Marker-assisted Selection Research Articles

Using Marker-Assisted Selection to Develop a Drought-Tolerant Rice Line with Enhanced Resistance to Blast and Brown Planthopper

Rice is a major global staple crop, but rising temperatures and freshwater shortages have made drought one of the most severe abiotic stresses affecting agriculture. Additionally, rice blast disease and brown planthopper infestations significantly impact yields. Therefore, developing water-saving, drought-resistant, high-yielding, and disease-resistant rice varieties is critical for sustainable rice production. The new water-saving and drought-resistant (WDR) rice ‘Huhan 1516’, bred using marker-assisted selection (MAS) and marker-assisted backcrossing (MABC) techniques, addresses these challenges. This variety is highly adaptable to drought-prone and water-scarce regions such as the Yangtze and Huai River basins. With its high yield, drought tolerance, and broad-spectrum resistance to rice blast (conferred by the Pi2 gene) and brown planthopper (BPH), ‘Huhan 1516’ is suitable for various farming systems and environments. Field trials show that this variety outperforms control varieties by 2.2% in yield and exhibits moderate resistance to both rice blast and brown planthopper. ‘Huhan 1516’ has been recognized as a new water-saving and drought-resistant rice variety by the state, and as a released cultivar, it has great potential for market promotion and application.

Identification of Plasma Protein Biomarkers for Predicting Lung Cancer.

Lung cancer remains a leading cause of cancer-related mortality worldwide, necessitating the development of effective early diagnostic strategies. Despite advancements in imaging and screening technologies, late-stage diagnoses remain common, limiting treatment options and reducing survival rates. Thus, there is a critical need for reliable, minimally invasive biomarkers to improve early detection and patient outcomes. Plasma protein biomarkers offer promising potential for early lung cancer detection and continuous disease monitoring. This study explored the potential of specific plasma protein markers as early indicators of lung cancer. Plasma samples were collected from normal healthy individuals and lung cancer patients, and protein purification and analysis were conducted using LC-MS/MS. A mixed-effect model was applied to select lung cancer-related protein markers based on label-free relative quantification values. We identified 29 proteins with potential for early lung cancer diagnosis, including complement proteins (CFB, C3, C8G, C1QA, C1R, C6), orosomucoid proteins (ORM1, ORM2), ceruloplasmin (CP), alpha-1-B glycoprotein (A1BG), and others. These proteins play diverse roles in immune response, inflammation, and cell signaling, suggesting their relevance in lung cancer pathophysiology. Our findings suggest the potential of plasma proteins as early diagnostic biomarkers for lung cancer. Further validation in larger cohorts is needed to confirm their clinical utility. Integrating these biomarkers into existing diagnostic modalities could enhance early detection accuracy, leading to improved patient outcomes.

Advances in Soybean Genetic Improvement

The soybean (Glycine max) is a globally important crop due to its high protein and oil content, which serves as a key resource for human and animal nutrition, as well as bioenergy production. This review assesses recent advancements in soybean genetic improvement by conducting an extensive literature analysis focusing on enhancing resistance to biotic and abiotic stresses, improving nutritional profiles, and optimizing yield. We also describe the progress in breeding techniques, including traditional approaches, marker-assisted selection, and biotechnological innovations such as genetic engineering and genome editing. The development of transgenic soybean cultivars through Agrobacterium-mediated transformation and biolistic methods aims to introduce traits such as herbicide resistance, pest tolerance, and improved oil composition. However, challenges remain, particularly with respect to genotype recalcitrance to transformation, plant regeneration, and regulatory hurdles. In addition, we examined how wild soybean germplasm and polyploidy contribute to expanding genetic diversity as well as the influence of epigenetic processes and microbiome on stress tolerance. These genetic innovations are crucial for addressing the increasing global demand for soybeans, while mitigating the effects of climate change and environmental stressors. The integration of molecular breeding strategies with sustainable agricultural practices offers a pathway for developing more resilient and productive soybean varieties, thereby contributing to global food security and agricultural sustainability.

Creating a Genetic Toolbox for the Carbon-Fixing, Nitrogen-Fixing and Dehalogenating Bacterium Xanthobacter autotrophicus.

