Breeding Of Varieties Research Articles

Comparative genome analysis of two peanut Ralstonia solanacearum strains with significant difference in pathogenicity reveals 16S rRNA dimethyltransferase RsmA involved in inducing immunity

BackgroundBacterial wilt disease, caused by Ralstonia solanacearum, seriously threaten the quality and yield of peanut (Arachis hypogaea L.). Identification of proteins inducing host immune response in R. solanacearum is an important way towards exploring resistance genes in peanut. In previous study, we found that the pathogenicity was significant different between peanut R. solanacearum ZKRS126 and ZKRS146. In this study, comparative genomics analysis was performed to reveal the difference of the genomes between ZKRS126 and ZKRS146, as well as the function of the strain specific gene rsmA in triggering immunity.ResultsCompared with ZKRS146, ZKRS126 caused less cell death in the peanut leaves and its proliferation and pathogenicity were significantly attenuated. Whole genome sequencing revealed that the genomes of ZKRS126 and ZKRS146 were composed of one chromosome, one megaplasmid and one small plasmid. The genome size of ZKRS126 (6,059,912 bp) was slightly larger than that of ZKRS146 (6,053,081 bp). Comparative genomics analysis showed that the genetic relationship between ZKRS126 and ZKRS146 was very close. In both ZKRS126 and ZKRS146, 73 Type III secretion system-secreted effectors (T3Es) were identified by retrieving the effector repertoire, respectively. The gene sequences of T3Es were identical between ZKRS126 and ZKRS146. Comparing all the coding genes between ZKRS126 and ZKRS146, 42 specific genes were identified in ZKRS126 and 43 in ZKRS146. Loss of the specific gene rsmA in ZKRS126 resulted in more virulence, and complementarity of rsmA in mutant strains recovered hypovirulence. The cAMP assay demonstrated RsmA was not a T3E. In Nicotiania benthamiana leaves, transient expression of rsmA significantly induced the up-regulated expression of marker genes in HR, PTI, SA, and JA pathways, indicating RsmA might trigger the plant immunity by activating the immune-related pathways.ConclusionsThis study not only obtained the complete genomes of two peanut R. solanacearum strains, but also revealed their differences in the genome levels through comparing analysis. The function verification of RsmA provided the way for the identification of immunity elicitors, which will accelerate the breeding of bacterial wilt-resistant peanut varieties in the future.Graphical

Current state of knowledge on cultural practices and sanitary threats of the horse in Algerian society

Abstract Algeria is a typical country of great and ancestral equestrian tradition where horses are a varied asset in terms of animal genetic resources, offering an important diversity of breeds in terms of their adaptation and their capacity for production in their natural environment. This literature review aims to illustrate the role played by the horse in Algerian culture and traditions from the past to the present and, to present main diseases studied throughout the country. The equine industry occupies a prominent place in the history and economy of North Africa, especially in Algeria, horse has a major role in sustainable development, particularly in the environmental field, by playing a particular role in the management of spaces and landscapes beneficial to the maintenance and development of biodiversity, but also in its relationship with humans. Especially in the Center and West of the country, horses are the main actors of "Fantasia", which ensures the continuity of an authentic military equestrian tradition, it is a simulation of traditional military action. According to the prevalence rates, the main diseases threatening horses’ health are Equine Influenza, West Nile Virus, Equine Viral Arteritis, Equine granulocytic anaplasmosis, Lyme disease, Toxoplasmosis, Microsporidiosis and Pinworms. However, low rates were observed for Rhinopneumonitis, Brucellosis, Surra and Cryptosporidiosis. Actually, horses deserve more attention from public authorities and civil society, to preserve this animal considered as a part of the national and humanitarian heritage.

A conserved nuclear factor YC subunit, NF-YC3, is essential for arbuscule development.

