Inbred Lines Research Articles

Effect of Introgression of Ty-1 and ty-5 Genes on Productivity, Quality, and Antioxidant Compounds in De la Pera Tomato Breeding Lines

Tomato (Solanum lycopersicum L.) is a crop that is affected by more than a hundred viral species. De la pera is a local varietal type of tomato that is very popular in southeastern Spain. However, it is highly susceptible to several viruses, such as Tomato yellow leaf curl virus (TYLCV), which is considered one of the most important diseases of tomato crops and is a limiting factor for production in both outdoor and protected crops, making it difficult to eradicate. This study shows the effect of gene introgression on the performance of traditional lines of De la pera by combining two genes that offer tolerance to TYLCV, Ty-1 and ty-5, on some yield and quality traits and on the antioxidant capacity of tomato fruits. Two pear tomato breeding families, UMH175 and UMH220, were evaluated. Four lines from each of the families with all homozygous combinations of the Ty-1 and ty-5 genes were studied. The results showed that the introgression of the ty-5 allele produced a slight negative effect on yield, mean fruit weight, total soluble solids, and titratable acidity, in contrast to Ty-1, which produced a large negative effect. None of the introgressions showed a negative effect on the antioxidant compounds. ty-5 is a promising gene for use in breeding programs.

Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life.

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

Genetic analysis of a maternal assistance score in sheep

Maternal behaviour is important for lamb survival, as ewes perform many behaviours that affect the chances of a lamb surviving. Collecting maternal behaviour data directly at lambing is time−consuming and not considered suitable for acquiring the large volumes of data that would be required for using as selection criteria within commercial breeding flocks. The aim of this study was to investigate if a simple scoring system is heritable and assesses the expression of behaviours that reduce the probability of lamb mortality. Ewe behaviour was scored on a 3-point Maternal Assistance Score (MAS): (1) the ewe shows a high level of maternal interest (assumed if no intervention required); (2) the ewe shows limited interest in her lamb; and (3) the ewe shows no interest in her lamb. A total of 19 453 MAS were collected over 12 years, across 24 farms (including both indoor and outdoor lambing systems) and 12 different breed lines that make up the Innovis breeding programme. Ewe parity, breed, number of lambs carried, flock, lambing batch, lambing day within flock and pre-mating weight all had a significant effect on MAS (P < 0.05). The maternal assistance score was shown to be heritable (h2 = 0.05) and repeatable (0.10), positively genetically correlated to lambing difficulty (rg = 0.29) and amount of assistance the lamb required to suckle from the ewe (rg = 0.88), and negatively genetically correlated with the number of lambs successfully reared (rg = 0.49). This study shows that an easy−to−measure score can be used by shepherds with large breeding flocks, based on whether the ewe requires further assistance to support her lamb rearing. The score could be used in breeding programmes to select for lamb rearing ability in the future and potentially lead to an improvement in lamb welfare through a reduction in mortality.

Kernel Trait and Genetic Variability Analysis in BC2F1 Maize Lines Derived from Zea nicaraguensis Crosses

Maize (Zea mays L.) is an important cereal crop with significant applications in food, feed and industrial applications. This study aimed to increase maize yield and quality by evaluating core traits in introgressed Zea nicaraguensis individual’s recipients of LM13 and LM14 maize inbred lines. Kernel type, shape, color, dimensions and weight were assessed in 35 BC2F1 plants using standardized descriptor guidelines. Analysis of genotypic and phenotypic coefficients of variation, heritability and genetic progress showed significant genetic diversity and the influence of environmental factors. Significant sources of variability highlighted by principal component analysis were kernel color, endosperm color, and 100-seed weight. High heritability and genetic progress in kernel color and length-to-width ratio indicate great selection potential. Reintroducing the diversity lost in cultivated maize inherent in Zea nicaraguensis has the potential to improve both its agronomic performance and quality. Future research should aim to identify genetic markers and examine the interaction between genetic and environmental influences to optimize maize varieties for specific environments and consumer preferences, ultimately contributing to global food security and agricultural sustainability.