Xanthobacter autotrophicus is a metabolically flexible microorganism with two key features: (1) The organism has adapted to grow on a wide variety of carbon sources including CO2, methanol, formate, propylene, haloalkanes and haloacids; and (2) X. autotrophicus was the first chemoautotroph identified that could also simultaneously fix N2, meaning the organism can utilize CO2, N2, and H2 for growth. This metabolic flexibility has enabled use of X. autotrophicus for gas fixation, the creation of fertilizers and foods from gases, and the dehalogenation of environmental contaminants. Despite the wide variety of applications that have already been demonstrated for this organism, there are few genetic tools available to explore and exploit its metabolism. Here, we report a genetic toolbox for use in X. autotrophicus. We first identified suitable origins of replication and quantified their copy number, and identified antibiotic resistance cassettes that could be used as selectable markers. We then tested several constitutive and inducible promoters and terminators and quantified their promoter strengths and termination efficiencies. Finally, we demonstrated that gene expression tools remain effective under both autotrophic and dehalogenative metabolic conditions to show that these tools can be used in the environments that make X. autotrophicus unique. Our extensive characterization of these tools in X. autotrophicus will enable genetic and metabolic engineering to optimize production of fertilizers and foods from gases, and enable bioremediation of halogenated environmental contaminants.

Comparative effects of cognitive and instability resistance training versus instability resistance training on balance and cognition in elderly women

This study investigates the effects of integrated instability resistance training and cognitive training (IRCT) versus isolated instability resistance training (IRT) on balance, gait, muscle strength, and cognitive functions in elderly women.This randomized controlled trial included 36 participants, with 18 in the IRCT group and 18 in the IRT group. The sample size was estimated to achieve a statistical power of 0.95 with a large effect size (0.40; n = 12 each group). The closed-eye single-leg stand test was measured for static balance, the closed-eye stepping test, and the Timed Up and Go Test (TUGT) were measured for dynamic balance. Dual-task balance was assessed by combining the TUGT with cognitive tasks (TUGT-C) and motor tasks (TUGT-M). Gait performance was evaluated using a gait function system. Lower limb muscle strength was measured with the 30-Second Chair Stand Test. Cognitive function was assessed through the Trail Making Test (TMT), Digit Span Test (DST), Stroop Color and Word Test (Stroop), and Digit Symbol Substitution Test (DSST). Results IRCT group showed better improvements in both cognitive (p < 0.001) and motor (p = 0.812 for baseline; p < 0.001 for post-intervention) dual-task abilities, IRCT also experienced better enhancement in certain cognitive functions, particularly in the TMT (p = 0.001) and DSST (p = 0.022) compared to the IRT group. Both groups demonstrated enhancements in walking abilities as shown on selective markers of the gait performance test (p < 0.05) and leg muscle strength via 30-Second Chair (p < 0.001 for time main effect). These results suggest that combining cognitive exercises with physical training more effectively addresses the complex challenges associated with aging in women. The study highlights the potential of comprehensive training approaches in boosting health and quality of life for the elderly, with implications for developing tailored exercise programs focused on reducing fall risks and enhancing quality of life in this population.

The influence of plant genomics on plant evolution

With the increasing demand for high-quality tea, the genetic basis of ideal traits of tea plants has been widely concerned. The research on tea tree genomics, specifically focusing on “Longjing 43”, provides significant insights into plant evolution and breeding. “Longjing 43” was chosen due to its complex genome and economic importance. The study successfully assembled its genome to the chromosome level, revealing a large and heterogeneous genome with numerous repetitive sequences. Comparative genomics showed that hybridization has been a key driver of genetic diversity and adaptability in tea plants. These findings are crucial for developing marker-assisted selection (MAS) techniques, improving traits such as disease resistance, flavor, and stress response. Moreover, the research underscores the role of tea tree genomics in preserving cultural heritage and promoting economic benefits through enhanced tea quality. This study contributes to the broader understanding of plant genomics by illustrating the evolutionary processes and potential applications in agriculture, conservation, and industry, thus offering a comprehensive tool for future plant breeding and genetic improvement strategies.

