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Core Ideas Construction of a GBS‐based high‐resolution genetic map of a tomato RIL population Development of an analytical pipeline to localize crossover events and construct genomic bins Fine mapping of QTL for fruit weight and lycopene content confirm use of the high‐resolution map Identification of SIZISO as the gene underlying the lycopene QTL Lyc12.1 RIL population, high‐resolution genetic map, and analytical pipeline available to the public Genotyping‐by‐sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato (Solanum lycopersicum L.) recombinant inbred line (RIL) population, derived from a cross between cultivar NC EBR‐1 and the wild tomato S. pimpinellifolium L. accession LA2093. A pipeline was developed to convert single nucleotide polymorphism (SNP) data into genomic bins, which could be used for fine mapping of quantitative trait loci (QTL) and identification of candidate genes. The pipeline, implemented in a python script named SNPbinner, adopts a hidden Markov model approach for calculation of recombination breakpoints followed by genomic bins construction. The total length of the newly developed high‐resolution genetic map was 1.2‐fold larger than previously estimated based on restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR)–based markers. The map was used to verify and refine QTL previously identified for two fruit quality traits in the RIL population, fruit weight (FW) and fruit lycopene content (LYC). Two well‐described FW QTL (fw2.2 and fw3.2) were localized precisely at their known underlying causative genes, and the QTL intervals were decreased by two‐ to tenfold. A major QTL for LYC content (Lyc12.1) was verified at high resolution and its underlying causative gene was determined to be ζ‐carotene isomerase (SlZISO). The RIL population, the high resolution genetic map, and the easy‐to‐use genotyping pipeline, SNPbinner, are made publicly available.

St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm‐season turfgrass species in the family Poaceae. This species is a popular choice for lawns in the Southern United States, due to its higher tolerance to shade, heat and humidity. However, there is little genomic information available to researchers and breeders, limiting knowledge on the genetic basis for favorable traits. We present a reference‐grade chromosome‐scale genome assembly for the popular freeze‐tolerant diploid cultivar Raleigh. The reference genome has been resolved into two haplotype assemblies (465.41 and 401.52 Mb), accounting for 95.2% and 82.1% of the expected haplotype genome size respectively, each anchored on the nine chromosomes and a total of 62,454 genes. Analysis of the assembly revealed 50.70% of the genome contained repeats. Analysis of the diversity within the species was investigated across 79 genotypes including commercial cultivars, breeding lines, and plant introductions by low‐coverage sequencing identifying 605,038 single nucleotide polymorphisms (SNPs). The SNPs were used to investigate genetic diversity across the panel and the effectiveness of low‐coverage sequencing on the high GC content species. SNPs classified genotypes into groups matching their phylogenetic and breeding history, with the plant introductions clustering into two groups on either side of the plot. Breeding lines for those whose parents existed in the panel clustered in between the two parents. These results showed that the cheaper, low‐coverage option can be used for this type of analysis. Together, all of the resources produced in this study allow the start of the genomics‐enabled genetic improvement for St. Augustinegrass. Core Ideas The first chromosome‐scale assemblies of both haplotypes of the Stenotaphrum secundatum genome were assembled. A total of 62,454 protein‐coding genes were annotated across both haplotypes. A uniform annotation filtering pipeline was developed for turfgrasses to facilitate future comparisons. A panel of 79 diploid representatives of the germplasm for S. secundatum were investigated for genetic diversity. A low‐coverage sequencing platform was tested for effectiveness in variant calling on high GC content species. Plain Language Summary The first published genome sequence of the popular turfgrass, St. Augustinegrass, has been completed. St. Augustinegrass is popular for its ability to thrive in sandy soils, while having a higher tolerance to heat, humidity, and shade than most other southern grown grasses. By using some of the newest sequencing technologies, the genome is currently of a higher quality than any other currently published warm‐season turfgrass genome. This reference genome provides a high‐quality closely related genome for future genomic work with warm‐season turfgrasses. This will allow for the expansion of the molecular toolkits that are available to turfgrass breeders to allow building tools to enable more efficient selection. We also found that a cheaper way of sequencing was sufficient for investigating differences among breeding materials to save money in future studies.