Quantitative Trait Loci Mapping and Comparative Transcriptome Analysis of Fruit Weight (FW) in Watermelon (Citrullus lanatus L.).

The watermelon (Citrullus lanatus L.) holds substantial economic value as a globally cultivated horticultural crop. However, the genetic architecture of watermelon fruit weight (FW) remains poorly understood. In this study, we used sh14-11 with small fruit and N14 with big fruit to construct 100 recombinant inbred lines (RILs). Based on whole-genome resequencing (WGR), 218,127 single nucleotide polymorphisms (SNPs) were detected to construct a high-quality genetic map. After quantitative trait loci (QTL) mapping, a candidate interval of 31-38 Mb on chromosome 2 was identified for FW. Simultaneously, the bulked segregant analysis (BSA) in the F2 population corroborated the identification of the same interval, encompassing the homologous gene linked to the known FW-related gene fas. Additionally, RNA-seq was carried out across 11 tissues from sh14-11 and N14, revealing expression profiles that identified 1695 new genes and corrected the annotation of 2941 genes. Subsequent differential expression analysis unveiled 8969 differentially expressed genes (DEGs), with 354 of these genes exhibiting significant differences across four key developmental stages. The integration of QTL mapping and differential expression analysis facilitated the identification of 14 FW-related genes, including annotated TGA and NAC transcription factors implicated in fruit development. This combined approach offers valuable insights into the genetic basis of FW, providing crucial resources for enhancing watermelon cultivation.

Effective population size in field pea

BackgroundEffective population size (Ne) is a pivotal parameter in population genetics as it can provide information on the rate of inbreeding and the contemporary status of genetic diversity in breeding populations. The population with smaller Ne can lead to faster inbreeding, with little potential for genetic gain making selections ineffective. The importance of Ne has become increasingly recognized in plant breeding, which can help breeders monitor and enhance the genetic variability or redesign their selection protocols. Here, we present the first Ne estimates based on linkage disequilibrium (LD) in the pea genome.ResultsWe calculated and compared Ne using SNP markers from North Dakota State University (NDSU) modern breeding lines and United States Department of Agriculture (USDA) diversity panel. The extent of LD was highly variable not only between populations but also among different regions and chromosomes of the genome. Overall, NDSU had a higher and longer-range LD than the USDA that could extend up to 500 Kb, with a genome-wide average r2 of 0.57 (vs 0.34), likely due to its lower recombination rates and the selection background. The estimated Ne for the USDA was nearly three-fold higher (Ne = 174) than NDSU (Ne = 64), which can be confounded by a high degree of population structure due to the selfing nature of pea.ConclusionsOur results provided insights into the genetic diversity of the germplasm studied, which can guide plant breeders to actively monitor Ne in successive cycles of breeding to sustain viability of the breeding efforts in the long term.

Discovering novel genomic regions explaining adaptation of bread wheat to conservation agriculture through GWAS

To sustainably increase wheat yield to meet the growing world population’s food demand in the face of climate change, Conservation Agriculture (CA) is a promising approach. Still, there is a lack of genomic studies investigating the genetic basis of crop adaptation to CA. To dissect the genetic architecture of 19 morpho-physiological traits that could be involved in the enhanced adaptation and performance of genotypes under CA, we performed GWAS to identify MTAs under four contrasting production regimes viz., conventional tillage timely sown (CTTS), conservation agriculture timely sown (CATS), conventional tillage late sown (CTLS) and conservation agriculture late sown (CALS) using an association panel of 183 advanced wheat breeding lines along with 5 checks. Traits like Phi2 (Quantum yield of photosystem II; CATS:0.37, CALS: 0.31), RC (Relative chlorophyll content; CATS:55.51, CALS: 54.47) and PS1 (Active photosystem I centers; CATS:2.45, CALS: 2.23) have higher mean values in CA compared to CT under both sowing times. GWAS identified 80 MTAs for the studied traits across four production environments. The phenotypic variation explained (PVE) by these QTNs ranged from 2.15 to 40.22%. Gene annotation provided highly informative SNPs associated with Phi2, NPQ (Quantum yield of non-photochemical quenching), PS1, and RC which were linked with genes that play crucial roles in the physiological adaptation under both CA and CT. A highly significant SNP AX94651261 (9.43% PVE) was identified to be associated with Phi2, while two SNP markers AX94730536 (30.90% PVE) and AX94683305 (16.99% PVE) were associated with NPQ. Identified QTNs upon validation can be used in marker-assisted breeding programs to develop CA adaptive genotypes.