Establishing reciprocal symbiosis with arbuscular mycorrhizal (AM) fungi is an important evolutionary strategy of most terrestrial plants to adapt to environmental stresses, especially phosphate (Pi) deficiencies. Identifying the key genes essential for AM symbiosis in plants and dissecting their functional mechanisms will be helpful for the breeding of new crop varieties with enhanced nutrient uptake efficiency. Here, we report a nuclear factor YC subunit-encoding gene, OsNF-YC3, whose expression is specifically induced in arbuscule-containing cells, plays an essential role in AM symbiosis. Knockout of OsNF-YC3 resulted in stunted arbuscule morphology and substantially decreased P accumulation, while overexpressing OsNF-YC3 enhanced mycorrhization and Pi uptake efficiency. OsNF-YC3 is directly regulated by OsPHRs, the major regulators of Pi starvation responses. Chromatin immunoprecipitation sequencing analysis uncovered multiple genes with crucial roles in arbuscule development as its potential downstream targets, including the AM-specific Pi transporter gene OsPT11. OsNF-YC3 can form a heterotrimer with the other two NF-Y subunits, OsNF-YA11 and OsNF-YB11, in yeast. Loss of OsNF-YA11 function also severely impaired arbuscule development in its mutants. Overall, our results highlight an essential role of OsNF-YC3 and its potential interacting NF-Y subunit, OsNF-YA11, in regulating AM symbiosis and arbuscule development.

A high-quality chromosome-level genome assembly of the traditional Chinese medicinal herb Zanthoxylum nitidum

Dried roots of Zanthoxylum nitidum (2n=2x=70, family Rutaceae) was referred as “Liang-Mian-Zhen” in Chinese, acting as a valuable species due to its notable pharmacological activities. Herein, we combined PacBio HiFi data together with Hi-C mapping technology to construct a chromosome-scale reference genome assembly for Z. nitidum. The assembly reached a length of 2.24 Gb, successfully anchoring 99.31% of sequences onto 35 pseudo-chromosomes. Among these, 26 chromosomes achieved telomere-to-telomere assembly, and 11 chromosomes were gap-free. The contigs N50 and scaffolds N50 reached 57.61 Mb and 78.00 Mb, respectively. Transposable elements comprised 81.44% of the Z. nitidum genome, and over 78% of them were long-terminal repeat retrotransposon elements. Furthermore, 32,737 protein-coding genes were identified and 99.38% of all were functionally annotated. The completeness of the genome assembly and final gene sets reached 97.83% and 96.47% based on Benchmarking Universal Single-Copy Orthologs (BUSCO), respectively. Taken together, our results provided a high-quality chromosome-level assembly of Z. nitidum genome and will be a valuable resource that will facilitate breeding varieties with higher alkaloids content.

PhenoBench: A Large Dataset and Benchmarks for Semantic Image Interpretation in the Agricultural Domain.

The production of food, feed, fiber, and fuel is a key task of agriculture, which has to cope with many challenges in the upcoming decades, e.g., a higher demand, climate change, lack of workers, and the availability of arable land. Vision systems can support making better and more sustainable field management decisions, but also support the breeding of new crop varieties by allowing temporally dense and reproducible measurements. Recently, agricultural robotics got an increasing interest in the vision and robotics communities since it is a promising avenue for coping with the aforementioned lack of workers and enabling more sustainable production. While large datasets and benchmarks in other domains are readily available and enable significant progress, agricultural datasets and benchmarks are comparably rare. We present an annotated dataset and benchmarks for the semantic interpretation of real agricultural fields. Our dataset recorded with a UAV provides high-quality, pixel-wise annotations of crops and weeds, but also crop leaf instances at the same time. Furthermore, we provide benchmarks for various tasks on a hidden test set comprised of different fields: known fields covered by the training data and a completely unseen field.

Перспективные сорта и гибридные формы абрикоса селекции Дагестанской селекционной опытной станции плодовых культур

Abstract. The article presents the results of a comprehensive assessment of breeding varieties and hybrid forms of apricot (Prunus armeniaca L.) for 2021-2023 based on the following traits: yield capacity, resistance to major diseases (clasteresporium and moniliosis), and fruit quality. The following varieties were distinguished by yield capacity: Tamasha (8.0 t/ha), Uzden (8.9 t/ha), Kokan kyurek (7.3 t/ha) (early ripening); Hukumat kyurek (10.2 t/ha) and hybrid 3/34 (9.2 t/ha) (mid-season ripening) and Esdelik (10.4 t/ha), Untsukulskiy late (10.6 t/ha), Dzhengutaevskiy (9.7 t/ha) (late ripening). Among the studied breeding varieties and hybrid forms, Tamasha (0.5 points) and Uzden (0.1 points) are noted for their comparatively high resistance to clasterosporium. For the other varieties and hybrid forms, this indicator is in the range from 1.0 points to 1.7 points. In terms of resistance to blossom blight, Tamasha and Uzden (0.5 points) stand out among the early varieties; among the mid-season ripening varieties, the seedling Khonobakha (0.5 points) and among the late varieties, Dzhengutaevskiy and Untsukulskiy pozdniy (0.5 points). Damage by fruit rot in most varieties and hybrid forms fluctuates between 0.1 and 0.5 points. Only three varieties have this indicator in the range from 0.8 to 1.0 points. The content of total sugar in fruits of breeding varieties and hybrid forms of apricot varied from 5.8 to 9.8%. The varieties with large fruit size (fruit weight over 35 g) Bukhara, Esdelik, Uzden, Salikh, Musa, Dzhengudaevskiy and hybrids 3/34 and 6/22 have been selected. The selected breeding varieties and hybrid forms of apricot will be recommended for inclusion in targeted crossings in order to increase the efficiency of the breeding process. Keywords: breeding variety, hybrid form, adaptability, clusteresporium, moniliosis, fruit rot, yield capacity

