Breeding Methods Research Articles

Rearing density and food variety impact growth, development, and survival of larvae in the declining amphibian, Pseudacris maculata.

Boreal chorus frogs (Pseudacris maculata Agassiz 1850) are a widespread amphibian in North America, but several populations are in decline. Specifically, we are developing captive breeding and reintroduction methods for the Great Lakes/St. Lawrence-Canadian Shield population. Here we present the effects of tadpole density, food variety, and addition of supplemental minerals to rearing water on the growth, development, and survival during the larval and metamorph/juvenile stages. We conducted two experiments using a factorial design. We found that low tadpole density (1vs. 2 tadpoles/L) and high food variety (fivefood items vs. three food items) significantly increased tadpole body length and Gosner stage after 2 weeks (p < .001), increased survival to metamorphosis (p < .001), decreased time to metamorphosis (p < .001), and increased weight after metamorphosis (p < .001). On average, tadpoles in the high density/low food treatment, compared to the low density/high food, were 25% smaller after 2 weeks, had 3.9× lower survival to metamorphosis, took 1.25× longer to reach metamorphosis, and weighed 1.5× less after metamorphosis. In contrast, neither density (0.5vs. 1 tadpole/L) nor mineral supplemented water affected growth and development, but tadpole survival was higher at 1 tadpole/L. Our findings demonstrate the feasibility of rearing boreal chorus frogs in captivity and provide guidelines for rearing this and similar species in a laboratory environment.

Validation of molecular markers associated with amylose content of F8 and F9 lines resulting from a crossing of Black Rice and Mentik Wangi

The development of black rice with a fluffier texture at Universitas Jenderal Soedirman, which began in 2004, was carried out by crossing local black rice with the Mentik Wangi variety. At present, six black rice advanced breeding lines are ready for multi-location yield trials. Meanwhile, developing molecular marker-based plant breeding methods can facilitate a more efficient selection process. An important stage in developing molecular markers is marker validation, which aims to test the effectiveness in determining phenotypes in various genotypic and in new populations that differ from others based on the link between the marker and the expected character identified. This research aimed to determine molecular markers that can differentiate the level of amylose content in populations of F8 and F9 lines. The research was carried out on 10 (ten) genotypes consisting of the control variety Logawa, IRPM 112-19- 56, black rice, Mentik Wangi, and six lines. The amplification of the RM190, Wx and SSIIa markers showed polymorphic band. Based on the simple linear regression analysis, in F9, the SSIIa marker had the highest coefficient of determination compared to other markers. Hence, it had the greatest possibility of being a marker for selecting rice based on amylose content.

Easy-to-Use CRISPR-Cas9 Genome Editing in the Cultured Pacific Abalone (Haliotis discus hannai).

The Pacific abalone is an important aquaculture shellfish and serves as an important model in basic biology study. However, the study of abalone is limited by lack of highly efficient and easy-to-use gene-editing tools. In this paper, we demonstrate efficient gene knockout in Pacific abalone using CRISPR-Cas9. We developed a highly effective microinjection method by nesting fertilized eggs in a low-concentration agarose gel. We identified the cilia developmental gene β-tubulin and light-sensitive transmembrane protein r-opsin as target genes and designed highly specific sgRNAs for modifying their genomic sequences. Sanger sequencing of the genomic regions of β-tubulin and r-opsin genes from injected larvae identified various genomic long-fragment deletions. In situ hybridization showed gene expression patterns of β-tubulin and r-opsin were significantly altered in the mosaic mutants. Knocking out β-tubulin in abalone embryos efficiently affected cilia development. Scanning electron microscopy and swimming behavior assay showed defecting cilia and decreased motility. Moreover, knocking out of r-opsin in abalone embryos effectively affected the expression and development of eyespots. Overall, this work developed an easy-to-use mosaic gene knockout protocol for abalone, which will allow researchers to utilize CRISPR-Cas9 approaches to study unexploited abalone biology and will lead to novel breeding methods for this aquaculture species.