Potential of Tropically-Adapted Exotic Acid Tolerance White Maize Donor Lines in Sub-tropical Breeding Programmes for Low pH Adaptation

Low pH in soils is attributed as the main contributor to the low yields characteristic in maize production regions of Angola. Here, eight white-kernel acid soil tolerant donor lines (ASTDLs) sourced from CIMMYT-Colombia (testers) were crossed with eight white elite lines adapted to the mid-altitude climatic conditions from CIMMYT-Zimbabwe, in order to identify donor lines, which can be potential sources of acid tolerance genes in breeding programmes in Angola. The two groups of parents were crossed using a line by tester (L&amp;times;T) mating design, yielding 47 crosses with sufficient seed, which were evaluated alongside eight acid tolerant commercial hybrids, during the 2014-16 cropping seasons at nine sites, representing acid and non-acid soils in Angola and Zimbabwe. Effects of general combining ability (GCA) due to lines and testers, as well as specific combining ability (SCA) on grain yield were significant (P &amp;lt; 0.05) under acid soils. From the CIMMYT-Zimbabwe breeding programme, inbred lines identified as ZW1, ZW4 and ZW5 together with the CIMMYT-Colombia ASTDLs (i.e., CW4 and CW8) seemed to be ideal parents for crosses that can do well under both the acid and non-acid soils. The best specific cross for acid soils was identified as ZW1 &amp;times; CW8 (CH142512), whereas for non-acid soils, ZW3 &amp;times; CW4 (CH142500) was identified. Interestingly, the cross ZW1 &amp;times; CW8 was also observed as stable under both acid and non-acid soil conditions. Overall, data showed potential of exotic acid tolerance donor lines for enhancing low-pH adaptation in sub-tropical maize populations.

A Preliminary Evaluation of Faba Bean as a Green Shell Bean in Virginia, USA

Even though faba bean (Vicia faba L.) is an important food crop on worldwide basis, its use as a vegetable i.e. use of green seeds as food is limited. We were interested in characterizing production and food quality traits of faba bean grown in eastern USA. Our main objective is to develop faba bean as a winter alternative crop for this region to diversify cropping system that currently mainly depends upon cereal grain crops. This necessitates existence of winter-hardy faba bean varieties. We conducted a preliminary experiment with two winter-hardy faba bean breeding lines to record production and seed composition traits. Two faba bean lines (VSX-BL and VSX-BH) were planted in the field in November 2022 and green pods were harvested in June 2023 at physiological maturity. Values of most of the traits under study were statistically similar between the two lines except for concentration of phosphorus. Results demonstrated that faba bean green pod and green seeds yields could be approximately 5700 and 2100 kg ha-1. The shelling percent in green faba bean pods was approximately 37 whereas seed number per pod was approximately 2.6. Concentrations (g 100 g-1) of fructose, glucose, and sucrose were 0.245, 0.668, 2.9021, respectively whereas concentrations of Fe and Zn (mg kg-1) were 103.7 and 69.7, respectively. Green faba bean seeds contained small amounts of RFO carbohydrates. Seed composition traits of green faba bean seeds compare well with green seeds of pea, soybean, and white lupin. Our results provide a positive proof of concept that production of green faba bean as an alternate winter food legume crop in eastern USA is possible.

