Genetic Improvement Strategies Research Articles

In-silico analysis of cattle blood transcriptome to identify lncRNAs and their role during bovine tuberculosis

Long noncoding RNAs (lncRNAs) are RNA molecules with a length greater than 200 nucleotides that do not code for functional proteins. Although, genes play a vital role in immune response against a disease, it is less known that lncRNAs also contribute through gene regulation. Bovine tuberculosis is a significant zoonotic disease caused by Mycobacterium bovis (M. bovis) in cattle. Here, we report the in-silico analysis of the publicly available transcriptomic data of calves infected with M. bovis. A total of 51,812 lncRNAs were extracted across all the samples. A total of 216 genes and 260 lncRNAs were found to be differentially expressed across all the 4 conditions—infected vs uninfected at 8- and 20-week post-infection (WPI), 8 vs 20-WPI of both infected and uninfected. Gene Ontology and Functional annotation showed that 8 DEGs were annotated with immune system GOs and 2 DEGs with REACTOME immune system pathways. Co-expression analysis of DElncRNAs with DEGs revealed the involvement of lncRNAs with the genes annotated with Immune related GOs and pathways. Overall, our study sheds light on the dynamic transcriptomic changes in response to M. bovis infection, particularly highlighting the involvement of lncRNAs with immune-related genes. The identified immune pathways and gene–lncRNA interactions offer valuable insights for further research in understanding host–pathogen interactions and potential avenues for genetic improvement strategies in cattle.

A NAC transcription factor MNAC3-centered regulatory network negatively modulates rice immunity against blast disease.

NAC transcription factors (TFs) are pivotal in plant immunity against diverse pathogens. Here, we report the functional and regulatory network of MNAC3, a novel NAC TF, in rice immunity. MNAC3, a transcriptional activator, negatively modulates rice immunity against blast and bacterial leaf blight diseases and pathogen-associated molecular pattern (PAMP)-triggered immune responses. MNAC3 binds to a CACG cis-element and activates the transcription of immune-negative target genes OsINO80, OsJAZ10, and OsJAZ11. The negative function of MNAC3 in rice immunity depends on its transcription of downstream genes such as OsINO80 and OsJAZ10. MNAC3 interacts with immunity-related OsPP2C41 (a protein phosphatase), ONAC066 (a NAC TF), and OsDjA6 (a DnaJ chaperone). ONAC066 and OsPP2C41 attenuate MNAC3 transcriptional activity, while OsDjA6 promotes it. Phosphorylation of MNAC3 at S163 is critical for its negative functions in rice immunity. OsPP2C41, which plays positive roles in rice blast resistance and chitin-triggered immune responses, dephosphorylates MNAC3, suppressing its transcriptional activity on the target genes OsINO80, OsJAZ10, and OsJAZ11 and promoting the translocation of MNAC3 from nucleus to cytoplasm. These results establish a MNAC3-centered regulatory network in which OsPP2C41 dephosphorylates MNAC3, attenuating its transcriptional activity on downstream immune-negative target genes in rice. Together, these findings deepen our understanding of molecular mechanisms in rice immunity and offer a novel strategy for genetic improvement of rice disease resistance.

Genome-Wide Association Analysis and Genetic Parameters for Egg Production Traits in Peking Ducks.

Egg production traits are crucial in the poultry industry, including age at first egg (AFE), egg number (EN) at different stages, and laying rate (LR). Ducks exhibit higher egg production capacity than other poultry species, but the genetic mechanisms are still poorly understood. In this study, we collected egg-laying data of 618 Peking ducks from 22 to 66 weeks of age and genotyped them by whole-genome resequencing. Genetic parameters were calculated based on SNPs, and a genome-wide association study (GWAS) was performed for these traits. The SNP-based heritability of egg production traits ranged from 0.09 to 0.54. The GWAS identified nine significant SNP loci associated with AFE and egg number from 22 to 66 weeks. These loci showed that the corresponding alleles were positively correlated with a decrease in the traits. Moreover, three potential candidate genes (ENSAPLG00020011445, ENSAPLG00020012564, TMEM260) were identified. Functional enrichment analyses suggest that specific immune responses may have a critical impact on egg production capacity by influencing ovarian function and oocyte maturation processes. In conclusion, this study deepens the understanding of egg-laying genetics in Peking duck and provides a sound theoretical basis for future genetic improvement and genomic selection strategies in poultry.

First Gynogenesis of Vanilla planifolia for Haploid Production and Ploidy Verification Protocol.