Design and Development of an Iot-Based Intelligent Incubator

The intelligent egg incubator is designed to improve existing egg incubators to transform the traditional breeding method into a modern and advanced breeding method. To reduce the chore that traditional breeding methods can cause, the use of an automatic incubator is therefore recommended to ensure the best possible hatching rate. Automatic incubators also allow you to control heat and humidity levels to reproduce ideal brooding conditions. The main objective of this work is to design an egg incubation system that performs better than manual incubation. The proposed system is an innovation that makes it possible to monitor the temperature, humidity and movement of the egg inside the incubator thanks to a data acquisition system taking into account the physiological conditions of the eggs. The proposed system is equipped with a Wi-Fi module via the ESP32, allowing the system to be manipulated remotely.

Gümüş Nitrat ve Ön Soğuk Uygulamalarının Çilek Anter Kültüründe Kallus Oluşumuna Etkileri

Strawberry (Fragaria x ananassa Duch.) which is one of the widely grown berry species in the world has economic and commercial importance. In commercial strawberry varieties, in order to increase yield and quality, it is necessary to obtain starting materials that are resistant/tolerant to biotic and abiotic stress factors. Biotechnological methods have an important place in strawberry breeding studies due to the long and costly process of classical breeding methods, the genetic expansion of seed production, high ploidy level and strong heterozygosity. Haploid plant production is an efficient breeding method that has been successfully applied to most plant species. However, due to the lack of sufficient haploid studies on strawberry and the fact that a specific protocol for this species has not yet been developed the necessary progress has not been made in this regard. In this study, the effectiveness of some factors determine the success in anther culture which has a significant place in obtaining haploid strawberries was investigated. For this reason, first, different sodium hypochlorite doses (NaOCl; 1%, 2%, 3%) and application durations (10, 15, 20 min) were used to determine the appropriate method for sterilisation, then cold pre-treatments (24, 36, 48, 72 hours at +4 °C) and different silver nitrate doses (AgNO3; 10, 20, 30, 40 mg l-1) were employed for callus induction in Festival strawberry variety. At the conclusion of the study it was observed that the lowest contamination rate (1%) was obtained by soaking in 1% sodium hypochlorite solution for 10 minutes. Cold pre-treatment of flower buds at +4 °C for 36 hours produced the highest callus induction rate (96%). The evaluation of the effect of AgNO3 application at different doses on the callus induction rate revealed that the highest callus induction (82%) was obtained from 20 mg l-1 AgNO3 dosage. This study showed that anther culture practices in strawberry can be improved by using cold pre-treatment, appropriate sterilization method and silver nitrate addition to the medium.

Dog Shows and Kennel Clubs in Shanghai: British Sport, Sportsmanship and the Changing Concept of Pets in China, 1887–1937

As in many colonial settings, it was the British who initiated dog shows as a sport at the Shanghai International Settlement in 1887. The main purpose behind this development was to increase the understanding and interest of Shanghai residents in dogs, and to spread scientific and refined methods of dog breeding. In this context, the overall aim was to promote the trade of purebred dogs within China. Through dog shows, some upper-middle class Chinese gradually began to consider dogs as pets rather than livestock, and conspicuous consumption of dog-related products and services was in vogue, accompanied by the emergence of dog restaurants, dog hospitals, and dog schools in Shanghai. The popularity of pet dogs and the rise of the pet economy in modern Shanghai was the result of multiple factors such as the elevated status of dogs in the city, the popularity of British sports represented by dog shows in Shanghai, and the general acceptance of western pet views and values among the Chinese elite. It was also a fusion of Chinese and Western cultural exchanges, and the epitome of Shanghai’s modernization process.

How do crop varieties developed through different breeding methods perform in field in terms of yield and biotic and abiotic stress? A systematic map protocol.