Productivity, seed quality and protein yield of pea samples developed by the FSBSI “ARC “Donskoy”

The purpose of the current study was to determine the quantitative and qualitative indicators of seeds of pea samples. The study was carried out in the southern part of the Rostov region in the fields of the FSBSI Agricultural Research Center “Donskoy” in 2021–2023. The objects of research were 12 pea samples developed by the ARC “Donskoy”. The zoned variety ‘Aksaisky Usatiy 5’ was used as a standard. Quality characteristics of peas, such as protein percentage in seeds and their ability to boil soft, are highly dependent on environmental conditions and often have a negative correlation with seed productivity. One of the goals in pea breeding is to change this inverse correlation between productivity and seed quality. The mean productivity of the varieties and lines in the Competitive Variety Testing through the years of study was 3.66 t/ha on average. The standard ‘Aksai Usatiy 5’ (3.46 t/ha) was reliably exceeded by such varieties and lines as ‘G-1181’ (4.17 t/ha), ‘Kazak’ (4.02 t/ha), ‘AKM’ (3.99 t/ha), ‘G-1313’ (3.80 t/ha). The samples with the highest protein percentage (second quality class, 22.0–25.0 %) were ‘Aksaysky Usatiy 5’ (23.7 %), ‘Skif’ (24.4 %), ‘Kazak’ (23.1 %), ‘AKM’ (23.6 %), ‘G-1141’ (24.3 %), ‘G-1172’ (25.0 %), ‘G-1181’ (22.3 %). The mean boiling time was 75 minutes. The minimum boiling time was 63 minutes for the varieties ‘Aksaisky Usatiy 5’, ‘Skif’, 65 minutes for the line ‘G-1234’ and 70 minutes for the line ‘G-1288’. The mean coefficient of the ability to boil soft over the years of study was 2.20, varying from 1.92 to 2.61. The mean protein yield over the years of study was 0.85 t/ha. The varieties ‘Kazak’ (0.94 t/ha), ‘AKM’ (0.93 t/ha) and breeding lines ‘G-1181’ (0.93 t/ha), ‘G-1313’ (0.90 t/ha) showed the best indicators. The maximum values of protein yield were identified at maximum productivity of 4.2–4.3 t/ha and 23.5–24.0% of protein in seeds.

Genetic Dissection of Major Rice QTLs for Strong Culms and Fine Mapping of qWS5 for Breeding Application in Transplanted System

BackgroundRice is one of the major staples that feeds about one half of the global populations, and it is important to identify the genetic loci for the traits related to yield improvement. Lodging will cause severe yield loss when it happens, and stem diameter has been characterized as an important trait for lodging resistance. However, most QTLs for stem diameter have not been finely dissected due to their sensitivity to environmental fluctuation.ResultIn this study, we performed QTL analysis for stem diameter using populations derived from Nipponbare (NIP) and strong culm variety YYP1, and confirmed the single and combined effect of three major QTLs by recombinant inbred lines (RILs). Based on the QTL location, we found that qWS5 is a novel QTL not well characterized before. To finely dissect the novel locus, several recombinant heterogeneous inbred families (HIFs) were selected from the RILs for linkage analysis and their derived nearly isogenic lines (NILs) were subjected to detailed trait investigation throughout different years. The HIF-NILs strategy confined the QTL to about 380 kb region supported by repeated genotype and phenotype data, and it lays the foundation for QTL cloning in the future. In addition, introgression of the QTL to an elite japonica variety SD785 was performed by successive backcrossing, and it confirmed the value of qWS5 in increasing stem diameter and other agronomic traits during rice breeding.ConclusionsWe prove that qWS5 is a novel QTL with relatively stable effect for stem diameter and the QTL can be finely mapped to small region by the HIF-NILs strategy. The result will facilitate the improvement of rice lodging resistance by molecular marker assisted selection breeding.

