identified Piz-t on chromosome 6 and a new QTL located between 3.3 Mb and 4.4 Mb on chromosome 12 (designated as qBR12_3.3–4.4). Analysis of 12 selected BC1F2:3 lines derived from P044 demonstrated that in the absence of Ptr and Piz-t, qBR12_3.3–4.4 alone reduced the disease severity index from approximately 6.3 to 3.9.ConclusionsPtrA is likely the primary gene responsible for the broad-spectrum and durable resistance of TNG84. Piz-t confers narrow-spectrum resistance, while qBR12_3.3–4.4 contributes partial resistance. The discovery of qBR12_3.3–4.4 has provided a new source of blast resistance, and the markers developed in this study can be utilized in future breeding programs.

Navigating access and benefit sharing in international trade of endemic species: The case of Colombia's poison frogs (Dendrobatidae)

AbstractWildlife is an important global commodity that generates significant revenue along the supply chain, including economic benefits in range states for sought‐after species. However, international trade in wild species is often associated with over‐exploitation and illegal extraction. To regulate, monitor, and ensure the sustainability of such trade, over 180 countries have ratified the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Using national data collected through CITES processes, we undertook a network analysis to evaluate the structure and dynamics of international trade in six CITES‐listed species of Colombian endemic poison frogs (Dendrobatidae). We assessed the magnitude of the international trade and the countries that were reporting legal imports/exports, both before and after Colombia allowed legal exports of these species, to examine the changes associated with Colombia's export legalization and to draw conclusions about the country's role and benefits from trade in these species. Our analyses show that, for over two decades, international trade of CITES‐listed species likely in contravention of the Convention resulted in significant exports—and likely greater financial benefits—accruing in non‐range states through reported captive breeding programs. Although the market was reconfigured when Colombia legalized the export of certain endemic frog species, non‐range states with founder stocks obtained from unknown and possibly illegal sources continue to account for a significant portion of the trade volume of some species (mostly, Phyllobates spp.). We discuss the importance of enforcing regulations and collaborations that promote better traceability of international commerce of endemic species to ensure the legitimacy of transactions, economic benefits for origin countries, and the conservation of species in the wild.

Near-complete telomere-to-telomere de novo genome assembly in Egyptian clover (Trifolium alexandrinum).

Egyptian clover (Trifolium alexandrinum L.), also known as berseem clover, is an important forage crop to Semi-arid conditions that was domesticated in ancient Egypt since 6,000 years BC and introduced and well adapted to numerous countries including India, Pakistan, Turkey, and Mediterranean region. Despite its agricultural importance, genomic research on Egyptian clover has been limited to developing efficient modern breeding programs. In the present study, we constructed near-complete telomere-to-telomere-level genome assemblies for two Egyptian clover cultivars, Helaly and Fahl. Initial assemblies were established by using highly-fidelity long-read technology. To extend sequence contiguity, we developed a gap-targeted sequencing (GAP-Seq) method, in which contig ends are targeted for sequencing to obtain long reads bridging two contigs. The total length of the resultant chromosome-level assemblies was 547.7Mb for Helaly and 536.3Mb for Fahl. These differences in sequence length can be attributed to the expansion of DNA transposons. Population genomic analysis using single-nucleotide polymorphisms revealed genomic regions highly differentiated between two cultivars and increased genetic uniformity within each cultivar. Gene ontologies associated with metabolic and biosynthetic processes and developmental processes were enriched in these genomic regions, indicating that these genes may determine the unique characteristics of each cultivar. Comprehensive genomic resources can provide valuable insights into genetic improvements in Egyptian clover and legume genomics.

Heritability and Genome-Wide Association Study of Dog Behavioral Phenotypes in a Commercial Breeding Cohort

Background: Canine behavior plays an important role in the success of the human–dog relationship and the dog’s overall welfare, making selection for behavior a vital part of any breeding program. While behaviors are complex traits determined by gene × environment interactions, genetic selection for desirable behavioral phenotypes remains possible. Methods: No genomic association studies of dog behavior to date have been reported on a commercial breeding (CB) cohort; therefore, we utilized dogs from these facilities (n = 615 dogs). Behavioral testing followed previously validated protocols, resulting in three phenotypes/variables [social fear (SF), non-social fear (NSF), and startle response (SR)]. Dogs were genotyped on the 710 K Affymetrix Axiom CanineHD SNP array. Results: Inbreeding coefficients indicated that dogs from CB facilities are statistically less inbred than dogs originating from other breeding sources. Heritability estimates for behavioral phenotypes ranged from 0.042 ± 0.045 to 0.354 ± 0.111. A genome-wide association analysis identified genetic loci associated with SF, NSF, and SR; genes near many of these loci have been previously associated with behavioral phenotypes in other populations of dogs. Finally, genetic risk scores demonstrated differences between dogs that were more or less fearful in response to test stimuli, suggesting that these behaviors could be subjected to genetic improvement. Conclusions: This study confirms several canine genetic behavioral loci identified in previous studies. It also demonstrates that inbreeding coefficients of dogs in CB facilities are typically lower than those in dogs originating from other breeding sources. SF and NSF were more heritable than SR. Risk allele and weighted risk scores suggest that fearful behaviors could be subjected to genetic improvement.

HISTOPATHOLOGIC FINDINGS IN 10 CASES OF MORTALITY IN CAPTIVE MALAYSIAN FIRE SNAILS (PLATYMMA TWEEDIEI).

Malaysian fire snails (Platymma tweediei), face threats to their environment, including habitat destruction and the illegal wildlife trade. Captive breeding projects are likely to play a role in the survival of this species; however, mortality in captive populations potentially presents a significant challenge. This paper presents the results of histopathologic examination of tissues from 10 P. tweediei casualties in a captive population at Chester Zoo. In October 2022, a captive breeding program was established with 20 wild-born P. tweediei. All adult founder animals died by July 2023, of which 10 were submitted for necropsy and histopathology of organs. Significant histologic abnormalities were present in all cases, primarily affecting the lung, integument, and heart. Histological analyses indicated a pneumonia-like condition was prevalent in all cases, suggesting potential environmental factors contributed to respiratory infections. A variety of possible etiologic or secondary infectious agents were present in sections including bacteria, fungi, and trematodes. There were some challenges in interpreting the histologic changes, emphasizing the need for more reference material and studies on the normal histologic anatomy of terrestrial gastropods. The findings underline the importance of understanding mortality events in captive populations to improve husbandry and environmental management. Additionally, the study recommends the submission of fresh specimens for necropsy to enhance diagnostic capabilities, such as bacterial culture, and suggests targeted sampling strategies for future research on captive snail species.

Meta-QTL mapping for wheat thousand kernel weight

Wheat domestication and subsequent genetic improvement have yielded cultivated species with larger seeds compared to wild ancestors. Increasing thousand kernel weight (TKW) remains a crucial goal in many wheat breeding programs. To identify genomic regions influencing TKW across diverse genetic populations, we performed a comprehensive meta-analysis of quantitative trait loci (MQTL), integrating 993 initial QTL from 120 independent mapping studies over recent decades. We refined 242 loci into 66 MQTL, with an average confidence interval (CI) 3.06 times smaller than that of the original QTL. In these 66 MQTL regions, a total of 4,913 candidate genes related to TKW were identified, involved in ubiquitination, phytohormones, G-proteins, photosynthesis, and microRNAs. Expression analysis of the candidate genes showed that 95 were specific to grain and might potentially affect TKW at different seed development stages. These findings enhance our understanding of the genetic factors associated with TKW in wheat, providing reliable MQTL and potential candidate genes for genetic improvement of this trait.

Assessment of Genetic Variability and Trait Associations in Chickpea (Cicer arietinum L.) Germplasms for Targeted Breeding Strategies

Chickpea (Cicer arietinum L.) is a pivotal legume crop with substantial contributions to global food security and agricultural sustainability due to its high protein content, adaptability and nitrogen-fixing ability. The efficiency of breeding programs in enhancing chickpea productivity and resilience relies heavily on understanding and utilizing genetic variability within the germplasm. This study investigates the extent of genetic variability among forty-three chickpea genotypes, focusing on key traits such as number of pods (NPP), biological yield (BY), harvest index (HI), days to flowering (DTF), days to maturity (DTM), that influence yield and other agronomic characteristics. Analysis of variance showed significant variability among genotypes for various traits. Higher phenotypic coefficients of variation (PCV) compared to genotypic coefficients (GCV) indicated the presence of environmental influence, particularly for traits like number of pods per plant (NPP) and biological yield (BY). High heritability was observed for days to flowering (DTF) and maturity (DTM), while genetic advance as percent of mean (GAM) varied, indicating additive gene action for some traits. Correlation and path analysis revealed positive relationships between plot yield and traits such as Days to Flowering (DTF), plant height (PH), and harvest index (HI). Principal component analysis (PCA) and cluster analysis indicated significant genetic diversity, grouping genotypes into clusters and identifying top performers like GJG1801 and NBEG 924. This study emphasizes the importance of genetic variability in breeding programs, aiding in the selection of elite genotypes for targeted traits improvement.

Evaluation of wheat blast resistance in the USDA hard winter wheat (Triticum aestivum L.) Northern and Southern Regional Performance Nurseries.

Wheat blast, caused by the Triticum pathotype of Pyricularia oryzae, is an emerging disease that threatens the global supply of wheat. The pathogen was first reported in Brazil and subsequently spread to the neighboring countries of Argentina, Bolivia, and Paraguay. More recently, wheat blast was reported in Asia and Africa, having been observed in Bangladesh and Zambia. The transcontinental spread of the pathogen has heightened awareness of the disease and has underscored the need to prepare for potential introductions into major wheat production regions. To this end, we have conducted greenhouse evaluations of the 2017 - 2020 hard winter wheat (Triticum aestivum L.) entries of the USDA-coordinated Northern and Southern Regional Performance Nurseries (NRPN and SRPN, respectively) of the U.S. Great Plains using an aggressive isolate of the pathogen, B-71, collected in Bolivia in 2012. Based on molecular marker analysis, all potentially resistant entries in both the NRPN and SRPN were in possession of the distal chromosomal translocation of 2NVS from Aegilops ventricosa, which has previously been associated with wheat blast resistance. No potentially new sources of resistance were evident in the 2017 - 2020 regional performance nurseries, which highlights the need for the continued use of 2NVS donor lines in Great Plains wheat breeding programs.

Profile Characterization of Cowpea Variety Suitable for Good Kossai: A Cowpea Pancake

Cowpea is a legume rich in nutrients that are very important from human nutrition and socio-economic point of view. The transformation of cowpea into Kossai involves several actors for its optimal valorization. This study aims to identify and synthesize the main traits sought by the actors of the links in the Kossai value chain. The methodology consisted of collecting data using a questionnaire administered to populations of 140 cowpea grain producers, 147 Kossai processors/resellers and 146 Kossai consumers selected in 14 sites and 28 focus groups discussions. The results showed that 88% of producers are men, 94% of consumers are men and 100% of processors are women. Actors in the sample have an average age of 46 years and a basic level of education, mainly traditional Coranic school and primary school. Cowpea local varieties are still predominantly used in the production and manufacture of Kossai. The processing of Kossai is done in six stages from winnowing to frying. Kneading and frying are the most delicate stage which requires more attention to obtain good Kossai. Main traits of cowpea variety expected by actors of Kossai value chain are large-caliber clean, white or reddish seed coat and consistency, high yield, precocity, etc. In addition, the grains must be suitable for Kossai manufacturing process, particularly mixing and frying with golden color of the final product. Breeding program of new cowpea varieties suitable for making Kossai should consider a large number of these traits in order to increase diversity, improve and sustain nutritional quality.

Identification of genomic regions affecting nitrogen excretion intensity in Brown Swiss dairy cows

Dairy cows with a lower nitrogen excretion intensity (Nexi) excrete less nitrogen, ammonia (NH3) and nitrous oxide (N2O), a highly potent greenhouse gas (GHG), per kg of milk produced and therefore represent a lower environmental impact while maintaining food security. To date, the genomics background of Nexi is unknown. Here we performed a genetic association study, overlap analysis and functional enrichment analysis for Nexi in 875 genotyped dairy cows with 2,147 lactations from 200 herds. We identified 1456 single nucleotide polymorphisms (SNPs) that significantly affect Nexi. We found 140 SNPs overlapping with 148 protein-coding genes. The MAN1A1 gene is a strong candidate gene for Nexi. Genotype CC of rs42786248, the most significantly associated SNP located in the MAN1A1 gene, had higher Nexi than genotypes AA (p < 0.001) and AC (p < 0.001). We identified 33 genes involved in biological processes related to nitrogen metabolism. Our results form the basis for further research on the genomics background of Nexi. The identified SNPs serve as potential targets for selective breeding programs, aimed at reducing Nexi and associated NH3 and N2O emissions in cattle production, thus contributing to more environmentally sustainable milk production.

Breeding objectives and economic value of important traits of Abergelle goats kept under a smallholder production system in Tigray, Ethiopia

Context In developing countries, the production of livestock can be improved by establishing a functional breeding program that involves communities in planning and implementation. Production objectives, farmers’ preferences for traits, and the economic value of the traits need to be studied and documented in designing a functional breeding program. Aim This study aims to identify production objectives, determine the preferred traits of smallholder farmers, and estimate the economic values of important traits for Abergelle goats in Tigray, Ethiopia. Methods An own-flock ranking exercise was used to identify the trait preferences of smallholder farmers. A bio-economic model was employed to estimate the economic values of important traits of Abergelle goats. Key results Abergelle goats were mainly kept for income generation followed by milk production. Appearance (size), color, libido, pedigree, and growth were the most important breeding-buck attributes, whereas milk yield, mothering ability (kid survival and growth), pedigree, coat color, kidding interval, and twinning were the important attributes for breeding does. Positive economic values of €0.25, €0.12, €0.45, €0.68, €0.17 and €2.00 per genetic standard deviation were obtained for 6-month weight, mature weight, daily milk yield, liter size, kidding interval, and pre-weaning kid survival per average doe place and year respectively. However, a negative economic value of −€0.017 per genetic standard deviation was achieved for 3–6-month average daily gain (ADG) per doe per year. Conclusions In this study, the most economically significant traits with positive economic values were pre-weaning survival, litter size, daily milk yield, 6-month weight, mature weight, and kidding interval. Implication Including these traits in the breeding goals can increase the profitability of the flock and improve the livelihood of Abergelle goat keepers.

Marker Assisted Selection: A Novel Approach for Crop Improvement

The process of marker-assisted selection, or marker-aided selection (MAS), selects a trait of interest indirectly by considering a marker linked to the trait (e.g., quality, productivity, disease resistance, and biotic stress tolerance) rather than the trait itself. This integration of marker data with traditional selection approaches has become a widely studied and recommended method for advancing breeding programs. This technique has been extensively researched and recommended for animal and plant breeding. Here, we combine marker data with conventional selection to choose the best candidate for a future breeding program. Nowadays, the majority of MAS investigations employ DNA-based markers such as microsatellites, single nucleotide polymorphisms (SNPs), random amplification of polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and restriction fragment length polymorphism (RFLP). In this case, we discussed several kinds, techniques, and other features of marker Assisted Selection.

Genomic prediction of genotyped and non-genotyped Jeju black cattle using single- and multi-trait methods for carcass traits

Jeju black cattle (JBC) are recognised as one of Korea’s native breeds that are well-suited to the local environmental conditions and known for their excellent meat quality. This study investigated the variance components and genomic prediction accuracy for carcase traits such as carcase weight (CWT), eye muscle area (EMA), backfat thickness (BF) and marbling score (MS) in JBC using various statistical models. We employed single-step genomic best linear unbiased prediction (ssGBLUP) and single-step Bayesian regression (SSBR) models, which utilised imputed genotypes for non-genotyped individuals. Phenotypic data were collected from 2045 JBC, and 3759 JBC individuals were genotyped using the Affymetrix 160K SNP Axiom array. Estimated heritability ranged from 0.24 to 0.40 for both single-trait and multi-trait models. Multi-trait models consistently demonstrated higher genomic prediction accuracy compared to single-trait models, underscoring the value of integrating multiple traits. For instance, CWT accuracy improved from 0.24 in single-trait PBLUP (st-PBLUP) to 0.47 in multi-trait ssGBLUP. Similarly, SSBR models showed significant improvements, with single-trait SSBR Bayes B achieving 0.46 and its multi-trait version reaching 0.49. EMA accuracy improved from 0.21 in st-PBLUP to 0.39 in the multi-trait SSBR Bayes C model. BF and MS also exhibited consistent accuracy improvements with multi-trait Bayesian regression models. These results demonstrate the superior accuracy of ssGBLUP and SSBR models compared to traditional BLUP, particularly for traits with higher heritability values. This findings offer valuable insights for enhancing genomic selection strategies and improving carcase traits in JBC breeding programs, contributing to the breed’s economic sustainability and meat production efficiency.

Rapid Conversion of the Popular Normal-Oleic Peanut Cultivar 308 to High-Oleic Variants via Floral Organ Injection of Pingyangmycin

The cultivated peanut (Arachis hypogaea L.) is a main cash crop globally, providing oil, protein, and various beneficial phytochemicals, with high-oleic peanut offering enhanced health benefits and oxidative stability. Despite these advantages, many widely cultivated peanut varieties remain normal-oleic, and the conversion of these varieties to high-oleic types without compromising yield and adaptability is of significant interest. This study evaluated the feasibility of using Pingyangmycin, a chemical mutagen, to induce high-oleic mutations in the popular peanut variety 308 through floral organ injection. The results showed that this method effectively generated high-oleic mutants with oleic acid content exceeding 75%. The mutants yielded more pods and kernels than the parental variety. Genotypic analysis confirmed mutations in the FAD2A and FAD2B genes, associated with the high-oleic phenotype. This novel approach, which reduces seed and reagent requirements and accelerates the breeding timeline, holds promise for enhancing peanut breeding programs and the development of high-oleic cultivars with superior quality and yield.