Abstract Background: Despite Nepal's considerable progress towards sustainable development goals in recent years, much more needs to be done to address the key development challenges. Agriculture plays an indispensable role in Nepal's development trajectory, but Nepal faces complex challenges in its agricultural landscape. Addressing these challenges requires a coordinated effort and the use of robust scientific evidence to support decision making - knowledge on effectiveness of crop varieties will help to direct support and resources where they are needed most. Despite heavy investment in seed technology, benefits to crop productivity and farmer income have been limited. Changing weather patterns and an overreliance on imported crops have led to a potentially fragile system. There is therefore a need for an overview of what research is being invested in, along with information about the effectiveness of new crop varieties, including imports. Methods: This systematic map will collate the literature from Nepal and its neighbouring countries to answer the question: "How do crop varieties developed through different breeding methods perform in field in terms of yield and biotic and abiotic stress?". We will search for evidence across a suite of bibliographic databases and grey literature resources using a tried-and-tested search strategy. Potentially relevant records will be screened against a set of a priori, explicit eligibility criteria, ensuring consistency in application prior to use. Relevant records will proceed to meta-data extraction and coding, followed by visualisation and narrative description of the evidence base as a whole. Knowledge gaps and clusters will be identified across pairs of variables including crop, breeding method, country and measurement methods to assess the volume and quality of evidence across the evidence base. This process will highlight areas where further research is needed, along with topics for which sufficient evidence exists to allow full synthesis of study findings in answer to questions regarding the effectiveness of different plant breeding methods in terms of yield and stress tolerance.

Genome-wide association study for the level of prolificacy in Cameroon’s native goat

ABSTRACT Income from goats highly depends on prolificacy, which is difficult to improve by traditional breeding methods. The study aimed to identify SNP markers for prolificacy, using a case–control genome-wide association study (GWAS) on 111 genotyped Cameroon native goat (CNG) does, based on the 50 K single nucleotide polymorphism (SNP) chip panel. None of the top SNPs reached the significant p-value of 5 × 10−8. The highest p-value was 0.0009. Despite the number of cases being about a quarter of the number of controls, the highest allele frequency of some of the top 20 variants in the cases was indicative of their potential role in the trait. These top variants included the following 15: rs268285661, rs268235169, rs268236449, rs268235135, rs268240394 in Sphingosine-1-phosphate phosphatase 2 (SGPP2) gene, rs268283635 in Solute carrier family 24 member 2 (SLC24A2) gene, rs268251678 in Androgen-induced gene 1 (AIG1) gene, rs268267018, rs268239617, rs268281364, rs268273029, rs268286941, rs268236144, rs268233233 in CEP126 gene and rs268278159, respectively. Our findings indicate that GWAS enable the identification of some loci within genes, with known biological functions and pathways in human being and mice animal model but far-ranging to what was previously hypothesized and tested in goat.

Genomic selection for growth characteristics in Korean red pine (Pinus densiflora Seibold & Zucc.).

Traditionally, selective breeding has been used to improve tree growth. However, traditional selection methods are time-consuming and limit annual genetic gain. Genomic selection (GS) offers an alternative to progeny testing by estimating the genotype-based breeding values of individuals based on genomic information using molecular markers. In the present study, we introduced GS to an open-pollinated breeding population of Korean red pine (Pinus densiflora), which is in high demand in South Korea, to shorten the breeding cycle. We compared the prediction accuracies of GS for growth characteristics (diameter at breast height [DBH], height, straightness, and volume) in Korean red pines under various conditions (marker set, model, and training set) and evaluated the selection efficiency of GS compared to traditional selection methods. Training the GS model to include individuals from various environments using genomic best linear unbiased prediction (GBLUP) and markers with a minor allele frequency larger than 0.05 was effective. The optimized model had an accuracy of 0.164-0.498 and a predictive ability of 0.018-0.441. The predictive ability of GBLUP against that of additive best linear unbiased prediction (ABLUP) was 0.86-5.10, and against the square root of heritability was 0.19-0.76, indicating that GS for Korean red pine was as efficient as in previous studies on forest trees. Moreover, the response to GS was higher than that to traditional selection regarding the annual genetic gain. Therefore, we conclude that the trained GS model is more effective than the traditional breeding methods for Korean red pines. We anticipate that the next generation of trees selected by GS will lay the foundation for the accelerated breeding of Korean red pine.