Biparental graph strategy to represent and analyze hybrid plant genomes.

Hybrid plants are found extensively in the wild, and they often demonstrate superior performance of complex traits over their parents and other selfing plants. This phenomenon, known as heterosis, has been extensively applied in plant breeding for decades. However, the process of decoding hybrid plant genomes has seriously lagged due to the challenges associated with genome assembly and the lack of appropriate methodologies for their subsequent representation and analysis. Here, we present the assembly and analysis of 2 hybrids, an intraspecific hybrid between 2 maize (Zea mays ssp. mays) inbred lines and an interspecific hybrid between maize and its wild relative teosinte (Z. mays ssp. parviglumis), utilizing a combination of PacBio High Fidelity sequencing and chromatin conformation capture sequencing data. The haplotypic assemblies are well phased at chromosomal scale, successfully resolving the complex loci with extensive parental structural variations (SVs). By integrating into a biparental genome graph, the haplotypic assemblies can facilitate downstream short-read-based SV calling and allele-specific gene expression analysis, demonstrating outstanding advantages over a single linear genome. Our work offers a comprehensive workflow that aims to facilitate the decoding of numerous hybrid plant genomes, particularly those with unknown or inaccessible parentage, thereby enhancing our understanding of genome evolution and heterosis.

Transcriptomic Analysis of Maize Inbred Lines with Different Leaf Shapes Reveals Candidate Genes and Pathways Involved in Density Tolerance

Transcriptomic Analysis of Maize Inbred Lines with Different Leaf Shapes Reveals Candidate Genes and Pathways Involved in Density Tolerance

Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in sorghum seeds

Cereal seeds are vital for food, feed, and agricultural sustainability because they store and provide essential nutrients to human and animal food and feed systems. Unraveling molecular processes in seed development is crucial for enhancing cereal grain yield and quality. We analyze spatiotemporal transcriptome and metabolome profiles during sorghum seed development in the inbred line ‘BTx623’. Morphological and molecular analyses identify the key stages of seed maturation, specifying starch biosynthesis onset at 5 days post-anthesis (dpa) and protein at 10 dpa. Transcriptome profiling from 1 to 25 dpa reveal dynamic gene expression pathways, shifting from cellular growth and embryo development (1–5 dpa) to cell division, fatty acid biosynthesis (5–25 dpa), and seed storage compounds synthesis in the endosperm (5–25 dpa). Network analysis identifies 361 and 207 hub genes linked to starch and protein synthesis in the endosperm, respectively, which will help breeders enhance sorghum grain quality. The availability of this data in the sorghum reference genome line establishes a baseline for future studies as new pangenomes emerge, which will consider copy number and presence-absence variation in functional food traits.

Evaluation of Grain Moisture Content at Maturity and Screening for Identification Indexes of Maize Inbred Lines

The grain moisture content of maize inbred lines at maturity is one of the most important indicators for mechanical harvesting of kernels. In this study, 116 maize inbred lines from a wide range of sources were used as research materials and 30 traits of grain moisture content were analyzed using multivariate statistical analysis. The results showed that all 30 traits had some correlations. Principal component analysis downscaled the 30 traits into 10 principal component factors, reflecting 77.674% of the information in the original traits. Cluster analysis categorized the 116 inbred lines into 5 major groups containing 26, 29, 31, 16 and 14 inbred lines. Based on the D value of the overall evaluation, discriminant analysis reclassified the maize inbred lines by principal component scores and 98 maize inbred lines were correctly discriminated with a probability of 84.48%, which can be regarded as a relatively reliable clustering result. The stepwise regression method was further used to screen seven traits: GMC2, GDR1, HMC3, NH, GDR2, CD and EL and to establish a comprehensive evaluation model for the grain moisture content of maize inbred lines. Among 116 maize inbred lines, 14, represented by H21 and MS71, had the lowest grain moisture content at maturity.