Genomic-Wide Association Studies For Resistance to Anthracnose in a Pseudo-F2 Mango Population

Goal: This study aimed to apply genome-wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with resistance to mango anthracnose. Theoretical Framework: The statistical methods of GWAS aim to identify associations among genotypes with phenotypes for marker-assisted selection (MAS) or genome dissection of important traits. Method: Ninety-four plants of a ‘Haden’ × ‘Tommy Atkins’ pseudo-F2 population were genotyped with 705 SNPs and phenotyped for resistance to Colletotrichum siamense, anthracnose causal agent, by spraying young leaves, three times at different periods, with 103 conidia/mL. Qualitative GWAS, with Plink Fisher’s exact test and Cochran-Armitage trend genotypic test, and quantitative GWAS, with Tassel general (GLM) and mixed linear models (MLM) were applied. F2 plants with symptoms mean absence &gt;75% were considered moderately resistant to the fungus. Results and discussion: Qualitative and quantitative GWAS methods combined enable the identification of two consensus SNP loci controlling 24.76% of total variance to mango anthracnose resistance. Other four SNPs, identified, exclusively in quantitative or qualitative analysis, explained 28.55% of total variance to mango anthracnose. These SNPs loci are promising candidate for further PCR primers design in order to apply MAS in mango. Research implications: This study facilitates the identification of consensus chromosomal regions associated with mango anthracnose resistance. The application of MAS in mango breeding will accelerate the development of new cultivars. Originality/Value: To our knowledge, this a pioneering GWAS study applied to anthracnose, which is the most significant and widespread fungal disease affecting mango fruit globally.

Characterization of the wheat-tetraploid Thinopyrum elongatum 7E(7D) substitution line with Fusarium head blight resistance

BackgroundFusarium head blight (FHB), a devastating disease of wheat production, is predominantly elicited by Fusarium graminearum (Fg). The tetraploid Thinopyrum elongatum is a tertiary gene resource of common wheat that possesses high affinity and displays high resistance traits against multiple biotic and abiotic stress. We aim to employ and utilize the novel FHB resistance resources from the wild germplasm of common wheat for breeding.ResultsDurum wheat-tetraploid Th. elongatum amphiploid 8801 was hybridized with common wheat cultivars SM482 and SM51, and the F5 generation was generated. We conducted cytogenetically in situ hybridization (ISH) technologies to select and confirm a genetically stable 7E(7D) substitution line K17-1069-5, which showed FHB expansion resistance in both field and greenhouse infection experiments and displayed no significant disadvantage in agronomic traits compared to their common wheat parents in the field. The F2 segregation populations (K17-1069-5 × SM830) showed that the 7E chromosome conferred dominant FHB resistance with dosage effect. We developed 19 SSR molecular markers specific to chromosome 7E, which could be conducted for genetic mapping and large breeding populations marker-assisted selection (MAS) during selection procedures in the future. We isolated a novel Fhb7 allele from the tetraploid Th. elongatum chromosome 7E (Chr7E) using homology-based cloning, which was designated as TTE7E-Fhb7.ConclusionsIn summary, our study developed a novel wheat-tetraploid Thinopyrum elongatum 7E(7D) K17-1069-5 substitution line which contains stable FHB resistance.

Genome-wide association study of pineapple breeding population

Pineapples (Ananas comosus (L.) Merr.) are one of the most important tropical fruits. Although pineapple breeding program has been conducted in Japan, sufficient genomic information has not been adopted for breeding. The objective of this study was to identify quantitative trait loci (QTL) for pineapple breeding-related traits that can be applied to different populations. Here, we performed a genome-wide association study using seven breeding populations, including 703 individuals with genome-wide 9574 SNPs. Eleven QTLs were detected for nine traits (flesh color, flesh color values (a*, b*), bolting days, days from bolting to harvest, fruit shell color, soluble solid content, acidity, ascorbic acid content, and fruit cracking). Phenotypic value of each genotype in each population was confirmed for each QTL. Six QTLs (acidity QTL ACID-1, ascorbic acid QTL AsA-1 and AsA-2, flesh color QTL FCOL-1 and FCOLb-1, and fruit-cracking QTL CRACK-1) showed significant intergenotypic variance among all populations with genotype segregation. The obtained QTLs and their genotype information will contribute to the selection of cross-breeding parents and marker-assisted selection in pineapple breeding programs.