Allelic variation in the promoter of WRKY22 enhances humid adaptation of Arabidopsis thaliana

Submergence tolerance is a complex trait governed by multiple genetic loci. Arabidopsis thaliana, widely distributed from arid to humid regions, offers an opportunity to explore the underlying genetic components and their interactive mechanisms. In this study, we utilized map-based cloning techniques to identify the WRKY22 genetic locus, which activates RAP2.12, a locus identified previously, possibly through ethylene signal transduction. WRKY22 expression is inhibited by ARRs but activated by the WRKY70 transcription factors. The cooperative interaction between these regulators enhances A. thaliana’s ability to adapt more effectively to contrasting habitats. A two-nucleotide deletion in the WRKY22 promoter region prevents its inhibition by phosphorylated ARRs, maintaining its high expression in humid accessions. This WRKY22 allele without ARRs binding element underwent strong natural selection during the southeastern colonization of A. thaliana to the humid Yangtze River basin. However, the WRKY70-activated WT box in the WRKY22 promoter region shows no variation between humid and arid accessions. These findings together establish one previously unreported molecular module composed by multiple regulators, with WRKY22 playing a key role in the ecological shift of A. thaliana. Expanding upon the identified locus, we overexpressed BnaC2.WRKY22 in Brassica napus and successfully achieved a significant improvement in submergence tolerance, highlighting a functional conservatism of this gene across related species. This further demonstrates the potential for transferring knowledge from model plants to crops for the breeding of flood-tolerant crop varieties.

Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations.

Ruminant livestock provide a rich source of products, such as meat, milk, and wool, and play a critical role in global food security and nutrition. Over the past few decades, genomic studies of ruminant livestock have provided valuable insights into their domestication and the genetic basis of economically important traits, facilitating the breeding of elite varieties. In this review, we summarize the main advancements for domestic ruminants in reference genome assemblies, population genomics, and the identification of functional genes or variants for phenotypic traits. These traits include meat and carcass quality, reproduction, milk production, feed efficiency, wool and cashmere yield, horn development, tail type, coat color, environmental adaptation, and disease resistance. Functional genomic research is entering a new era with the advancements of graphical pangenomics and telomere-to-telomere (T2T) gap-free genome assembly. These advancements promise to improve our understanding of domestication and the molecular mechanisms underlying economically important traits in ruminant livestock. Finally, we provide new perspectives and future directions for genomic research on ruminant genomes. We suggest how ever-increasing multiomics datasets will facilitate future studies and molecular breeding in livestock, including the potential to uncover novel genetic mechanisms underlying phenotypic traits, to enable more accurate genomic prediction models, and to accelerate genetic improvement programs.

ERD14 regulation by the HY5- or HY5-MED2 module mediates the cold signal transduction of asparagus bean.

