Resource For Breeding Research Articles

Eastern filbert blight resistant Corylus avellana identified from 20 years of germplasm introduction and evaluation at Rutgers University, New Jersey, USA

The stem canker disease eastern filbert blight (EFB), caused by Anisogramma anomala, is a major impediment of European hazelnut (Corylus avellana) production in the United States. While most European hazelnut cultivars are highly susceptible to the pathogen, which remains confined to North America, EFB resistant and tolerant genotypes occur in the gene pool at low frequency. At Rutgers University, New Brunswick, NJ, USA, 5,226 trees were grown from open pollinated seeds collected from Russia, Crimea, Poland, Turkey, Estonia, Latvia, Lithuania, Moldova, Azerbaijan, Italy, and the Republic of Georgia between 2002 to 2010. The trees were field planted, exposed to A. anomala under high pathogen pressure, and evaluated for disease response 5-6 years after their establishment. At this point, around four percent were found to be EFB resistant totaling 216 accessions that spanned a wide diversity of seedlots from most countries and regions. However, recent observations show many of these once-resistant selections have since succumbed to EFB. In this study, the long-term disease response of this germplasm was evaluated to identify trees remaining resistant and tolerant and document changes in EFB response over time in relation to their origin. All trees were rated for presence of EFB according to a scale of 0 to 5 where 0 = no EFB and 5 = all stems have cankers. Data were assembled from three sets: first reports from 5-6 years after each planting year, a reassessment in 2017, and a final evaluation in January 2024. Overall, the results showed a significant reduction in resistant individuals from the original reports. By 2017, the population of 216 trees was reduced to 154 and by 2024 it decreased further to 91. Notably, this shift from resistant to susceptible phenotype was severe and abrupt and patterns were observed within related seed lots. These patterns were also apparent in trees where their resistance (R) genes were mapped. Specifically, all selections with R genes mapped to linkage group (LG) 6 now expressed severe EFB, while those with R genes mapped to LG 2 or 7 remained free of disease. These results strongly suggest pathogenic variation present over time played a role in the breakdown of resistance. Fortunately, despite loss of some of the germplasm, a wide variety of trees spanning most collection origins still remain free of EFB. These 91 trees from 56 distinct seedlots originating from 7 countries are formally documented in this manuscript to facilitate their long-term preservation, continued evaluation and sharing, and to increase global awareness of this valuable genetic resource for future research and breeding.

Genetic Assessment and Positioning of Algerian Barley Landraces with Respect to Landraces from the Middle East and Europe Using RAPD and SSR Markers

Landraces are a critical genetic resource for resilience breeding, offering solutions to prepare agriculture for the challenges posed by climate change. Their efficient utilisation depends on understanding their history and genetic relationships. The current study investigates the phylogenetic relationships of barley landraces from Algeria, varieties from the Near and Middle East, traditional landraces, and modern cultivars from Europe. Using a core set of 33 varieties, including the wild ancestor Hordeum spontaneum from Armenia, genetic diversity was analysed with Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR) markers spanning all barley chromosomes. Based on the SSR-based phylogeny, the Algerian varieties are well clustered with those from the Near East, while distinct from the European varieties. The findings from RAPD markers partially support these results. Using exclusively traditional landraces, where a region of origin can be defined, the SSR markers are analysed separately for each chromosome individually, and the resulting clades are represented by the respective region of origin. This strategy resolves qualitative differences in geographic resolution, depending on the chromosome. While marker HvB23D (chromosome 4) separated the wild H. spontaneum from all domesticated genotypes, markers Bmag19 and Hv13GIII (chromosome 3) reveal four distinct geographic clusters (Maghreb, Near and Middle East, West Europe, Central Europe). These biogeographic patterns suggest a model, where divergence of domesticated barley due to human activity interacted with introgression of individual chromosomes from wild barley, yielding adaptive diversity. These biogeographic patterns suggest a model in which the divergence of domesticated barley, driven by human activity, interacts with the introgression of chromosomes from wild barley, resulting in the creation of adaptive genetic diversity. Our research advances our knowledge of barley landraces’ functional genomics and highlights their potential in molecular breeding, particularly for developing resilient varieties suited to diverse environmental conditions.