Current knowledge and breeding strategies for management of aphid-transmitted viruses of pepper (Capsicum spp.) in Africa

Aphid-transmitted viruses cause significant losses in pepper production worldwide, negatively affecting yield and quality. The emergence of new aphid-transmitted viruses or development of variants as well as the occurrence in mixed infections make management a challenge. Here, we overview the current status of the distribution, incidence and phylogeny of aphids and the viruses they transmit in pepper in Africa; outline the available genetic resources, including sources of resistance, resistance genes and molecular markers; and discuss the recent advances in understanding the genetic basis of resistance to the predominant African viruses infecting pepper. Pepper veinal mottle virus (PVMV; Potyvirus); Potato virus Y (PVY; Potyvirus), Chili veinal mottle virus (ChiVMV; Potyvirus), Cucumber mosaic virus (CMV; Cucumovirus) and Pepper veins yellow virus (PeVYV; Polerovirus) have been reported to be the most widespread and devastating aphid-transmitted viruses infecting pepper across Africa. Co-infection or mixed infection between aphid-transmitted viruses has been detected and the interrelationship between viruses that co-infect chili peppers is poorly understood. Establishing and evaluating existing and new diversity sets with more genetic diversity is an important component of developing host resistance and implementing integrated management strategies. However, more work needs to be done to characterize the aphid-transmitted viral strains across Africa and understand their phylogeny in order to develop more durable host resistance. In addition, a limited number of QTLs associated with resistance to the aphid-transmitted virus have been reported and QTL data are only available for PVY, ChiVMV and CMV mainly against European and Asian strains, although PVMV is likely the most important aphid-transmitted viral disease in Africa. There is a need to identify germplasm resources with resistance against various aphid-transmitted virus strains, and subsequent pyramiding of the resistance using marker-assisted selection could be an effective strategy. The recent advances in understanding the genetic basis of the resistance to the virus and the new breeding techniques that can be leveraged to accelerate breeding for aphid-transmitted virus in pepper are proposed as strategies to more efficiently develop resistant cultivars. The deployment of multi-genetic resistances in pepper is an effective and desirable method of managing viral-diseases in Africa and limit losses for farmers in a sustainable manner.

Revolutionizing livestock sustainability: Pioneering breeding strategies for superior forage biomass and quality

Livestock primarily rely on forage crops as a source of feed and nutrition. The milk productivity of a cow or meat production in goat/sheep could directly be associated with the availability of a sufficient quantity of quality green fodders with essential nutrients in a balanced ratio. Feeding the cereal/grass: legume fodders in the required proportion will not only improve productivity but also the reproductive capacity of animals. However, many countries of the world experience a huge gap between demand and availability of green fodder. In this context, emphasis should be placed on developing efficient forage genotypes with increased biomass and quality as per the requirements of animals, duly considering their digestibility. Breeding approaches encompassing required classical approaches, including wide hybridization to exploit natural genetic variability, biotechnological tools such as transgenic technology, marker-assisted selection, genomic selection, and various omics techniques alongside high-throughput phenotyping using multispectral cameras, would help to sustain livestock productivity by meeting out the present and future fodder requirements coupled with enhanced nutrients

Establishing the green algae Chlamydomonas incerta as a platform for recombinant protein production.

ABSTRACTChlamydomonas incerta, a genetically close relative of the model green algaChlamydomonas reinhardtii, shows significant potential as a host for recombinant protein expression. Because of the close genetic relationship betweenC. incertaandC. reinhardtii, this species offers an additional reference point for advancing our understanding of photosynthetic organisms, and also provides a potential new candidate for biotechnological applications. This study investigates C. incerta’s capacity to express three recombinant proteins: the fluorescent protein mCherry, the hemicellulose-degrading enzyme xylanase, and the plastic-degrading enzyme PHL7. We have also examined the capacity to target protein expression to various cellular compartments in this alga, including the cytosol, secretory pathway, cytoplasmic membrane, and cell wall. When compared directly withC. reinhardtii,C. incertaexhibited a distinct but notable capacity for recombinant protein production. Cellular transformation with a vector encoding mCherry revealed thatC. incertaproduced approximately 3.5 times higher fluorescence levels and a 3.7-fold increase in immunoblot intensity compared toC. reinhardtii. For xylanase expression and secretion, bothC. incertaandC. reinhardtiishowed similar secretion capacities and enzymatic activities, with comparable xylan degradation rates, highlighting the industrial applicability of xylanase expression in microalgae. Finally,C. incertashowed comparable PHL7 activity levels toC. reinhardtii, as demonstrated by the in vitro degradation of a polyester polyurethane suspension, Impranil® DLN. Finally, we also explored the potential of cellular fusion for the generation of genetic hybrids betweenC. incertaandC. reinhardtiias a means to enhance phenotypic diversity and augment genetic variation. We were able to generate genetic fusion that could exchange both the recombinant protein genes, as well as associated selectable marker genes into recombinant offspring. These findings emphasizeC. incerta’s potential as a robust platform for recombinant protein production, and as a powerful tool for gaining a better understanding of microalgal biology.GRAPHICAL ABSTRACT