Cold stress affects the growth, development, and yield of asparagus bean (Vigna unguiculata subsp. sesquipedalis). Mediator (MED) complex subunits regulate the cold tolerance of asparagus bean, but the underlying regulatory mechanisms remain unclear. Here, VunMED2 positively responds to cold stress of asparagus beans. Under cold acclimation and freezing treatment, the survival rate, ROS scavenging activity, and expression levels of VunMED2 were increased in VunMED2 transgenic plants. Natural variation in the promoter of VunMED2 in two different cold-tolerant asparagus beans was observed. Under cold stress, the expression of the GUS reporter gene was higher in cold-tolerant plants than in cold-sensitive plants, and the expression of the GUS reporter gene was tissue-specific. VunHY5 positively influenced the expression of VunMED2 by binding to the E-box motif, and the transcriptional activation of the promoter was stronger in the cold-tolerant variety than in cold-sensitive plants. VunHY5 overexpression improved plant freezing resistance by increasing the antioxidant capacity and expression of dehydrin genes. VunHY5 and VunMED2 play a synergistic role in binding to the G-box/ABRE motif and transcriptionally activating the expression of VunERD14. VunERD14 complemented the med2 mutant, which could positively respond to plant freezing resistance by reducing membrane lipid peroxidation and improving the antioxidant capacity. Therefore, the VunHY5-VunERD14 module and the VunHY5-VunMED2-VunERD14 positive cascade effect are involved in the cold signal transduction in asparagus bean. Our findings have implications for the breeding of asparagus bean varieties with improved cold tolerance.

Impacts of High Temperatures on the Growth and Development of Rice and Measures for Heat Tolerance Regulation: A Review

As one of the world’s principal food crops, rice sustains over half of the global population. With global climate change intensifying, the frequency of extreme high temperatures is increasing, posing significant threats to the growth and development, yield, and quality of rice, thereby jeopardizing global food security. This study reviews the impacts of high temperatures on rice at different developmental stages and summarizes previous research on heat tolerance cultivation techniques for rice. Currently, to enhance heat tolerance in rice, the following strategies were primarily adopted: (1) the exploration of heat-tolerant genetic resources and breeding of heat-tolerant varieties; (2) cooling through canopy temperature management via enhanced transpiration regulated by water management; (3) the scientific application of fertilizers to promote the accumulation of assimilates in rice; (4) the application of exogenous regulators to bolster the antioxidant capacity of rice. The implementation of these strategies not only helps to ensure rice yield and quality but also provides robust support for addressing the challenges that global warming poses to agricultural production.

Exploring the distribution of polymorphism across diverse breeds Worldwide in the bovine NR5A2 gene and its correlation with number of mature follicles and corpus albicans

The Nuclear receptor subfamily 5 group A member 2 (NR5A2) gene plays a pivotal role in ovarian development, ovulation, and reproductive traits. There is a lack of studies on its impact on ovarian traits and reproductive traits in cattle. This study aimed to explore NR5A2 gene polymorphisms associations with reproductive traits and investigate the distribution of NR5A2 gene polymorphisms across diverse bovine breeds worldwide. We identified a novel 17-bp deletion within the NR5A2 gene specifically in Chinese Holstein cows (n = 1033) leading to the observation of two genotypes DD and ID. Subsequent association analysis revealed a significant correlation between the ‘ID’ genotype at this locus and a larger number of corpus albicans (p = 0.042) in diestrus, as well as a higher number of mature follicles (p = 0.038) in estrus. In addition, we also found that the distribution of this deletion exhibits strong regionality across different cattle breeds globally. These findings indicate that the 17-bp deletion mutation within the NR5A2 gene is significantly associated with an increased corpus luteum diameter and a greater number of mature follicles, suggesting its potential utility as a valuable DNA marker for enhancing cow fertility.

Functions of MdTINY, a member of the apple dehydration responsive element binding-A4

The dehydration responsive element binding (DREB) transcription factors play an important role in plant growth and development and are extensively involved in plant responses to abiotic stress. The DREB family contains six subfamilies, and TINY belongs to the DREB-A4 subfamily. The Arabidopsis thaliana TINY gene, AtTINY, plays a role in regulating plant growth and responses to stress. In order to investigate the evolutionary characterization of the DREB-A4 subfamily and the biological function of the MdTINY gene in apple (Malus domestica), in this study, we used the databases GDDH13 and TAIR and online tools (Expasy and WoLF PSORT) to study the biological information of the DREB-A4 subfamily in apple. In addition, the tertiary structures of the proteins were predicted. The apple DREB-A4 subfamily contained 22 genes, all of which had a conserved AP2 domain, and subcellular localization predictions showed that DREB-A4 subfamily proteins were mainly located in the nucleus. The transgenic calli of MdTINY were obtained by the Agrobacterium-mediated transformation method, and the main biological functions of MdTINY were explored by quantitative real-time PCR (qRT-PCR) combined with anthocyanin content determination. MdTINY shared the highest amino acid sequence similarity with AtTINY. The coding region of MdTINY had a full length of 759 bp, encoding 252 amino acid residues. Analysis of the promoter elements and expression patterns indicated that MdTINY was responsive to light and multiple stress conditions. MdTINY was localized in the nucleus and had transcriptional autoactivation activity. The overexpression of MdTINY in calli inhibited normal growth and promoted anthocyanoside accumulation. These results indicated that MdTINY negatively regulated apple plant growth and promoted fruit coloring, providing a candidate gene for the breeding of apple varieties with high quality of fruit color.