Vanilla orchids are members of the Vanilloideae orchid subfamily, and they hold significant economic value as a spice crop in tropical regions. Despite the presence of 180 known species within this subfamily, commercial production focuses on only three species (Vanilla planifolia, V. odorata, and V. pompona) and one hybrid (V. × tahitensis), prized for their aromatic qualities and bioactive compounds. Limited modern breeding initiatives have been undertaken with vanilla orchids, although recent advancements in genomic research are shedding light on this crop's potential. The protracted breeding cycle of vanilla, coupled with increasing demand for germplasm, underscores the importance of research and breeding efforts in vanilla. This paper outlines a protocol for haploid production in V. planifolia using unfertilized ovaries in tissue culture conditions. Additionally, we present a methodology to confirm the haploid nature of putative haploid lines through stomatal size comparison, chromosome counting, and flow cytometry analysis, proving the successful development of haploid vanilla plants. These findings contribute to the advancement of breeding programs and genetic improvement strategies for the vanilla industry.

Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two rainbow trout aquaculture lines confirms oligogenic architecture with several moderate effect quantitative trait loci

Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV), which can cause substantial mortality and economic losses in rainbow trout aquaculture and fisheries enhancement hatchery programs. In a previous study on a commercial rainbow trout breeding line that has undergone selection, we found that genetic resistance to IHNV is controlled by the oligogenic inheritance of several moderate and many small effect quantitative trait loci (QTL). Here we used genome wide association analyses in two different commercial aquaculture lines that were naïve to previous exposure to IHNV to determine whether QTL were shared across lines, and to investigate whether there were major effect loci that were still segregating in the naïve lines. A total of 1,859 and 1,768 offspring from two commercial aquaculture strains were phenotyped for resistance to IHNV and genotyped with the rainbow trout Axiom 57K SNP array. Moderate heritability values (0.15–0.25) were estimated. Two statistical methods were used for genome wide association analyses in the two populations. No major QTL were detected despite the naïve status of the two lines. Further, our analyses confirmed an oligogenic architecture for genetic resistance to IHNV in rainbow trout. Overall, 17 QTL with notable effect (≥1.9% of the additive genetic variance) were detected in at least one of the two rainbow trout lines with at least one of the two statistical methods. Five of those QTL were mapped to overlapping or adjacent chromosomal regions in both lines, suggesting that some loci may be shared across commercial lines. Although some of the loci detected in this GWAS merit further investigation to better understand the biological basis of IHNV disease resistance across populations, the overall genetic architecture of IHNV resistance in the two rainbow trout lines suggests that genomic selection may be a more effective strategy for genetic improvement in this trait.

Morphology, Reproductive Biology and Anatomy of the Foxtail Orchid, Rhynchostylis retusa (L.) Blume

Background: Rhynchostylis retusa (L.) Blume, commonly known as the fox-tail orchid, is a promising epiphytic native species for breeding programs. Its’ population is diminishing in the native habitat due to unscrupulous overexploitation and habitat destruction. Hence, conservation of this species attains prime importance. To achieve the foregoing task, phenotypic traits in relation to adaptation are to be elucidated. Methods: In the present investigation, the morphological characters were documented and the correlation between each trait was determined. Furthermore, the anatomy of leaves and roots was documented, as was the stomatal structure and distribution on the abaxile and adaxile surfaces of the leaves. Biometric features of floral characters and reproductive biology such as anthesis, stigma receptivity, pollen production per pollinium, pollen viability, pollination mechanisms, self and cross-compatibility; male sterility, etc. were studied and documented. Observations on capsule development, nature of seeds, seed viability, etc. were also determined. Result: The seed viability tests revealed that about 40% of the seeds are viable. The observations gathered during this investigation can be used to develop conservation, sustainable utilization and genetic improvement strategies for this crop.

Genome-wide analysis of the GRAS gene family in white clover (Trifolium repens L.) provides insight into its critical role in response to cold stress