Overview of Genetics and Breeding of Carrot (Daucas Carota L.): A Review

Carrot is one of the most important vegetable crops consumed in the world. It is grown for its taproot which contains carbohydrate in large amount. Carrot is domesticated in ancient year and originated in Asian countries. The crop is highly diversified in color, shape, size, nutritional content and so on. Crop diversity identification was done through morphological identification and DNA markers. Carrot is well known for its beta carotene content. To increase the crop yield and quality many breeding programs have been established and achieved some objectives through conventional breeding methods and using some biotechnological tools. So there is a need to have better understanding of crop genetic characteristics and breeding methods are useful in germplasm collection, conservation and utilization, particularly in case of carrot. Since carrot is highly cross pollinated crop appropriate breeding program and method should be used to improve crop yield and quality especially in developing countries like Ethiopia.

Registration of ‘KS Big Bow’ hard white winter wheat

Abstract‘KS Big Bow’ (Reg. no. CV‐1206, PI 701521), a hard white winter wheat (Triticum aestivum L.) cultivar, was developed by the wheat breeding program at the Agricultural Research Center–Hays, Kansas State University, and released by the Kansas Agricultural Experiment Station in 2022. KS Big Bow was selected from a single cross of KS050223M‐2/KS11HW15 using a modified bulk breeding method. The main objective of this cross is to release a competitive hard white winter wheat cultivar with adaptation to the dryland production in western Kansas. KS Big Bow is an F5‐derived line and was tested in yield trials from 2017 to 2022 in Kansas before its release. It has performed well in dryland yield trials in western Kansas. KS Big Bow has a medium to medium‐early maturity and medium plant height. Its test weight and straw strength are good. KS Big Bow has a good disease‐resistant package including resistance to Wheat streak mosaic virus, moderate resistances to stripe rust (caused by Puccinia striiformis Westend. f. sp. tritici Erikss.) and stem rust (caused by P. graminis Pers f. sp. tritici Eriks. &amp; E. Henn.), and intermediate resistance to Barley yellow dwarf virus. Its milling and baking qualities are about average.

An ethnoveterinary study on medicinal plants used by the Bai people in Yunlong County northwest Yunnan, China

BackgroundThe Bai people in Yunlong County, northwest Yunnan, China, have used medicinal plants and traditional remedies for ethnoveterinary practices. The Bai have mastered ethnoveterinary therapeutic methods in livestock breeding since ancient times. The Bai’s traditional ethnoveterinary knowledge is now facing extinction, and their unique ethnoveterinary practices have rarely been recorded. This study documented animal diseases, EMPs, and related traditional knowledge in Yunlong County, China.MethodsEthnobotanical fieldwork was conducted in six villages and townships of Yunlong County between 2021 and 2022. Data were obtained through semi-structured interviews, participatory observations, and keyperson interviews. A total of 68 informants were interviewed, and the informant consensus factor and use reports (URs) were used to evaluate the current ethnoveterinary practices among the local communities. Information on livestock diseases, medicinal plants, and traditional ethnoveterinary medicine knowledge were also obtained.ResultsA total of 90 plant species belong to 51 families, 84 genera were recorded as being used as EMPs by the Bai people, and Asteraceae plants are most frequently used. A total of 68 informants were interviewed, including 58 men (85.3%) and 10 women (14.7%). The most commonly used EMPs parts included the roots, whole plants, leaves, and stems, and the common livestock diseases identified in this field investigation included trauma and fracture, gastrointestinal disorders, respiratory disorders, parasitic diseases, miscellaneous, venomous snake bites, reproductive diseases, infectious diseases, skin disease, and urinary diseases. Most of the EMPs are herbs (77.78%). Courtyard is one of the habitats of medicinal plants in Yunlong County.ConclusionTraditional knowledge of ethnoveterinary medicine is related to the local sociocultural characteristics of the Bai. Plants are used in cultural traditions, which, in turn, nourish the plant culture. Cultural diversity and biodiversity are interdependent. This traditional knowledge is at risk of disappearance because of the increasing extension of Western veterinary medicine, lifestyle changes, and mainstream cultural influences. Therefore, it is important to continue research on ethnoveterinary practices.

