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ABSTRACT Grain hardness (GH) plays an important role in wheat quality evaluation. Identification of new genes or quantitative trait loci (QTL) for GH is an effective strategy for wheat quality breeding. Here, we used a recombinant inbred line (RIL) population derived from a cross between two hard wheat Yangmai 4 (YM4) and Yanzhan 1 (YZ1) to identify QTL for GH. No QTL was detected on 5D chromosome, as parents YM4 and YZ1 possessed the two hard alleles Pinb‐D1b and Pinb‐D1p at the Hardness‐5D (Ha‐5D) locus, respectively. A total of three GH QTL were identified, among which QGh.yaas‐4B and QGh.yaas‐7D could be detected in all experiments and for mean value, explaining 8.69%–15.07% of the phenotypic variances. QGh.yaas‐4D, co‐located with Rht‐D1, was detected in one experiment and for mean value, explaining 9.94%–11.39% of the phenotypic variances. We were not able to precisely validate QGh.yaas‐4B due to its large mapping interval. Kompetitive allele‐specific PCR (KASP) markers for QGh.yaas‐7D were successfully developed, and then QGh.yaas‐4D and QGh.yaas‐7D were validated in a panel of 101 wheat cultivars/lines (all carrying Pina‐D1a and Pinb‐D1a alleles). Cultivars/lines harbouring the positive alleles of QGh.yaas‐4D and QGh.yaas‐7D increased GH by 85.16% relative to the ones without any positive allele. These results provide new loci and resources in molecular breeding for wheat hardness. [ABSTRACT FROM AUTHOR]

Groundnut (Arachis hypogaea L.) is an important oilseed crop. A specific type of groundnut, known as high-oleate groundnut, is particularly sought-after for its antioxidant properties and benefits to human health due to its favorable fatty acid profile. To breed high-oleic acid varieties of groundnut, two elite varieties of Tamil Nadu, India, TMVGn 13 and GJG 33, were hybridized with a high-oleic groundnut donor released in India, Girnar 4. The resulting progenies were then backcrossed with their recurrent parents for two generations, using marker-assisted backcross selection. Six progenies in the TMVGn 13 × Girnar 4 cross and nine progenies in the GJG 33 × Girnar 4 cross were identified as homozygous mutants for ahFAD2A and ahFAD2B genes, respectively. Three lines with high oleic acid content (>70%), good oil content (48–50%), and pod yield per plant were selected from these progenies. Following multi-location and adaptive research yield trials, these lines may be released as high-oleic acid varieties. [ABSTRACT FROM AUTHOR]

Omics methodologies, such as genomics, transcriptomics, proteomics, metabolomics, lipidomics and microbiomics, have revolutionized biological research by allowing comprehensive molecular analysis in livestock animals. However, despite being widely used in various animal species, research on donkeys has been notably scarce. China, renowned for its rich history in donkey husbandry, plays a pivotal role in their conservation and utilization. China boasts 24 distinct donkey breeds, necessitating conservation efforts, especially for smaller breeds facing extinction threats. So far, omics approaches have been employed in studies of donkey milk and meat, shedding light on their composition and quality. Similarly, omics methods have been utilized to explore the molecular basis associated with donkey growth, meat production, and quality traits. Omics analysis has also unraveled the critical role of donkey microbiota in health and nutrition, with gut microbiome studies revealing associations with factors such as pregnancy, age, transportation stress, and altitude. Furthermore, omics applications have addressed donkey health issues, including infectious diseases and reproductive problems. In addition, these applications have also provided insights into the improvement of donkey reproductive efficiency research. In conclusion, omics methodologies are essential for advancing knowledge about donkeys, their genetic diversity, and their applications across various domains. However, omics research in donkeys is still in its infancy, and there is a need for continued research to enhance donkey breeding, production, and welfare in China and beyond. [ABSTRACT FROM AUTHOR]

Soil salinization is a widespread hindrance that endangers agricultural production and ecological security. High salt concentrations in saline soils are primarily caused by osmotic stress, ionic toxicity and oxidative stress, which have a negative impact on plant growth and development. In order to withstand salt stress, plants have developed a series of complicated physiological and molecular mechanisms, encompassing adaptive changes in the structure and function of various plant organs, as well as the intricate signal transduction networks enabling plants to survive in high-salinity environments. This review summarizes the recent advances in salt perception under different tissues, physiological responses and signaling regulations of plant tolerance to salt stress. We also examine the current knowledge of strategies for breeding salt-tolerant plants, including the applications of omics technologies and transgenic approaches, aiming to provide the basis for the cultivation of salt-tolerant crops through molecular breeding. Finally, future research on the application of wild germplasm resources and muti-omics technologies to discover new tolerant genes as well as investigation of crosstalk among plant hormone signaling pathways to uncover plant salt tolerance mechanisms are also discussed in this review. [ABSTRACT FROM AUTHOR]

Summary: Forests face many threats. While traditional breeding may be too slow to deliver well‐adapted trees, genomic selection (GS) can accelerate the process. We describe a comprehensive study of GS from proof of concept to operational application in western redcedar (WRC, Thuja plicata).Using genomic data, we developed models on a training population (TrP) of trees to predict breeding values (BVs) in a target seedling population (TaP) for growth, heartwood chemistry, and foliar chemistry traits. We used cross‐validation to assess prediction accuracy (PACC) in the TrP; we also validated models for early‐expressed foliar traits in the TaP.Prediction accuracy was high across generations, environments, and ages. PACC was not reduced to zero among unrelated individuals in TrP and was only slightly reduced in the TaP, confirming strong linkage disequilibrium and the ability of the model to generate accurate predictions across breeding generations. Genomic BV predictions were correlated with those from pedigree but displayed a wider range of within‐family variation due to the ability of GS to capture the Mendelian sampling term.Using predicted TaP BVs in multi‐trait selection, we functionally implemented and integrated GS into an operational tree‐breeding program. [ABSTRACT FROM AUTHOR]

