Breeding Goal Research Articles

Genetics of gait score in broilers: Genetic parameters of gait score in purebred broiler lines.

Genetics of gait score in broilers: Genetic parameters of gait score in purebred broiler lines.

Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing.

Speed and endurance are the primary goals in racehorse breeding. The Grassland-Thoroughbred is a newly developed breed in northern China that combines speed, endurance, and environmental adaptability. However, current research on the genetic background of this breed and the genes associated with athletic performance remains limited. We conducted whole-genome resequencing on Mongolian (MG), Thoroughbred (TB), Xilingol (XL), and Grassland-Thoroughbred (CY) horses, generating 3813.74 Gb of clean data after quality control. The number of transitions was significantly higher than that of transversions. The SNPs were mainly located in intergenic regions, followed by intronic regions. Principal component analysis, population structure analysis, and phylogenetic tree results indicated that the CYs had a distinct genetic background from MGs, TBs, and XLs, but based on PCA and phylogenetic clustering, they showed greater genetic similarity to Thoroughbreds. Using fixation index (Fst) and nucleotide diversity ratio (π ratio) analyses between CYs and the other three horse populations, 70, 76, and 80 candidate genes were identified from the intersection of the two methods, respectively. A total of 179 candidate genes were obtained from the union of the three groups. Candidate genes associated with athletic performance (ATF2, NDUFS7, PRKG1, IGFN1, MTOR, TTN) and growth and development (MTOR, IGFN1, COL21A1, NEDD4, PIEZO1) were screened. These genes are related to athletic ability and developmental processes in the CY population. Our study reveals genomic information associated with important traits in Grassland-Thoroughbreds and identifies valuable candidate genes, laying a foundation for future breeding and trait association studies.

Orchestrating anthocyanin biosynthesis in fruit of fruit trees: Transcriptional, post-transcriptional, and post-translational regulation.

Orchestrating anthocyanin biosynthesis in fruit of fruit trees: Transcriptional, post-transcriptional, and post-translational regulation.

Onerice breeding framework: An end‐to‐end system to develop better varieties faster

AbstractBreeding in the Consultative Group on International Agricultural Research (CGIAR) system is an intricate process that integrates the contributions of market research, pre‐breeding, breeding, breeding operations, and seed systems. Therefore, a well‐defined framework is critical for the effective and efficient operation of a breeding program. The OneRice Breeding Framework developed at the International Rice Research Institute (IRRI) integrates these components, from initial market research to establish breeding goals, creating breeding strategies for improved product design and development, and swiftly testing and replacing products through effective seed systems. The framework represents a cutting‐edge breeding approach that offers comprehensive guidance on harnessing modern tools and technologies, including genomic selection, speed breeding, sparse testing, and so on. Additionally, the framework outlines strategies for systematically integrating novel genetic variation into elite breeding programs through pre‐breeding efforts. It is adaptable across different crops and is dynamic, allowing adjustments in the breeding program based on target objectives, resource availability, and tools. The OneRice Breeding Framework is a comprehensive end‐to‐end framework that integrates all the components to enhance genetic gains and develop and disseminate better products faster to address food, nutrition, and income security. Consequently, the OneRice Breeding Framework is the fundamental blueprint for modern rice (Oryza sativa) crop breeding.

Optimisation of variance component estimation and genomic prediction in a commercial crossbred population of Durocx(LandracexYorkshire) three-way pigs.

Optimisation of variance component estimation and genomic prediction in a commercial crossbred population of Durocx(LandracexYorkshire) three-way pigs.

Assessment of Biochemical Composition of Fruits of Hippophae rhamnoides (Elaeagnaceae juss.), Viburnum opulus (Viburnaceae raf.) and Lonicera caerulea subsp. altaica (Caprifoliaceae juss.).