The GRAS transcription factor (TF) is a plant-specific regulator that plays a critical role in plant growth, development and response to various abiotic stresses. While the functions of many GRAS TFs have been extensively studied in numerous model plants with fully sequenced genomes, the GRAS TFs in white clover (Trifolium repens L.) remain elusive despite the sequencing of its genome. To bridge this knowledge gap, homologs of GRAS TFs from Arabidopsis were employed and subjected to a genome-wide blast against white clover proteins. This analysis identified and characterized 102 putative GRAS genes, designated as TrGRAS, based on the presence of GRAS domains in positive blast hits. Concurrently, an exploration of their gene structures, classification, evolutionary relationships and conservative motifs provided insights into the distinctive features of TrGRAS in white clover. Furthermore, gene duplication analysis revealed an expansion of TrGRAS genes in the PAT1 and LISCL subfamilies, indicating functional diversity within the white clover genome. Lastly, RNA-seq and quantitative reverse transcription-PCR (qRT-PCR) experiments confirmed their higher expression during the early or intermittent responses to cold stress, suggesting their potential and crucial roles in determining the cold tolerances of white clover. The analysis of TrGRAS genes, coupled with expression studies, contributes to the functional characterization of TrGRAS genes in white clover. This knowledge is pivotal for informing genetic improvement strategies in future breeding efforts aimed at enhancing cold tolerance in white clover.

Genetic characterization of Zeyheria tuberculosa progenies and evaluation for formation of a seed orchard

Zeyheria tuberculosa, a native species of Brazil known for its significant potential in silviculture and genetic improvement, holds prominence among various species. In this study, our objective was to assess the diversity, genetic structure, and feasibility of establishing a seedling seed orchard (SSO) for this species. A total of 71 progenies were collected from different locations and were used in our experiment in Ijaci - MG. We genotyped 92 individuals (nine families with eight individuals, two families with seven individuals, and one family with six individuals), specifically selecting those with the highest predicted genetic values, using ten ISSR primers. The molecular markers employed effectively detected polymorphism (PIC = 0.44). The population exhibited moderate to high genetic diversity, as evidenced by observed (AO = 2.00) and effective alleles (AE = 1.61), Nei's diversity index (H* = 0.35), and Shannon's diversity index (I* = 0.52). Molecular variance analysis indicated significant genetic differentiation between the progenies (Φst = 0.19), yet the majority of the variation was observed within them (80.1%). Employing a Bayesian approach, we identified the formation of two distinct genetic groups, further confirming the non-genetic structure of the population. These findings affirm the potential of the Z. tuberculosa progenies to contribute to the establishment of a seedling seed orchard, supporting genetic improvement strategies and the conservation of the species' genetic diversity.

A novel histone methyltransferase gene CgSDG40 positively regulates carotenoid biosynthesis during citrus fruit ripening

The flesh color of pummelo (Citrus maxima) fruits is highly diverse and largely depends on the level of carotenoids, which are beneficial to human health. It is vital to investigate the regulatory network of carotenoid biosynthesis to improve the carotenoid content in pummelo. However, the molecular mechanism underlying carotenoid accumulation in pummelo is not fully understood. In this study, we identified a novel histone methyltransferase gene, CgSDG40, involved in carotenoid regulation by analyzing the flesh transcriptome of typical white-fleshed pummelo, red-fleshed pummelo and extreme-colored F1 hybrids from a segregated pummelo population. Expression of CgSDG40 corresponded to flesh color change and was highly coexpressed with CgPSY1. Interestingly, CgSDG40 and CgPSY1 are located physically adjacent to each other on the chromosome in opposite directions, sharing a partially overlapping promoter region. Subcellular localization analysis indicated that CgSDG40 localizes to the nucleus. Overexpression of CgSDG40 significantly increased the total carotenoid content in citrus calli relative to that in wild type. In addition, expression of CgPSY1 was significantly activated in overexpression lines relative to wild type. Taken together, our findings reveal a novel histone methyltransferase regulator, CgSDG40, involved in the regulation of carotenoid biosynthesis in citrus and provide new strategies for molecular design breeding and genetic improvement of fruit color and nutritional quality.

Genetic evaluations of dairy goats with few pedigree data: different approaches to use molecular information.

One of the limitations of implementing animal breeding programs in small-scale or extensive production systems is the lack of production records and genealogical records. In this context, molecular markers could help to gain information for the breeding program. This study addresses the inclusion of molecular data into traditional genetic evaluation models as a random effect by molecular pedigree reconstruction and as a fixed effect by Bayesian clustering. The methods were tested for lactation curve traits in 14 dairy goat herds with incomplete phenotypic data and pedigree information. The results showed an increment of 37.3% of the relationships regarding the originals with MOLCOAN and clustering into five genetic groups. Data leads to estimating additive variance, error variance, and heritability with four different models, including pedigree and molecular information. Deviance Information Criterion (DIC) values demonstrate a greater fitting of the models that include molecular information either as fixed (genetic clusters) or as random (molecular matrix) effects. The molecular information of simple markers can complement genetic improvement strategies in populations with little information.