Microglia and Macrophages in Human Pineal Gland

Background. The causal role of the inflammatory process in the central nervous system (CNS) in the pathogenesis of most nervous and mental diseases, as well as in aging, has been established in the last two decades. The most important immune cells in the CNS are microglial cells and macrophages. To date, microglia and macrophages have been studied in various areas of the central nervous system, but have not been studied in the human pineal gland. The purpose of the study was to investigate the morphological features, types and localization of human pineal gland microglial cells using immunohistochemistry. Material and methods. The work was carried out on samples of the human brain pineal gland aged from 16 to 61 years (n=7). An immunohistochemical reaction was performed on sections of the pineal gland using antibodies to Iba-1 and TMEM119, the selective markers of microgliocytes. The frequency of occurrence of immunostained cells was analyzed using statistical methods. Results. It has been established that the majority of phagocytic cells of the structurally normal human pineal gland are not macrophages, but microgliocytes, which are represented by both resting and activated forms. Microglia in the human pineal gland are typically localized in connective tissue trabeculae, both at and away from blood vessels. Microgliocytes are also found in the parenchyma of the pineal gland among the hormone-synthesizing pinealocytes. There was a statistically significant decrease in the number of Iba-1- and especially TMEM119-immunoreactive cells with aging. Conclusion. The present study is the first to examine microglial cells and macrophages in the human pineal gland. The prevalence of microglial cells over macrophages has been established. The morphological features and localization of the identified types of microglial cells indicate their participation primarily in immune defense, and also, probably, in the regulation of pinealocyte functions. In addition, data have been obtained indicating the participation of microglial cells in increasing inflammation in the human pineal gland during aging.

Genome-wide mapping of quantitative trait loci conferring resistance to stripe rust in spring wheat line PI 660072.

Two major QTL for resistance to stripe rust were mapped on chromosome 2BL and 4BL in spring wheat PI 660072, and their KASP markers were developed. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide. Identifying resistance genes is crucial for developing resistant cultivars to control the disease. Spring wheat PI 660072 (Triticum aestivum) has been identified to possess both adult-plant resistance (APR) and all-stage resistance (ASR) to stripe rust. To elucidate the genetic basis of the resistance in PI 660072, a mapping population consisting of 211 F5-F7 recombinant-inbred lines (RILs) was developed from a cross of PI 660072 with susceptible spring wheat Avocet S. The mapping population was phenotyped for stripe rust responses across five field environments from 2020 to 2022 and genotyped using the 15K SNP (single nucleotide polymorphism) array to map stripe rust resistance loci. The mapping population was also tested at the seedling stage with predominant Chinese Pst races CYR31, CYR32, CYR34 and PST-YX1-3-1 in the greenhouse. Stripe rust resistance genes were identified using the quantitative trait locus (QTL) mapping approach. Two QTL were identified with QYrPI660072.swust-2BL mapped on the long arm of chromosome 2B for ASR and QYrPI660072.swust-4BL on the long arm of chromosome 4B for APR. To facilitate marker-assisted selection breeding, Kompetitive allele specific PCR (KASP) markers, KASP-1269 for QYrPI660072.swust-2BL and KASP-3209 for QYrPI660072.swust-4BL, were developed. These markers could be used to introgress the effective resistance QTL into new wheat cultivars.