The bluish‐white appearance of some plants, known as glaucousness, results from the scattering effect of visible light due to plant surface waxes. This adaptive trait can contribute to tolerance of abiotic stresses in wheat (Triticum aestivum L.) such as drought, solar radiation, and heat. In this study, we identified quantitative trait loci (QTLs) and marker‐trait associations for flag leaf and spike glaucousness in two biparental populations and a panel of elite winter wheat lines. For all populations, spike and flag leaf glaucousness were visually scored on a 0–4 scale in multiple environments. Our QTL analyses and association mapping identified a significant locus on the long arm of chromosome 3A (QFlg.ncb‐3A) in all populations, explaining up to 36.6 percent of phenotypic variation for flag leaf glaucousness. Further, in one biparental population we identified three QTLs associated with spike glaucousness, located on chromosomes 1B, 2A, and 4D (QSpg.ncb‐1B, QSpg.ncb‐2A, QSpg.ncb‐4D) where they explained up to 22.8, 20.7, and 14.2 phenotypic variation, respectively. The QSpg.ncb‐1B QTL is located within the t1RS·1BL translocation from rye (Secale cereale L.) and demonstrates how glaucousness variation can be associated with an alien introgression in wheat. Our results suggest that QFlg.ncb‐3A is a primary determinant of flag leaf and, to a lesser extent, spike glaucousness in the evaluated germplasm. Collectively, our results expand the understanding of the genetic control of glaucousness in wheat flag leaf and spikes tissues, suggesting both unique and shared loci may underly the degree of glaucousness on the different plant parts. Core Ideas A major quantitative trait locus (QTL) (QFlg.ncb‐3A) for flag leaf and spike glaucousness was detected on chromosome 3A in three populations. Unique to spike glaucousness, three additional QTLs were detected in the LA population on chromosomes 1B, 2A, and 4D. Epistasis among QTL was observed for spike and leaf glaucousness. QSpg.ncb‐1B on t1RS·1BL establishes spike glaucousness variation associated with alien introgression in wheat. Plain Language Summary The bluish‐white appearance of some plants, known as glaucousness, results from the scattering effect of visible light due to plant surface waxes. This adaptive trait can contribute to tolerance of abiotic stresses in wheat such as drought, solar radiation, and heat. In this work, we rated the bluish‐white versus green color of leaves and spikes in panel of wheat breeding lines and in progeny from crosses between lines that differed in color. Using DNA markers, we were able to determine that a region of wheat chromosome 3A was the primary determinant of flag leaf and, to a lesser extent, spike glaucousness in the evaluated material. Three different chromosome regions associated only with high wax levels on the spikes. Collectively, our results expand the understanding of the genetic control of the glaucousness trait.

Virginia-type peanut, , is the second largest market class of peanut cultivated in the United States. It is mainly used for large-seeded, in-shell products. Historically, Virginia-type peanut cultivars were developed through long-term recurrent phenotypic selection and wild species introgression projects. Contemporary genomic technologies represent a unique opportunity to revolutionize the traditional breeding pipeline. While there are genomic tools available for wild and cultivated peanuts, none are tailored specifically to applied Virginia-type cultivar development programs. Here, the first Virginia-type peanut reference genome, \"Bailey II\", was assembled. It has improved contiguity and reduced instances of manual curation in chromosome arms. Whole-genome sequencing and marker discovery was conducted on 66 peanut lines which resulted in 1.15 million markers. The high marker resolution achieved allowed 34 unique wild species introgression blocks to be cataloged in the genome, some of which are known to confer resistance to one or more pathogens. To enable marker-assisted selection of the blocks, 111 PCR Allele Competitive Extension assays were designed. Forty thousand high quality markers were selected from the full set that are suitable for mid-density genotyping for genomic selection. Genomic data from representative advanced Virginia-type peanut lines suggests this is an appropriate base population for genomic selection. The findings and tools produced in this research will allow for rapid genetic gain in the Virginia-type peanut population. Genomics-assisted breeding will allow swift response to changing biotic and abiotic threats, and ultimately the development of superior cultivars for public use and consumption.