Assessment of the resistance of inbred table beet lines to cercosporosis (Cercospora beticola Sacc.) in field and laboratory conditions

Assessment of the resistance of inbred table beet lines to cercosporosis (Cercospora beticola Sacc.) in field and laboratory conditions

Combining Ability and Hybrid Breeding in Tunisian Melon (Cucumis melo L.) for Fruit Traits

A half-diallel cross study of seven melon inbred lines was carried out. The seven parents and their 21 F1 hybrids were evaluated for precocity of maturity, average weight per fruit, and fruit quality (fruit size, rind thickness, and soluble solids). The Diallel analysis was investigated for breeding values of these melon genotypes via general and specific combining ability, relationships between general and specific combining ability, and heterosis for the evaluated traits. The analysis of variance of the traits evaluated indicated highly significant differences among genotypes, suggesting the presence of adequate genetic variation for breeding. Additive genetic effects were most important with respect to fruit weight, while genetic dominance and epistasis effects mainly controlled fruit quality traits (fruit size, rind thickness, and TSS). Parent 1 (P1) and parent 3 (P3) had significant positive general combining ability effects for fruit weight. Also, P3 had positive general combining ability effects for fruit length and diameter, and cavity diameter. P3 was found to show maximum significant GCA in the desirable direction for all the traits except for TSS. Evaluation of heterosis (%) revealed that hybrid P1 × P3 can be considered as the best-performing hybrid for average fruit weight, TSS, and precocity, which also exhibited the highest positive and significant SCA effect for these traits. These results suggested that, among the melon genotypes studied, there is the potential to generate superior new varieties in hybrid production.

Morpho-physiological characterization and selection of heat tolerant wheat lines using selection indices

Heat stress is one of the major constraints in wheat production due to its adverse effect on grain yield and component traits. Moreover, it negatively affects the physiological, biochemical and quality traits of wheat. Therefore, selection of heat tolerant wheat lines is one of the major breeding goals for wheat scientist. In present study, 238 recombinant inbred lines were evaluated along with their parents WH 711 × WH 542 under timely and late sown (heat stress) condition. The heat tolerance indices were calculated based on grain yield under normal and stress conditions. The mean grain yield of 238 wheat lines was reduced by 20.54% suggesting critical effect of heat stress on grain yield. The harmonic mean (HM), stress tolerance index (STI), mean productivity (MP), geometric mean productivity (GMP), and mean relative performance (MRP) were correlated significantly and positively with grain yield under stress and normal conditions. Whereas, Tolerance index (TOL) was correlated negatively with grain yield under stress conditions and positively under normal condition. Based on STI, MP, HM, GMP and MRP, wheat lines WL 92, WL 119, WL 114, WL 110, WL 6 were identified as heat tolerant and could be utilized as potential lines for increasing heat stress tolerance of future wheat breeding programs.

First Report of Pantoea ananatis causing leaf streak disease on wheat (Triticum aestivum) in the United States of America.