The development of an in vitro floral culture transformation system for quinoa

AbstractBecause of its high-quality seed protein and ability to thrive in marginal habitats, Chenopodium quinoa has been identified as an important emerging grain crop for global food security. However, the lack of an efficient and robust transformation system has been a barrier for conducting the advanced genetic studies needed to better understand and improve the species for agronomic traits. Here we present a novel transformation system based on Agrobacterium-mediated transformation of in vitro floral culture. Quinoa floral cultures were established from inflorescences that naturally formed on plants grown in vitro. When placed on a cytokinin-containing medium, chopped inflorescences rapidly generated highly meristematic floral cultures, primarily composed of floral buds, flowers at various developmental stages, inflorescence shoots, and leafy structures. Transformation of these cultures with Agrobacterium carrying selectable and visual markers (NPTII and GUS) produced independent, stably transformed meristematic cultures resistant to paromomycin after an extended selection period (about 3 mo with sub-culture occurring every 15 d). Transformation frequency was about 20% and was calculated as the number of independent transformed events per initial number of floral culture explants used for transformation. In vitro flowers and inflorescences from putative transgenic events self-pollinated naturally and produced viable seeds that germinated without dormancy. We also demonstrated that flowering shoots could be successfully grafted onto wild rootstock to increase the number of seeds generated from T0 floral shoots. Molecular and phenotypic analysis of the progeny confirmed that the transgenes were stably integrated and inherited according to expected Mendelian ratios.

Identification of genes governing YMD resistance in soybean cultivar SL 958.

Yellow mosaic disease (YMD) is the most devastating disease of soybean under north Indian conditions. A recombinant inbred line population derived from SL 958 (R) × AGS 456 (S) was used to map the genes imparting YMD resistance. Genotyping by sequencing (GBS) of 148 individuals and the parents was used to identify polymorphic SNPs in the population. These were used to generate linkage maps and subsequently map the QTL. A QTL, MYMIV 1-1.1, was mapped onto chromosome 6. The QTL was mapped at a genetic distance of 114.31 cM, with likelihood ratio of 81.34 (LOD 17.68), explaining 33.80% of the variation for the trait, with an additive effect of 1.22. MYMIV 1-1.1 was flanked by SNPs Gm06_12614920 explaining 33.80% of variation and Gm06_12887789 explaining 31.04% of the variation. The QTL region spanned for a total of 2.798 Mbp. The QTL was mapped in an approximately 4 cM region. Flanking SNPs can be developed into linked markers for effective marker-assisted selection. Out of the genes in the QTL region, Glyma.06G161700 (Suppressor of Gene Silencing/SGS3) is the strongest contender for the resistance gene. This is the first study documenting GBS-based mapping of YMD resistance in soybean. © 2024 Society of Chemical Industry.

Harnessing Genomic Resources and Molecular Breeding Techniques for Advancing Crop Resilience and Productivity

Crop improvement and adaptation are critical to ensure global food security in the face of climate change, population growth, and resource limitations. Exploiting genomic resources and molecular breeding techniques offers immense potential to accelerate the development of resilient, high-yielding crop varieties. This review provides an overview of the current state and future prospects of leveraging genomics and molecular breeding for crop improvement, with a focus on major food crops. We discuss key genomic resources such as reference genomes, transcriptomes, and pan-genomes, as well as powerful molecular breeding approaches like marker-assisted selection, genomic selection, and genome editing. Integrating these tools into crop breeding pipelines can greatly enhance the precision and efficiency of developing improved varieties with desirable traits such as abiotic stress tolerance, disease resistance, and enhanced nutritional quality. We also highlight successful examples of applying these techniques in crops like rice, wheat, maize, and legumes. Furthermore, we explore the role of big data, machine learning, and systems biology in extracting actionable insights from the vast genomic data being generated. Finally, we discuss the challenges and opportunities in translating genomic discoveries into improved crop varieties, emphasizing the need for multidisciplinary collaborations, capacity building, and public-private partnerships. Harnessing the power of genomics and molecular breeding will be pivotal in developing climate-resilient crops to feed the growing global population sustainably.

Research Progress on Genomic Regions and Candidate Genes Related to Milk Composition Traits of Dairy Goats Based on Functional Genomics: A Narrative Review.