Evidence of subpopulation diversification and traces of introgression within Canarian camel breed zoometric standard: scope and opportunities for selection

Extant diversity for phenotypic traits is an essential criterion to be considered when ordering priorities for conservation and improvement of animal genetic resources. Concretely, the characterisation of the distinctive body morphometry of a particular group of animals can aid in the design of selective breeding programs, given the strong correlation between body morphology and productive function. The present research aims to characterise an endangered autochthonous camel breed (Canarian camel), mainly relegated to leisure riding, for its body morphology, with a double objective: to explore the phenotypic diversity and structure of the breed for zoometric traits and assess the zoometric profile of this genetic resource that supports its differentiation from other camel breeds. Overall, the results highlight the existence of a high degree of diversity, which may be linked to genetic factors for zoometric traits in an endangered autochthonous breed with traditional in situ breeding schemes, which predicts the success of the implementation of genetic improvement schemes for such functional characteristics. This phenotypic diversity in body morphology could also be a tool for the evaluation of new functional niches within the efforts of functional valorisation of this camel breed for its sustainable conservation. Body morphology traits in the studied camel breed are significantly influenced by sex, physiological status and coat colour.

Morphometric differentiation of three chicken ecotypes of Ethiopia using multivariate analysis.

Twenty-one morphometric traits were measured on 770 extensively managed indigenous chickens in the western zone of Tigray, comprising 412 hens and 358 cocks in three agro-ecologies. The quantitative traits for male and female chicken ecotypes were separately analyzed using multivariate analysis with SAS 2008. Four and seven principal components accounted for about 74.26% and 69.77% of the total variability in morphometric traits for males and females, respectively. Earlobe length, wingspan, skull length, and shank length werethe most important traits for discriminating among female chicken ecotypes, while wingspan, neck length, earlobe length, spur length, body length, and shank length were the most important discriminatory traits among male chicken ecotypes. The discriminant analysis accurately classified 97.3% of female and 100% of male chicken ecotypes. Cluster analysis revealed the genetic heterogeneity of indigenous chicken populations in both sexes. This finding suggests the presence of morphological variations among the indigenous chicken populations in the different agro-ecological zones, classified as distinct indigenous chicken ecotypes (Lowland, Midland, and Highland). Further DNA-based studies are needed to confirm and complement these morphological variations for effective conservation and the development of sustainable genetic improvement strategies for indigenous chicken populations in the region.

Characterization of runs of homozygosity islands in American mink using whole-genome sequencing data.

The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole-genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. Subsequent to quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for further analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3-1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. Within these segments, we identified 63 ROH islands housing 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2 and SLC24A4), body size/weight (MYLK4, PRIM2, FABP2, EYS and PHF3), immune capacity (IL2, IL21, PTP4A1, SEMA4C, JAK2, CCNA2 and TNIP3) and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2 and HSPA4L). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed 56 and 9 significant terms (FDR-corrected p-value < 0.05), respectively, among which cGMP-PKG signalling pathway, regulation of actin cytoskeleton, and calcium signalling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to our understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.

Aleutian disease: Risk factors and ImmunAD strategy for genetic improvement of tolerance in American mink (Neogale vison).

Aleutian disease (AD) is a devastating infectious disease in American mink (Neogale vison) industry caused by Aleutian mink disease virus (AMDV). Two crucial steps toward controlling infectious diseases in farm animals are: (i) assessment of the infection risk factors to minimize the likelihood of infection and (ii) selection of animals with superior immune responses against pathogens to build tolerant farms. This study aimed to investigate AD risk factors and evaluate a novel "ImmunAD" approach for genetic improvement of AD tolerance. Phenotypic records and pedigree information of 1,366 and 24,633 animals were included in this study. The risk of animal's age, sex, color type, and year of sampling on AMDV infection was assessed using a logistic regression model and counter immune-electrophoresis (CIEP) test results. ImmunAD phenotype was calculated based on AMDVG enzyme-linked immunosorbent assay (ELISA) and CIEP test results, and breeding values for ImmunAD were estimated using an animal model. Animals were classified into high-coordinated (HCIR), average-coordinated (ACIR), and low-coordinated immune responders (LCIR) using ImmunAD's breeding values, and the impact of selection of HCIR on live grade of pelt quality (PQ), harvest weight (HW), and harvest length (HL) breeding values were evaluated. Age of > 1 year, male sex, and year of sampling were identified as significant risk factors of AD (p < 0.05). A moderate-to-high heritability (0.55±0.07) was estimated for ImmunAD, while a higher heritability was observed among the CIEP-positive animals (0.76±0.06). Significantly higher breeding values were observed for PQ and HL among HCIR than those for LCIR and ACIR (p < 0.05). Our findings indicate the critical role of male breeders in AD distribution within mink farms. Regular screening of AD in male breeders before pairing them with females during breeding seasons can help disease control. ImmunAD strategy can be applied to genetic improvement of AD tolerance, with favorable impacts on some growth and production traits. Higher genetic gains can be achieved in populations with higher AD seroprevalences.