Genomic prediction in multi-environment trials in maize using statistical and machine learning methods

In the context of multi-environment trials (MET), genomic prediction is proposed as a tool that allows the prediction of the phenotype of single cross hybrids that were not tested in field trials. This approach saves time and costs compared to traditional breeding methods. Thus, this study aimed to evaluate the genomic prediction of single cross maize hybrids not tested in MET, grain yield and female flowering time. We also aimed to propose an application of machine learning methodologies in MET in the prediction of hybrids and compare their performance with Genomic best linear unbiased prediction (GBLUP) with non-additive effects. Our results highlight that both methodologies are efficient and can be used in maize breeding programs to accurately predict the performance of hybrids in specific environments. The best methodology is case-dependent, specifically, to explore the potential of GBLUP, it is important to perform accurate modeling of the variance components to optimize the prediction of new hybrids. On the other hand, machine learning methodologies can capture non-additive effects without making any assumptions at the outset of the model. Overall, predicting the performance of new hybrids that were not evaluated in any field trials was more challenging than predicting hybrids in sparse test designs.

Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits.

Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.

Characterization of yield and fruit quality parameters of Vietnamese elite tomato lines generated through phenotypic selection and conventional breeding methods

Characterization of yield and fruit quality parameters of Vietnamese elite tomato lines generated through phenotypic selection and conventional breeding methods

The expression of lignin biosynthesis genes during plant development and effects of downregulated cinnamyl alcohol dehydrogenase (CAD) gene in bahiagrass (Paspalum notatum Flügge)

AbstractBahiagrass (Paspalum notatum Flügge) is a warm‐season grass where high lignin content limits its forage quality, negatively affecting animal performance. To create a new breeding method by genome editing, isolation and characterization of lignin biosynthesis genes and identification of their molecular relationships are essential. The caffeic acid O‐methyltransferase (COMT) and cinnamyl alcohol dehydrogenase (CAD) cDNA clones were isolated from bahiagrass, and their protein sequences showed high similarity to other C4 monocot species through phylogenetic analysis. Gene expression analysis of phenylalanine ammonia‐lyase (PAL), COMT and CAD, involved in crucial stages of lignin biosynthesis and lignin content, was conducted at different plant developmental stages. The highest gene expression levels of these genes were observed in the vegetative (V) and early reproductive stages, while the lignin content increased until the middle reproductive stage and remained constant thereafter. Additionally, to further understand the molecular relationships in lignin biosynthesis, the effect of CAD downregulation was analyzed in transgenic bahiagrass lines introduced with sorghum CAD antisense and RNAi vector obtained from a previous report. This led to a reduced lignin content and affected the expression of PAL and COMT working upstream of CAD. In the V stage, PAL expression was lower in transgenic lines compared to wild type (WT), while COMT expression showed no significant differences. However, PAL and COMT expression of transgenic lines in the middle reproductive stage (R2) was significantly higher than in the WT. These findings suggest that the downregulation of CAD gene expression affects PAL and COMT expression and induces a feedback system in the R2 stage. Lignin content influenced the phenotype of the transgenic plants with significantly reduced lignin, exhibiting a dwarf phenotype with shorter plant heights. The findings of this study can be applied to genome editing for the development of practical new breeding materials with improved digestibility in bahiagrass.

