Marker-assisted selection: an approach for precision plant breeding in the twenty-first century

Review: Strategies for limiting dietary cadmium in cereals

Cadmium (Cd) is a toxic metal, which in some production areas reaches levels above allowed limits in cereals. Thus, reducing its concentration in cereals is crucial for mitigating health risks and complying with food safety regulations. This review evaluates strategies to reduce Cd accumulation in cereal grains by mitigating soil Cd contamination and its bioavailability to plants. It covers methods for Cd estimation in soil and explores biological, chemical, and genetic approaches to limit Cd uptake by crops. The effectiveness of these strategies depends on genetic factors, soil properties, and crop type. Key approaches include traditional breeding, genome editing, digital and predictive soil mapping, and silicon (Si) and selenium (Se) supplementation. Traditional breeding, enhanced by modern genetic tools, enables the development of high-yielding, low-Cd cultivars but is time-consuming. Genome editing, particularly CRISPR-Cas9, offers precise gene modifications to reduce Cd uptake but faces regulatory constraints. Digital and predictive soil mapping provide high-resolution maps for targeted interventions but require extensive calibration. Silicon supplementation is a promising approach, as it competes with Cd for uptake sites, and limits Cd translocation to edible plant parts. Additionally, Si enhances plant tolerance to abiotic stresses, making it a multifunctional solution. Selenium supplementation can also reduce Cd accumulation while offering health benefits. However, the effectiveness of both Si and Se vary with dosage and crop type. An integrated approach combining these strategies is essential for effective Cd reduction in cereals. Continued research, technological advancements, and supportive policies are crucial for ensuring safe and sustainable cereal production.

Discovery of major QTL and a massive haplotype associated with cannabinoid biosynthesis in drug-type Cannabis

Cannabis (Cannabis sativa L.), once sidelined by decades of prohibition, has now gained recognition as a multifaceted and promising plant in both medical research and commercial applications following its recent legalization. This study leverages a genome-wide association study (GWAS) on 174 drug-type Cannabis accessions from the legal Canadian market, focusing on identifying quantitative trait loci (QTL) and candidate genes associated with eleven cannabinoid traits using 282K common single-nucleotide polymorphisms. This approach aims to transform our understanding of Cannabis genetics. We have pinpointed 33 significant markers that significantly influence cannabinoid production, promising to drive the development of Cannabis varieties with specific cannabinoid profiles. Among the notable findings is a massive haplotype of ∼60 Mb on chromosome 7 in Type I (i.e., tetrahydrocannabinol [THC]-dominant) accessions, highlighting a major genetic influence on cannabinoid profiles. These insights offer valuable guidance for Cannabis breeding programs, enabling the use of precise genetic markers to select and refine promising Cannabis varieties. This approach promises to speed up the breeding process, reduce costs significantly compared to traditional methods, and ensure that the resulting Cannabis varieties are optimized for specific medical and recreational needs. This study marks a significant stride toward fully integrating Cannabis into modern agricultural practices and genetic research, paving the way for future innovations.

Molecular and physiological basis of heterosis in hybrid rice performance

Heterosis is often exploited to produce high-yielding crops with better performance than their inbred counterparts. Commercial rice breeding has made use of this phenomenon as well, primarily through the use of cytoplasmic male sterility (CMS) and environment-sensitive genic male sterility (EGMS). However, a limited understanding of the molecular and physiological basis of heterosis prevents researchers from harnessing the full potential of hybrid breeding. This review examines the various explanations and mechanisms of heterosis in rice, including evidence fitting the established theories of heterosis and the use of modern omics approaches to characterizing heterosis and heterosis-related traits. Overdominance was the most frequently cited mechanism behind yield-related traits and various molecular and physiological markers associated with heterosis were identified.

Genome-wide association study of biological nitrogen fixation traits in mini-core cowpea germplasm

Biological Nitrogen Fixation (BNF) efficiency in legume crops such as cowpea (Vigna unguiculata L. Walp) has been less documented yet is key in improving yield performance and restoring soil fertility in sub-Saharan Africa. Nevertheless, little progress has been made in understanding the gene control of the BNF traits in cowpea to sustain the development of smart agriculture in this part of the world. This study aimed to identify cowpea genotypes and map genomic regions for BNF traits for developing high nitrogen-fixing cultivars. A total of 241 mini-core cowpea genotypes were inoculated with Bradyrhizobium spp in a screen house for two cycles. Phenotypic data collected on the number of nodules (NN) per plant, nodule efficiency (NE) in percentage, and nodule dry weight (NDW) per plant revealed significant differences implying high genetic variability in the mini-core population for nodulation capacity. Fifteen significant association signals were identified for BNF traits on nine chromosomes except Vu02 and Vu09 when two multi-locus models were considered. Markers accounting for over 15% variation for BNF traits included 2_31410 (2.32Mb) on Vu05 and 2_45545 (24.93Mb) on Vu06 for NN, 2_06530 (56.64Mb) and 2_27028 (34.31Mb) on Vu01 for NE and 2_50837 (10.07Mb) on Vu01 and 2_11699 (34.41Mb) on Vu07 for NDW, respectively. Additionally, positional candidate genes near the peak markers that encode genes associated with BNF in cowpea included Vigun06g121800, Vigun01g160600, Vigun10g014400, Vigun07g221500, Vigun07g221300 and Vigun11g096700. The genotype TVu-1477 was identified to have favorable alleles for both three studied traits. The significant markers identified in this study can be converted to Kompetitive Allele Specific-PCR (KASP) markers to accelerate the development of high-yielding cowpea varieties that also enhance soil fertility.

Genome-wide identification and characterization of NAC transcription factor-derived microsatellites in wheat (Triticum aestivum L.)

Bread wheat (Triticum aestivum L.) is one of the widely consumed staple foods, providing 20% of the total protein and calories in human nutrition. Seeing its importance in the global food supply, the enrichment of functional genomic resources is vital for meeting future demands and ensuring sustainable production. In addition to the presence of functional domains, the presence of microsatellites within transcription factors makes them valuable candidates for enriching functional marker resources. The NAC transcription factor family regulates a variety of physiological processes in cereal crops. Hence, the present study aims to develop and characterize Triticum aestivum NAC MicroSatellites (TaNACMS) to enrich functional marker resources for genetic diversity analysis, marker-assisted selection, and evolutionary studies. In total, 520 SSRs were identified from 451 TaNAC sequences, and a set of 66 TaNACMS was used for cross-transferability in wild/related wheat species. The cross-transferability rate of 90.22% revealed high locus conservation. Further, 16 TaNACMS were utilized for the characterization of genetic diversity in Indian wheat varieties. These TaNACMS produced 40 alleles (2.5 alleles per locus) with an average observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) of 0.392, 0.417, and 0.380, respectively. The genetic analysis of wheat genotypes, using principal coordinates analysis (PCoA), neighbor-joining (NJ) clustering, and Bayesian-based STRUCTURE, has revealed three distinct genetic clusters. Two of these clusters consist of Indian wheat varieties, while the third cluster comprises wild/related wheat species. In conclusion, the high rate of transferability of TaNACMS can be effectively utilized for gene flow both within and between species, highlighting evolutionary connections between cultivated wheat and related species. Additionally, these SSRs will aid the marker repository and benefit the wheat improvement programs through marker-assisted selection (MAS).

Polymorphism analysis of GDF9 and BMP15 genes and their association with litter size in crossbreed goats in Malaysia

The goat industry plays a crucial role in Malaysia's economy, with breeds such as Katjang and Boer being integral to the chevon supply. However, achieving self-sufficiency in goat meat production is still challenging due to the insufficient local carcass supply. To address this issue, a crossbreeding program has been initiated to improve reproductive performance in local breeds. In mammals, there are BMP15 and GDF9 genes, which are the components of the TGF-β superfamily that are key regulators of ovulation and litter size. This study aimed to improve reproductive performance in crossbred goats from Katjang and Boer populations in Sabah, Malaysia, by analyzing genetic variations in the BMP15 and GDF9 genes. A total of sixty female cross-Katjang goats, with recorded litter size and parities, were sampled. Five milliliters of blood was taken from the jugular vein using K2-EDTA tubes. Genetic analysis was performed using conventional PCR at the Biotechnology Research Institute, University Malaysia Sabah, followed by sequencing at Apical Scientific, Malaysia. Four novel polymorphic loci were identified within the GDF9 gene: G320C, A352G, G366T, and G375T. All of these loci resulted in missense mutations, causing a change in amino acid sequences. Notably, the A352G and G375T loci showed significant associations with litter size, with the AG genotype at position 352 and the GG genotype at position 375 emerging as potential markers for selective breeding. However, the polymorphic information content (PIC)values indicated low genetic diversity (< 0.25) at these loci. Interestingly, no polymorphisms were detected in the BMP15 gene, suggesting a monomorphic state (wild-type genotype) in the Cross-Katjang goat population. This finding indicates that BMP15 may not play a significant role in litter size variation in this crossbreed, shifting the focus towards GDF9 as a more relevant genetic marker for enhancing reproductive traits. This study provides important insights into the genetic factors influencing reproductive traits in crossbred goats, with potential applications in marker-assisted selection to improve reproductive and productivity performance.