Characterization of the chitinase gene family in Saccharum reveals the disease resistance mechanism of ScChiVII1.

A chitinase gene ScChiVII1 which is involved in defense against pathogen stress was characterized in sugarcane. Chitinases, a subclass of pathogenesis-related proteins, catalyze chitin hydrolysis and play a key role in plant defense against chitin-containing pathogens. However, there is little research on disease resistance analysis of chitinase genes in sugarcane, and the systematic identification of their gene families has not been reported. In this study, 85 SsChi and 23 ShChi genes, which were divided into 6 groups, were identified from the wild sugarcane species Saccharum spontaneum and Saccharum hybrid cultivar R570, respectively. Transcriptome analysis and real-time quantitative PCR revealed that SsChi genes responded to smut pathogen stress. The chitinase crude extracted from the leaves of transgenic Nicotiana benthamiana plants overexpressing ScChiVII1 (a homologous gene of SsChi22a) inhibited the hyphal growth of Fusarium solani var. coeruleum and Sporisorium scitamineum. Notably, the chitinase and catalase activities and the jasmonic acid content in the leaves of ScChiVII1 transgenic N. benthamiana increased after inoculation with F solani var. coeruleum, but the salicylic acid, hydrogen peroxide, and malondialdehyde contents decreased. Comprehensive RNA sequencing of leaves before (0day) and after inoculation (2days) revealed that ScChiVII1 transgenic tobacco enhanced plant disease resistance by activating transcription factors and disease resistance-related signaling pathways, and modulating the expression of genes involved in the hypersensitive response and ethylene synthesis pathways. Taken together, this study provides comprehensive information on the chitinase gene family and offers potential genetic resources for disease resistance breeding in sugarcane.

Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb.

Microsatellites [simple sequence repeats (SSRs)] are one of the most widely used sources of genetic markers, particularly prevalent in plants. Despite their importance in various applications, a comprehensive genome-wide identification of coding sequence (CDS)-associated SSR markers in the Argania spinosa L. genome has yet to be conducted. In this study, 66 280 CDSs containing 5351 SSRs within 4535 A. spinosa L. CDSs were identified. Among these, tri-nucleotide motifs (58.96%) were the most common, followed by hexa-nucleotide (15.71%) and di-nucleotide motifs (13.32%). The predominant SSR motif in the tri-nucleotide category was AAG (24.4%), while AG (94.1%) was the most abundant among di-nucleotide repeats. Furthermore, the extracted CDSs containing SSRs were subjected to functional annotation; 3396 CDSs (74.88%) exhibited homology with known proteins, 3341 CDSs (73.7%) were assigned Gene Ontology terms, 1004 CDSs were annotated with Enzyme Commission numbers, and 832 (18.3%) were annotated with KEGG pathways. A total of 3475 primer pairs were designed, out of which 3264 were successfully validated in silico against the A. spinosa L. genome, with 99.6% representing high-resolution markers yielding no more than three products. Additionally, the SSR markers demonstrated a low rate of transferability through in-silico verification in two species within the Sapotaceae family. Furthermore, we developed an online database, the "Argania spinosa L. SSR database: https://as-fmmdb.shinyapps.io/asssrdb/" (AsSSRdb) to provide access to the CDS-associated SSRs identified in this study. Overall, this research provides valuable marker resources for DNA fingerprinting, genetic studies, and molecular breeding in argan and related species. Database URL: https://as-fmmdb.shinyapps.io/asssrdb/.

Multi-Omics Analyses Offer Novel Insights into the Selection of Sugar and Lipid Metabolism During Maize Domestication and Improvement.

Over thousands of years of domestication, maize has undergone significant environmental changes. Understanding the genetic and metabolic trace during maize evolution can better contribute to molecular breeding and nutrition quality improvement. This study examines the metabolic profiles and transcriptomes of maize kernels from teosinte, landrace, and maize accessions at 15 days post-pollination. Differentially accumulated metabolites were enriched in sugar and lipid metabolism pathways. The metabolic selection profile exhibited four distinct patterns: continuous increases, constant decrease, initial decline or stability followed by an increase, and initial growth or stability followed by a subsequent decline. Sugars and JA were positive selection while LPCs/LPEs were negative selection during evolution. The expression level of genes related to sugar accumulation was significantly higher in maize, contrasting with enhanced glycolysis and lipid metabolism activity in teosinte. The correlation network highlighted distinct hormonal regulation of sugar and lipid metabolism. We identified 27 candidate genes associated with sugar, lipid, and JA that have undergone strong selection by population genomic regions. The positive selection of the PLD may explain the negative selection of LPCs/LPEs due to substrate competition. These findings enhance our understanding of the evolutionary trajectory of primary metabolism in maize and provide valuable resources for breeding and improvement.