Direction of salmon aquaculture development in the world

The growth of the world's population implies the search for alternative sources of nutrition. One such area is the development of aquaculture. The world aquaculture, as well as other branches of agriculture, has gone through stages of its formation from farming by primitive methods to use of modern technologies. Salmon farming occupies an important place in industrial fish farming, and the volume of farmed products is increasing every year. This review summarises the main milestones in the salmon aquaculture industry, describes the trends that have guided breeding programmes and shows the genetic approaches that have been used in fish farming. The introduction of genetic methods in salmonid fish breeding depends on the level of development of the countries where fish farms are located. Abroad there is a great experience of investment policy aimed at creation and introduction of projects up to the final (operational) stage of introduction of molecular genetics methods into salmon breeding, including the use of genomic selection. While in Russia the concept of genetic improvements in aquaculture is only being discussed. In this review an important place is given to generalisation of the accumulated material on genetic methods of salmonid fish research, as well as directions of application of genetic markers in salmon farming. The issues of searching for candidate genes, quantitative trait loci (QTL) associated with gaining muscle weight and fish resistance to diseases are discussed. The directions and ways of solving breeding problems are shown. Intensive development of scientific approaches to aquaculture development abroad is a vector for setting goals to expand business investment in the development of molecular genetic approaches to salmonid fish breeding in Russia.

Crop DNA extraction with lab-made magnetic nanoparticles.

Molecular breeding methods, such as marker-assisted selection and genomic selection, require high-throughput and cost-effective methods for isolating genomic DNA from plants, specifically from crop tissue or seed with high polysaccharides, lipids, and proteins. A quick and inexpensive high-throughput method for isolating genomic DNA from seed and leaf tissue from multiple crops was tested with a DNA isolation method that combines CTAB extraction buffer and lab-made SA-coated magnetic nanoparticles. This method is capable of isolating quality genomic DNA from leaf tissue and seeds in less than 2 hours with fewer steps than a standard CTAB extraction method. The yield of the genomic DNA was 582-729 ng per 5 leaf discs or 216-1869 ng per seed in soybean, 2.92-62.6 ng per 5 leaf discs or 78.9-219 ng per seed in wheat, and 30.9-35.4 ng per 5 leaf discs in maize. The isolated DNA was tested with multiple molecular breeding methods and was found to be of sufficient quality and quantity for PCR and targeted genotyping by sequencing methods such as molecular inversion probes (MIPs). The combination of SA-coated magnetic nanoparticles and CTAB extraction buffer is a fast, simple, and environmentally friendly, high-throughput method for both leaf tissues and seed(s) DNA preparation at low cost per sample. The DNA obtained from this method can be deployed in applied breeding programs for marker-assisted selection or genomic selection.

Crop Improvement: Comparison of Transgenesis and Gene Editing

The development and improvement of molecular biology methods have led to the creation of new technologies that make it possible to modify plant genomes by transferring and integrating into the genomes’ heterologous genes from various expression systems (genetic engineering), as well as inducing knockouts of one or more target genes of interest (genomic editing). The development of genome-editing methods is a new milestone in the development of modern breeding methods and certainly relies on the knowledge and technologies developed for transgenesis. This review will discuss issues related to the advantages and disadvantages of both technologies for improving the economically valuable traits of important crops.

Study of the process of formation of a unique congenital polydactyly in mini-pigs

The formation of a unique anomaly of the structure of the distal extremities – polydactyly in mini-pigs of the selection of the Institute of Cytology and Genetics (ICiG) SB RAS was studied. The genealogy of two looked animals with polydactyly (six–toed on the fore and hind limbs) - a black boar and a white pig, demonstrated the hereditary nature of the manifestation of this anomaly, differing depending on the method of breeding in several generations, is analysed. Anatomisation of distal fragments of the limbs of these two pigs culled at the age of 15-16 months showed the formation of differentiation of trophic structures of blood supply to the accessory fingers and tendon-ligamentous apparatus, including ligaments of the finger-lift muscle. The prepared samples were processed for histological staining and microscopy, which showed the interior features of the formation of connective and bone tissues of the phalanges of additional fingers on the fore and hind limbs, characteristic of each studied animal. The results are discussed in connection with topical issues of veterinary pathogenetics of farm animals and the context of the interest of classical and modern biology in polydactyly.