Development of genome-wide SSR markers through in silico mining of guava (Psidium guajava L.) genome for genetic diversity analysis and transferability studies across species and genera

Guava (Psidium guajava L.) is one of the economically major fruit crops, abundant in nutrients and found growing in tropical-subtropical regions around the world. Ensuring sufficient genomic resources is crucial for crop species to enhance breeding efficiency and facilitate molecular breeding. However, genomic resources, especially microsatellite or simple sequence repeat (SSR) markers, are limited in guava. Therefore, novel genome-wide SSR markers were developed by utilizing chromosome assembly (GCA_016432845.1) of the "New Age" cultivar through GMATA, a comprehensive software. The software evaluated about 397.8 million base pairs (Mbp) of the guava genome sequence, where 87,372 SSR loci were utilized to design primers, ultimately creating 75,084 new SSR markers. After in silico analysis, a total of 75 g-SSR markers were chosen to screen 35 guava genotypes, encompassing wild Psidium species and five jamun genotypes. Of the 72 amplified novel g-SSR markers (FHTGSSRs), 53 showed polymorphism, suggesting significant genetic variation among the guava genotypes, including wild species. The 53 polymorphic g-SSR markers had an average of 3.04 alleles per locus for 35 selected guava genotypes. Besides, in this study, the mean values recorded for major allele frequency, gene diversity, observed heterozygosity, and polymorphism information content were 0.73, 0.38, 0.13, and 0.33, respectively. Among the wild Psidium species studied, the transferability of these novel g-SSR loci across different species was found to be 45.83% to 90.28%. Furthermore, 17 novel g-SSR markers were successfully amplified in all the selected Syzygium genotypes, of which only four markers could differentiate between two Syzygium species. A neighbour-joining (N-J) tree was constructed using 53 polymorphic g-SSR markers and classified 35 guava genotypes into four clades and one outlier, emphasizing the genetic uniqueness of wild Psidium species compared to cultivated genotypes. Model-based structure analysis divided the guava genotypes into two distinct genetic groups, a classification that was strongly supported by Principal Coordinate Analysis (PCoA). In addition, the AMOVA and PCoA analyses also indicated substantial genetic diversity among the selected guava genotypes, including wild Psidium species. Hence, the developed novel genome-wide genomic SSRs could enhance the availability of genomic resources and assist in the molecular breeding of guava.

Integrated Phenotypic and Molecular Evaluation of Powdery Mildew Resistance in Egyptian Barley: Identification of Resistance-Associated Markers

Powdery mildew, caused by Blumeria graminis f. sp. hordei (Bgh), severely impacts global barley Hordeum vulgare L. (Hv) production. This investigation evaluated Egyptian barley genotypes to identify novel resistance sources and molecular markers for breeding programs. Phenotypic assessments at the seedling (growth stage, GS 32) and adult plant (GS 55-59) stages under controlled and field conditions, combined with SSR marker analysis, revealed distinct resistance profiles. Genotypes Giza 123, Giza 125, and G8 exhibited strong resistance, with Giza 123 displaying Mlo-mediated immunity. Susceptible genotypes (Giza 126, G1, G2, and G4) showed rapid disease progression (IT4; up to 80% severity). Intermediate genotypes (G5, G6, and G9) suggested quantitative resistance. Simple sequence repeat (SSR) analysis linked the EBmac0603 primer 160 bp allele to resistance and the 149 bp allele to susceptibility. The EBmac0603 primer 185 bp allele correlated with partial resistance, highlighting its utility in marker-assisted selection (MAS). The integration of phenotypic and molecular data identified Giza 123 and G8 as prime candidates for breeding, emphasizing the need for strategies like gene pyramiding or quantitative resistance incorporation in susceptible lines. This study underscores the value of Egypt's barley diversity in advancing durable disease resistance through targeted breeding and molecular tools.

In Vitro Culture of Aegle marmelos Against Media Composition Stress: Molecular Identification, Media, and Enzyme Optimization for Higher Growth Yields

Aegle marmelos, known for its spiky appearance, is a versatile tree found worldwide. In the Indian medical tradition, this therapeutic tree is utilized to treat various ailments. It is commonly propagated through seeds, although they have a limited lifespan and are susceptible to insect damage. Due to the variability of seed offspring, standardized varieties are not readily available. Molecular identification was performed for the plant species to be as a fingerprint identification based on genomic basic. Hence, this study manipulated the in vitro multiplication for enhancing Aegle marmelos traits through variation in media type and composition. In phase one of the experiment, successful micropropagation has been easily achieved with shoot tip culture on two growth in vitro media: Murashige and Skoog (MS) medium and woody plant medium (WPM) with different concentrations (one-fourth, one-half, three-fourths, and full power media) with two sucrose concentration 20 and 30 g/L. The growth parameters measured indicated a heightened response to both MS and WPM media, each with its distinct composition. The genetic variation via intersimple sequence repeat (ISSR) molecular marker in the first phase was 35.5%. In phase two, the hormonal treatment was applied for the best media choice from Phase 1. During the second phase of multiplication and rooting stages with phytohormones, the optimal treatments were chosen to maximize yields. In the multiplication stage, the most favorable conditions, as determined by morphological parameters, were achieved with full MS medium supplemented with 30 g sucrose, 0.1 mg/L Kin, and 0.75 mg/L BAP. In contrast, for the rooting stage, the optimal treatment consisted of one-fourth MS medium supplemented with 15 g sucrose, 0.5 mg/L Kin, 0.1 g/L activated charcoal, and 15 mg/L IBA. Physiological parameters exhibited variability, with each metabolite displaying distinct optimal conditions. Catalase plays a crucial role in decomposing hydrogen peroxide to protect cells, tissues, and organs. This research effectively enhanced the in vitro micropropagation of Aegle marmelos by determining the most efficacious medium formulations and hormonal treatments for shoot multiplication and roots, while also illustrating the influence of WPM on catalase enzyme activity enhancement.

Wheat Drought Tolerance: Unveiling a Synergistic Future with Conventional and Molecular Breeding Strategies

The development of wheat cultivars capable of withstanding drought conditions is necessary for global food security. Conventional breeding, emphasizing the exploitation of inherent genetic diversity by selecting wheat genotypes exhibiting superior drought-related traits, including root architecture, water use efficiency, and stress-responsive genes, has been used by breeders. Simultaneously, molecular techniques such as marker-assisted selection and gene editing are deployed to accelerate the identification and integration of specific drought-responsive genes into elite wheat lines. Cutting-edge genomic tools play a pivotal role in decoding the genetic basis of wheat drought tolerance, enabling the precise identification of key genomic regions and facilitating breeding decisions. Gene-editing technologies, deployed judiciously, ensure the targeted enhancement of desirable traits without compromising the overall genomic integrity of wheat varieties. This review introduces a strategic amalgamation of conventional and molecular breeding approaches for developing drought-tolerant wheat. The review aims to accelerate progress by seamlessly merging traditional breeding methods with advanced molecular tools, and it also underscores the potential of a synergistic future for enhancing wheat drought resilience, providing a roadmap for the development of resilient wheat varieties essential for sustainable agriculture in the 21st century.

Molecular, biophysical, and biochemical studies on irradiated Zea mays seeds using various sources of gamma rays for dosimetrical applications

Gamma rays are a powerful tool for enhancing crop quality and production. They can cause mutations that improve plant traits and are commonly used in agriculture. The present study aimed to examine the effects of gamma irradiation on maize hybrids' triple white seeds (Giza 321) using different doses (10, 20, and 50 Gy) from different radiation sources 60Co or 137Cs). The maize treated with gamma rays from the Co-60 source at 10 Gy exhibited the lowest shoot length percentage of 37.5%, compared to control groups, while root lengths were unaffected at 10 and 50 Gy Cs-137 doses. In addition, the study revealed that gamma irradiation stimulated the excess production of proline, protein, and antioxidant enzymes, which revealed the defense strategy of the plant that tolerates stress. The study also revealed that gamma rays caused a significant reduction in chlorophyll content for all doses, while carotenoid content increased. DNA tail length indicated that minimal damage occurred at 50 Gy of 60Co and 137Cs, respectively. Moreover, the analysis of tail DNA% and tail moment showed that the lowest damage was determined for 20 Gy of 60Co and 137Cs, respectively. SDS-PAGE analysis showed that the 20 Gy Co treatments had the largest number of bands (15), while the 20 Gy Cs dose had the minimum number of bands (10). Ultimately, the proline content and peroxidase enzymes respond exponentially with the dose, making them potential radiation biomarkers for dosimetric purposes. However, further dosimetric features of these two parameters are necessary to be defined in future work. The present results showed that the treatment of plants with gamma rays enhanced the defense system of the maize at a specific dose, thereby, a large-scale study is recommended for using this radiation to enhance the defense and/or the tolerance of a wide range of crops as well as evaluate its safety, applicability, and reproducibility at field scale.

Latin America: a hub for agrobiotechnological innovations

BACKGROUND

Modern biotechnology is one of the last century's major advances in human science. Particularly in the agronomical field, the landscape of crop improvement technologies has witnessed a great expansion, driven by the integration of molecular and genetic engineering methodologies into the breeding toolbox. Latin America (LATAM) serves as a pioneering region in incorporating such techniques with several countries swiftly embracing these technologies.

SCOPE

This review aims to give a comprehensive overview of the elements that influenced agrobiotech acceptance in LATAM countries and how such cases could provide support for upcoming technologies to be considered worldwide.

CONCLUSIONS

Nearly 50 years of biotech breakthroughs have provided humankind with an impressive portfolio of tools already integrated into several life-science areas. The agronomical field has greatly progressed thanks to technologies derived from genetically modified organisms and great promises are being made to also incorporate genome-editing products. LATAM provides a prime example of how early introduction of novelties in the crop production chain can result in improved yields, paving the way for future developments to be easily integrated into the technological ecosystem of a region. The example set by LATAM can also be useful for the present gene-editing regulatory scenario. With several countries presently on the path to approving these methods in their current crop systems, basing their next steps on the example of LATAM could represent a safe and practical pathway towards a new agronomical revolution.

Fine mapping of the unique Ur-11 gene conferring broad resistance to the rust pathogen of common bean

KEY MESSAGE

Fine mapping positioned the Ur-11 rust resistance gene in common bean to a narrow 9 kb genomic region and enabled the development of a KASP marker tightly linked to Ur-11 for use in gene pyramiding to achieve durable rust resistance. The extensive virulence diversity of the fungal pathogen Uromyces appendiculatus threatens common bean (Phaseolus vulgaris) production. The Ur-11 gene present in the Guatemalan common bean accession PI 181996 conferred resistance to 89 of 90 virulent races of U. appendiculatus. We describe here the fine mapping of Ur-11 and the development and validation of a DNA marker tightly linked to Ur-11. An F2 population from the cross between the susceptible Pinto 114 with the resistant PI 181996 was inoculated with four races of U. appendiculatus. This study established that the rust resistance in PI 181996 was conferred by Ur-11. We then fine mapped Ur-11 using F2 plants and F2:3 families, high-throughput SNP genotyping, SSRs and KASPs marker development, whole-genome sequencing, and local haplotype analysis. Ur-11 was positioned in a narrow 9.01 Kb genomic region on chromosome Pv11 flanked by KASP markers SS322 and SS375. This genomic region included a candidate gene encoding a nucleotide-binding site and leucine rich-repeat domain with pathogen resistance functions. The validation of the SS322 KASP marker was performed on a panel of 206 diverse common bean cultivars that were inoculated with four races of U. appendiculatus. The SS322 marker was 97.5% accurate in identifying the presence of Ur-11 in common bean plants. These results suggest that S322 will be a highly effective molecular marker for the development of common bean cultivars with Ur-11 alone and combining Ur-11 with other rust resistance genes that would confer broad and durable resistance to the hypervirulent bean rust pathogen.

Genomic insights into pigeon breeding: GWAS for economic traits and the development of a high-throughput liquid phase array chip

Due to the monogamous mating system and late maturity of pigeons, their breeding cycle is longer compared to that of other poultry species, which has hindered the optimization of growth traits and meat quality. While traditional breeding methods are commonly used, they lack precision and are time-consuming. This study integrates phenotypic data from Tarim pigeons and White King pigeons with genomic information, using genome-wide association analysis (GWAS) to identify genetic markers associated with key economic traits, thereby accelerating the breeding process. The results reveal significant correlations between body type characteristics (e.g., live weight and chest depth) and carcass traits, supporting their use as indirect selection criteria. GWAS identified several candidate genes, including PPARGC1A and ADGRA3, linked to muscle development and metabolic regulation. To enhance breeding efficiency, this study developed a Liquid Phase Chip (LPC), designed to use high-throughput technology for identifying genetic markers related to carcass traits. Although the LPC is not yet commercially available, the 50 K pigeon LPC from this study could provide crucial theoretical support for its future application. Ultimately, the LPC will serve as an important tool for precision and efficiency in pigeon breeding, driving the development and optimization of the pigeon industry.

Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large-scale soybean dataset

The surge in high-throughput technologies has empowered the acquisition of vast genomic datasets, prompting the search for genetic markers and biomarkers relevant to complex traits. However, grappling with the inherent complexities of high dimensionality and sparsity within these datasets poses formidable hurdles. The immense number of features and their potential redundancy demand efficient strategies for extracting pertinent information and identifying significant markers. Feature selection is important in large genomic data as it helps in enhancing interpretability and computational efficiency. This study focuses on addressing these challenges through a comprehensive investigation into genomic feature selection methodologies, employing a rich soybean (Glycine max L. Merr.) dataset comprising 966 lines with over 5.5 million single nucleotide polymorphisms. Emphasizing the "small n large p" dilemma prevalent in contemporary genomic studies, we compared the efficacy of traditional genome-wide association studies (GWAS) with two prominent machine learning tools, random forest and extreme gradient boosting, in pinpointing predictive features. Utilizing the expansive soybean dataset, we assessed the performance of these methodologies in selecting features that optimize predictive modeling for various phenotypes. By constructing predictive models based on the selected features, we ascertain the comparative prediction accuracies, thereby illuminating the strengths and limitations of these feature selection methodologies in the realm of genomic data analysis.

Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program

Genomic selection can enhance the rate of genetic gain of cane and sucrose yield in sugarcane (Saccharum L.), an important industrial crop worldwide. We assessed the predictive ability (PA) for six traits, such as theoretical recoverable sugar (TRS), number of stalks (NS), stalk weight (SW), cane yield (CY), sugar yield (SY), and fiber content (Fiber) using 20,451 single nucleotide polymorphisms (SNPs) with 22 statistical models based on the genomic estimated breeding values of 567 genotypes within and across five stages of the Louisiana sugarcane breeding program. TRS and SW with high heritability showed higher PA compared to other traits, while NS had the lowest. Machine learning (ML) methods, such as random forest and support vector machine (SVM), outperformed others in predicting traits with low heritability. ML methods predicted TRS and SY with the highest accuracy in cross-stage predictions, while Bayesian models predicted NS and CY with the highest accuracy. Extended genomic best linear unbiased prediction models accounting for dominance and epistasis effects showed a slight improvement in PA for a few traits. When both NS and TRS, which can be available as early as stage 2, were considered in a multi-trait selection model, the PA for SY in stage 5 could increase up to 0.66 compared to 0.30 with a single-trait model. Marker density assessment suggested 9091 SNPs were sufficient for optimal PA of all traits. The study demonstrated the potential of using historical data to devise genomic prediction strategies for clonal selection early in sugarcane breeding programs.

Micronutrient Biofortification in Wheat: QTLs, Candidate Genes and Molecular Mechanism

Micronutrient deficiency (hidden hunger) is one of the serious health problems globally, often due to diets dominated by staple foods. Genetic biofortification of a staple like wheat has surfaced as a promising, cost-efficient, and sustainable strategy. Significant genetic diversity exists in wheat and its wild relatives, but the nutritional profile in commercial wheat varieties has inadvertently declined over time, striving for better yield and disease resistance. Substantial efforts have been made to biofortify wheat using conventional and molecular breeding. QTL and genome-wide association studies were conducted, and some of the identified QTLs/marker-trait association (MTAs) for grain micronutrients like Fe have been exploited by MAS. The genetic mechanisms of micronutrient uptake, transport, and storage have also been investigated. Although wheat biofortified varieties are now commercially cultivated in selected regions worldwide, further improvements are needed. This review provides an overview of wheat biofortification, covering breeding efforts, nutritional evaluation methods, nutrient assimilation and bioavailability, and microbial involvement in wheat grain enrichment. Emerging technologies such as non-destructive hyperspectral imaging (HSI)/red, green, and blue (RGB) phenotyping; multi-omics integration; CRISPR-Cas9 alongside genomic selection; and microbial genetics hold promise for advancing biofortification.

Development of Simple Sequence Repeat (SSR) Markers from a Genome Survey of a Cymbidium kanran Makino Population in Jeju Island, Republic of Korea

The Cymbidium kanran Makino, an economically significant ornamental plant, is observed in small numbers in its natural habitat on Jeju Island in South Korea. C. kanran of Jeju is afforded protection due to a decline in its population resulting from environmental changes and illegal poaching. We developed simple sequence repeat (SSR) markers to analyze the differences to other C. kanran through molecular genetic studies. Based on the results of the Random amplified polymorphic DNA (RAPD) analysis and whole genome sequencing, 86 initial SSR marker candidates were selected in silico. After excluding those that were structurally unsuitable, 40 were reselected through polymorphism testing. Finally, 25 markers were selected based on the diversity test and their applicability to real samples. The newly developed markers will prove invaluable in substantiating the distinctiveness of C. kanran from Jeju, as well as in the processes of conservation, restoration, and the identification of cultivars.

A functional SNP of the core promoter region within goat CDC25A gene affects litter size

The Cell division cycle 25A (CDC25A) gene has been considered as a candidate gene associated with reproductive traits for goat breeding. In this study, five truncated fragments divided at position-2285 nt to +198 nt were amplified and cloned into the luciferase reporter vectors to identify the core promoter. The luciferase reporter assay showed that the core promoter of CDC25A was located at position-663 nt to-237 nt. Afterwards, a single nucleotide polymorphism (NC_030829.1:g.51731829A > C) at the core promoter was detected using sequencing and KASP in a population of 1,016 goats and luciferase reporter vectors carrying the A allele or C allele were transfected into cells, respectively. The results displayed that the higher relative luciferase activity was observed in plasmids carrying the A allele rather than the C allele. The litter size of individuals with the AA genotype was significantly better than those with other genotypes, which corresponded to increased transcriptional activity in plasmids carrying the A allele. In short, our study provides a potential molecular genetic marker for improving reproductive efficiency in goat breeding.

Improvement of crop production in controlled environment agriculture through breeding

Controlled environment agriculture (CEA) represents one of the fastest-growing sectors of horticulture. Production in controlled environments ranges from highly controlled indoor environments with 100% artificial lighting (vertical farms or plant factories) to high-tech greenhouses with or without supplemental lighting, to simpler greenhouses and high tunnels. Although food production occurs in the soil inside high tunnels, most CEA operations use various hydroponic systems to meet crop irrigation and fertility needs. The expansion of CEA offers promise as a tool for increasing food production in and near urban systems as these systems do not rely on arable agricultural land. In addition, CEA offers resilience to climate instability by growing inside protective structures. Products harvested from CEA systems tend to be of high quality, both internal and external, and are sought after by consumers. Currently, CEA producers rely on cultivars bred for production in open-field agriculture. Because of high energy and other production costs in CEA, only a limited number of food crops have proven themselves to be profitable to produce. One factor contributing to this situation may be a lack of optimized cultivars. Indoor growing operations offer opportunities for breeding cultivars that are ideal for these systems. To facilitate breeding these specialized cultivars, a wide range of tools are available for plant breeders to help speed this process and increase its efficiency. This review aims to cover breeding opportunities and needs for a wide range of horticultural crops either already being produced in CEA systems or with potential for CEA production. It also reviews many of the tools available to breeders including genomics-informed breeding, marker-assisted selection, precision breeding, high-throughput phenotyping, and potential sources of germplasm suitable for CEA breeding. The availability of published genomes and trait-linked molecular markers should enable rapid progress in the breeding of CEA-specific food crops that will help drive the growth of this industry.

Development and validation of PCR marker array for molecular selection towards spring, vernalization-independent and winter, vernalization-responsive ecotypes of white lupin (Lupinus albus L.)

White lupin (Lupinus albus L.) is an ancient grain legume that is still undergoing improvement of domestication traits, including vernalization-responsiveness, providing frost tolerance and preventing winter flowering in autumn-sowing agriculture, and vernalization-independence, conferring drought escape by rapid flowering in spring-sowing. A recent genome-wide association study highlighted several loci significantly associated with the most contrasting phenotypes, including deletions in the promoter of the FLOWERING LOCUS T homolog, LalbFTc1, and some DArT-seq/silicoDArT loci. The present study aimed to develop and validate a versatile PCR marker array enabling molecular selection of spring- and winter-type white lupin ecotypes. Candidate DArT-seq and silicoDArT loci were transformed into cleaved amplified polymorphic sequence (CAPS) or derived CAPS markers. Developed markers, together with those previously published for LalbFTc1 INDELs and quantitative trait loci from linkage maps, were implemented for screening of white lupin germplasm panel subjected to 2-year phenotyping of phenology traits. Three DArT-seq, two silicoDArT and seven LalbFTc1 INDEL markers were positively validated, constituting a convenient PCR-based marker assay for rapid and accurate reselection of white lupin germplasm towards early flowering and thermoneutrality or late flowering and vernalization-responsiveness, as well as for tracking high genetic and phenotypic diversity within white lupin landraces, revealed in the present study.

Genetic and metabolic factors influencing skin yellowness in yellow-feathered broilers

The degree of yellowness of the skin is an important factor affecting the market popularity and sales price of yellow-feathered broilers. Despite its commercial importance, the specific pigments and genetic mechanisms involved remain unclear. This study identified lutein as the primary carotenoid in the skin and established serum lutein concentration as a molecular marker for predicting skin yellowness in carcasses. Through RNA sequencing of broilers with varying yellowness, we identified key genes like CYP26A1, CYP1B1, CYP2C18, CYP2W1, HSD17B2, AOX1, KMO, PLIN1, and RET, which may regulate carotenoid absorption and deposition. Additionally, a single nucleotide polymorphism in the CYP1A1 gene was significantly associated with skin yellowness in Ma-Huang chickens. Overall, this study examined the primary pigment types that influence the skin yellowness of yellow-feathered broilers, emphasizing that lutein can serve as a molecular marker for skin yellowness and providing insights into the regulatory factors that regulate skin yellowness. These findings provide essential theoretical support for the breeding of skin color traits in yellow-feathered broilers.

Revolutionizing cotton cultivation: A comprehensive review of genome editing technologies and their impact on breeding and production

Cotton (Gossypium hirsutum L.), a vital global cash crop, significantly impacts both the agricultural and industrial sectors, providing essential fiber for textiles and valuable byproducts such as cottonseed oil and animal feed. The cultivation of cotton supports millions of livelihoods worldwide, particularly in developing regions, making it a cornerstone of rural economies. Despite its importance, cotton production faces numerous challenges, including biotic stresses from pests and diseases, and abiotic stresses like drought, salinity, and extreme temperatures. These challenges necessitate innovative solutions to ensure sustainable production. Genome editing technologies, particularly CRISPR/Cas9, have revolutionized cotton breeding by enabling precise genetic modifications. These advancements hold promise for developing cotton varieties with enhanced resistance to pests, diseases, and environmental stresses. Early genome editing tools like ZFNs and TALENs paved the way for more precise modifications but were limited by complexity and cost. The introduction of CRISPR/Cas-based technology with its simplicity and efficiency, has dramatically transformed the field, making it the preferred tool for genome editing in crops. Improved version of the technology like CRISPR/Cas12a, CRISPR/Cas13, base and prime editing, developed from CRISPR/Cas systems, provide additional tools with distinct mechanisms, further expanding their potential applications in crop improvement. This comprehensive review explores the impact of genome editing on cotton breeding and production. It discusses the technical challenges, including off-target effects and delivery methods for genome editing components, and highlights ongoing research efforts to overcome these hurdles. The review underscores the potential of genome editing technologies to revolutionize cotton cultivation, enhancing yield, quality, and resilience, ultimately contributing to a sustainable future for the cotton industry.

Marker assisted pyramiding of major resistance genes of tomato leaf curl and late blight diseases for stabilising tomato production

Globally, tomato leaf curl disease (ToLCD) caused by begomoviruses and late blight disease caused by Phytophthora infestans are important limiting factors for tomato production. Development of disease resistant cultivars is an important objective of tomato breeding programmes. Resistance genes such as Ty2 and Ty3 against ToLCD, and Ph2 and Ph3 resistant genes against late blight were utilized in this study to develop tomato lines with ToLCD and late blight resistance. Two F2 populations derived from the crosses viz., VRT4-20-18 × (LA3152 × LA4286) and LA3152 × VRT-78-2 were used as base material. Marker assisted selection was employed throughout the generation advancement programme to select plants with the targeted genes. Gene based molecular markers AW910upF2R3, Ty3-SCAR and Ph3SCAR were used to select genotypes containing the Ty2, Ty3 and Ph3 genes, respectively. The dTG-63/HinfI CAPS marker linked to Ph2 gene was used to select the Ph2 gene containing genotypes. Advanced lines with all the four genes and/ or in different combinations with desirable agronomic traits were developed. Further, these selected genotypes were also tested for resistance to both the diseases under natural epiphytotic and artificially inoculated conditions. Lines with the Ty-3 alone or in combination with the Ty-2 performed well against ToLCD with DSI < 1, whereas lines with both the Ph2 and Ph3 genes performed well against late blight with DSI < 1. Developed advanced lines in the study can play a greater role in stabilizing tomato production by minimizing the losses caused by these diseases.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-025-01548-8.

Genome editing in Sub-Saharan Africa: a game-changing strategy for climate change mitigation and sustainable agriculture

Sub-Saharan Africa's agricultural sector faces a multifaceted challenge due to climate change consisting of high temperatures, changing precipitation trends, alongside intensified pest and disease outbreaks. Conventional plant breeding methods have historically contributed to yield gains in Africa, and the intensifying demand for food security outpaces these improvements due to a confluence of factors, including rising urbanization, improved living standards, and population growth. To address escalating food demands amidst urbanization, rising living standards, and population growth, a paradigm shift toward more sustainable and innovative crop improvement strategies is imperative. Genome editing technologies offer a promising avenue for achieving sustained yield increases while bolstering resilience against escalating biotic and abiotic stresses associated with climate change. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein (CRISPR/Cas) is unique due to its ubiquity, efficacy, alongside precision, making it a pivotal tool for Sub-Saharan African crop improvement. This review highlights the challenges and explores the prospect of gene editing to secure the region's future foods.

The Tetratricopeptide repeat protein TaTPR-B1 regulates spike compactness in bread wheat

Spike compactness (SC) is strongly associated with wheat (Triticum aestivum L.) grain yield. In this study, we conducted a quantitative trait locus (QTL) analysis using a doubled haploid (DH) population derived from a cross between two common wheat varieties with contrasting spike morphology, revealing 16 stable QTLs associated with SC. The effect of a major QTL, QSc.cau-6B.1, was validated in 231 F7 recombinant inbred lines (RILs) derived from the same cross as the DH population. Using two residual heterozygous lines (RHLs), we delimited QSc.cau-6B.1 to an approximately 0.5-Mbp physical interval containing four high-confidence genes. The tetratricopeptide repeat-TraesCS6B03G1214400 (TaTPR-B1) was the priority candidate gene according to sequence and expression variations between near-isogenic lines. Accordingly, TaTPR-B1 knockout in the common wheat variety 'CB037' significantly increased SC compared to the wild type (WT). Conversely, TaTPR-B1 overexpression in the common wheat variety 'Fielder' significantly decreased SC compared to the WT. Moreover, we developed a PCR-based marker targeting the 32-bp insertion/deletion (InDel) between the two TaTPR-B1 alleles, which could be practical and valuable in modern wheat breeding programs for diagnostic purposes. Collectively, these findings provide insight into the genetic basis of SC in common wheat and present a valuable target with a breeder-friendly diagnostic marker for gene pyramid breeding.

Overview of research on virus-resistant breeding of melon

The development of virus-resistant melon varieties not only poses challenges in balancing melon quality and resistance but also contributes to sustainable agricultural development. This research focuses on the exploration and application of various breeding techniques to enhance the virus resistance of melon varieties. Molecular markers associated with virus resistance genes have been identified and utilized in marker-assisted selection, enabling more efficient and targeted breeding. Genetic engineering approaches have also shown promise, introducing specific resistance genes into melon genomes. In addition, traditional breeding methods, such as hybridization and selection, continue to play an important role in creating virus-resistant melon lines. The combination of these approaches holds great potential for developing melon varieties with improved virus resistance, thereby increasing yield and quality, and reducing the economic losses caused by viral infections in melon production.

Evaluation of stripe rust resistance and analysis of resistance genes in wheat genotypes from Pakistan and Southwest China

Introduction

Stripe rust, caused by Puccinia striiformis f. sp. tritici, poses a significant threat to wheat quality and production worldwide. The rapid evolution of Pst races caused several resistance genes to be ineffective.

Methods

This study evaluated stripe rust resistance genes in 349 Pakistan and Southwest China genotypes. We utilized previously published functional and linked molecular markers to detect 13 major stripe rust resistance genes: Yr5, Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, Yr29, Yr30, Yr36, Yr48, Yr65, and YrSp. Field evaluations assessed IT and resistance levels, while the impact of gene combinations on resistance was also analyzed.

Results

Field evaluations showed that over 60% of Chuanyu wheat, 50% of recent Pakistani cultivars, and 20% of historic Pakistani lines were resistant to current stripe rust races. In Chuanyu wheat, the dominant genes were Yr17, YrSp, and Yr48; however, Yr17, Yr26, and YrSp were overused, while Yr36 was absent, and Yr18 was rare. In historic lines, Yr5, Yr17, Yr18, and Yr26 were prevalent, with Yr15, Yr26, and YrSp demonstrating effective resistance against current stripe rust races. Furthermore, the study identified specific combinations of Yr genes (Yr26+Yr48, Yr29+Yr5, Yr26+Yr30, and Yr30+Yr17) that enhanced resistance to Pst.

Discussion

This research highlights effective resistance genes and gene combinations for stripe rust in wheat and emphasizes the deployment of durable resistance. The findings guide the strategic use of these genes in breeding programs aimed at developing durable resistance in wheat genotypes in Pakistan and Southwest China.

High-resolution genetic map and SNP chip for molecular breeding in Panax ginseng, a tetraploid medicinal plant

Ginseng (Panax ginseng) renowned as the king of medicinal plants. Ginseng grows slowly under shade conditions, requiring at least 4 years to produce a limited number of seeds. Molecular breeding of ginseng faces challenges due to its the tetraploid genome and the absence of an efficient molecular marker system. To overcome these obstacles, we adopted genotyping-by-sequencing to delve into genetic mapping and survey genetic diversity. We constructed a comprehensive genetic map comprising 24 linkage groups, each corresponding to one of the 24 chromosomes in the ginseng genome, based on 1216 nonredundant SNPs obtained from an F 2 mapping population. Additionally, 431 103 SNPs were identified from 119 diverse ginseng genotypes. From these, 192 informative subgenome-specific single copy SNPs were selected to develop a SNP chip. The SNP chip was used to genotype a large ginseng collection, encompassing registered cultivars, breeding lines, wild-simulated ginseng, and wild ginseng from various countries and regions. We evaluated the utility of the assay for molecular breeding with 919 ginseng genotypes. This breeder-friendly SNP chip promises versatility, enabling purity assessments of seeds and products, the authentication of species and cultivars, and the determination of homozygosity and homogeneity rates for breeding lines. Genotype data for 1200 ginseng genotypes are now stored in our database. This SNP chip lays the foundation for a molecular breeding in ginseng and will facilitate the breeding process in this medicinal crop.

How Rice Responds to Temperature Changes and Defeats Heat Stress

With the intensification of the greenhouse effect, a series of natural phenomena, such as global warming, are gradually recognized; when the ambient temperature increases to the extent that it causes heat stress in plants, agricultural production will inevitably be affected. Therefore, several issues associated with heat stress in crops urgently need to be solved. Rice is one of the momentous food crops for humans, widely planted in tropical and subtropical monsoon regions. It is prone to high temperature stress in summer, leading to a decrease in yield and quality. Understanding how rice can tolerate heat stress through genetic effects is particularly vital. This article reviews how rice respond to rising temperature by integrating the molecular regulatory pathways and introduce its physiological mechanisms of tolerance to heat stress from the perspective of molecular biology. In addition, genome selection and genetic engineering for rice heat tolerance were emphasized to provide a theoretical basis for the sustainability and stability of crop yield-quality structures under high temperatures from the point of view of molecular breeding.

Tae-miR396b regulates TaGRFs in spikes of three wheat spike mutants

Tillering and spike differentiation are key agronomic traits for wheat (Triticum aestivum L.) production. Numerous studies have shown that miR396 and growth-regulating factor genes (GRFs) are involved in growth and development of different plant organs. Previously, we have reported that wheat miR396b (tae-miR396b) and their targets TaGRFs (T. aestivum GRFs) play important roles in regulating wheat tillering. This study was to investigate the regulatory roles of tae-miR396b and TaGRFs played during wheat spike development. Wheat cultivar Guomai 301 (wild type, WT) and its three sipke mutants dwarf round spike mutant (drs), apical spikelet sterility mutant (ass) and prematurely terminated spike differentiation mutant (ptsd1) were studied. Three homeologous genes of tae-miR396b on the long arms of chromosomes 6A, 6B, and 6D were identified, and they encoded the same mature miRNA. Complementary sequences of mature tae-miR396b were identified in 23 TaGRFs, indicating they were the target genes of tae-miR396b. Tae-miR396b had different regulatory effects on TaGRFs between Guomai 301 and its mutants. TaGRF2-7A was confirmed to be the target gene of tae-miR396b by molecular interaction assay. The expression levels of tae-miR396b and TaGRFs were different between WT and mutants drs, ass and ptsd1 at the floret primordium visible (S1), the two awns/spikelet reaching apical meristem of the spikelet (S2), and the green anther stage (S3). The expression level of tae-miR396b in WT was significantly higher than that in mutants drs and ass. The most TaGRFs were negatively regulated by tae-miR396b. The abnormal expressions of TaGRF1 (6A, 6D), TaGRF2 (7A, 7B, 7D), TaGRF4 (6A, 6B), TaGRF5 (4A, 7A, 7D), and TaGRF10 (6A, 6B, 6D) were important causes for abnormal spike development in the three mutants. This study laid foundation for further elucidating functions of tae-miR396b and TaGRFs underlying wheat spike development. Regulating tae-miR396b and TaGRFs will be a new approach for wheat high yield breeding.

Identification of QTL-allele systems of seed size and oil content for simultaneous genomic improvement in Northeast China soybeans

Northeast China (NEC) is the major production area for soybeans in China, whereas its soybean germplasm has played key roles in world soybean production, especially in the Americas. For plant breeding, genomic selection involves two stages, cross design and progeny selection, with the former determining the latter's potential. In NEC, one of the major breeding purposes is for 100-seed weight (100SW) and seed oil content (SOC). A diverse sample with 361 NEC soybean germplasm accessions was evaluated for their 100SW and SOC in Tieling, Liaoning, China. Both traits exhibited significant phenotypic, genotypic, and G × E variation, with a trait heritability of 82.38% and 86.26%, respectively. A restricted two-stage multi-locus genome-wide association study (RTM-GWAS) with 15,501 SNPLDB (SNP linkage disequilibrium block) markers identified 80 and 92 QTLs with 230 and 299 alleles for 100SW and SOC, respectively. Corresponding to some increase of the two traits, almost all the alleles in the early maturity groups (MG 0 + 00 + 000) were inherited from the late MGs (MG I+II+III), indicating that genetic recombination was the major motivator in addition to a few allele emergence and some allele exclusion fluctuations among early MGs. Using the 95th percentile as indicator, the prediction of recombination potentials showed that 30.43 g 100SW and 27.73% SOC might be achieved, respectively. Three strategies of simultaneous genomic improvement of both traits in designing optimal crosses, namely, 100SW-first, SOC-first, and 100SW-SOC-balance, were proved to be efficient. Thus, the optimal cross design could be extended to multiple traits based on a relatively thorough identification of the QTL-alleles using RTM-GWAS.

Identification of powdery mildew resistance quantitative trait loci in melon and development of resistant near-isogenic lines through marker-assisted backcrossing

BACKGROUND

Melon (Cucumis melo L.), an important cucurbit crop, faces production limitations due to powdery mildew (PM). Developing resistant varieties offers a sustainable, genetics-based alternative to chemical treatments. Therefore, identifying PM resistance quantitative trait loci (QTL) and creating trait-associated markers are essential for efficient melon PM resistance improvement through marker-assisted backcrossing (MABC).

RESULTS

Three F2 populations, A6, B2, and C4, were generated for QTL mapping of PM resistance. Major QTL were identified on chromosome 2 in A6, chromosome 5 in B2, and chromosomes 5 and 12 in C4. A series of TaqMan® assays targeting regions on chromosomes 2, 5, and 12 were developed and validated for foreground and recombinant selection, complemented by the double digest restriction-site associated DNA genotyping system to evaluate the recurrent parent genome recovery. Three MABC programs using resistant donor parents from A6 and C4 crossed with elite susceptible recurrent parents with green and orange fruit flesh were implemented. After two to three cycles of MABC, individual QTL was successfully introgressed into elite genetic backgrounds, giving six PM resistance lines in each green- and orange-fleshed background. PM inoculation on the twelve near-isogenic lines confirmed their resistance to PM.

CONCLUSIONS

We have identified major PM resistance QTL for melon on chromosomes 2, 5, and 12 and have introgressed individual QTL to elite genetic backgrounds using MABC in three and a half years. This study demonstrates the power of combining high-throughput genotyping with breeding efforts and showcases the efficiency of molecular breeding.

CATSPER2 and SPEF2 are potential molecular markers for boar sperm quality: a population association study

PURPOSE

This study investigates the role of cation channel sperm associated 2 (CATSPER2) and sperm flagella 2 (SPEF2) genes in boar spermatogenesis, focusing on their association with sperm quality traits in boars.

METHODS

Utilizing targeted next-generation sequencing, we identified and genotyped two polymorphisms in CATSPER2 (rs341636020G > A, rs326912346G > T) and three variants in SPEF2 (rs320839956A > G, rs334209514C > A, rs325319860C > T) across three boar breeds (Duroc, n = 181; Landrace, n = 87; Large White, n = 52).

RESULTS

Our results confirmed the presence of the specified single nucleotide polymorphisms (SNPs), adhering to association study criteria. In CATSPER2, significant associations were detected between rs341636020G > A and sperm curvilinear velocity (VCL) in Duroc and Landrace boars, and between rs326912346G > T and straight velocity (VSL) in Duroc and Large White boars. For SPEF2, rs320839956A > G was significantly linked to sperm viability in Duroc and Landrace and to sperm concentration (SCON) in Large White boars. Additionally, rs334209514C > A and rs325319860C > T showed significant associations with SCON and VCL respectively, in Doruc and Landrace boars.

CONCLUSIONS

Overall, our findings suggest that CATSPER2 and SPEF2 SNPs significantly impact boar sperm quality traits. These genetic markers have the potential to enhance boar fertility through selective breeding programs, contributing to the optimization of reproductive performance in pigs.

Genetic marker: a genome mapping tool to decode genetic diversity of livestock animals

Genotyping is the process of determining the genetic makeup of an organism by examining its DNA sequences using various genetic markers. It has been widely used in various fields, such as agriculture, biomedical and conservation research, to study genetic diversity, inheritance, the genetic basis of disease-associated traits, evolution, adaptation, etc., Genotyping markers have evolved immensely and are broadly classified as random markers (RFLP, RAPD, AFLP, etc.) and functional markers (SCoT, CDDP, SRAP, etc.). However, functional markers are very limited in genotype studies, especially in animal science, despite their advantages in overcoming the limitations of random markers, which are directly linked with phenotypic traits, high specificity, and similar logistic requirements. The current review surveyed the available random and functional markers for genotyping applications, focusing on livestock including plant and microbe domains. This review article summarises the application, advantages, and limitations of developed markers and methods for genotyping applications. This review aims to make the reader aware of all available markers, their design principles, and methods, and we discuss the marker inheritance patterns of RLFP and AFLP. The review further outlines the marker selection for particular applications and endorses the application of functional markers in genotyping research.

Unraveling the Secrets of Early-Maturity and Short-Duration Bread Wheat in Unpredictable Environments

In response to the escalating challenges posed by unpredictable environmental conditions, the pursuit of early maturation in bread wheat has emerged as a paramount research endeavor. This comprehensive review delves into the multifaceted landscape of strategies and implications surrounding the unlocking of early maturation in bread wheat varieties. Drawing upon a synthesis of cutting-edge research in genetics, physiology, and environmental science, this review elucidates the intricate mechanisms underlying early maturation and its potential ramifications for wheat cultivation in dynamic environments. By meticulously analyzing the genetic determinants, physiological processes, and environmental interactions shaping early maturation, this review offers valuable insights into the complexities of this trait and its relevance in contemporary wheat breeding programs. Furthermore, this review critically evaluates the trade-offs inherent in pursuing early maturation, navigating the delicate balance between accelerated development and optimal yield potential. Through a meticulous examination of both challenges and opportunities, this review provides a comprehensive framework for researchers, breeders, and agricultural stakeholders to advance our understanding and utilization of early maturation in bread wheat cultivars, ultimately fostering resilience and sustainability in wheat production systems worldwide.

Marker-Assisted Selection of Jacalin-Related Lectin Genes OsJRL45 and OsJRL40 Derived from Sea Rice 86 Enhances Salt Tolerance in Rice

Soil salinization limits rice growth and is an important restriction on grain yield. Jacalin-related lectins are involved in multiple stress responses, but their role in salt stress responses and use as molecular markers for salt tolerance remain poorly understood. Salt stress treatments and RT-qPCR analyses of Sea Rice 86 (SR86), 9311, and Nipponbare (Nip) showed that OsJRL45 and OsJRL40 enhanced tolerance of salt stress in SR86. Molecular markers based on sequence differences in SR86 and the salt-sensitive variety, 9311, in the intergenic region between OsJRL45 and OsJRL40 were validated in recombinant inbred lines derived from SR86 and 9311, hybrid populations, and common rice varieties. Yeast two-hybrid and bimolecular fluorescence complementation demonstrated that OsJRL45 and OsJRL40 interacted. Co-transformation of Nip with OsJRL45 and OsJRL40 derived from SR86 had no effect on the mature phenotype in T2 plants; however, salt stress at the three-leaf stage led to significant increases in CAT, POD, SOD, and Pro contents, but reduced MDA content in transgenic plants. Transcriptomic analysis identified 834 differentially expressed genes in transgenic plants under salt stress. GO and KEGG enrichment analyses indicated that metabolic pathways related to antioxidant responses and osmotic balance were crucial for salt-stress tolerance. Thus, molecular markers based on nucleotide differences in OsJRL45 and OsJRL40 provide a novel method for identifying salt-tolerant rice varieties.

Integrating targeted genetic markers to genotyping-by-sequencing for an ultimate genotyping tool

New selection methods, using trait-specific markers (marker-assisted selection (MAS)) and/or genome-wide markers (genomic selection (GS)), are becoming increasingly widespread in breeding programs. This new era requires innovative and cost-efficient solutions for genotyping. Reduction in sequencing cost has enhanced the use of high-throughput low-cost genotyping methods such as genotyping-by-sequencing (GBS) for genome-wide single-nucleotide polymorphism (SNP) profiling in large breeding populations. However, the major weakness of GBS methodologies is their inability to genotype targeted markers. Conversely, targeted methods, such as amplicon sequencing (AmpSeq), often face cost constraints, hindering genome-wide genotyping across a large cohort. Although GBS and AmpSeq data can be generated from the same sample, an efficient method to achieve this is lacking. In this study, we present the Genome-wide & Targeted Amplicon (GTA) genotyping platform, an innovative way to integrate multiplex targeted amplicons into the GBS library preparation to provide an all-in-one cost-effective genotyping solution to breeders and research communities. Custom primers were designed to target 23 and 36 high-value markers associated with key agronomical traits in soybean and barley, respectively. The resulting multiplex amplicons were compatible with the GBS library preparation enabling both GBS and targeted genotyping data to be produced efficiently and cost-effectively. To facilitate data analysis, we have introduced Fast-GBS.v3, a user-friendly bioinformatic pipeline that generates comprehensive outputs from data obtained following sequencing of GTA libraries. This high-throughput low-cost approach will greatly facilitate the application of DNA markers as it provides required markers for both MAS and GS in a single assay.

Cold tolerance of woodland strawberry (Fragaria vesca) is linked to Cold Box Factor 4 and the dehydrin Xero2

Domesticated strawberry is susceptible to sudden frost episodes, limiting the productivity of this cash crop in regions where they are grown during early spring. In contrast, the ancestral woodland strawberry (Fragaria vesca) has successfully colonized many habitats of the Northern Hemisphere. Thus, this species seems to harbour genetic factors promoting cold tolerance. Screening a germplasm established in the frame of the German Gene Bank for Crop Wild Relatives, we identified, among 70 wild accessions, a pair with contrasting cold tolerance. By following the physiological, biochemical, molecular, and metabolic responses of this contrasting pair, we identified the transcription factor Cold Box Factor 4 and the dehydrin Xero2 as molecular markers associated with superior tolerance to cold stress. Overexpression of green fluorescent protein fusions with Xero2 in tobacco BY-2 cells conferred cold tolerance to these recipient cells. A detailed analysis of the metabolome for the two contrasting genotypes allows the definition of metabolic signatures correlated with cold tolerance versus cold stress. This work provides a proof-of-concept for the value of crop wild relatives as genetic resources to identify genetic factors suitable to increase the stress resilience of crop plants.

Quantifying Genetic Parameters for Blackleg Resistance in Rapeseed: A Comparative Study

Selection is a fundamental part of the plant breeding process, enabling the identification and development of varieties with desirable traits. Thanks to advances in genetics and biotechnology, the selection process has become more precise and efficient, resulting in faster breeding progress and better adaptation of crops to environmental challenges. Genetic parameters related to gene additivity and epistasis play a key role and can influence decisions on the suitability of breeding material. In this study, 188 rapeseed doubled haploid lines were assessed in field conditions for resistance to Leptosphaeria spp. Through next-generation sequencing, a total of 133,764 molecular markers (96,121 SilicoDArT and 37,643 SNP) were obtained. The similarity of the DH lines at the phenotypic and genetic levels was calculated. The results indicate that the similarity at the phenotypic level was markedly different from the similarity at the genetic level. Genetic parameters related to additive gene action effects and epistasis (double and triple) were calculated using two methods: based on phenotypic observations only and using molecular marker observations. All evaluated genetic parameters (additive, additive-additive and additive-additive-additive) were statistically significant for both estimation methods. The parameters associated with the interaction (double and triple) had opposite signs depending on the estimation method.

CRISPR-Cas9-mediated editing of GmARM improves resistance to multiple stresses in soybean

The growth and development of soybean plants can be affected by both abiotic and biotic stressors, such as saline-alkali stress and Phytophthora root rot. In this study, we identified a stress-related gene-GmARM-whose promoter contained several hormone-response and stress-regulatory elements, including ABRE, TCA element, STRE, and MBS. qRT-PCR analysis showed that the expression of GmARM was the highest in seeds at 55 days after flowering. Furthermore, this gene was upregulated after exposure to saline-alkali stress and Phytophthora root rot infection at the seedling stage. Thus, we generated GmARM mutants using the CRISPR-Cas9 system to understand the role of this gene in stress response. T3 plants showed significantly improved salt tolerance, alkali resistance, and disease resistance, with a significantly higher survival rate than the wildtype plants. Moreover, mutations in GmARM affected the expression of related stress-resistance genes, indicating that GmARM mutants achieved multiple stress tolerance. Therefore, this study provides a foundation for further exploration of the genes involved in resistance to multiple stresses in soybean that can be used for breeding multiple stress-resistance soybean varieties.

Prospects for mineral biofortification of wheat: classical breeding and agronomy

Low intake of micro- and macroelements and vitamins in food negatively affects the health of more than two billion people around the world provoking chronic diseases. For the majority of the world's population, these are soft and durum wheats that provide beneficial nutrients, however their modern high-yielding varieties have a significantly depleted grain mineral composition that have reduced mineral intake through food. Biofortification is a new research trend, whose main goal is to improve the nutritional qualities of agricultural crops using a set of classical (hybridization and selection) methods as well and the modern ones employing gene/QTL mapping, bioinformatic analysis, transgenesis, mutagenesis and genome editing. Using the classical breeding methods, biofortified varieties have been bred as a part of various international programs funded by HarvestPlus, CIMMYT, ICARDA. Despite the promise of transgenesis and genome editing, these labor-intensive methods require significant investments, so these technologies, when applied to wheat, are still at the development stage and cannot be applied routinely. In recent years, the interest in wheat biofortification has increased due to the advances in mapping genes and QTLs for agronomically important traits. The new markers obtained from wheat genome sequencing and application of bioinformatic methods (GWAS, meta-QTL analysis) has expanded our knowledge on the traits that determine the grain mineral concentration and has identified the key gene candidates. This review describes the current research on genetic biofortification of wheat in the world and in Russia and provides information on the use of cultivated and wild-relative germplasms to expand the genetic diversity of modern wheat varieties.

Whole-genome sequencing of two captive black soldier fly populations: Implications for commercial production

Black soldier fly (BSF; Hermetia illucens) is a promising insect species for food and feed production as its larvae can convert different organic waste to high-value protein. Selective breeding is one way to optimize production, but the potential of breeding is only starting to be explored and not yet utilized for BSF. To assist in monitoring a captive population and implementing a breeding program, genomics tools are imperative. We conducted whole genome sequencing of two captive populations separated by geographical distance - Denmark (DK) and Texas, USA (TX). Various population genetics analyses revealed a moderate genetic differentiation between two populations. Moreover, we observed higher inbreeding in the DK population, and the detection of a subpopulation within DK population aligned well with the recent foundation of the DK population from two captive populations. Additionally, we generated gene ontology annotation and variants annotation for wider potential applications. Our findings establish a robust marker set for research in population genetics, facilitating the monitoring of inbreeding and laying the groundwork for practical breeding programs for BSF.

QTL-Seq identified a genomic region on chromosome 1 for soil-salinity tolerance in F2 progeny of Thai salt-tolerant rice donor line "Jao Khao"

Introduction

Owing to advances in high-throughput genome sequencing, QTL-Seq mapping of salt tolerance traits is a major platform for identifying soil-salinity tolerance QTLs to accelerate marker-assisted selection for salt-tolerant rice varieties. We performed QTL-BSA-Seq in the seedling stage of rice from a genetic cross of the extreme salt-sensitive variety, IR29, and "Jao Khao" (JK), a Thai salt-tolerant variety.

Methods

A total of 462 F2 progeny grown in soil and treated with 160 mM NaCl were used as the QTL mapping population. Two high- and low-bulk sets, based on cell membrane stability (CMS) and tiller number at the recovery stage (TN), were equally sampled. The genomes of each pool were sequenced, and statistical significance of QTL was calculated using QTLseq and G prime (G') analysis, which is based on calculating the allele frequency differences or Δ(SNP index).

Results

Both methods detected the overlapping interval region, wherein CMS-bulk was mapped at two loci in the 38.41-38.85 Mb region with 336 SNPs on chromosome 1 (qCMS1) and the 26.13-26.80 Mb region with 1,011 SNPs on chromosome 3 (qCMS3); the Δ(SNP index) peaks were -0.2709 and 0.3127, respectively. TN-bulk was mapped at only one locus in the overlapping 38.26-38.95 Mb region on chromosome 1 with 575 SNPs (qTN1) and a Δ(SNP index) peak of -0.3544. These identified QTLs in two different genetic backgrounds of segregating populations derived from JK were validated. The results confirmed the colocalization of the qCMS1 and qTN1 traits on chromosome 1. Based on the CMS trait, qCMS1/qTN1 stably expressed 6%-18% of the phenotypic variance in the two validation populations, while qCMS1/qTN1 accounted for 16%-20% of the phenotypic variance in one validation population based on the TN trait.

Conclusion

The findings confirm that the CMS and TN traits are tightly linked to the long arm of chromosome 1 rather than to chromosome 3. The validated qCMS-TN1 QTL can be used for gene/QTL pyramiding in marker-assisted selection to expedite breeding for salt resistance in rice at the seedling stage.

Deciphering the genetic basis of agronomic, yield, and nutritional traits in rice (Oryza sativa L.) using a saturated GBS-based SNP linkage map

Developing high-yielding rice varieties that possess favorable agronomic characteristics and enhanced grain Zn content is crucial in ensuring food security and addressing nutritional needs. This research employed ICIM, IM, and multi-parent population QTL mapping methods to identify important genetic regions associated with traits such as DF, PH, NT, NP, PL, YLD, TGW, GL, GW, Zn, and Fe. Two populations of recombinant inbred lines consisting of 373 lines were phenotyped for agronomic, yield and grain micronutrient traits for three seasons at IRRI, and genotyped by sequencing. Most of the traits demonstrated moderate to high broad-sense heritability. There was a positive relationship between Zn and Fe contents. The principal components and correlation results revealed a significant negative association between YLD and Zn/Fe. ICIM identified 81 QTLs, while IM detected 36 QTLs across populations. The multi-parent population analysis detected 27 QTLs with six of them consistently detected across seasons. We shortlisted eight candidate genes associated with yield QTLs, 19 genes with QTLs for agronomic traits, and 26 genes with Zn and Fe QTLs. Notable candidate genes included CL4 and d35 for YLD, dh1 for DF, OsIRX10, HDT702, sd1 for PH, OsD27 for NP, whereas WFP and OsIPI1 were associated with PL, OsRSR1 and OsMTP1 were associated to TGW. The OsNAS1, OsRZFP34, OsHMP5, OsMTP7, OsC3H33, and OsHMA1 were associated with Fe and Zn QTLs. We identified promising RILs with acceptable yield potential and high grain Zn content from each population. The major effect QTLs, genes and high Zn RILs identified in our study are useful for efficient Zn biofortification of rice.

afila, the origin and nature of a major innovation in the history of pea breeding

The afila (af) mutation causes the replacement of leaflets by a branched mass of tendrils in the compound leaves of pea - Pisum sativum L. This mutation was first described in 1953, and several reports of spontaneous af mutations and induced mutants with a similar phenotype exist. Despite widespread introgression into breeding material, the nature of af and the origin of the alleles used remain unknown. Here, we combine comparative genomics with reverse genetic approaches to elucidate the genetic determinants of af. We also investigate haplotype diversity using a set of AfAf and afaf cultivars and breeding lines and molecular markers linked to seven consecutive genes. Our results show that deletion of two tandemly arranged genes encoding Q-type Cys(2)His(2) zinc finger transcription factors, PsPALM1a and PsPALM1b, is responsible for the af phenotype in pea. Eight haplotypes were identified in the af-harbouring genomic region on chromosome 2. These haplotypes differ in the size of the deletion, covering more or less genes. Diversity at the af locus is valuable for crop improvement and sheds light on the history of pea breeding for improved standing ability. The results will be used to understand the function of PsPALM1a/b and to transfer the knowledge for innovation in related crops.

In Vitro Culture Technology and Advanced Biotechnology Tools Toward Improvement in Gladiolus (Gladiolus species): Present Scenario and Future Prospects

In the world's flower trade, gladiolus (Gladiolus spp.) is ranked first among bulbous flowers and eighth among cut flowers, with more than 30,000 different cultivars being grown. Mass multiplication and commercialization are restricted by the traditional propagation methods. However, the large-scale proliferation and improvement of the gladiolus have been accomplished with the aid of plant tissue culture and other biotechnological techniques. The current review includes a thorough examination of the growth and development parameters required for successful in vitro gladiolus development as well as cormel formation. Moreover, focus is being given to various techniques and methods such as in vitro cytogenetic stability and modification of chromosome number, in vitro mutagenesis and selection of pest resistance, in vitro identification and selection to develop virus-free germplasm, cryopreservation, synthetic seed technology, identifying virus diseases by RT-PCR, somaclonal variation, and protoplast and somatic hybridization. Molecular markers and their applications for genetic diversity analysis, relationships between different genotypes, and clonal stability analysis in Gladiolus species have been conducted by several research groups worldwide and are also being discussed. The article also covers efforts to enhance the functionality of plant phenotypes through genetic transformation. Future prospects for further improvement of ornamental gladiolus are also explored. Overall, the current review provides insight into the applications of basic and advanced biotechnological tools for gladiolus improvement.

A Sustainable Strategy for Marker-Assisted Selection (MAS) Applied in Grapevine (Vitis spp.) Breeding for Resistance to Downy (Plasmopara Viticola) and Powdery (Erysiphe Necator) Mildews

Plant breeders utilize marker-assisted selection (MAS) to identify favorable or unfavorable alleles in seedlings early. In this task, they need methods that provide maximum information with minimal input of time and economic resources. Grape breeding aimed at producing cultivars resistant to pathogens employs several resistance loci (Rpv, Ren, and Run) that are ideal for implementing MAS. In this work, a sustainable MAS protocol was developed based on non-purified DNA (crude), multiplex PCR of SSR markers, and capillary electrophoresis, and its application on grapevine seedlings to follow some main resistance loci was described. The optimized protocol was utilized on 8440 samples and showed high efficiency, reasonable throughput (2-3.2 min sample), easy handling, flexibility, and tolerable costs (reduced by at least 3.5 times compared to a standard protocol). The Rpv, Ren, and Run allelic data analysis did not show limitations to loci combination and pyramiding, but segregation distortions were frequent and displayed both low (undesired) and high rates of inheritance. The protocol and results presented are useful tools for grape breeders and beyond, and they can address sustainable changes in MAS. Several progenies generated have valuable pyramided resistance and will be the subject of new studies and implementation in the breeding program.

The addition of Psathyrostachys Huashanica Keng 6Ns large segment chromosomes has positive impact on stripe rust resistance and plant spikelet number of common wheat

BACKGROUND

Developing novel germplasm by using wheat wild related species is an effective way to rebuild the wheat resource bank. The Psathyrostachys huashanica Keng (P. huashanica, 2n = 2x = 14, NsNs) is regarded as a superior species to improve wheat breeding because of its multi-resistance, early maturation and numerous tiller traits. Introducing genetic components of P. huashanica into the common wheat background is the most important step in achieving the effective use. Therefore, the cytogenetic characterization and influence of the introgressed P. huashanica large segment chromosomes in the wheat background is necessary to be explored.

RESULTS

In this study, we characterized a novel derived line, named D88-2a, a progeny of the former characterized wheat-P. huashanica partial amphiploid line H8911 (2n = 7x = 49, AABBDDNs). Cytological identification showed that the chromosomal composition of D88-2a was 2n = 44 = 22II, indicating the addition of exogenous chromosomes. Genomic in situ hybridization demonstrated that the supernumerary chromosomes were a pair of homologues from the P. huashanica and could be stably inherited in the common wheat background. Molecular markers and 15 K SNP array indicated that the additional chromosomes were derived from the sixth homoeologous group (i.e., 6Ns) of P. huashanica. Based on the distribution of the heterozygous single-nucleotide polymorphism sites and fluorescence in situ hybridization karyotype of each chromosome, this pair of additional chromosomes was confirmed as P. huashanica 6Ns large segment chromosomes, which contained the entire short arm and the proximal centromere portion of the long arm. In terms of the agronomic traits, the addition line D88-2a exhibited enhanced stripe rust resistance, improved spike characteristics and increased protein content than its wheat parent line 7182.

CONCLUSIONS

The new wheat germplasm D88-2a is a novel cytogenetically stable wheat-P. huashanica 6Ns large segment addition line, and the introgressed large segment alien chromosome has positive impact on plant spikelet number and stripe rust resistance. Thus, this germplasm can be used for genetic improvement of cultivated wheat and the study of functional alien chromosome segment.

Refinement of rice blast disease resistance QTLs and gene networks through meta-QTL analysis

Rice blast disease is the most devastating disease constraining crop productivity. Vertical resistance to blast disease is widely studied despite its instability. Clusters of genes or QTLs conferring blast resistance that offer durable horizontal resistance are important in resistance breeding. In this study, we aimed to refine the reported QTLs and identify stable meta-QTLs (MQTLs) associated with rice blast resistance. A total of 435 QTLs were used to project 71 MQTLs across all the rice chromosomes. As many as 199 putative rice blast resistance genes were identified within 53 MQTL regions. The genes included 48 characterized resistance gene analogs and related proteins, such as NBS-LRR type, LRR receptor-like kinase, NB-ARC domain, pathogenesis-related TF/ERF domain, elicitor-induced defense and proteins involved in defense signaling. MQTL regions with clusters of RGA were also identified. Fifteen highly significant MQTLs included 29 candidate genes and genes characterized for blast resistance, such as Piz, Nbs-Pi9, pi55-1, pi55-2, Pi3/Pi5-1, Pi3/Pi5-2, Pikh, Pi54, Pik/Pikm/Pikp, Pb1 and Pb2. Furthermore, the candidate genes (42) were associated with differential expression (in silico) in compatible and incompatible reactions upon disease infection. Moreover, nearly half of the genes within the MQTL regions were orthologous to those in O. sativa indica, Z. mays and A. thaliana, which confirmed their significance. The peak markers within three significant MQTLs differentiated blast-resistant and susceptible lines and serve as potential surrogates for the selection of blast-resistant lines. These MQTLs are potential candidates for durable and broad-spectrum rice blast resistance and could be utilized in blast resistance breeding.