Goat milk has gained global attention for its unique nutritional properties and potential health benefits. Advancements in functional genomic technologies have significantly progressed genetic research on milk composition traits in dairy goats. This review summarizes various research methodologies applied in this field. Genome-wide association studies (GWAS) have identified genomic regions associated with major milk components, with the diacylglycerol acyltransferase 1 (DGAT1) gene and casein gene cluster consistently linked to milk composition traits. Transcriptomics has revealed gene expression patterns in mammary tissue across lactation stages, while the role of non-coding RNAs (such as miRNAs and circRNAs) in regulating milk composition has been confirmed. Proteomic and metabolomic studies have not only helped us gain a more comprehensive understanding of goat milk composition characteristics but have also provided crucial support for the functional validation of genes related to milk components. The integration of multi-omics data has emerged as an effective strategy for elucidating complex regulatory networks from a systems biology perspective. Despite progress, challenges remain, including refining reference genomes, collecting large-scale phenotypic data, and conducting functional validations. Future research should focus on improving reference genomes, expanding study populations, investigating functional milk components, exploring epigenetic regulation and non-coding RNAs, and studying microbiome-host genome interactions. These efforts will inform more precise genomic and marker-assisted selection strategies, advancing genetic improvements in milk composition traits in dairy goats.

Genome-wide association study of salt tolerance at the seed germination stage in lettuce.

Developing lettuce varieties with salt tolerance at the seed germination stage is essential since lettuce seeds are planted half an inch deep in soil where salt levels are often highest in the salinity-affected growing regions. Greater knowledge of genetics and genomics of salt tolerance in lettuce will facilitate breeding of improved lettuce varieties with salt tolerance. Accordingly, we conducted a genome-wide association study (GWAS) in lettuce to identify marker-trait association for salt tolerance at the seed germination stage. The study involved 445 diverse lettuce accessions and 56,820 single nucleotide polymorphism (SNP) markers obtained through genotype-by-sequencing technology using lettuce reference genome version v8. GWAS using two single-locus and three multi-locus models for germination rate (GR) under salinity stress, 5 days post seeding (GR5d_S) and a salinity susceptibility index (SSI) based on GR under salinity stress and control conditions, 5 days post seeding (SSI_GR5d) revealed 10 significant SNPs on lettuce chromosomes 2, 4, and 7. The 10 SNPs were associated with five novel QTLs for salt tolerance in lettuce, explaining phenotyping variations of 5.85%, 4.38%, 4.26%, 3.77%, and 1.80%, indicating the quantitative nature of these two salt tolerance-related traits. Using the basic local alignment search tool (BLAST) within 100 Kb upstream and downstream of each of the 10 SNPs, we identified 25 salt tolerance-related putative candidate genes including four genes encoding for major transcription factors. The 10 significant salt tolerance-related SNPs and the 25 candidate genes identified in the current study will be a valuable resource for molecular marker development and marker-assisted selection for breeding lettuce varieties with improved salt tolerance at the seed germination stage.

Association of Ovocalyxin-32 Gene Variants with Egg Quality Traits in Indigenous Chicken Breeds.

This study sought to evaluate the genetic variations of the ovocalyxin-32 gene and its association with egg quality traits in indigenous chicken populations, focusing on exons 1 and 6. Genotype frequencies of SNPs (G/T and A/G) within these exons were assessed for their conformity to the Hardy-Weinberg equilibrium (HWE) across several strains. While most strains exhibited close adherence to HWE expectations, some like light-brown and gray strains indicated substantial discrepancies, particularly for the TT genotype, which points towards the possible effects of genetic drift as well as selection pressures. This study also analyzed the influence of such SNPs on egg quality parameters. A thinner eggshell, reduced shell weight, and decreased breaking strength were associated with the G/T SNP in exon 1, suggesting a likely negative effect on egg quality in T allele carriers. Conversely, the AG genotype displayed better performance in shell thickness, weight and egg weight in the A/G SNP in exon 1, whilst yolk height was best improved by the AA genotype compared to breaking strength. For instance, in exon 6, the A/G SNP enhanced the shell and yolk quality among AG genotypes, while the CC genotype resulted in better eggshell characteristics with enlarged yolks because the C/T SNP was linked. Nonetheless, there were no significant deviations from the HWE despite these associations, which suggested that most breeds had a stable genetic background. Further, considering SNPs' additive and dominant effects in this research, it was indicated that additive effects account for phenotypic expressions given by the G/T SNP located at exon 1. In contrast, significant additive and dominant effects were observed under the A/G SNP situated at the exon. Generally, it therefore could be concluded from this study that specific SNPs within the ovocalyxin-32 gene may act as good markers for marker-assisted selection (MAS) that can improve desired characteristics-such as those of egg quality-in indigenous chicken breeds. This study demonstrated that both additive and dominance effects must be taken into account when performing genetic analyses, thereby emphasizing the complexity of phenotypic variation caused by genetic mechanisms in native chicken races.