Wheat (Triticum aestivum) loses 21.5% yield to pests and diseases annually (Savary et al. 2019). Among the wheat diseases, bacterial leaf streak (BLS) is a growing problem, costing $78.5 million in losses (https://cropprotectionnetwork.org/). In July 2022, we sampled winter wheat leaf samples at Volga (44.30, -96.92), South Dakota, USA with an estimated disease incidence of 40% (n=100). The typical symptoms were water-soaking with large necrotic and chlorotic streaks extending the length of the leaves and were strikingly similar to BLS. To isolate the pathogen, leaves were cut lengthwise into 1 cm pieces and surface-sterilized using a 10% NaOCl solution for 3 min, followed by 70% ethanol for 3 min, and then rinsed with sterile distilled water and placed in 500 ul of sterile distilled water for 5 min and using a sterile loop the water was streaked over a plate of Nutrient Agar (NA). Following Duveiller et al. (1997), the streaked plate was incubated in the dark at 28℃ for 48 h. Observed single colonies were sub-cultured thrice onto fresh NA plates to obtain a pure culture. We named the culture SD101. Bacteria were found to be gram-negative with a colony morphology initially raised, smooth, and white that later turned yellow. DNA was extracted using the Wizard HMW DNA Extraction Kit (Promega, Madison, WI) following the manufacturer's protocol, and sequenced using Nanopore MinION R9.4 (Oxford Nanopore Technology). We used the Rapid Annotation Using Subsystems Technology approach (Aziz eal. 2008) to extract the 16S rDNA, DNA gyrase subunit B (gyrB), and translation initiation factor IF-2 (infB) gene sequences that were deposited in GenBank under accession numbers PP329908.1 for 16S rDNA, PP496481 for infB, and PP328920.1 for gyrB. Homology analysis using CLC Genomics Workbench 22.0.2 (QIAGEN) and BLASTn against the GenBank nucleotide database resulted in a 99.74% match (1543/ 1547 bp) of the 16S sequence, 99.59% match (2674/ 2685 bp) of the infB sequence, and 99.42% match (2396/ 2410 bp) of the gyrB sequence with Pantoea ananatis strain AJ13355 (AP012032). To test pathogenicity, seeds of spring wheat breeding line SD4892 were planted in 30 cm × 30 cm pots in a greenhouse under a 16 h light photoperiod. The inoculum was prepared from 48-h-old NA plates of SD101 rinsed with 1X Phosphate Buffer Saline (PBS buffer), adjusted to an OD600 = 1.0, and amended with two drops of Tween 20 (polyoxyethylene sorbitol ester, Millipore Sigma). PBS with Tween 20 was used as a negative control. The inoculum was sprayed on 15 replicates of 15-day-old seedlings, kept at 95% relative humidity for 48 h, then moved to the greenhouse at 23 to 25°C. The symptoms appeared as water soaking that later turned to necrotic streaks with surrounding chlorosis on all 15 inoculated plants while control plants remained healthy. The pathogen was re-isolated from the leaves as described above. The 16S rDNA, infB, and gyrB sequences amplified and sequenced were identical to the gene sequences from the whole genome sequencing. The experiment was repeated with the same results, completing Koch's postulates. Although P. ananatis is pathogenic on corn, rice, and other plant species in the United States (Coutinho et al. 2009), and was reported pathogenic on wheat in Poland (Krawczyk et al. 2020), this is the first report of its pathogenicity on wheat in the United States. The prevalence, and incidence of BLS disease caused by P. ananatis in wheat is needed to estimate its threat to wheat production and to develop management strategies.

A single gene determines allorecognition in hydrozoan jellyfish Cladonema radiatum inbred lines.

Allorecognition-the ability of an organism to discriminate between self and nonself-is crucial to colonial marine animals to avoid invasion by other individuals in the same habitat. The cnidarian hydroid Hydractinia has long been a major research model in studying invertebrate allorecognition, establishing a rich knowledge foundation. In this study, we introduce a new cnidarian model Cladonema radiatum (C. radiatum). C. radiatum is a hydroid jellyfish which also forms polyp colonies interconnected with stolons. Allorecognition responses-fusion or regression of stolons-are observed when stolons encounter each other. By transmission electron microscopy, we observe rapid tissue remodeling contributing to gastrovascular system connection in fusion. Meanwhile, rejection responses are regulated by reconstruction of the chitinous exoskeleton perisarc, and induction of necrotic and autophagic cellular responses at cells in contact with the opponent. Genetic analysis identifies allorecognition genes: six Alr genes located on the putative allorecognition complex and four immunoglobulin superfamily genes on a separate genome region. C. radiatum allorecognition genes show notable conservation with the Hydractinia Alr family. Remarkedly, stolon encounter assays of inbred lines reveal that genotypes of Alr1 solely determine allorecognition outcomes in C. radiatum.