Research Progress of CRISPR/Cas9 Application in Rice Cultivation

Rice, being one of the world's most important staple crops, plays an important role in global food security and sustainable agriculture. The CRISPR/Cas9 gene editing technology has attracted widespread attention globally. With its precision and simplicity, rice breeding and research now heavily rely on the CRISPR gene editing method. The rice genome has been fully sequenced and intensively studied. Genome editing in rice holds great potential for variety improvement and agricultural production. In recent years, many studies have reported successful cases of gene knockout, point mutations, and targeted genome insertions using CRISPR-mediated genetic improvement strategies in rice. Using CRISPR gene editing technology to introduce new beneficial traits in rice, such as increased quality and nutritional value, disease resistance, stress tolerance, and greater control of rice growth and development has shown great potential. However, despite the broad prospects of CRISPR technology in rice, there are still many challenges and technical limitations to overcome, and issues regarding precision and safety remain unresolved. This review intended to provide an overview of the CRISPR technology's principles, methods, and researched progress in rice, as well as to analyze its possible benefits and difficulties in rice breeding while also providing information on its potential future applications.

Development of selection strategies for genetic improvement in production traits of Mecheri sheep based on a Bayesian multi trait evaluation

The progression of genetic selection techniques to enhance farm animal performance traits is guided by the present level of genetic variation and maternal impact in each trait, as well as the genetic association between traits. This study was conducted on a population of Mecheri sheep maintained from 1980 to 2018 at Mecheri Sheep Research Station, Pottaneri, India, to determine variance and covariance components, as well as genetic parameters for various production performance traits. A total of 2616 lambs, produced by 1044 dams and 226 sires, were examined in the study and the production traits of Mecheri sheep assessed include birth weight (BW), weaning weight (WW), six-month weight (SMW), nine-month weight (NMW), and yearling weight (YW). The Bayesian approach, using the Gibbs sampler, analyzed six animal models with different combinations of additive direct and maternal additive effects. Direct genetics, maternal genetics, and residual effects models were the major contributors to total phenotypic variation for all the production traits studied. Direct heritability estimates of birth weight, WW, SMW, NMW, and YW were 0.25, 0.20, 0.12, 0.14, and 0.13, respectively. The maternal heritability estimated for BW, WW, SMW, NMW, and YW were 0.17, 0.10, 0.12, 0.14, and 0.14, respectively. The maternal effects had a major impact on the pre-weaning production traits. The genetic correlations estimated between different pairs of production traits studied ranged from 0.19 to 0.93. The body weight at birth exhibited a higher genetic relationship with weaning weight than post-weaning growth characteristics, and the genetic correlation between weaning weight and post-weaning attributes was moderate to high (0.52 to 0.72). Based on the additive genetic variance in weaning weight and the correlation estimates of weaning weight with post-weaning traits, weaning weight was proposed as a selection criterion for improving growth traits in Mecheri sheep.

Enrichment of grape berries and tomato fruit with health-promoting tartaric acid by expression of the Vitis vinifera transketolase VvTK2 gene

Tartaric acid (TA) is a major non-fermentable plant soluble acid that abundantly occur in grapes and wines, imparting low pH and tart flavour to berries thereby regulating numerous quality attributes of wine, such as flavour, microbial stability, and aging potential. Evaluation of acidity in mature fruits of 21 wine grape (Vitis vinifera) varieties revealed significant variation between ‘Beichun’ and ‘Gewürztraminer’, which was correlated with TA content. RNA-seq analysis of fruits from the two cultivars at different developmental stages revealed that a transketolase gene, VvTK2, was significantly dominantly expressed in the high TA phenotype ‘Beichun’ variety. Subcellular localization assay showed that VvTK2 protein was located in the chloroplast. Virus-induced VvTK2 gene silencing significantly decreased the expression of 2-keto-L-gulonic acid reductase (Vv2-KGR) as well as L-idonate dehydrogenase (VvL-IdnDH3) and inhibited TA accumulation, while its transient over-expression in grape showed the opposite results. Heterologous VvTK2 over-expression in tomato demonstrated its obvious capacity to induce TA synthesis. Overall, these results highlights a novel role of VvTK2 in modulating TA biosynthesis, which could be an excellent strategy for future genetic improvement of grape flavour.