Genome-wide analysis of fatty acid desaturase genes in moso bamboo (Phyllostachys edulis) reveal their important roles in abiotic stresses responses

BackgroundBamboo is an important nontimber forestry product worldwide, while growth, development and geographic distribution of bamboo are often affected by abiotic stresses. Fatty acid desaturases have important roles in regulating plant abiotic stress tolerance, especially low-temperature. However, there is no report on genome-wide of FAD genes in bamboo under abiotic stresses.ResultsA toltal of 43 PeFAD genes were identified in moso bamboo genome, which were unevenly located in 17 scaffolds. Phylogenetic analysis indicated that PeFAD genes were divided into 6 groups and ADS/FAD5 group was absence in momo bamboo, and gene structure and histidine-motifs remained highly conserved in each group. The expansion of PeFAD genes was mainly caused by tandem and segmental duplications of SAD/FAB2 group. We also identified 59 types of miRNAs targeting PeFAD genes. RNA-seq data indicated that PeFAD genes were transcribed in various organs/tissues with different degrees, and responded to abiotic stresses and hormone treatments, including cold, salt, drought, SA, ABA, BR, NAA and GA. Co-expression analysis under cold stress showed that PeCBF3 might directly bind the promoter of top cold-responsive PeSLD1 gene that contained LTR cis-element and DRE core element. The qRT-PCR assay also validated the expression pattern of PeSLD1 and its upstream regulatory gene PeCBF3.ConclusionIn this study, we performed comprehensive genome-wide survey of PeFAD genes in moso bamboo and analyzed their expression patterns in various tissues and organs, and under abiotic stresses and phytohormones treatment. The qRT-PCR assay validated the cold inducibility of PeSLD1 and PeCBF3. This work showed critical roles of PeFAD genes in abiotic stresses responses. This is the first report on genome-wide analysis of PeFAD genes in moso bamboo, which will provide critical gene resources for molecular breeding of stress-toleranct moso bamboo.

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.

LcASR enhances tolerance to abiotic stress in Leymus chinensis and Arabidopsis thaliana by improving photosynthetic performance.

As a crucial forage grass, Leymus chinensis plays significant roles in soil and water conservation owing to its robust stress resistance. However, the underlying molecular mechanisms of its stress tolerance remain unclear. In this study, a novel gene, designated as LcASR (Abiotic Stress Resistance in Leymus chinensis), imparting resilience to both high light and drought, was identified. Under normal growth conditions, heterologous overexpression of LcASR in Arabidopsis (HO lines) showed no significant difference in appearance compared to wild-type. Nevertheless, HO lines accumulate significantly higher chlorophyll content during the dark-to-light transition compared to the wild-type, indicating that the LcASR protein participates in chlorophyll synthesis during chloroplast development. Meanwhile, transgenic Arabidopsis and L. chinensis plants exhibited resistance to abiotic stresses such as high light and drought. Photosystem complexes analysis revealed that LHCII proteins remained stable within their respective complexes during high light stress. We hypothesize that LcASR may play a role in fine tuning of chlorophyll synthesis to enable plant adaptation to diverse stress conditions. Moreover, overexpression of LcASR in L. chinensis led to agronomically valuable traits such as deeper green color, higher biomass accumulation, prolonged withering period, and extended grazing durations. This study uncovers a novel gene in L. chinensis that enhances forage yield and provides valuable genetic resources for sheepgrass breeding.