Background/Objectives: This study explores the biochemical diversity of Hippophae rhamnoides, Viburnum opulus, and Lonicera caerulea subsp. altaica to identify genotypes rich in bioactive compounds for breeding nutritionally valuable cultivars. Methods: Selected forms and cultivars of each species were evaluated for key biochemical traits. Analyses included quantification of vitamins (C, B9, B12), sugars, organic acids, carotenoids, and flavonoids using HPLC and TLC. Results: In H. rhamnoides, vitamin C content ranged widely, with 'Pamyati Baytulina Sh-9-81' reaching 156.0 mg/%, while 'Shetlastinka No. 7' showed the most favorable sugar-to-vitamin C ratio. 'Krasnoplodnaya K-14-81' had the highest carotenoids (55.3 mg/100 g), and 'Dolgozhdannaya No. 5' was notable for flavonoid richness. In V. opulus, considerable variation was observed in vitamin content, sugars, and dry matter; 'Zhemchuzhnoe Ozhele' and 'Shtambovaya' were rich in rutin and robinin. In L. caerulea subsp. altaica, forms No. 5, 7, and 9 stood out for vitamin C, sugar, and flavonoid content. Hyperoside, isorhamnetin, and myricetin were common, while kaempferol and hypolaetin were form-specific. Conclusions:H. rhamnoides demonstrated the highest variability in biochemical composition, while L. caerulea subsp. altaica showed a particularly rich flavonoid profile. These species offer valuable genetic resources for developing biofortified cultivars suited to both nutritional and adaptive breeding goals.

Rice kernel morphometrics: Exploring the physical dimensions of indigenous traditional landrace diversity through physio metric studies

Development and widespread adoption of modern rice varieties has led bottlenecking of many beneficial alleles and there is a significant decline in the cultivation of traditional landraces, which results in substantial loss of genetic diversity. The varied consumer preference in terms of eating habit and other preparations in rice sustains the diversity in the grains. Hence, present day market trend in rice revolves around the choice of consumers which are mainly based on the physical characteristics of rice. To categorize rice based on kernel characteristics, in this study, a total of 500 rice genotypes were taken for assessing the physical properties of kernel viz., seed length, seed width, length/width ratio, seed thickness, bulk density, geometric mean diameter, sphericity, aspect ratio and hundred seed weight. All the traits exhibited ample amount of significant variations (P<0.05). High GCV was exhibited by bulk density and high heritability was observed by hundred seed weight, seed thickness, bulk density and seed width indicating that these traits were highly influenced by genetic factor and less influence of environment. Among these traits, hundred seed weight, seed thickness, bulk density and seed width exhibited high heritability coupled with high genetic advance as per cent of mean indicating the additive gene action and amenable for selection. Principal component analysis observed that the first three principle components explained most of the total variations present in the studied genotypes. Specifically, the first principal component (PC1) contributed the most, representing 35.24% of the variability followed by PC2 and PC3. In view of size and shape, most rice genotypes exhibited kernels that were predominantly short and narrow, succeeded by those that were short and of medium width. To categorise the seed diversity among the kernels of landraces, Mahalanobis D2 statistics analysis was performed. Based on this the 500 rice landraces were grouped into five distinct clusters. Among the clusters, the Cluster II predominantly comprised kernels of medium and short lengths, medium widths. In contrast, Cluster V predominantly featured grains of very short lengths, narrow to very narrow widths. From the five clusters, four genotypes per cluster emphasising high mean value for bold and slender shape were selected for observation of cooking quality traits. During cooking, grain expands in all the dimensions but usually more in length. The gelatinization temperature based on alkali digestion values showed that 16 rice genotypes had low alkali spreading values, leading to stickier rice. Meanwhile, four genotypes exhibited intermediate alkali spreading values, which are preferred for parboiling. Therefore, an understanding on the kernel architecture and grouping them based on the physical dimensions like seed thickness, seed width, and bulk density, as well as kernel colour along with hundred seed weight will be useful in formulating breeding programme for kernel traits or consumer preferences. This selection aimed to align breeding goals with market needs, guaranteeing economic feasibility and sustainability in rice farming. Keywords: Rice, physical properties,variability, principle components, diversity, cooking traits

Repeatability and genetic parameters for phenotypes of methane emission in crossbred beef×dairy slaughter calves.

Repeatability and genetic parameters for phenotypes of methane emission in crossbred beef×dairy slaughter calves.

QTL Mapping and Candidate Gene Analysis for Cotton Fiber Quality and Early Maturity Using F2 and F3 Generations.

Cotton is the most important natural fiber-producing crop globally. High-quality fiber and early maturity are equally important breeding goals in the cotton industry. However, it remains challenging to synchronously improve these traits through conventional breeding techniques. To identify additional genetic information relating to fiber quality and early maturity, 11 phenotypic traits for the F2 and F3 generations were tested, and quantitative trait loci (QTL) mapping was performed. Candidate genes were analyzed using published RNA-seq datasets and qRT-PCR assays. All 11 tested traits showed bi-directional transgressive segregation, and most traits followed an approximately normal distribution. Overall, significant positive and significant negative correlations were observed among these traits. During cotton breeding, varieties with strong boll-setting ability can be selected from early-maturing materials that have high-quality fiber. A total of 102 QTLs were mapped, including 4 major and 3 stable QTLs. qFL-D13-1 was mapped in both the F2 and F3 generations, achieving a 3.94% to 11.39% contribution rate to the phenotypic variation. Three genes located in the QTL regions were identified based on their high expression levels in the three evaluated RNA-seq datasets. Ghir_A04G014830.1, covered by qHNFFB-A4-1 and qFU-A4-1, encoded ACLA-1. Ghir_D13G015010.1, encoding VTC2, and Ghir_D13G016670.1, encoding GA2OX1, were in the stable QTL qFL-D13-1 region. The qRT-PCR results suggested that these three genes may be involved in regulating seed development, fiber initiation, and fiber elongation. Overall, these findings contribute additional information for the breeding of high-yield, high fiber quality, and early-maturity varieties, as well as serve as a foundation for research on the underlying molecular mechanisms.

Precise genome editing of Dense and Erect Panicle 1 promotes rice sheath blight resistance and yield production in japonica rice.

The primary goals of crop breeding are to enhance yield and improve disease resistance. However, the "trade-off" mechanism, in which signalling pathways for resistance and yield are antagonistically regulated, poses challenges for achieving both simultaneously. Previously, we demonstrated that knock-out mutants of the Dense and Erect Panicle 1 (DEP1) gene can significantly enhance rice resistance to sheath blight (ShB), and we mapped DEP1's association with panicle length. In this study, we discovered that dep1 mutants significantly reduced rice yield. Nonetheless, truncated DEP1 was able to achieve both ShB resistance and yield increase in japonica rice. To further explore the function of truncated DEP1 in promoting yield and ShB resistance, we generated CRISPR/Cas9-mediated genome editing mutants, including a full-length deletion mutant of DEP1, named dep1, and a truncated version, dep1-cys. Upon inoculation with Rhizoctonia solani, the dep1-cys mutant demonstrated stronger ShB resistance than the dep1 mutant. Additionally, dep1-cys increased yield per plant, whereas dep1 reduced it. Compared to the full DEP1 protein, the truncated DEP1 (dep1-cys) demonstrated a decreased interaction affinity with IDD14 and increased affinity with IDD10, which are known to positively and negatively regulate ShB resistance through the activation of PIN1a and ETR2, respectively. The dep1-cys mutant exhibited higher PIN1a and lower ETR2 expression than wild-type plants, suggesting that dep1-cys modulated IDD14 and IDD10 interactions to regulate PIN1a and ETR2, thereby enhancing ShB resistance. Overall, these data indicate that precise genome editing of DEP1 could simultaneously improve both ShB resistance and yield, effectively mitigating trade-off regulation in rice.

Characterization of German sheep production systems and derivation of respective economic values for breeding traits.

The aim of this study was to derive economic weights for sheep breeding goal traits for specific cluster types. The herd clustering approach considered 25 German sheep herds including descriptors related to area-based factors, management factors, herd information and socio-economic characteristics. The evaluation criterion suggested the application of agglomerative hierarchical clustering with the respective allocation of 25 herds to 3 different clusters. The clusters mainly differed with regard to herd size, production focus, and organic versus conventional management practices. The ongoing contingent valuation approach to derive cluster specific economic weights for 12 breeding goal traits based on the willingness to pay (WTP) considering 25 German sheep farmers, a hypothetical budget of 1000 € for the improvement of a trait per 1 genetic SD, and linear mixed model applications. Significant cluster differences for the WTP (P < 0.01) were only identified for the trait feed utilisation with regard to clusters 2 (least-squares mean = 101.65 €) and 3 (least-squares mean = 9.46 €). Least-squares means for individual breeding goal traits were summed up into four overall breeding goal categories. The highest trait importance was expressed for "functional", but displaying a variation among cluster. All clusters rated the trait category "health and welfare" including tail length very similar (range from 24 % to 29 %), with even stronger emphasize on "health and welfare" over "performance" in clusters 1 and 3. In consequence, we suggest to modify sheep breeding goals with a shift from production towards health, welfare and functionality, by consideration of production system particularities.

Applied Research Note: Predicting carcass portion weights for purebred turkey (Meleagris gallopavo) lines using a 2D imaging system

Applied Research Note: Predicting carcass portion weights for purebred turkey (Meleagris gallopavo) lines using a 2D imaging system

Breeding objectives, selection criteria and reproductive performance of indigenous sheep in west Wallaga zone, Oromia, Ethiopia

ABSTRACT The study aimed to assess the breeding goals, selection criteria and reproductive performance of indigenous sheep in west Wallaga zone, Ethiopia. A qualitative survey approach through questionnaire administration was used to collect data. The analysis primarily involved descriptive statistics and chi-square tests. Based on index values, sheep were primarily produced for income generation, followed by meat production and saving, but with different ranking orders among the study areas. Results of this study showed that sheep milk was not produced throughout the year across the study areas. The findings also revealed that uncontrolled mating alongside communal grazing and access to water points was the most prevalent sheep breeding practices. Overall appearance, coat colour and growth rate for the breeding rams and growth rate, age at first sexual maturity and lambing interval for ewes were the most selection criteria in all study districts. The overall mean (±SE) age at first lambing, reproductive life span, litter size and average lifetime crop density were 14.68 ± 0.02 months, 9.8 ± 0.16 years, 8.83 ± 0.44 and 11.7 ± 0.30, respectively, which were significantly (P < 0.05) different among the districts. Hence, farmers’ indigenous knowledge needs to be considered in designing sustainable breeding strategy to improve productivity of sheep in the study areas.

Improving genomic selection in hexaploid wheat with sub-genome additive and epistatic models.

The goal of wheat breeding is the development of superior cultivars tailored to specific environments, and the identification of promising crosses is crucial for the success of breeding programs. Although genomic estimated breeding values were developed to estimate additive effects of genotypes before testing as parents, application has focused on predicting performance of candidate lines, ignoring nonadditive genetic effects. However, nonadditive genetic effects are hypothesized to be especially important in allopolyploid species due to the interaction between homeologous genes. The objectives of this study were to model additive and additive-by-additive epistatic effects to better delineate the genetic architecture of grain yield in wheat and to improve the accuracy of genome-wide predictions. The data set utilized consisted of 3,740 F5:6 experimental lines tested in the K-State wheat breeding program across the years 2016 and 2018. Covariance matrices were calculated based on whole- and sub-genome marker data, and the natural and orthogonal interaction approach was used to estimate variance components for additive and additive-by-additive epistatic effects. Incorporating epistatic effects in additive models resulted in nonorthogonal partitioning of genetic effects but increased total genetic variance and reduced deviance information criteria. Estimation of sub-genome effects indicated that genotypes with the greatest whole-genome effects often combine sub-genomes with intermediate to high effects, suggesting potential for crossing parental lines that have complementary sub-genome effects. Modeling epistasis in either whole-genome or sub-genome models led to a marginal (3%) improvement in genomic prediction accuracy, which could result in significant genetic gains across multiple cycles of breeding.

Stability, performance and participatory evaluation of potato varieties under rain-fed and irrigation conditions at Southeast, Ethiopia

The goal of potato breeding is to develop widely adaptable, highly productive cultivars that farmers would prefer. The objective of this study was to evaluate the performance and stability of potato varieties linking the preferences of smallholder farmers in rain-fed and irrigated environments. Using a randomized complete block design in three replicates, twelve potato cultivars were assessed in 10 settings in Southeast Ethiopia during the Meher and Belg seasons in 2019 and 2020. The environments, genotypes, and GEI all revealed significant differences (p&lt;0.001) in the pooled analysis of the variance of tuber yield. The tuber yield variances for GEI, environment, and genotypic impacts were 15.48%, 7.61%, and 59.49% explained by the AMMI analysis, respectively. The environments were grouped into three distinct categories. A total of 99.6% of the variance was the cumulative contribution of PC1, PC2, PC3, PC4, and PC5 sharing 80.8%, 11.3%, 4.3%, 2.2%, and 1.0%, respectively High-yielding and widely adapted were Gera, Gudanie, Bubu, Belete, Shenkolla, Guassa, and Maracharre varieties, according to the AMMI, BLUP, GGE biplot, and WAAS. However, dynamic types that were particularly affected by environmental variations include Jalenie, Dagim, Gorebella, Awash, and Zemen. A stability measure of metric and preference based on various traits identified Gudanie and Guassa varieties. The scores of the small holder farmers were consistent throughout the test environments. The canonical correlation analysis indicated the significant association between the metric traits collected by the breeder and the small- holder farmer preferences. The study provides baseline data for potato breeding, and the varieties must be evaluated in the nation's mega-environments for additional recommendations. Int. J. Agril. Res. Innov. Tech. 14(2): 85-98, December 2024

Determination of blood biochemical indices and research of egg quality-related candidate gene CDH5 in Putian black duck

Determination of blood biochemical indices and research of egg quality-related candidate gene CDH5 in Putian black duck

Maize2035: A decadal vision for intelligent maize breeding.

Maize2035: A decadal vision for intelligent maize breeding.

Genetic Variation in a Crossing Population of Camellia oleifera Based on ddRAD Sequencing and Analysis of Association with Fruit Traits.

Tea oil is an important high-quality edible oil derived from woody plants. Camellia oleifera is the largest and most widely planted oil-producing plant in the Camellia genus in China, and its seeds are the most important source for obtaining tea oil. In current research, improving the yield and quality of tea oil is the main goal of oil tea genetic breeding. The aim of this study was to investigate the degree of genetic variation in an early crossing population of C. oleifera and identify single nucleotide polymorphisms (SNPs) and genes significantly associated with fruit traits, which can provide a basis for marker-assisted selection and gene editing for achieving trait improvement in the future. In this study, we selected a crossing population of approximately 40-year-old C. oleifera with a total of 330 samples. Then, ddRAD sequencing was used for SNP calling and population genetic analysis, and association analysis was performed on fruit traits measured repeatedly for two consecutive years. The research results indicate that over 8 million high-quality SNPs have been identified, but the vast majority of SNPs occur in intergenic regions. The nucleotide polymorphism of this population is at a low level, and Tajima's D values are mostly greater than 0, indicating that the change in this population was not suitable for the model of central evolution. The population structure analysis shows that the population has seven theoretical sources of genetic material and can be divided into seven groups, and the clustering analysis results support the population structure analysis results. Association analysis identified significant SNPs associated with genes related to the seed number of a single fruit and seed kernel oil content. Our findings provide a basis for molecular breeding and future genetic improvement of cultivated oil tea.

Genetic Mapping for Seed Aging Tolerance Under Multiple Environments in Sweet Corn

Seed vigor significantly impacts seed production and storage. Enhancing seed vigor is a pivotal goal in sweet corn breeding, as improved seed sowing quality is crucial for agricultural development, aiding in better resilience against storage adversities and facilitating long-term germplasm preservation. In this study, a recombinant inbred line (RIL) population, including 158 families, was derived from the aging-tolerant line K62 and the aging-sensitive line K107. Utilizing SNP arrays, genotypes were identified, and a genetic linkage map was constructed. Composite interval mapping was employed to detect quantitative trait loci (QTLs) associated with five seed vigor traits, namely the seedling fresh weight (SFW), germination potential (GP), germination rate (GR), germination index (GI), and vigor index (VI), at three days after artificial aging treatment. Upon analysis, a total of 42 QTLs affecting seed vigor indices were identified over two years. Of these, six were linked to SFW, while the GP, GR, GI, and VI each comprised nine QTLs. Nine QTL clusters were identified, with significant contributions (&gt;10%) from Loci02.1, Loci05.2, Loci06.1, and Loci10.1, ranging from 9.50% to 24.20%, 8.89% to 11.54%, 9.16% to 15.55%, and 7.54% to 17.77%, respectively. Candidate genes were explored within QTL cluster regions based on the aging-induced transcriptomic sequencing data of K62 and K107. Through Gene Ontology enrichment, gene annotation, and expression profiling clustering analyses, 12 positive candidate genes linked to seed aging tolerance were identified. This study provides a foundational understanding of the genetic mechanisms of seed aging tolerance and the innovation of an elite germplasm for seed aging tolerance in sweet corn.

Genome-Wide Association and Genomic Prediction of Alfalfa (Medicago sativa L.) Biomass Yield Under Drought Stress.

Developing drought-resistant alfalfa (Medicago sativa L.) that maintains high biomass yield is a key breeding goal to enhance productivity in water-limited areas. In this study, 424 alfalfa breeding families were analyzed to identify molecular markers associated with biomass yield under drought stress and to predict high-merit plants. Biomass yield was measured from 18 harvests from 2020 to 2023 in a field trial with deficit irrigation. A total of 131 significant markers were associated with biomass yield, with 80 markers specifically linked to yield under drought stress; among these, 19 markers were associated with multiple harvests. Finally, genomic best linear unbiased prediction (GBLUP) was employed to obtain predictive accuracies (PAs) and genomic estimated breeding values (GEBVs). Removing low-informative SNPs [SNPs with p-values > 0.05 from the additive Genome-Wide Association (GWAS) model] for GBLUP increased PA by 47.3%. The high number of markers associated with yield under drought stress and the highest PA (0.9) represent a significant achievement in improving yield under drought stress in alfalfa.