Understanding the evolution of domestic dogs

This article discusses the process of domestication, and the outcomes of domestication, and the evolutionary history of dogs. The essay also describes the processes that led to the evolution of domestic dogs and investigates the causes of the enormous variety of dog breeds. This research shows the complex interactions between humans and dogs throughout the history by analyzing genetic, and social aspects. It also provides insights into how this special relationship has formed the diversity of breeds that exist today. Additionally, the article provides a detailed examination of the Chinese Village Dog, an indigenous breed of China, highlighting its unique evolutionary pathway, genetic diversity, and cultural significance. Through the analysis of ancient texts and archaeological findings, this research sheds light on the longstanding relationship between Chinese Village Dogs and human communities, as well as the ongoing challenges and conservation efforts aimed at preserving indigenous Asian dog breeds.

Breeding potential of red- and white-skinned onion (Allium cepa L.) genotypes for economic traits using multivariate analysis

ABSTRACT The improvement of onion (Allium cepa L.) depends on the characterization and evaluation of the germplasm to find superior genotypes with desired horticultural qualities and utilization of diversity in future breeding. The study aimed to evaluate advanced breeding lines (consisting of both red- and white-skinned types) through genetic component analyses and genetic divergence using multivariate analysis to identify genotypes that can be utilized in breeding for table and dehydration purposes, respectively. Genotypes ‘(EM-AVT-2) REC-21-48,’ ‘(RIET) RVA-21-01,’ and ‘(EM-AVT-2) REC-21-46’ were found to be high yielders. Higher estimates of the genotypic coefficient of variation, heritability and genetic advance for the percentage of the double bulb, total soluble solid, and reducing sugar contents indicate additive gene action, and selection based on these parameters would be more reliable. The plant height, polar diameter, equatorial diameter, and neck thickness emerged as important selection indices. Principal components such as the plant height, number of leaves per plant, percentage of bolting and double bulb had values of >1, accounting for 81.73% of the total variation. Based on mean values and multivariate analysis, onion genotypes ‘(EM-AVT-2) REC-21-46’ (red-skinned), ‘(EM-AVT-2) REC-21-52’ (red-skinned), ‘(WIET) WVA-21-47’ (white-skinned), ‘(WAVT-2) WVC-21-74’ (white-skinned), ‘(WIET) WVA-21-39’ (white-skinned) and ‘(WHTSS-AVT-2) WTC-21-84’ (white-skinned) could be utilized as potential genitors in future breeding for table and dehydration purpose.

Integrating QTL mapping and transcriptome analysis to provide molecular insights into gynophore-pod strength in cultivated peanut (Arachis hypogaea L.).

Gynophore-pod strength is one of important mechanical properties that affect mechanized harvesting quality in peanut. Yet its molecular regulation remains elusive. We measured gynophore-pod strength across three environments using a recombinant inbred line (RIL) population derived from a cross between Yuanza9102 and Xuzhou68-4, followed by QTL mapping. Lines with extreme gynophore-pod strength from the RILs were selected to perform anatomical analysis and transcriptome analysis to elucidate the underlying molecular mechanisms governing gynophore-pod strength. Both genotypic factor and environments affected gynophore-pod strength significantly, and its broad sense heritability (h2 ) was estimated as 0.77. Two QTLs that were stable in at least two environments were detected. qGPS.A05-1 was mapped 4cM (about 1.09Mb) on chromosome A05, and qGPS.B02-1 was mapped 3cM (about 1.71Mb) on chromosome B02. Anatomical analysis showed higher lignin content in lines with extreme high gynophore-pod strength compared to those with extreme low gynophore-pod strength. Additionally, comparative transcriptome analysis unveiled that phenylpropanoid biosynthesis was the main pathway associated with high gynophore-pod strength. Further, we predicted VJ8B3Q and H82QG0 as the candidate genes for qGPS.A05-1 and qGPS.B02-1, respectively. The two stable QTLs and their associated markers could help modify gynophore-pod strength. Our findings may offer genetic resources for the molecular-assisted breeding of new peanut varieties with improved mechanized harvesting quality.