Thaumatin-like protein family genes VfTLP4-3 and VfTLP5 are critical for faba bean's response to drought stress at the seedling stage

Thaumatin-like proteins (TLPs) are a diverse family of pathogenesis-related proteins (PR-5) found in various plant species. Faba bean is an economically important crop known for its nutritional value and resilience to harsh environmental conditions, including drought. In this study, we conducted a comprehensive analysis of the gene structure, phylogenetics, and expression patterns of TLP genes in faba bean, with a specific focus on their response to drought stress. A total of 10 TLP genes were identified and characterized from the faba bean transcriptome, which could be classified into four distinct groups based on their evolutionary relationships. Conserved cysteine residues and REDDD motifs, which are characteristic features of TLPs, were found in most of the identified VfTLP members, and these proteins were likely to reside in the cytoplasm. Two genes, VfTLP4-3 and VfTLP5, exhibited significant upregulation under drought conditions. Additionally, ectopically expressing VfTLP4-3 and VfTLP5 in tobacco leaves resulted in enhanced drought tolerance and increased peroxidase (POD) activity. Moreover, the protein VfTLP4-3 was hypothesized to interact with glycoside hydrolase family 18 (GH18), endochitinase, dehydrin, Barwin, and aldolase, all of which are implicated in chitin metabolism. Conversely, VfTLP5 was anticipated to associate with peptidyl-prolyl cis-trans isomerase-like 3, a molecule linked to the synthesis of proline. These findings suggest that these genes may play crucial roles in mediating the drought response in faba bean through the regulation of these metabolic pathways, and serve as a foundation for future genetic improvement strategies targeting enhanced drought resilience in this economically important crop.

Cattle Genetic Improvement Strategies for Sustainable Development in Tropics: Review

Inefficient use of genetic variation among and within breeds of different breeds is an obstacle to enhancing the livestock population in underdeveloped countries. The best productive and adaptable animals for each environment must be identified for breeding objectives. Changing numerous aspects of production is required for successful livestock genetic improvement. In developing countries, genetic improvement efforts are unlikely to succeed unless they are supplemented by better diet, herd health, and management. Improvement strategies that are now taken for granted in developed countries are not implemented in most developing countries. The high expense of such procedures is one of the main reasons for their poor adoption rates. As a result, the economic evaluation of improvement programs is critical. Population increase, market development, technological change, and a shifting resource base are all examples. These dynamics that drive a specific livestock production system, as well as the entire subsector, must be anticipated and identified in development strategies. It is vital to understand the direction and speed with which these elements may change, both at the sectoral and farm levels, for future initiatives to respond appropriately. As a result, improving local cattle genetic value and devising genetic improvement methods accordingly is critical for the country's and sector's long-term development. Insufficient research has negative impacts on different breed types in diverse and dynamic livestock production systems assessment in developing countries, which creates significant knowledge gaps about breed-change interventions. Hence, supporting researchers, research institutions and higher education institutions is crucial to the success of policy in reducing the knowledge gap and strengthening the relationships between the livestock owners and government. Moreover, the development of national livestock strategies, effective policies, and the establishment of breeding cooperatives have an impact on the development and implementation of national livestock strategies for sustainable development.

PSXII-7 Characterization of Runs of Homozygosity Islands in American Mink Using Whole-Genome Sequencing Data

Abstract The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy to detect the variants shared among the individuals of a population, and thereby to reveal important genomic regions for complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, ROH islands, and the gene content of those candidate regions using whole-genome sequencing data of 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. After quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for subsequent analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3–1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. We identified 63 ROH islands that harbored 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2, SLC24A4, SLC24A3, PDE5A), body size/body weight (MYLK4, PRIM2, FABP2, BBS7, EYS, PHF3), immune capacity (IL2, PTP4A1, SEMA4C, CD274, JAK2, MAD2L1, CCNA2, TNIP3), and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2, LARP1B, HSPA4L, CAMK2D). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed multiple significant terms (P ≤ 0.05), among which cGMP-PKG signaling pathway, regulation of actin cytoskeleton, and calcium signaling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to an understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.