Bakanae disease, caused by Fusarium fujikuroi, is a major threat to rice production globally, especially in Egypt. No rice variety is completely resistant to bakanae disease. Here, we assessed resistance in 11 Egyptian rice genotypes, identified a novel F. fujikuroi strain using molecular techniques, and developed molecular markers for resistance breeding. ISSR and InDel PCR were used to determine the genetic distance between the genotypes and develop molecular markers for bakanae disease resistance. qRT-PCR was used to assess the gene expression of four resistance candidate genes. Sakha 103 and Sakha 104 were the most tolerant genotypes, while Sakha 101 and Sakha 108 were the most susceptible to bakanae disease. ISSR and InDel PCR showed high polymorphism values among genotypes and distinctive bands in the most tolerant varieties. Gene expression analysis revealed up-regulation of LOC_Os01g41770, LOC_Os01g41780, and LOC_Os01g41790, which encode leucine-rich repeat receptor-like proteins, in susceptible varieties. Additionally, LOC_Os01g41800, encoding a putative cytochrome P450 monooxygenase, was up regulated in tolerant genotypes after inoculation. This study provides tools for screening rice genotypes for bakanae disease resistance and improving resistance breeding programs. The identified molecular markers and candidate genes could potentially be used in future breeding programs to develop new, Bakanae-resistant rice varieties, which is essential for sustainable rice production. [ABSTRACT FROM AUTHOR]

Despite extensive introductions of Eucalyptus germplasm to Brazil in the last 50 years, relatively little is known about the genetic diversity within current breeding programs, particularly for non-mainstream species. A prime example is Eucalyptus benthamii, a subtropical species with a restricted natural range, endangered due to anthropogenic population fragmentation. We used microsatellite markers to reconstruct the pedigrees and estimate diversity within the two most representative pools of E. benthamii germplasm managed in separate, commercial Brazilian breeding populations. The analysis, together with evidence from Australian Tree Seed Centre (ATSC), historical germplasm export data confirmed that the genetic diversity within the two populations is modest. In the two breeding populations, the estimated status number was in the range of 8.5–22.0 per population considering marker-based co-ancestry. Extensive close relatedness and family structure were identified within and across the two populations, confirming that they share a high proportion of founder ancestors. This is likely a result of the narrow genetic base of the initial introductions and subsequent directional selection and breeding. With the increasing importance of E. benthamii in Brazilian plantation forestry, and as further breeding will likely reduce the status number, our study highlights the need for infusions to augment the existing genetic diversity. Complementary to sourcing infusions, implementing breeding strategies that take advantage of the marker-based information reported in this study to carefully manage the pedigree should help to minimise inbreeding. Exchanging unrelated individuals between the two Brazilian breeding populations would also be advantageous. [ABSTRACT FROM AUTHOR]

Main conclusion: Leveraging advanced breeding and multi-omics resources is vital to position millet as an essential “nutricereal resource,” aligning with IYoM goals, alleviating strain on global cereal production, boosting resilience to climate change, and advancing sustainable crop improvement and biodiversity. The global challenges of food security, nutrition, climate change, and agrarian sustainability demand the adoption of climate-resilient, nutrient-rich crops to support a growing population amidst shifting environmental conditions. Millets, also referred to as “Shree Anna,” emerge as a promising solution to address these issues by bolstering food production, improving nutrient security, and fostering biodiversity conservation. Their resilience to harsh environments, nutritional density, cultural significance, and potential to enhance dietary quality index made them valuable assets in global agriculture. Recognizing their pivotal role, the United Nations designated 2023 as the “International Year of Millets (IYoM 2023),” emphasizing their contribution to climate-resilient agriculture and nutritional enhancement. Scientific progress has invigorated efforts to enhance millet production through genetic and genomic interventions, yielding a wealth of advanced molecular breeding technologies and multi-omics resources. These advancements offer opportunities to tackle prevailing challenges in millet, such as anti-nutritional factors, sensory acceptability issues, toxin contamination, and ancillary crop improvements. This review provides a comprehensive overview of molecular breeding and multi-omics resources for nine major millet species, focusing on their potential impact within the framework of IYoM. These resources include whole and pan-genome, elucidating adaptive responses to abiotic stressors, organelle-based studies revealing evolutionary resilience, markers linked to desirable traits for efficient breeding, QTL analysis facilitating trait selection, functional gene discovery for biotechnological interventions, regulatory ncRNAs for trait modulation, web-based platforms for stakeholder communication, tissue culture techniques for genetic modification, and integrated omics approaches enabled by precise application of CRISPR/Cas9 technology. Aligning these resources with the seven thematic areas outlined by IYoM catalyzes transformative changes in millet production and utilization, thereby contributing to global food security, sustainable agriculture, and enhanced nutritional consequences. The portrayal of millets in the context of the International Year of Millets (IYoM) framework includes a roadmap for their enhancement through future interventions, utilizing multi-omics resources. [ABSTRACT FROM AUTHOR]

Summary: Gene silencing is crucial in crop breeding for desired trait development. RNA interference (RNAi) has been used widely but is limited by ectopic expression of transgenes and genetic instability. Introducing an upstream start codon (uATG) into the 5′untranslated region (5′UTR) of a target gene may 'silence' the target gene by inhibiting protein translation from the primary start codon (pATG).Here, we report an efficient gene silencing method by introducing a tailor‐designed uATG‐containing element (ATGE) into the 5′UTR of genes in plants, occupying the original start site to act as a new pATG.Using base editing to introduce new uATGs failed to silence two of the tested three rice genes, indicating complex regulatory mechanisms. Precisely inserting an ATGE adjacent to pATG achieved significant target protein downregulation. Through extensive optimization, we demonstrated this strategy substantially and consistently downregulated target protein expression. By designing a bidirectional multifunctional ATGE4, we enabled tunable knockdown from 19% to 89% and observed expected phenotypes. Introducing ATGE into Waxy, which regulates starch synthesis, generated grains with lower amylose, revealing the value for crop breeding.Together, we have developed a programmable and robust method to knock down gene expression in plants, with potential for biological mechanism exploration and crop enhancement. See also the Commentary on this article by Li & Wei, 243: 2052–2054. [ABSTRACT FROM AUTHOR]

Rice is one of the most important food crops in the world, and its yield restricts global food security. However, various diseases and pests of rice pose a great threat to food security. Among them, bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious bacterial diseases affecting rice globally, creating an increasingly urgent need for research in breeding resistant varieties. Phytohormones are widely involved in disease resistance, such as auxin, abscisic acid (ABA), ethylene (ET), jasmonic acid (JA), and salicylic acid (SA). In recent years, breakthroughs have been made in the analysis of their regulatory mechanism in BLB resistance in rice. In this review, a series of achievements of phytohormones in rice BLB resistance in recent years were summarized, the genes involved and their signaling pathways were reviewed, and a breeding strategy combining the phytohormones regulation network with modern breeding techniques was proposed, with the intention of applying this strategy to molecular breeding work and playing a reference role for how to further improve rice resistance. [ABSTRACT FROM AUTHOR]

Introduction: Fruit color significantly influences the quality of horticultural crops, which affects phytochemical diversity and consumer preferences. Despite its importance, the genetic basis of the white-colored fruit in tomatoes remains poorly understood. Methods: In this study, we demonstrate that white-fleshed tomato varieties accumulate fewer carotenoids than yellow-fleshed varieties. We developed various segregating populations by hybridizing red, yellow, and white fruit tomato cultivars. Results: Genetic analysis revealed that the white fruit color trait is controlled by a single gene that dominates both red and yellow fruits. Bulk segregant RNA sequencing provided a preliminary map of a 3.17 Mb region on chromosome 3 associated with the white color trait. Based on kompetitive allele-specific PCR (KASP) markers, we narrowed the candidate gene region to 819 kb. Within this region, we identified a 4906-bp sequence absence variation near Phytoene Synthase 1 (SlPSY1) specific to white-colored tomatoes. Genotyping of the progeny and natural populations using a single nucleotide polymorphism adjacent to this absence of variation confirmed its key role in white fruit formation. Discussion: Collectively, our findings provide insights into white fruit trait formation in tomatoes, enabling tomato breeders to precisely introduce white fruit traits for commercial exploitation. [ABSTRACT FROM AUTHOR]

Enhancing crop nitrogen use efficiency (NUE) in agricultural sciences is a pivotal challenge, particularly for high-demand crops like potatoes (Solanum tuberosum L.), the world's third most significant food crop. This study delves into the molecular responses of potatoes to low nitrogen (LN) stress, employing an integrative approach that combines transcriptomics and metabolomics to compare two cultivars with divergent NUE traits: XS6, known for its high NUE, and NS7, characterized by lower NUE. Our research unveils that XS6 exhibits higher chlorophyll and N content, increased tuber yield, and elevated N assimilation capacity under LN stress conditions compared to NS7. Through transcriptome analysis, we identified critical genes involved in C and N metabolism that had higher expression in XS6. A significant discovery was the high-affinity nitrate transporter 2.7 gene, which showed elevated expression in XS6, suggesting its key role in enhancing NUE. Metabolomics analysis further complemented these findings, revealing a sophisticated alteration of 1252 metabolites under LN stress, highlighting the dynamic interplay between carbon and N metabolism in coping with N scarcity. The integration of transcriptomic and metabolomic data underscored the crucial role of trehalose in mitigating N deficiency and enhancing NUE. This study provides novel insights into the molecular mechanisms governing NUE in potatoes, offering valuable perspectives for molecular breeding to enhance NUE in potatoes and potentially other crops. [ABSTRACT FROM AUTHOR]

Cotton breeding for the development of early-maturing varieties is an effective way to improve multiple cropping indexes and alleviate the conflict between grains and cotton in the cultivated fields in China. In the present study, we aimed to identify upland cotton quantitative trait loci (QTLs) and candidate genes related to early-maturity traits, including whole growth period (WGP), flowering timing (FT), node of the first fruiting branch (NFFB), height of the node of the first fruiting branch (HNFFB), and plant height (PH). An early-maturing variety, CCRI50, and a late-maturing variety, Guoxinmian 11, were crossed to obtain biparental populations. These populations were used to map QTLs for the early-maturity traits for two years (2020 and 2021). With BSA-seq analysis based on the data of population 2020, the candidate regions related to early maturity were found to be located on chromosome D03. We then developed 22 polymorphic insertions or deletions (InDel) markers to further narrow down the candidate regions, resulting in the detection of five and four QTLs in the 2020 and 2021 populations, respectively. According to the results of QTL mapping, two candidate regions (InDel_G286-InDel_G144 and InDel_G24-InDel_G43) were detected. In these regions, three genes (GH_D03G0451, GH_D03G0649, and GH_D03G1180) have non-synonymous mutations in their exons and one gene (GH_D03G0450) has SNP variations in the upstream sequence between CCRI50 and Guoxinmian 11. These four genes also showed dominant expression in the floral organs. The expression levels of GH_D03G0451, GH_D03G0649 and GH_D03G1180 were significantly higher in CCRI50 than in Guoxinmian 11 during the bud differentiation stages, while GH_D03G0450 showed the opposite trend. Further functional verification of GH_D03G0451 indicated that the GH_D03G0451-silenced plants showed a delay in the flowering time. The results suggest that these are the candidate genes for cotton early maturity, and they may be used for breeding early-maturity cotton varieties.

Crop pedigrees incorporate information on the kinship and genetic evolutionary history of breeding materials. Complete and accurate pedigree information is vital for effective genetic improvement of crops and maximal exploitation of heterosis in crop production. It is difficult for breeders to accurately extrapolate the selection of germplasm resources with missing genealogical information based on breeding experience. In this study, an algorithm called PidTools was developed, consisting of five sets of algorithms from three core modules, for accurate pedigree identification analysis. The algorithms and associated tools are suitable for all crops, for the reconstruction and visualization of a complete pedigree for breeding materials. The algorithm and tools were validated with the model crop maize. A genotype database was constructed using Maize6H-60K array data from 5791 maize inbred lines. The pedigree of the maize inbred line Jing72464 was identified without prior provision of any parental information. The pedigree information for Zheng58 was fully identified at the genome-wide scale. With regard to group identification, the parents of a doubled-haploid group were identified based on the genotyping data. The pedigree of 21 Dan340 derived lines were visualized using PidTools. The algorithms are incorporated into a user-friendly online analytical platform, PidTools-WS, with an associated customizable toolkit program, PidTools-CLI. These analytical tools and the present results provide useful information for future maize breeding. The PidTools online analysis platform is available at https://PidTools.plantdna.site/.

Plant breeding, often known as the science of plant development, is the study and practice of modifying a plant’s genetic makeup through a variety of breeding techniques to produce higher-quality, more prolific, and more resistant to harsh environmental circumstances. Classical breeding programs are indispensable techniques for increasing yields and improving plant characteristics, but they are progressing too slowly to meet the increasing food demand of the rapidly growing world population alone. Considering that the development periods of plants are generally long in traditional plant breeding, the opportunity to develop higher quality and more productive species that are more resistant to abiotic and biotic stress factors is very limited. Because there are multiple steps required in producing new plant varieties, including hybridization, selection, and testing, the process of creating a new variation takes several years. However, it is important to rapidly develop plant varieties with desirable characteristics to meet the increasing food demand of the rapidly growing world population, so the application of biotechnological methods integrated into plant breeding and combined with traditional methods can help reduce food shortages. Today, with the quick acceleration of biotechnology, molecular DNA marker technology has been developed in plant breeding and very important developments have been experienced. Thanks to the development of molecular tools for genetic research aimed at improving agricultural traits in plants related to crop yield, crop quality, or tolerance to adverse environmental conditions, we now have a much better understanding of plant genetics and the architecture and function of plant genomes. Therefore, it is of critical importance to revise current breeding procedures by incorporating molecular markers into breeding programs in the future.

The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity.

Rice and wheat provide nearly 40% of human calorie and protein requirements. They share a common ancestor and belong to the Poaceae (grass) family. Characterizing their genetic homology is crucial for developing new cultivars with enhanced traits. Several wheat genes and gene families have been characterized based on their rice orthologs. Rice–wheat orthology can identify genetic regions that regulate similar traits in both crops. Rice–wheat comparative genomics can identify candidate wheat genes in a genomic region identified by association or QTL mapping, deduce their putative functions and biochemical pathways, and develop molecular markers for marker-assisted breeding. A knowledge of gene homology facilitates the transfer between crops of genes or genomic regions associated with desirable traits by genetic engineering, gene editing, or wide crossing.

Abstract Improving rice quality remains a crucial breeding objective, second only to enhancing yield, yet progress in quality improvement lags behind yield. The high temperature and ripening conditions in Southern China often result in poor rice quality, impacting hybrid rice production and utilization. Therefore, to address this challenge, analyzing the molecular basis of high-quality traits is essential for molecular design breeding of high-quality hybrid rice varieties. In this study, we investigated the molecular basis of grain shape, amylose content, gel consistency, gelatinization temperature, and aroma, which influence rice quality. We discovered that quality related alleles gs3, GW7 TFA , gw8, chalk5, Wx b , ALK TT , and fgr can enhance rice quality when applied in breeding programs. Polymerization of gs3, GW7 TFA , gw8, and chalk5 genes improves rice appearance quality. The gs3 and GW7 TFA allele polymerization increasing the grain’s length-width ratio, adding the aggregation of gw8 allele can further reducing grain width. The chalk5 gene regulates low chalkiness, but low correlation to chalkiness was exhibited with grain widths below 2.0 mm, with minimal differences between Chalk5 and chalk5 alleles. Enhancing rice cooking and eating quality is achieved through Wx b and ALK TT gene polymerization, while introducing the fgr(E7) gene significantly improved rice aroma. Using molecular marker-assisted technology, we aggregated these genes to develop a batch of indica hybrid rice parents with improved rice quality are obtained. Cross-combining these enhanced parents can generate new, high-quality hybrid rice varieties suitable for cultivation in Southern China. Therefore, our findings contribute to a molecular breeding model for grain quality improvement in high-quality indica hybrid rice. This study, along with others, highlights the potential of molecular design breeding for enhancing complex traits, particularly rice grain quality.

The sustainable maintenance breeding of pigeonpea germplasm, genetic stocks, released cultivars, and hybrid parents is a tough job. The prime reason for their genetic contamination is the insect‐aided cross‐pollination. Although various public and private seed agencies are involved in maintenance breeding to produce different grades of pigeonpea seeds, but the limitation of resources and low priority make it difficult to meet the national seed requirements. This manuscript, aside from reviewing the present pigeonpea maintenance breeding methods, their limitations, and accomplishments, also highlights some advanced breeding and genomics approaches to enhance the efficiency of maintenance breeding. [ABSTRACT FROM AUTHOR]

In recent years, the integration of advances in biotechnology, genomic research, and the application of molecular markers with classical plant breeding methods has formed the basis of a multidisciplinary field called plant molecular breeding or genome-based plant breeding. This approach is widely used in breeding programs for various crops including sugar beet. The complete sequencing of the B. vulgaris genome provided a valuable tool for sugar beet genomics research. Additionally, advances in genome sequencing, the development of markers based on single nucleotide polymorphisms, and robotic methods for high-throughput genotyping have reduced the cost of genotypic evaluations for sugar beet. In Iran, the most damaging diseases affecting sugar beet include rhizomania, beet cyst nematode, root-knot nematode, and Rhizoctonia. Breeding for resistance to these diseases has been a significant focus. Over the past decades, researchers at the Iranian Sugar Beet Seed Institute and the University of Padua, Italy, have identified RAPD, SCAR, STS, and SNP molecular markers linked to resistance genes for these diseases using sugar beet mapping populations and other genotypes. In recent years, these selected markers have been used for molecular screening of thousands of single plants from various genotypes to determine the presence of the aforementioned resistance genes in breeding populations and commercial hybrids. [ABSTRACT FROM AUTHOR]

Consumer perception of beef is heavily influenced by overall meat quality, a critical factor in the cattle industry. Genomics has the potential to improve important beef quality traits and identify genetic markers and causal variants associated with these traits through genomic selection (GS) and genome-wide association studies (GWAS) approaches. Transcriptomics, proteomics, and metabolomics provide insights into underlying genetic mechanisms by identifying differentially expressed genes, proteins, and metabolic pathways linked to quality traits, complementing GWAS data. Leveraging these functional genomics techniques can optimize beef cattle breeding for enhanced quality traits to meet high-quality beef demand. This paper provides a comprehensive overview of the current state of applications of omics technologies in uncovering functional variants underlying beef quality complexities. By highlighting the latest findings from GWAS, GS, transcriptomics, proteomics, and metabolomics studies, this work seeks to serve as a valuable resource for fostering a deeper understanding of the complex relationships between genetics, gene expression, protein dynamics, and metabolic pathways in shaping beef quality. [ABSTRACT FROM AUTHOR]

Sea cucumber has emerged as a crucial economic species in aquaculture in China because of its remarkable nutritional and medicinal value. However, wild sea cucumber populations have experienced a decline due to overfishing and environmental factors, underscoring the urgent need for genetic resource conservation and biotechnology innovation within the sea cucumber aquaculture and breeding industry. The development of the sea cucumber industry is still impeded by challenges and difficulties. Nevertheless, significant progress has been made through the utilization of molecular markers, which have effectively addressed a number of fisheries and aquaculture issues. In recent years, diverse types of molecular markers including mitochondrial DNA, microsatellites, and SNP markers have been developed and extensively applied in various aspects of sea cucumber research. These markers play vital roles in genetic sex identification, germplasm resource evaluation, population structure assessment, as well as marker-assisted breeding in marine ranching and sea cucumber aquaculture and breeding industry. This review provides an overview of the fundamental principles, functions, and characteristics associated with various markers employed across various sea cucumber species while also discussing their applications within different aspects of the sea cucumber fisheries, aquaculture, and breeding industry. [ABSTRACT FROM AUTHOR]

The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity. [ABSTRACT FROM AUTHOR]

Improving rice quality remains a crucial breeding objective, second only to enhancing yield, yet progress in quality improvement lags behind yield. The high temperature and ripening conditions in Southern China often result in poor rice quality, impacting hybrid rice production and utilization. Therefore, to address this challenge, analyzing the molecular basis of high-quality traits is essential for molecular design breeding of high-quality hybrid rice varieties. In this study, we investigated the molecular basis of grain shape, amylose content, gel consistency, gelatinization temperature, and aroma, which influence rice quality. We discovered that quality related alleles gs3, GW7TFA, gw8, chalk5, Wxb, ALKTT, and fgr can enhance rice quality when applied in breeding programs. Polymerization of gs3, GW7TFA, gw8, and chalk5 genes improves rice appearance quality. The gs3 and GW7TFA allele polymerization increasing the grain's length-width ratio, adding the aggregation of gw8 allele can further reducing grain width. The chalk5 gene regulates low chalkiness, but low correlation to chalkiness was exhibited with grain widths below 2.0 mm, with minimal differences between Chalk5 and chalk5 alleles. Enhancing rice cooking and eating quality is achieved through Wxb and ALKTT gene polymerization, while introducing the fgr(E7) gene significantly improved rice aroma. Using molecular marker-assisted technology, we aggregated these genes to develop a batch of indica hybrid rice parents with improved rice quality are obtained. Cross-combining these enhanced parents can generate new, high-quality hybrid rice varieties suitable for cultivation in Southern China. Therefore, our findings contribute to a molecular breeding model for grain quality improvement in high-quality indica hybrid rice. This study, along with others, highlights the potential of molecular design breeding for enhancing complex traits, particularly rice grain quality. [ABSTRACT FROM AUTHOR]

BACKGROUND: Starch, dry matter content (DMC), proteins, and sugars are among the major influences on yam tuber quality. Genetic improvement programs need simple, rapid, and low‐cost tools to screen large populations. The objectives of this work were, using a quantitative trait loci mapping approach (QTL) on two diploid full‐sib segregating populations, (i) to acquire knowledge about the genetic control of these traits; (ii) to identify markers linked to the genomic regions controlling each trait, which are useful for marker‐assisted selection (MAS); (iii) to validate the QTLs on a diversity panel; and (iv) to identify candidate genes from the validated QTLs. RESULTS: Heritability for all traits was moderately high to high. Significant correlations were observed between traits. A total of 25 QTLs were identified, including six for DMC, six for sugars, six for proteins, and seven for starch. The phenotypic variance explained by individual QTLs ranged from 14.3% to 28.6%. The majority of QTLs were validated on a diversity panel, showing that they are not specific to the genetic background of the progenitors. The approximate physical location of validated QTLs allowed the identification of candidate genes for all studied traits. Those detected for starch content were mainly enzymes involved in starch and sucrose metabolism, whereas those detected for sugars were mainly involved in respiration and glycolysis. CONCLUSION: The validated QTLs will be useful for breeding programs using MAS to improve the quality of yam tubers. The putative genes should be useful in providing a better understanding of the physiological and molecular basis of these important tuber quality traits. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Wheat is a major food crop that plays a crucial role in the human diet. Various breeding technologies have been developed and refined to meet the increasing global wheat demand. Several studies have suggested breeding strategies that combine generation acceleration systems and molecular breeding methods to maximize breeding efficiency. However, real-world examples demonstrating the effective utilization of these strategies in breeding programs are lacking. In this study, we designed and demonstrated a synergized breeding strategy (SBS) that combines rapid and efficient breeding techniques, including speed breeding, speed vernalization, phenotypic selection, backcrossing, and marker-assisted selection. These breeding techniques were tailored to the specific characteristics of the breeding materials and objectives. Using the SBS approach, from artificial crossing to the initial observed yield trial under field conditions only took 3.5 years, resulting in a 53% reduction in the time required to develop a BC2 nearisogenic line (NIL) and achieving a higher recurrent genome recovery of 91.5% compared to traditional field conditions. We developed a new wheat NIL derived from cv. Jokyoung, a leading cultivar in Korea. Milyang56 exhibited improved protein content, sodium dodecyl sulfate-sedimentation value, and loaf volume compared to Jokyoung, which were attributed to introgression of the Glu-B1i allele from the donor parent, cv. Garnet. SBS represents a flexible breeding model that can be applied by breeders for developing breeding materials and mapping populations, as well as analyzing the environmental effects of specific genes or loci and for trait stacking. [ABSTRACT FROM AUTHOR]

Microsatellites, known as simple sequence repeats (SSRs), are short tandem repeats of 1 to 6 nucleotide motifs found in all genomes, particularly eukaryotes. They are widely used as co-dominant markers in genetic analyses and molecular breeding. Triticeae, a tribe of grasses, includes major cereal crops such as bread wheat, barley, and rye, as well as abundant forage and lawn grasses, playing a crucial role in global food production and agriculture. To enhance genetic work and expedite the improvement of Triticeae crops, we have developed TriticeaeSSRdb, an integrated and user-friendly database. It contains 3,891,705 SSRs from 21 species and offers browsing options based on genomic regions, chromosomes, motif types, and repeat motif sequences. Advanced search functions allow personalized searches based on chromosome location and length of SSR. Users can also explore the genes associated with SSRs, design customized primer pairs for PCR validation, and utilize practical tools for wholegenome browsing, sequence alignment, and in silico SSR prediction from local sequences. We continually update TriticeaeSSRdb with additional species and practical utilities. We anticipate that this database will greatly facilitate trait genetic analyses and enhance molecular breeding strategies for Triticeae crops. Researchers can freely access the database at http://triticeaessrdb.com/. [ABSTRACT FROM AUTHOR]

The Manipulated Genic Male Sterile Maintainer (MGM) system, a next-generation hybrid seed technology, enables efficient production of sortable seeds from genic male sterile (GMS) lines. However, implementing robust MGM systems in commercial maize inbred lines requires stable transformation, a genotype-specific and laborious process. This study aimed to integrate MGM technology into the commercial maize inbred line Z372, developing both GMS and MGM lines. We utilized the MGM line ZC01-3A-7, which contains the MS26ΔE5 editor T-DNA and MGM T-DNA, previously established in the highly transformable ZC01 recipient plants. Through a combination of crossing and backcrossing with Z372, we targeted the fertility gene Ms26 within the Z372 genome for mutation using the in vivo CRISPR/Cas9 activity within the MS26ΔE5 editor T-DNA construct. This approach facilitated precise editing of the Ms26 locus, minimizing linkage drag associated with the Ms26 mutation. Whole-genome SNP analysis achieved a 98.74% recovery rate for GMS and 96.32% for MGM in the BC2F2 generation. Importantly, the Z372-GMS line with the ms26ΔE5 mutation is non-transgenic, avoiding linkage drag and demonstrating production readiness. This study represents a significant advancement in maize breeding, enabling the rapid generation of GMS and MGM lines for efficient hybrid seed production. [ABSTRACT FROM AUTHOR]

Rice and wheat provide nearly 40% of human calorie and protein requirements. They share a common ancestor and belong to the Poaceae (grass) family. Characterizing their genetic homology is crucial for developing new cultivars with enhanced traits. Several wheat genes and gene families have been characterized based on their rice orthologs. Rice–wheat orthology can identify genetic regions that regulate similar traits in both crops. Rice–wheat comparative genomics can identify candidate wheat genes in a genomic region identified by association or QTL mapping, deduce their putative functions and biochemical pathways, and develop molecular markers for marker-assisted breeding. A knowledge of gene homology facilitates the transfer between crops of genes or genomic regions associated with desirable traits by genetic engineering, gene editing, or wide crossing. [ABSTRACT FROM AUTHOR]

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This study addresses the critical issue of high-temperature stress in Japanese flounder (Paralichthys olivaceus), a factor threatening both their survival and the growth of the aquaculture industry. The research aims to identify genetic markers associated with high-temperature tolerance, unravel the genetic regulatory mechanisms, and lay the foundation for breeding Japanese flounder with increased resistance to high temperatures. In this study, using a genome-wide association study was performed to identify single nucleotide polymorphisms (SNPs) and genes associated with high−temperature tolerance for Japanese flounder using 280 individuals with 342 311 high-quality SNPs. The traits of high-temperature tolerance were defined as the survival time and survival status of Japanese flounder at high water temperature (31℃) for 15 days cultivate. A genome-wide association study identified six loci on six chromosomes significantly correlated with survival time under high-temperature stress. Six candidate genes were successfully annotated. Additionally, 34 loci associated with survival status were identified and mapped to 15 chromosomes, with 22 candidate genes annotated. Functional analysis highlighted the potential importance of genes like traf4 and ppm1l in regulating apoptosis, impacting high-temperature tolerance in Japanese flounder. These findings provide a valuable theoretical framework for integrating molecular markers into Japanese flounder breeding programmes, serving as a molecular tool to enhance genetic traits linked to high-temperature tolerance in cultured Japanese flounder.

The breeding of flax and industrial hemp in China began in the 1950s. After the end of the 20th century, the development of related breeding technologies has been accelerating. The current main breeding techniques include cross breeding, mutagenesis, distant hybridization, utilization of male sterile flax, haploid breeding, hybrid breeding, tissue culture, transgene, gene editing, molecular marker assisted selection, and other technologies. Despite many new breeding techniques, cross breeding still are the main breeding method for flax and industrial hemp now. This paper introduced the production status, breeding history, germplasm collection, standard formulation, breeding methods, and new varieties of flax and industrial hemp. Analyzed some problems in flax and industrial hemp breeding, and put forward some suggestions.

Parthenocarpy and stenospermocarpy are the two mechanisms underlying the seedless fruit set program. Seedless fruit occurs naturally and can be produced using hormone application, crossbreeding, or ploidy breeding. However, the two types of breeding are time-consuming and sometimes ineffective due to interspecies hybridization barriers or the absence of appropriate parental genotypes to use in the breeding process. The genetic engineering approach provides a better prospect, which can be explored based on an understanding of the genetic causes underlying the seedlessness trait. For instance, CRISPR/Cas is a comprehensive and precise technology. The prerequisite for using the strategy to induce seedlessness is identifying the crucial master gene or transcription factor liable for seed formation/development. In this review, we primarily explored the seedlessness mechanisms and identified the potential candidate genes underlying seed development. We also discussed the CRISPR/Cas-mediated genome editing approaches and their improvements.

Introduction: Folate supplementation is crucial for the human body, and the chemically synthesized folic acid might have undesirable side effects. The use of molecular breeding methods to modify the genes related to the biosynthesis of folate by probiotics to increase folate production is currently a focus of research. Methods: In this study, the folate-producing strain of Limosilactobacillus reuteri B1-28 was isolated from human breast milk, and the difference between B1-28 and folA gene deletion strain AFolA was investigated by phenotyping, in vitro probiotic evaluation, metabolism and transcriptome analysis. Results: The results showed that the folate producted by the AFolA was 2-3 folds that of the B1-28. Scanning electron microscope showed that AFolA had rougher surface, and the acid-producing capacity (p = 0.0008) and adhesion properties (p = 0.0096) were significantly enhanced than B1-28. Transcriptomic analysis revealed that differentially expressed genes were mainly involved in three pathways, among which the biosynthesis of ribosome and aminoacyl-tRNA occurred in the key metabolic pathways. Metabolomics analysis showed that folA affected 5 metabolic pathways, involving 89 different metabolites. Discussion: In conclusion, the editing of a key gene of folA in folate biosynthesis pathway provides a feasible pathway to improve folate biosynthesis in breast milk-derived probiotics. [ABSTRACT FROM AUTHOR]

Genetic diversity levels are critical for characterizing and utilizing germplasm collections and for making improvements related to elite germplasms. The current study investigated the genetic diversity level and phylogenetic relationships in ten Turkish sweet corn varieties (Zea mays var. saccharata) using 15 ISSR markers and trnL-F intergenic spacer regions, respectively. A total of 75 loci were identified, of which 57 (76%) were polymorphic. The highest polymorphism ratio (100%) was found using UBC811, UBC817, and UBC823 ISSR markers, while the lowest ratio (45.4%) was identified using UBC829. According to trnL-F intergenic spacer region analyses, nucleotide diversity was found as p: 0.030 for Nei and: 0.036 for Watterson, respectively. In trnL-F intergenic spacer regions, several polymorphic (variable) sites were identified 28 of which 57% (16/28) were parsimony informative sites and 399 sites were invariable (monomorphic). The phylogenetic analysis revealed that two major groups were observed named groups A and B and ten sweet corn genotypes clustered along with known maize genotypes in subgroup B2 with 98% bootstrap value. Consequently, the ISSR data obtained in this study revealed that Turkish sweet corn genotypes exhibit extensive genetic diversity, and the trnL-F intergenic spacer region was successfully utilized to differentiate between maize genotypes from various origins and whole plant taxa. [ABSTRACT FROM AUTHOR]

The expression of Bacillus thuringiensis (Bt) toxins in transgenic cotton confers resistance to insect pests. However, it has been demonstrated that its effectiveness varies among cotton cultivars and different tissues. In this study, we evaluated the expression of Bt protein in 28 cotton cultivars and selected 7 cultivars that differed in Bt protein expression for transcriptome analysis. Based on their Bt protein expression levels, the selected cultivars were categorized into three groups: H (high Bt protein expression), M (moderate expression), and L (low expression). In total, 342, 318, and 965 differentially expressed genes were detected in the H vs. L, M vs. L, and H vs. M comparison groups, respectively. And three modules significantly associated with Bt protein expression were identified by weighted gene co-expression network analysis. Three hub genes were selected to verify their relationships with Bt protein expression using virus-induced gene silencing (VIGS). Silencing GhM_D11G1176, encoding an MYC transcription factor, was confirmed to significantly decrease the expression of Bt protein. The present findings contribute to an improved understanding of the mechanisms that influence Bt protein expression in transgenic cotton. [ABSTRACT FROM AUTHOR]

Dioscorea bulbifera (Dioscoreaceae), a versatile herbaceous climber native to Africa and Asia, holds significant nutritional and medicinal value. Despite extensive characterization and genetic variability analyses of African accessions, studies on the genetic variation of this species in China are limited. To address this gap, we conducted low-coverage whole genome sequencing on D. bulbifera accessions from diverse regions across mainland China and Taiwan island. Our initial investigation encompassed comprehensive comparative plastome analyses of these D. bulbifera accessions, and developing plastome resources (including plastome-derived repetitive sequences, SSRs, and divergent hotspots). We also explored polymorphic nuclear SSRs and elucidated the intraspecific phylogeny of these accessions. Comparative plastome analyses revealed that D. bulbifera plastomes exhibited a conserved quadripartite structure with minimal size variation mainly attributed to intergenic spacer regions, reinforcing prior observations of a high degree of conservation within a species. We identified 46 to 52 dispersed repeats and 151 to 163 plastome-derived SSRs, as well as highlighted eight key divergent hotspots in these D. bulbifera accessions. Furthermore, we developed 2731 high-quality candidate polymorphic nuclear SSRs for D. bulbifera. Intraspecific phylogenetic analysis revealed three distinct clades, where accessions from Southeast China formed a sister group to those from South China and Taiwan island, and collectively, these two clades formed a sister group to the remaining accessions, indicating potential regional genetic divergence. These findings not only contributed to the understanding of the genetic variation of D. bulbifera, but also offered valuable resources for future research, breeding efforts, and utilization of this economically important plant species. [ABSTRACT FROM AUTHOR]

Paw San Hmwe (PSH) is an indigenous rice variety from Myanmar with a good taste, a pleasant fragrance, and excellent elongation ability during cooking. However, its low yield potential and strong photoperiod sensitivity reduce its productivity, and it is vulnerable to climate changes during growth. To improve the photoperiod insensitivity, yield, and plant stature of PSH, the high-yield genes Grain number 1a (Gn1a) and Wealthy Farmer's Panicle (WFP), together with the photoperiod insensitivity trait, were introgressed into PSH via marker-assisted backcross breeding and phenotype selection. For the photoperiod insensitivity trait, phenotypic selection was performed under long-day conditions during the dry season. After foreground selection of Gn1a and WFP via simple sequence repeat genotyping, genotyping-by-sequencing was conducted to validate the introgression of target genes and determine the recurrent parent genome recovery of the selected lines. The improved lines were insensitive to photoperiod, and the Gn1a and WFP introgression lines showed significantly higher numbers of primary panicle branches and spikelets per panicle than the recurrent parent, with comparative similarity in cooking and eating qualities. This study successfully improved PSH by decreasing its photoperiod sensitivity and introducing high-yield genes via marker-assisted selection. The developed lines can be used for crop rotation and double-season cropping of better-quality rice. [ABSTRACT FROM AUTHOR]

Lignin is complex, three-dimensional biopolymer existing in plant cell wall. Lignin biosynthesis is increasingly highlighted because it is closely related to the wide applications in agriculture and industry productions, including in pulping process, forage digestibility, bio-fuel, and carbon sequestration. The functions of lignin in planta have also attracted more attentions recently, particularly in plant defense response against different pathogens. In this brief review, the progress in lignin biosynthesis is discussed, and the lignin's roles in disease resistance are thoroughly elucidated. This issue will help in developing broad-spectrum resistant crops in agriculture. [ABSTRACT FROM AUTHOR]

Maize is one of the important food crops after rice and wheat. It has good nutritive value in terms of starch, proteins, vitamins, and micronutrients which makes this crop important for industrial use. Many elite maize inbred lines and hybrids have already been developed which are having several combinations of nutritional quality traits, viz., quality protein maize (QPM), provitamin A, low phytate, and vitamin E using molecular marker-assisted breeding (MAB), especially in India, and China. Hence, the identification of quantitative trait loci (QTLs) for various quality traits is an important aspect. Several QTLs have been identified for quality traits and introgressed into elite germplasm by various research groups to develop multi-nutrient-rich maize genotypes. The use of potential QTLs in molecular breeding with advanced phenotyping platforms for quick identification or quality check may help the breeders to develop and commercialize biofortified maize. In this review, comprehensive information about QTLs for different quality traits in maize has been discussed for their potential utility in maize breeding programs. [ABSTRACT FROM AUTHOR]