Spinach (Spinacia oleracea L.) is a member of the Caryophyllales family, a basal eudicot asterid that consists of sugar beet (Beta vulgaris L. subsp. vulgaris), quinoa (Chenopodium quinoa Willd.), and amaranth (Amaranthus hypochondriacus L.). With the introduction of baby leaf types, spinach has become a staple food in many homes. Production issues focus on yield, nitrogen‐use efficiency and resistance to downy mildew (Peronospora effusa). Although genomes are available for the above species, a chromosome‐level assembly exists only for quinoa, allowing for proper annotation and structural analyses to enhance crop improvement. We independently assembled and annotated genomes of the cultivar Viroflay using short‐read strategy (Illumina) and long‐read strategies (Pacific Biosciences) to develop a chromosome‐level, genetically anchored assembly for spinach. Scaffold N50 for the Illumina assembly was 389 kb, whereas that for Pacific BioSciences was 4.43 Mb, representing 911 Mb (93% of the genome) in 221 scaffolds, 80% of which are anchored and oriented on a sequence‐based genetic map, also described within this work. The two assemblies were 99.5% collinear. Independent annotation of the two assemblies with the same comprehensive transcriptome dataset show that the quality of the assembly directly affects the annotation with significantly more genes predicted (26,862 vs. 34,877) in the long‐read assembly. Analysis of resistance genes confirms a bias in resistant gene motifs more typical of monocots. Evolutionary analysis indicates that Spinacia is a paleohexaploid with a whole‐genome triplication followed by extensive gene rearrangements identified in this work. Diversity analysis of 75 lines indicate that variation in genes is ample for hypothesis‐driven, genomic‐assisted breeding enabled by this work. Core Ideas Quality of genome assemblies directly affect quality of annotation. Analysis of resistance genes confirms a bias in resistant gene motifs more typical of monocots. Spinacia is a paleohexaploid with extensive gene rearrangements. Variation in genes is ample for hypothesis‐driven genomic‐assisted breeding.

The genomic sequences segregating in experimental populations are often highly divergent from the community reference and from one another. Such divergence is problematic under various short-read-based genotyping strategies. In addition, large structural differences are often invisible despite being strong candidates for causal variation. These issues are exacerbated in specialty crop breeding programs with fewer, lower-quality sequence resources. Here, we examine the benefits of complete genomic information, based on long-read assemblies, in a biparental mapping experiment segregating at numerous disease resistance loci in the non-model crop, melon ( Cucumis melo ). We find that a graph-based approach, which uses both parental genomes, results in 19% more variants callable across the population and raw allele calls with a 2 to 3-fold error-rate reduction, even relative to single reference approaches using a parent genome. We show that structural variation has played a substantial role in shaping two Fusarium wilt resistance loci with known causal genes. We also report on the genetics of powdery mildew resistance, where copy number variation and local recombination suppression are directly interpretable via parental genome alignments. Benefits observed, even in this low-resolution biparental experiment, will inevitably be amplified in more complex populations. The power of pangenomic graphs to improve genetic mapping is still unclear. Here, the authors demonstrate its value in identification of genetic variants associated with disease resistance traits in melon using PanPipes, a pangenome construction and low-coverage genotype-by-sequencing pipeline.

Background Spinach ( Spinacia oleracea L.) is a dioecious species with an XY sex chromosome system, but its Y chromosome has not been fully characterized. Our knowledge about the history of its domestication and improvement remains limited. Results A high-quality YY genome of spinach is assembled into 952 Mb in six pseudo-chromosomes. By a combination of genetic mapping, Genome-Wide Association Studies, and genomic analysis, we characterize a 17.42-Mb sex determination region (SDR) on chromosome 1. The sex chromosomes of spinach evolved when an insertion containing sex determination genes occurred, followed by a large genomic inversion about 1.98 Mya. A subsequent burst of SDR-specific repeats (0.1–0.15 Mya) explains the large size of this SDR. We identify a Y-specific gene, NRT1/PTR 6.4 which resides in this insertion, as a strong candidate for the sex determination or differentiation factor. Resequencing of 112 spinach genomes reveals a severe domestication bottleneck approximately 10.87 Kya, which dates the domestication of spinach 7000 years earlier than the archeological record. We demonstrate that a strong selection signal associated with internode elongation and leaf area expansion is associated with domestication of edibility traits in spinach. We find that several strong genomic introgressions from the wild species Spinacia turkestanica and Spinacia tetrandra harbor desirable alleles of genes related to downy mildew resistance, frost resistance, leaf morphology, and flowering-time shift, which likely contribute to spinach improvement. Conclusions Analysis of the YY genome uncovers evolutionary forces shaping nascent sex chromosome evolution in spinach. Our findings provide novel insights about the domestication and improvement of spinach.

Premise The shape of young cotton (Gossypium) fibers varies within and between commercial cotton species, as revealed by previous detailed analyses of one cultivar of G. hirsutum and one of G. barbadense. