Breeding Plans Research Articles

Methods of Calculating Prediction Error Variance and Prediction Accuracy for Restricted Best Linear Unbiased Prediction of Breeding Values.

Prediction error variance (PEV) and prediction accuracy (PA) of breeding values (BVs) are essential for formulating breeding plans and predicting response to selection. However, restricted best linear unbiased prediction method (RBLUP method) carries many unknowns: in particular, the formulas for calculating PEV and PA are not clear. New findings were obtained using the RBLUP method. The uniqueness of RBLUP of BVs was proven. The formulas of PEV and PA for the RBLUP of BVs were derived from restricted mixed model equations. A method was also devised for easily calculating the PEV and PA for the RBLUP of BVs. Finally, the relationship between the RBLUP and ordinary BLUP of BVs was derived. It has become easier to calculate the PEV and PA for the RBLUP of BVs. This method is particularly effective for calculating the PEV and PA when applying the RBLUP method to achieve relative desired changes in all traits. This has also made it possible to predict the response to selection using the RBLUP method.

Decision trees for determining the fate of laboratory animals.

Facilities involved in laboratory animal research often face ethical challenges such as: what should I do with the animals that are no longer suitable for experimental purposes? One of the common answers to this question is to kill them. And while numerous scientifically justifiable reasons exist for killing laboratory animals, we must not overlook our ethical responsibility towards these sentient beings. Animal facility managers and scientists frequently find themselves in a moral dilemma, torn between furthering their research and addressing the well-being of experimental animals required for their studies. We elaborated a concept consisting of six decision trees and recommendations for making informed decisions about the need to kill laboratory animals in research facilities, considering legal and ethical considerations. The concept is based on the German regulatory perspective. However, the measures and decisions for animal welfare can be implemented in all laboratory animal facilities. These recommendations suggest several courses of action, including implementing consistent breeding plans, exploring alternative uses, reassigning surplus animals and their organs, and establishing appropriate housing capacity limits that ensure species-appropriate care. We encourage scientists and animal facility managers to develop and implement decision-making frameworks and procedures tailored to their specific facilities, in the hope that this work will promote a thoughtful and responsible approach to the complex challenges associated with the killing of laboratory animals, advancing scientific progress and the humane treatment of these animals.

Genetic architecture of yield and yield contributing traits in chickpea (Cicer arietinum L.)

Genetic architecture of yield and yield contributing characters of five crosses in chickpea were performed by generation mean analysis. Non-significant χ2 values were noted for plant weight at harvest (PWH), number of pods per plant (NPd/P) and number of seeds per plant (NS/P) in cross-2; for number of secondary branches at first flower (NSBFF) and number of secondary branches at maximum flower (NSBMF) in cross-3 and for number of primary branches at maximum flower (NPBMF) in cross-4. Among these, PWH in cross-2; NSBFF and NSBMF in cross-3 and NPBMF in cross-4 were also non-significant regarding C and D scales. Non-significant scale coupled with non-significant χ2 values indicated only additive-dominance relationship for those characters and crosses that would likely be helpful in doing successful breeding plan easily for the development of potential lines in chickpea. Gene effects viz., additive [d], dominance [h], additive × additive [i] and dominance × dominance [l] were significant for different crosses and characters indicating involvement of additive, dominance, additive × additive and dominance × dominance gene interactions in the control of these traits. Most of the studied characters exhibited duplicate type of epistasis therefore, recurrent selection for these traits is suggested. Effective factor (K1) was less than one for all the characters and crosses indicating minimum one group of gene controlled the characters. Both broad (h2b) and narrow (h2n) sense heritability in majority cases were found to be high which indicates that selection for high heritability showing traits is likely to be effective. Mid-parent (MP) and better-parent (BP) heterosis found to be non-significant in maximum cases. All the characters and crosses showed non-significant inbreeding depression (ID) indicating a good sign for further genetic work.

Exploring the genetic variability of the PRNP gene at codons 127, 142, 146, 154, 211, 222, and 240 in goats farmed in the Lombardy Region, Italy

Scrapie is a transmissible spongiform encephalopathy affecting sheep and goats. The prion protein-encoding gene (PRNP) plays a crucial role in determining susceptibility and resistance to scrapie. At the European level, surveillance of scrapie is essential to prevent the spread of the disease to livestock. According to the Regulation EU 2020/772 polymorphisms K222, D/S146 could function as resistance alleles in the genetic management of disease prevention. In Italy, a breeding plan for scrapie eradication has not been implemented for goats. However, surveillance plans based on the PRNP genotype have been developed as a preventive measure for scrapie. This research aimed to describe the polymorphisms at 7 positions within the PRNP gene in 956 goats of the Alpine, Saanen and mixed populations farmed in the Lombardy Region in Italy. PRNP polymorphisms were detected using single nucleotide polymorphism markers included in the Neogen GGP Goat 70 k chip. The K222 allele occurred in all populations, with frequencies ranging from 2.1 to 12.7%. No animals carried the S/D146 resistance allele. However, it has been demonstrated that polymorphisms in the other positions analysed could influence resistance or susceptibility to scrapie outbreaks in different ways. Ten potentially distinct haplotypes were found, and the most prevalent of the three populations was H2, which differed from the wild type (H1) in terms of mutation (S vs P) at codon 240. This study provided additional information on the genetic variability of the PRNP gene in these populations in the Lombardy region of Italy, contributing to the development of genetic control measures for disease prevention.

A genome-guided strategy for climate resilience in American chestnut restoration populations

American chestnut (Castanea dentata) is a deciduous tree species of eastern North America that was decimated by the introduction of the chestnut blight fungus (Cryphonectria parasitica) in the early 20th century. Although millions of American chestnuts survive as root collar sprouts, these trees rarely reproduce. Thus, the species is considered functionally extinct. American chestnuts with improved blight resistance have been developed through interspecific hybridization followed by conspecific backcrossing, and by genetic engineering. Incorporating adaptive genomic diversity into these backcross families and transgenic lines is important for restoring the species across broad climatic gradients. To develop sampling recommendations for ex situ conservation of wild adaptive genetic variation, we coupled whole-genome resequencing of 384 stump sprouts with genotype-environment association analyses and found that the species range can be subdivided into three seed zones characterized by relatively homogeneous adaptive allele frequencies. We estimated that 21 to 29 trees per seed zone will need to be conserved to capture most extant adaptive diversity. We also resequenced the genomes of 269 backcross trees to understand the extent to which the breeding program has already captured wild adaptive diversity, and to estimate optimal reintroduction sites for specific families on the basis of their adaptive portfolio and future climate projections. Taken together, these results inform the development of an ex situ germplasm conservation and breeding plan to target blight-resistant breeding populations to specific environments and provides a blueprint for developing restoration plans for other imperiled tree species.

QTL analysis on a lemon population provides novel insights on the genetic regulation of the tolerance to the two-spotted spider mite attack

BackgroundAmong the Citrus species, lemon (Citrus limon Burm f.) is one of the most affected by the two-spotted spider mite (Tetranychus urticae Koch). Moreover, chemical control is hampered by the mite’s ability to develop genetic resistance against acaricides. In this context, the identification of the genetic basis of the host resistance could represent a sustainable strategy for spider mite control. In the present study, a marker-trait association analysis was performed on a lemon population employing an association mapping approach. An inter-specific full-sib population composed of 109 accessions was phenotyped through a detached-leaf assays performed in modified Huffaker cells. Those individuals, complemented with two inter-specific segregating populations, were genotyped using a target-sequencing approach called SPET (Single Primer Enrichment Technology), the resulting SNPs were employed for the generation of an integrated genetic map.ResultsThe percentage of damaged area in the full-sib population showed a quantitative distribution with values ranging from 0.36 to 9.67%. A total of 47,298 SNPs were selected for an association mapping study and a significant marker linked with resistance to spider mite was detected on linkage group 5. In silico gene annotation of the QTL interval enabled the detection of 13 genes involved in immune response to biotic and abiotic stress. Gene expression analysis showed an over expression of the gene encoding for the ethylene-responsive transcription factor ERF098-like, already characterized in Arabidopsis and in rice for its involvement in defense response.ConclusionThe identification of a molecular marker linked to the resistance to spider mite attack can pave the way for the development of marker-assisted breeding plan for the development of novel selection coupling favorable agronomical traits (e.g. fruit quality, yield) with a higher resistance toward the mite.

Genetic assessment of eight zoo populations of golden snub-nosed monkey (Rhinopithecus roxellana) implication to the conservation management of captive populations.

Captive breeding programs play an important role in preserving the genetic diversity of endangered species. It is of utmost importance to conduct genetic assessment for captive populations in order to develop scientific breeding plans and conservation management strategies. Here, we genotyped 10 microsatellite loci and sequenced 368 bp of mitochondrial DNA control region for the golden snub-nosed monkey (Rhinopithecus roxellana) from eight captive populations in China, and compared the genetic indices of captive populations with a wild population. Meanwhile, we performed paternity tests to verify the genealogical records and established genetic lineages. A total of 157 individuals were identified from 161 fecal samples, including 135 captive individuals (approximately 25% of captive individuals in China). Microsatellite analysis showed that the nine populations had moderate levels of genetic diversity, with polymorphism information content (PIC) ranging from 0.43 to 0.542; the genetic diversity of captive populations (average PIC: 0.503) was slightly higher than that of the wild population (PIC: 0.438). The Structure analysis indicated that individuals of the eight captive populations contained two different genetic components. We conducted either single-blind or double-blind paternity testing on 40 offspring of captive individuals and found that five offspring from two zoos (Nanjing Hongshan Forest Zoo and Shanghai Wild Animal Park) showed discrepant kinships from their pedigree records, probably due to the inaccuracies in pedigree records. By constructing genetic pedigrees, inbred offspring were found in Beijing Zoo, Shanghai Zoo, Hangzhou Zoo, and Chengdu Zoo. Analysis based on mitochondrial DNA showed a high level of genetic diversity in the eight captive populations (mean nucleotide diversity: 0.047). However, no nucleotide diversity was found in the wild population. This study conducted a genetic survey for captive golden snub-nosed monkeys and will significantly benefit the genetic conservation management for captive populations in the future.

Genetic diversity of common carp Cyprinus carpio in the base population of a selective breeding programme in India

A selective breeding program for developing a suitable strain of Cyprinus carpio (Linnaeus, 1758) for inland saline aquaculture in India is in progress. At ICAR-CIFE, various geographical populations of common carp of India, viz. Madhya Pradesh (MP), Haryana (HR), Tripura (TR), Andhra Pradesh (AP), Manipur (MN), and Maharashtra (MH) formed the base population for selective breeding. The present study assesses the genetic diversity of these stocks using truss morphometry and mitochondrial DNA D loop marker analysis. The images of 600 fish were captured and digitized. The landmarks were identified, and an image network was constructed for truss analysis using tpsDig2 and PAST software. The data was subjected to scale transformation and factor analysis using SAS for Academics. The top 3 factors could explain 85.40% of the total variation. The results indicate stock-wise and sex-wise groupings. The mitochondrial DNA (D-loop) sequence analysis was conducted on 169 samples using MEGA6 software. The overall average haplotype and nucleotide diversity of the population were 0.08129 and 0.01134, respectively. Among stocks, the MP stock had a maximum of four haplotypes. The AMOVA results reveal that the stock AP is unique, and the other stocks form a single grouping. The information generated from the present study delineates genetic diversity among stocks and will aid in designing breeding plans.

Sink-source connectivity for restocking of Pinna nobilis in the western Mediterranean Sea

The critically endangered endemic bivalve Pinna nobilis from the Mediterranean Sea suffered a sudden population decline after a mass mortality event in early autumn 2016. Conservation efforts aimed at preventing extinction included safeguarding resistant individuals and implementing a breeding plan to contribute to the repopulation of the species. This study utilized a model combining Lagrangian dispersion and connectivity analyses to pinpoint optimal restocking sites in the Western Mediterranean. Our approach allowed to identify locations capable of sustaining and generating larvae for broader repopulation in key areas of the Western Mediterranean Sea prior to the mass mortality event. Six important repopulation locations from Murcia, Valencia and Balearic Islands were selected for reintroduction efforts. The results obtained in this study show how the network could be self-sufficient and able to self-replenish itself of recruits. Overall, our work can be used to direct the reintroduction of resistant animals in the Western Mediterranean Sea.

Analysis of seven populations of cultured redclaw crayfish, Cherax quadricarinatus, using newly developed microsatellite markers

Cherax quadricarinatus, also known as the redclaw crayfish, is native to northern Australia and southern Papua New Guinea and is an important freshwater aquaculture species in many countries. Studying the genetic structure of the current cultured population can improve the breeding plan for redclaw crayfish to better manage the hybridization and germplasm bank and promote their rational utilization; however, microsatellite resources for redclaw crayfish remain insufficient. The purpose of this study was to analyze the genetic diversity of different redclaw crayfish populations in China. After screening 18 pairs of microsatellite markers from redclaw crayfish transcriptome data, 240 samples from seven main breeding areas (Changsha, Guangzhou, Haikou, Huzhou, Jiangmen, Wuxi, and Zhanjiang) were evaluated and detected using these microsatellite markers. In total, 97 alleles were detected, of which the minimum number was two and the maximum number was twelve. The observed heterozygosity ranged from 0.258 to 0.807, with an average of 0.559, and the expected heterozygosity ranged from 0.288 to 0.815, with an average value of 0.558. The polymorphic information content values of seven populations ranged from 0.268 to 0.791, with an average of 0.511. Moreover, pairwise genetic differentiation within the population was between 0.007 and 0.031. The UPGMA clustering results showed that the Zhanjiang population stands alone on a branch, but the genetic variation between branches is very small. Meanwhile, STRUCTURE analysis further revealed that the genetic backgrounds of each population are essentially identical, with no noticeable genetic differentiation arising from geographic differences. These results provide a basic assessment of the genetic diversity of the main cultured populations of redclaw crayfish and a molecular foundation for future genetic monitoring and selective breeding research.

Optimization and evaluation of alternative village-based breeding plans: the case of goats in Afar region, Ethiopia

The study aims to design and evaluate alternative village-based breeding plans for Afar goats in Aba’ala, Afar region, Ethiopia. The alternative breeding plans were designed and evaluated using ZPLAN+ computer program following the gene flow method and selection index procedures. Input parameters were sourced from a production system survey study, own-flock ranking exercises and literature. The breeding goal traits included six-month weight, daily milk yield and proportions of weaned kids. Four alternatives were designed based on the variation of the number of the traits in the selection index (recording) while keeping all traits in the aggregate breeding goal. Furthermore, the proposed alternative plans were evaluated by varying the years of breeding buck service period. Higher annual genetic gain was estimated for six-month weight (0.2983 kg) in alternative 4, for daily milk yield (0.0083 kg or 8.3 g) and proportion of lambs weaned (0.0142%) in alternative 1 when the years of buck use for breeding was set to two years. Higher selection accuracy was obtained in alternative 1 when all the traits were included in the selection index while lower selection accuracy was achieved in alternative 4 when six-month weight only was included in the selection index. The highest profit per doe per year was achieved in alternative 1 (1.221€) while the lowest was obtained in alternative 4 (0.885 €) when six-month weight only is included in the selection index. The simulation results gave an acceptable range of genetic gains with little difference across the alternatives. Therefore, village breeding programs with a few traits in the recording and two years of breeding buck use are deemed practicable. The proposed breeding plans should be part of the national development strategies and involvement of local research institutions and universities is very crucial to ensure adequate technical support.

Analysis of β-casein gene for A1 and A2 allelic variants in Holstein-Local crossbred cattle of Bangladesh using allele-specific PCR

Beta-casein (CSN2) is one of the important bovine milk proteins synthesized by β-casein gene. The aim of this study was to investigate the A1 and A2 allelic variants of CSN2 gene in Holstein-Friesian and Local (HF×L) crossbred cattle of Bangladesh. Allele specific polymerase chain reaction (AS-PCR) was carried out for genotyping of allelic variants. A total of 390 blood samples of HF×L crossbred cattle was included from govt., military and private dairy farms. Six different crossbred genotypes were identified in the studied population as 50%HF×50%L, 62.5%HF×37.5%L, 68.75%HF×31.25%L, 75%HF×25%L, 81.25%HF×18.75%L and 87.5%HF×12.5%L. The mean frequencies of the A1A1, A1A2, and A2A2 genotypes were 0.11, 0.48, and 0.41, respectively, while the corresponding frequencies of the A1 and A2 alleles were 0.34 and 0.66, respectively. The frequency of desirable A2A2 genotype reduced from 0.60 (50%HF×50%L) to 0.38 (87.5%HF×12.5%L) with the advancement of exotic HF inheritance from 50 to 87.5%. In contrast, the frequency of A1A1 and A1A2 genotypes increased proportionately with the progression of HF inheritance level. The undesirable A1A1 genotype frequency was found highest in the HF crossbreds of private dairy farms (0.13) compared to government (0.08) and military dairy farm (0.07) that signifies the availability of upper graded cows in the private dairy farms. Altogether, this study provides current scenario of A1 and A2 allelic variants of HF×L crossbreds of Bangladesh that could be utilized to design suitable breeding plans in crossbreeding programs for production of premium quality milk.

Variability in Indian wheat germplasm for important quality and physiological traits

Knowledge of variability in wheat genotypes is important for proposing crosses intended for development of heterotic combinations with improved stability. The present study consists of 120 wheat genotypes comprised of landraces, genetic stocks, released varieties, and improved genotypes. For the research experiment was conducted field in two rabi seasons (2019–2020 and 2020–2021) at ICAR-IIWBR, Karnal and a total of 120 genotypes were assessed using a randomized block approach for four quality (Zinc, iron, protein content and nitrogen) and six different physiological traits (Normalized difference vegetation index [NDVI]-1, NDVI-2, Soil Plant Analysis development [SPAD]-1, SPAD-2, Canopy Temperature [CT]-1, and CT-2) beside grain yield (GY). The occurrence of significant genetic variability amongst the several genotypes for nutritional and physiological characters indicates the inevitability for utilization of a considerable degree of genetic variation through the process of selection. The genotypic and phenotypic coefficients of variation (Genotypic coefficient of variation and Phenotypic coefficient of variation) exhibited their peak values for the trait GY, tailed by, grain zinc content, nitrogen (%), and SPAD-2. The high heritability values, in conjunction with substantial genetic advances, are indicative of the significance of GY, zinc, nitrogen, and protein content are key traits that hold potential for crop enhancement purposes. The total set of 120 genotypes clustered into 12 discrete sets on the basis of quality and physiological traits using the clustering technique and principal component analysis program available in the Statistical Package for Agricultural Research. Principal components axis 1 to principal component axis 4 unveiled about 71.31% of the total variability. Based on the findings of this study, it can be inferred that the released varieties showed greater performance in terms of grain output, although some landraces displayed higher values for the quality features. Hence, to acquire a comprehensive range of superior quality (Zn, PC, N, and Fe) cum high-yielding segregants, the selected genotypes from clusters “C” and “L” could function as better lines of parentage to organize breeding plans.

Laying performance, genetic parameters, and the expression of FSHβ, LHβ, FSHR, and LHR genes in Japanese quails selected for early egg production

Investigating the impact of early egg production selection (the first 90 d of laying) on egg production features, cumulative selection response (CSR), and the mRNA expression of gonadotropins (FSHβ and LHβ), and their receptors (FSHR and LHR), in Japanese quails was the goal. The selection experiment involved 1293 females in all, 257 from the base group and 1036 from the 4 selected generations. Age and body weight at sexual maturity (ASM, BWSM), weight of the first egg (WFE), days to the first 10 eggs (DF10E), egg mass for the first 10 eggs (EMF10E), egg weight (EW), egg number at the first 90 d of laying (EN90D), and egg mass at the first 90 d of laying (EM90D) were all recorded. Most egg production traits had heritability estimates that were low to moderate and ranged from 0.17 to 0.33., where the highest estimates were reported for EN90D (0.33) and BWSM (0.32). With the exception of EN90D, low to moderate positive genetic correlations were observed between ASM and other egg production traits (0.17-0.44). The fourth generation showed significantly (P < 0.05) lower ASM and DF10E but higher BWSM, WFE, EN90D, EM10E, and EM90D when compared with the base generation. CSR were significant (P < 0.05) for ASM (-6.67 d), BWSM (27.13 g), WFE (0.93 g), DF10E (-1.25 d), EN90D (7.24 egg), EM10E (10.57 g), and EM90D (140.0 g). FSHβ, LHβ, FSHR, and LHR gene mRNA expression was considerably (P < 0.05) greater in the fourth generation compared to the base generation. In conclusion, selection programs depending on the efficiency of egg production (EN90D) could improve the genetic gain of egg production traits and upregulate the mRNA expression of FSHβ, LHβ, FSHR, and LHR genes in selected quails (fourth generation). These findings might help to enhance breeding plans and create commercial lines of high egg production Japanese quails.

Dual-Stream Fusion Network with ConvNeXtV2 for Pig Weight Estimation Using RGB-D Data in Aisles.

In the field of livestock management, noncontact pig weight estimation has advanced considerably with the integration of computer vision and sensor technologies. However, real-world agricultural settings present substantial challenges for these estimation techniques, including the impacts of variable lighting and the complexities of measuring pigs in constant motion. To address these issues, we have developed an innovative algorithm, the moving pig weight estimate algorithm based on deep vision (MPWEADV). This algorithm effectively utilizes RGB and depth images to accurately estimate the weight of pigs on the move. The MPWEADV employs the advanced ConvNeXtV2 network for robust feature extraction and integrates a cutting-edge feature fusion module. Supported by a confidence map estimator, this module effectively merges information from both RGB and depth modalities, enhancing the algorithm's accuracy in determining pig weight. To demonstrate its efficacy, the MPWEADV achieved a root-mean-square error (RMSE) of 4.082 kg and a mean absolute percentage error (MAPE) of 2.383% in our test set. Comparative analyses with models replicating the latest research show the potential of the MPWEADV in unconstrained pig weight estimation practices. Our approach enables real-time assessment of pig conditions, offering valuable data support for grading and adjusting breeding plans, and holds broad prospects for application.

Variations in Composition, Antioxidant Profile, and Physical Traits of Goat Milk within the Semi-Intensive Production System in Mountainous Areas during the Post-Weaning to End-of-Lactation Period.

Dairy products from mountain-origin milk are known for their superior composition and quality. This study aimed to examine changes in composition, nutritional quality, and antioxidant properties of milk from semi-intensively managed goats in mountainous regions during the post-weaning to end-of-lactation period. Bulk tank milk samples from 10 farms were collected bi-weekly in the period from March to September. The farms were situated in regions with an average altitude of 772.20 m above sea level. The results revealed significant variations in milk composition, with fluctuations in fat, protein, lactose, and total solids. Milk yield per doe showed seasonal differences, with the highest yield in April and the lowest in September. Fatty acid composition exhibited changes throughout the sampling period, with variations in polyunsaturated fatty acids. Nutritional indices, such as the atherogenicity index and thrombogenicity index, remained within the recommended values. Antioxidant properties, including total phenolic content, DPPH, FRAP, and ABTS, showed significant differences, with higher values toward the end of the study. Milk pH, electrical conductivity, brix value, and refractive index also exhibited variations, while density and freezing point remained relatively stable. The study provided valuable information that can be used to develop breeding and feeding plans to achieve uniform milk quality in mountainous regions.

Massese sheep characteristics and demo-genetic trends in the province of Pisa (Italy)

Preserving animal breeds is key to a country’s economy, environment and culture. The present study collects all the available information on the Massese sheep breed and analyzes their demo-genetic trends in Pisa since 1976. Data were provided by Asso.Na.Pa. Descriptive statistics were analysed using Jmp software. The pedigree parameters of a total of 10,393 animals (whole population-WP) were analyzed using CFC, ENDOG and Pedigree viewer software. Animals born in the last fifteen years represented the Reference Population (RP), while animals with one or two unknown parents constituted the Base Population (BP). Demographic results showed an inconstant trend of offspring registration in the Herd book with two periods of a dramatic decline in lamb registrations and a substantially short productivity with a mean number of registered newborns of 1.5 and 18.2 for ewes and rams, respectively. A total of 6456 animals represented the RP, of which only 1059 animals (16.4%) had both known parents. The BP consisted of 7156 animals, thus highlighting the lack of sire and dam registration which prevented an accurate evaluation of the genetic parameters. The average inbreeding coefficient in the WP was 0.78%, and 0.046% in the RP. The number of inbreds was 575 in the WP and 17 in the RP. The present study represents a tool for breeders and technicians aimed at conserving and exploiting the genetic resources of Massese sheep through efficient breeding plans.

Genetic characteristics of complete mtDNA genome sequence of Indonesian local rabbit (Oryctolagus cuniculus)

BackgroundIndonesian local rabbit (Oryctolagus cuniculus) is a local breed in Indonesia. We reveal the mitochondrial genome sequence of the Indonesian local Rabbit for the first time. A better understanding of the mechanisms underlying these beneficial aspects of local breeds over imported ones requires detailed genetic investigations, of which mtDNA genome sequencing is of particular importance. Such an investigation will solve the major issues of misidentification with Javanese hares (Lepus nigricollis) and maternal lineage. In addition, this information will guide better statistics on the Indonesian local rabbit breed population and strategies for its conservation and breeding plans. This study aimed to identify and explore the characteristics of the mtDNA genomes of Indonesian local rabbits. ResultThis study observed that the length of the mtDNA genome is 17,469 bp, consisting of two ribosomal RNA (12S rRNA, 16S rRNA), 22 transfer RNA genes (trnR, trnG, trnK, trnD, trnS, trnY, trnC, trnN, trnA, trnW, trnM, trnQ, trnl, trnL, trnV, trnF, trnP, trnT, trnE, trnL, trnS, trnH), 13 protein-coding genes (PCGs) (ND4l, ND3, COX3, ATP6, ATP8, COX2, COX1, ND2, ND1, CYTB, ND6, ND5, ND4), a replication origin, and a noncoding control region (D-loop). ConclusionsmtDNA genome of Indonesian local rabbit was the longest and had the most extended D-loop sequence among the other references of Oryctolagus cuniculus. Other specific differences were also found in the percentage of nucleotides and variation in most of the PCGs when they were aligned with Oryctolagus cuniculus references from GenBank. Indonesian local Rabbits strongly suspected brought from Europe during the colonial period in Indonesia.

Genetic diversity and population structure of selected tef core germplasm lines based on microsatellite markers.

Tef is an indigenous and important food, feed, and cash crop for smallholder Ethiopian farmers. Knowledge of the natural genetic composition of the crop provides the option to further exploit its genetic potential through breeding. However, there are insufficient reports on the genetic variability of Ethiopian tef using a medium-throughput marker system. Hence, the current study was designed to evaluate the genetic variability of released and core germplasm that was collected earlier. Eighty-one tef genotypes collected from eight Ethiopian ecological zones and released varieties were targeted using 14 SSR markers. The study yielded a total of 122 alleles across the entire locus and population. The molecular variance analysis indicated the existence of large genetic differentiation (FIS and FIT = 0.87), with 86% and 13% of the total variation accounted for among genotypes within the population and across all genotypes used for this study, respectively. However, low genetic differentiation among the populations (FST = 0.014, which accounts for 1%) was observed. Multivariate analyses such as clustering and PCoA did not cluster genotypes into distinct groups according to their geographical areas of population. This is presumably due to gene flow among populations. In conclusion, our findings show that there is significant genetic diversity within populations, particularly in the Jimma, Tigray, and released varieties, as well as the presence of private alleles and heterozygosity. The study also indicates the existence of genotypic admixture in the studied materials. The identification of private alleles and their differentiation will be helpful in selecting breeding materials and creating breeding plans.

Case study of the market situation of calves from Alpine dairy farms and the effect of dams’ grazing during the last three months of gestation on auction parameters

The main aim of the study was to assess the recent evolution of cattle breeding in Alpine areas based on the number, quality and price of calves sold at local auctions in the South Tyrol region over the last decade, as case study. In addition, the effect of grazing during dam’s late gestation on calves’ auction quality was investigated to assess whether the inclusion of pasture in Alpine production system has an impact on auction parameters of calves beside its well-known positive effects on cattle welfare and the environment. Similarly, to other geographical areas, the study revealed that the numbers of crossbred calves (especially from specialised dairy breeds) has increased over the last years also in the Alpine area, because of more targeted breeding plans with an intensive use of beef bulls’ semen. Further, purebred calves from dual-purpose breeds (Simmental, Alpine Grey, Pinzgauer) received a higher remuneration in terms of price and market value at auction than purebred calves from specialised Holstein Friesian and Brown Swiss cows. A part of these animals could be available to support an innovative alpine meat supply chain which, if grass-fed, could further strengthen the current landscape maintenance service provided by the mountain livestock husbandry. Dams grazing during the last 90 days of gestation had a limited negative effect on calves’ liveweight and quality traits at auctions. All these results provide useful technical insights to support the switch from dairy to suckler herd system as future productive alternative for some small-scale mountain cattle farms whose viability is essential for the provision of several ecosystem services in the fragile Alpine environment.