Genome-Wide Analysis of the Multidrug and Toxic Compound Extrusion Gene Family in the Tea Plant

The multidrug and toxic compound extrusion (MATE) family is the latest class of novel secondary transporters discovered in plants. However, there is currently no comprehensive analysis of the MATE gene family in the tea plant. In this study, 68 CsMATE genes were identified from the tea plant genome using bioinformatic methods. In general, we analyzed the evolutionary relationships, intron–exon structure, distribution in chromosomes, conserved domains, and gene expression patterns in different tissues and stresses of the CsMATE gene family. The 68 CsMATEs were phylogenetically divided into four major clusters (Class I to Class IV). The CsMATE genes within the same class exhibit similar structural features, while displaying certain distinctions across different classes. Evolutionary analysis indicated that the CsMATE gene family expanded mainly through gene duplication events, in addition to proximal duplication. Through the analysis of cis-acting elements, it was found that CsMATE genes may be involved in the growth, development, and stress response. Furthermore, we observed that certain CsMATE genes could be induced to exhibit expression under abiotic stress conditions such as low temperature, high salinity (NaCl), osmotic stress (PEG), and methyl jasmonate treatment (MeJA). The findings presented herein offer a crucial theoretical foundation for elucidating the biological functions of CsMATE genes, particularly in response to abiotic stress, and furnish valuable potential genetic resources for tea plant resistance breeding.

SoyOD: An Integrated Soybean Multi-omics Database for Mining Genes and Biological Research.

Soybean is a globally important crop for food, feed, oil, and nitrogen fixation. A variety of multi-omics studies has been carried out, generating datasets ranging from genotype to phenotype. In order to efficiently utilize these data for basic and applied research, a soybean multi-omics database with extensive data coverage and comprehensive data analysis tools was established. The Soybean Omics Database (SoyOD) integrates important new datasets with existing public datasets to form the most comprehensive collection of soybean multi-omics information. Compared to existing soybean databases, SoyOD incorporates an extensive collection of novel data derived from the deep-sequencing of 984 germplasms, 162 novel transcriptome datasets from seeds at different developmental stages, 53 phenotypic datasets, and more than 2500 phenotypic images. In addition, SoyOD integrates existing data resources, including 59 assembled genomes, genetic variation data from 3904 soybean accessions, 225 sets of phenotypic data, and 1097 transcriptomic sequences covering 507 different tissues and treatment conditions. Moreover, SoyOD can be used to mine candidate genes for important agronomic traits, as shown in a case study on plant height. Additionally, powerful analytical and easy-to-use toolkits enable users to easily access the available multi-omics datasets, and to rapidly search genotypic and phenotypic data in a particular germplasm. The novelty, comprehensiveness, and user-friendly features of SoyOD make it a valuable resource for soybean molecular breeding and biological research. SoyOD is publicly accessible at https://bis.zju.edu.cn/soyod.

MADS-box encoding gene Tunicate1 positively controls maize yield by increasing leaf number above the ear

The leaves above the ear serve as a major source of carbohydrates for grain filling in maize. However, increasing the number of leaves above the ear to strengthen the source and improve maize yield remains challenging in modern maize breeding. Here, we clone the causative gene of the quantitative trait locus (QTL) associated with the number of leaves above the ear. The causative gene is the previously reported MADS-box domain-encoding gene Tunicate1 (Tu1), which is responsible for the phenotype of pod corn or Tunicate maize. We show that Tu1 can substantially increase the leaf number above the ear while maintaining the source‒sink balance. A distal upstream 5-base pair (bp) insertion of Tu1 originating from a popcorn landrace enhances its transcription, coregulates its plastochron activators and repressors, and increases the number of leaves above the ear. Field tests demonstrate that the 5-bp insertion of Tu1 can increase grain yields by 11.4% and 9.5% under regular and dense planting conditions, respectively. The discovery of this favorable Tu1 allele from landraces suggests that landraces represent a valuable resource for high-yield breeding of maize.

Assessment and preservation of the gene pool of the domestic <i>Kholmogorsk</i> cattle breed in the Arkhangelsk region