Classification of Dog Breeds Using Convolutional Neural Network Models and Support Vector Machine.

When classifying breeds of dogs, the accuracy of classification significantly affects breed identification and dog research. Using images to classify dog breeds can improve classification efficiency; however, it is increasingly challenging due to the diversities and similarities among dog breeds. Traditional image classification methods primarily rely on extracting simple geometric features, while current convolutional neural networks (CNNs) are capable of learning high-level semantic features. However, the diversity of dog breeds continues to pose a challenge to classification accuracy. To address this, we developed a model that integrates multiple CNNs with a machine learning method, significantly improving the accuracy of dog images classification. We used the Stanford Dog Dataset, combined image features from four CNN models, filtered the features using principal component analysis (PCA) and gray wolf optimization algorithm (GWO), and then classified the features with support vector machine (SVM). The classification accuracy rate reached 95.24% for 120 breeds and 99.34% for 76 selected breeds, respectively, demonstrating a significant improvement over existing methods using the same Stanford Dog Dataset. It is expected that our proposed method will further serve as a fundamental framework for the accurate classification of a wider range of species.

Runs of Homozygosity Islands in Autochthonous Spanish Cattle Breeds.

Understanding the genetic architecture of autochthonous European cattle breeds is important for developing effective conservation strategies and sustainable breeding programs. Spanish beef cattle, which trace their origins to ancient migrations from the Near East with later admixture from African populations, exhibit a rich genetic diversity shaped by environmental adaptation and selective breeding. Runs of Homozygosity (ROH) are extended stretches of identical genetic material inherited from both parents. They serve as indicators of inbreeding and selection signatures within populations. ROH islands, or regions of the genome where ROH segments are highly concentrated across individuals within a breed, indicate genomic regions under selective pressure. This study explores the distribution of ROH islands across seven Spanish beef cattle breeds (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Retinta, Pirenaica, and Rubia Gallega). By analyzing high-density SNP data, we characterized ROH patterns and identified genomic regions with high levels of homozygosity, which may indicate selection pressures or common ancestry. Our findings revealed breed-specific ROH patterns as well as shared ROH islands, underscoring genetic relationships and differentiation among the breeds. Notably, Morucha displayed the highest number of ROH, while Asturiana de los Valles had the fewest. FROH values, which indicate genomic inbreeding, varied among the breeds, with Morucha and Retinta being associated with higher values. We identified 57 ROH islands, with shared regions among populations that suggest common ancestral selection pressures. Key genes within these regions, like MSTN, are associated with muscle growth, body weight, and fertility. This study offers valuable insights for breeding strategies and conservation efforts, highlighting the genetic diversity and historical background of Spanish cattle breeds.

Screening and Evaluation of Salt-Tolerant Wheat Germplasm Based on the Main Morphological Indices at the Germination and Seedling Stages.

The successful screening and evaluation of salt-tolerant germplasm at the germination and seedling stages is of great importance for promoting the breeding of wheat varieties with salt tolerance. In this study, 70 wheat varieties bred in different regions were evaluated for salt tolerance through hydroponic exposure to different concentrations of salt. The relative water absorption, water absorption rate, dehiscence rate, germination rate, and germination index of seeds, and plant height, root length, stem diameter, and biomass of seedlings were determined at the germination and seedling stages of wheat, and the salt tolerance was identified and evaluated using multivariate statistical analysis. The germination ability and seedling growth potential of wheat germplasms decreased with the aggravation of salt stress. Based on the comprehensive salt tolerance index at the germination stage, our study identified 35 varieties to be salt-tolerant. There were nine varieties further screened for having strong salt tolerance according to the comprehensive salt tolerance index at the germination and seedling stages. SN41, Emam, YN301, and JM262 were superior in salt-tolerance, and YM39, LM30, JM60, YN999, and SD29 were salt-tolerant. Our study suggests that the biomass of seedlings can be used as a key parameter for assessing wheat germplasm's ability to withstand salt. Our results can provide some basic materials for cultivating new germplasm with salt tolerance and excavating the related genes of wheat.

Identification and genetic diversity analysis of specific walnut F1 progeny based on SSR molecular markers: taking heart-shaped walnuts and Jinghong 1 as examples

To gain a deeper understanding of the genetic diversity and authenticity of natural pollinated F1 progeny populations of specific walnuts (heart-shaped walnuts and Jinghong 1), as well as the genetic relationship between F1 offspring and their maternal parent. 32 heart-shaped walnut F1 offspring, 45 Jinghong 1 F1 offspring, and their maternal parent were selected as materials, and 14 pairs of SSR markers were used for genetic diversity and parent-child relationship analysis. The results showed that Jr05, Jr11, Jr29, Jr44, Jr45, Jr52, Jr53, Jr55, and Jr56 could be used as SSR markers for the identification of hybrid offspring in heart-shaped walnuts. Jr35, Jr40, Jr45, Jr50, Jr52, and Jr53 could be used as SSR markers for the identification of hybrid offspring of Jinghong 1. XX21 had the closer genetic relationship with heart-shaped walnuts, and HR20 had the closer genetic relationship with Jinghong 1. Besides, the classification results of F1 offspring based on UPGMA clustering and STRUCTURE were different. This study not only laid the foundation for parental identification of specific walnut F1 progeny, but also provided theoretical reference for fixing hybrid advantages, germplasm innovation, and new variety breeding.

QTL mapping and genome-wide association analysis reveal genetic loci and candidate gene for resistance to gray leaf spot in tropical and subtropical maize germplasm

Key messageUsing QTL mapping and GWAS, two candidate genes (Zm00001d051039 and Zm00001d051147) were consistently identified across the three different environments and BLUP values. GWAS analysis identified the candidate gene, Zm00001d044845. These genes were subsequently validated to exhibit a significant association with maize gray leaf spot (GLS) resistance.Gray leaf spot (GLS) is a major foliar disease of maize (Zea mays L.) that causes significant yield losses worldwide. Understanding the genetic mechanisms underlying gray leaf spot resistance is crucial for breeding high-yielding and disease-resistant varieties. In this study, eight tropical and subtropical germplasms were crossed with the temperate germplasm Ye107 to develop a nested association mapping (NAM) population comprising 1,653 F2:8 RILs, consisting of eight recombinant inbred line (RIL) subpopulations, using the single-seed descent method. The NAM population was evaluated for GLS resistance in three different environments, and genotyping by sequencing of the NAM population generated 593,719 high-quality single-nucleotide polymorphisms (SNPs). Linkage analysis and genome-wide association studies (GWASs) were conducted to identify candidate genes regulating GLS resistance in maize. Both analyses identified 25 QTLs and 149 SNPs that were significantly associated with GLS resistance. Candidate genes were screened 20 Kb upstream and downstream of the significant SNPs, and three novel candidate genes (Zm00001d051039, Zm00001d051147, and Zm00001d044845) were identified. Zm00001d051039 and Zm00001d051147 were located on chromosome 4 and co-localized in both linkage (qGLS4-1 and qGLS4-2) and GWAS analyses. SNP-138,153,206 was located 0.499 kb downstream of the candidate gene Zm00001d051039, which encodes the protein IN2-1 homolog B, a homolog of glutathione S-transferase (GST). GSTs and protein IN2-1 homolog B scavenge reactive oxygen species under various stress conditions, and GSTs are believed to protect plants from a wide range of biotic and abiotic stresses by detoxifying reactive electrophilic compounds. Zm00001d051147 encodes a probable beta-1,4-xylosyltransferase involved in the biosynthesis of xylan in the cell wall, enhancing resistance. SNP-145,813,215 was located 2.69 kb downstream of the candidate gene. SNP-5,043,412 was consistently identified in three different environments and BLUP values and was located 8.788 kb downstream of the candidate gene Zm00001d044845 on chromosome 9. Zm00001d044845 encodes the U-box domain-containing protein 4 (PUB4), which is involved in regulating plant immunity. qRT-PCR analysis showed that the relative expression levels of the three candidate genes were significantly upregulated in the leaves of the TML139 (resistant) parent, indicating that these three candidate genes could be associated with resistance to GLS. The findings of this study are significant for marker-assisted breeding aimed at enhancing resistance to GLS in maize and lay the foundation for further elucidation of the genetic mechanisms underlying resistance to gray leaf spot in maize and breeding of new disease-resistant varieties.