The article presents the results of monitoring immunogenetic studies on the origin of Kholmogory cattle to establish their breed genetic passport for the EAB locus of blood groups. The importance of determining of the breeding animals statute taking into account the forms of the identified state of erythrocyte antigens for the purpose of registration in the federal state information and analytical system of breeding resources of the Russian Federation is noted. In breeding farms of the Arkhangelsk region over the past 29 years, the total number of animals tested for the reliability of origin was 57,311. The percentage of reliability in the monitored livestock numbers varied from 86.95% (1995-2000) to 97.28% (2016-2020). To establish the genetic passport of breeding female tribal species of the breed with up to 75% Holstein bloodline approved for breeding purposes when working with Kholmogory cattle, we conducted immunogenetic testing, which revealed 46 alleles of the EAB locus. The total frequency of the EAB locus alleles in animals of groups 1-2 with specific (typical) for the Kholmogory breed and with unique alleles was 69.38%. In group 3 of animals with alleles of the approved Holstein breed, the total frequency was set at 30.6%, in group 4 with alleles of unapproved breeds – 0.02%. It was established that the concentration of alleles G2O2, B2O2, B2G2KA’B’G’O’G’’, B2E’2G’, B2O2Y2D’, Q is very low, they are found only in some individuals. The degree of homozygosity (theoretical) is 5.6%, the number of effective alleles is 17.9.

Resource pulses drive spatio‐temporal dynamics of non‐native bark beetles and wood borers

Abstract Clear‐fell harvesting of non‐native plantation forests in the southern hemisphere creates large amounts of woody debris that is used for breeding by non‐native bark beetles and wood borers. Limited competition and a shortage of natural enemies allow some invasive pine bark beetles and wood borers to become highly abundant and cause phytosanitary issues. Replicated transects (550–750 m long) of funnel traps baited with alpha‐pinene and ethanol spanning even‐aged Pinus radiata stands were established in New Zealand's largest plantation forest and monitored from pre‐harvest until up to 5 years post‐harvesting to test the effects of harvesting residue resource pulses on the spatio‐temporal population dynamics of Hylurgus ligniperda, Hylastes ater and Arhopalus ferus. Generalised additive mixed model analyses of trap captures of >687,000 H. ligniperda, >7600 H. ater and >5000 A. ferus individuals showed greatly elevated populations for the first 2–3 years post‐harvest. Subsequently, populations returned to very low levels once the resource pulse was exhausted. Spatial patterns of captures reflecting beetle dispersal from breeding material showed a curvilinear decline along the breeding resource gradient by up to 95% from the interior of a recently harvested stand into an adjacent, previously harvested stand with exploited resources. Synthesis and applications. The results show that forest management characterised by ongoing harvesting of neighbouring stands facilitates the build‐up of large populations of bark beetles and wood borers of phytosanitary concern. This is due to recurrent resource pulses caused by the supply of substantial amounts of breeding material from tree felling. Our findings can inform forest planning aimed at avoiding such harvesting patterns, by assisting with the development and implementation of strategies for the management of beetle populations across the landscape. Most beetles dispersed <400 m beyond the source stand edge, although some beetles are likely to have dispersed further. Keeping a distance of 1–2 km between recently felled stands and those scheduled for felling would be expected to reduce rapid population growth. This knowledge can also be used to reduce seedling attack, minimise infestation of logs, and ultimately, mitigate pathway and biosecurity risks, with important implications for forest product exports and quarantine measures.

Pan-transcriptome analysis provide insights into resistance and fruit quality breeding of pear (Pyrus pyrifolia)

Pyrus pyrifolia, commonly known as sand pear, is a key economic fruit tree in temperate regions and possesses highly diverse germplasm resources for pear quality improvement. However, research on the relationship between resistance and fruit quality traits during the breeding of fruit species like pear is limited. Pan-transcriptomes effectively capture genetic information from coding regions and reflect variations in gene expression between individuals. Here, we constructed a pan-transcriptome composed of 506 samples from different tissues of sand pear, and explored the intrinsic relationships among phenotypes and the selection for disease resistance during improvement based on expression presence/absence variation (ePAVs). The pan-transcriptome contains 156,744 transcripts, among which the novel transcripts show significant enrichment in the defense response. Interestingly, disease resistance genes are highly expressed in landraces of pear but have been selected against during the improvement of this perennial tree species. We found that genetically diverse landraces can be divided into two subgroups and inferred that they have undergone different dispersal processes. Through co-expression network analysis, we confirmed that the formation of stone cells in pears, the deposition of fruit anthocyanins, and the ability to resist stress are interrelated. They are jointly regulated by several modules, and the expression of regulatory genes has a significant correlation. Moreover, we identified candidate genes such as HKL1 that may affect sugar content and are missing from the reference genome. Our study provides insights into the associations between complex fruit traits, while providing a database resource for pear disease resistance and fruit quality breeding.

Progress on the mining of functional genes of Lonicera japonica.

Lonicera japonica Thunb. is a semi-evergreen climbing shrub belonging to the Caprifoliaceae family, whose dried flower buds or flowers on the verge of blooming are known as Jin Yin Hua in traditional Chinese medicine. This plant is not only a high-value and widely used medicinal material but also possesses characteristics that make it suitable for both medicinal and culinary purposes. Currently, there is a robust market demand for Jin Yin Hua, yet the breeding technology for new varieties of Lonicera japonica lags behind, necessitating the integration of modern breeding techniques. With the advancement of genomics in Lonicera japonica, an increasing number of functional genes have been identified, amassing a rich reservoir of genetic resources for molecular breeding of this species. In this review, we summarize the progress in Lonicera japonica genomics, functional gene mining, and the establishment of genetic transformation systems. In light of the existing challenges and deficiencies in the research of functional genes and quality breeding of Lonicera japonica, it is imperative to establish a germplasm resource bank, a mutant library, and an efficient genetic transformation system for this plant. Intensive research into the mining and identification of functional genes should be conducted, and molecular markers closely linked to the functional genes of Lonicera japonica should be developed. This will lay a foundational basis for the identification and cultivation of breakthrough varieties with superior qualities in Lonicera japonica.

FS2 encodes an ARID-HMG transcription factor that regulates fruit spine density in cucumber

Fruit spine density is an important commercial trait for cucumber (Cucumis sativus L.). However, most North China-type cucumbers, which are grown over large areas, have a dense-spine phenotype, which directly affects the appearance quality, storage, and transportation of fruits. Here, we isolated a novel few spines mutant (fs2) from the wild-type (WT) inbred line WD1, a North China-type cucumber with high density fruit spines, by ethyl methanesulfonate (EMS) mutagenic treatment. Genetic analysis revealed that the phenotype of fs2 was controlled by a single recessive nuclear gene. We fine-mapped the fs2 locus using F2 and BC1 populations (1802 and 420 individuals, respectively) and showed that the candidate gene of FS2 (Csa4G652850) encoded an ARID-HMG transcription factor containing an A/T-rich interaction domain (ARID) and a high mobility group box domain (HMG). One SNP (C to T) and one InDel (a 40-bp deletion) in the coding region of FS2 resulted in amino acid variation and premature translation termination in the fs2 mutant, respectively. FS2 was highly expressed in the apical buds and young ovaries. In addition, the experiments suggest that FS2 participates in the regulation of fruit spine initiation by activating the expression of the Tril gene in cucumber. This work not only provides an important reference for understanding the molecular mechanisms of fruit spine development but also provides an important resource for fruit appearance quality breeding in cucumber.

Wild rice GL12 synergistically improves grain length and salt tolerance in cultivated rice

The abounding variations in wild rice provided potential reservoirs of beneficial genes for rice breeding. Maintaining stable and high yields under environmental stresses is a long-standing goal of rice breeding but is challenging due to internal trade-off mechanisms. Here, we report wild rice GL12W improves grain length and salt tolerance in both indica and japonica genetic backgrounds. GL12W alters cell length by regulating grain size related genes including GS2, and positively regulates the salt tolerance related genes, such as NAC5, NCED3, under salt stresses. We find that a G/T variation in GL12 promoter determined its binding to coactivator GIF1 and transcription factor WRKY53. GIF1 promotes GL12W expression in young panicle and WRKY53 represses GL12W expression under salt stresses. The G/T variation also contributes to the divergence of indica and japonica subspecies. Our results provide useful resources for modern rice breeding and shed insights for understanding yield and salt tolerance trade-off mechanism.

Genome-Wide Identification and Expression Profiling Analysis of the CCT Gene Family in Solanum lycopersicum and Solanum melongena.

CCT family genes play crucial roles in photoperiodic flowering and environmental stress response; however, there are limited reports in Solanum species with considerable edible and medicinal value. In this study, we conducted genome-wide characterization and expression profiling analysis of the CCT gene family in two Solanum species: tomato (Solanum lycopersicum L.) and eggplant (Solanum melongena L.). A total of 27 SlCCT and 29 SmCCT genes were identified in the tomato and eggplant genomes, respectively. Phylogenetic analysis showed that the CCT gene family could be divided into six subgroups (COL I, COL II, COL III, PRR, CMF I, and CMF II) in Oryza sativa and Arabidopsis thaliana. The similarity in the distribution of exon-intron structures and conserved motifs within the same subgroup indicated the conservation of SlCCT and SmCCT genes during evolution. Intraspecies collinearity analysis revealed that six pairs of SlCCT genes and seven pairs of SmCCT genes showed collinear relationships, suggesting that segmental duplication played a vital role in the expansion of the SlCCT and SmCCT family genes. Cis-acting element prediction indicated that SlCCT and SmCCT were likely to be involved in multiple responses stimulated by light, phytohormones, and abiotic stress. RT-qPCR analysis revealed that SmCCT15, SlCCT6/SlCCT14, and SlCCT23/SmCCT9 responded significantly to salt, drought, and cold stress, respectively. Our comprehensive analysis of the CCT gene family in tomato and eggplant provides a basis for further studies on its molecular role in regulating flowering and resistance to abiotic stress, and provides valuable candidate gene resources for tomato and eggplant molecular breeding.

Genome-wide dissection of genes shaping inflorescence morphology in 242 Chinese south–north sorghum accessions

The inflorescences morphology (IM) of sorghum (Sorghum bicolor L. Moench) affects its resistance to pests, diseases, and grain yields. However, the specific genetic factors underlying in IM are not yet fully elucidated. Here we conducted a comprehensive genome-wide association analysis (GWAS) to identify the stable and adaptive Quantitative Trait Loci (QTL) for five IM traits (panicle length, the number of cob nodes, the number of primary branches, the largest length of the primary branch, and panicle type) in a sorghum panel, which adapted to different environments from the south to north in China. Totally, 2,015,850 high quality single nucleotide polymorphisms (SNPs) were obtained. Population structure analysis showed that two distinct genetic sub-populations were divided according to their geographic origin. Seventy-one QTLs distributed in 41 genetic regions on 9 chromosomes were identified. These regions harbored 21 high-confident candidate genes that were homologous to rice domestication genes, including 7 related to IM. Two domestication-related genes (Sobic.003G052700 and Sobic.006G247700) were located into two major QTL regions (QTL3.4721839 and QTL6.58709500) which were identified in multi-environments. Allelic variations in the two genes displayed a geographical pattern, indicating that different IM traits were selected by south and north sorghum breeders, such as south sorghums had long and loose panicles in order to adapt the hot and humid climate, while north sorghums had short and compact panicle to increase planting density and grain yield per unit area due to dry climate. This work provides new breeding strategies and resources for developing locally adapted sorghum varieties.

LC-MS metabolomics uncovers potential biomarkers of semen cryo-injury in goats.

Semen cryopreservation acts a crucial role in enhancing breed improvement and conserving genetic resources. However, it often leads to decreased sperm activity and reduced pregnancy rates. Despite significant advancements in semen freezing techniques for goats, the precise factors and mechanisms causing cryo-injury remain unclear. In this study, we examined the motility characteristics of fresh semen versus frozen-thawed semen and investigated changes in the metabolite profiles of seminal plasma using liquid chromatograph-mass spectrometry (LC-MS). A total of 364 differentially expressed metabolites (DEMs) were identified between fresh and frozen-thawed semen samples. Among these, 185 metabolites were significantly up-regulated, while 179 were down-regulated (p<0.05). The majority of these DEMs belonged to lipids and lipid-like molecules, as well as organic acids and derivatives. The Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that these DEMs were primarily involved in pathways related to amino acid synthesis and metabolism. Additionally, metabolite set enrichment analysis (MSEA) underscored the critical role of amino acid synthesis and metabolic pathways in semen cryopreservation. Specific metabolites such as alanine, proline, phenylalanine, tryptophan, tyrosine, adenosine, citric acid, flavin adenine dinucleotide (FAD), and choline emerged as potential biomarkers for sperm cryo-injury in goats. These findings provide valuable insights into enhancing the quality of semen cryopreservation in goats, contributing to improved breeding and genetic resource conservation efforts.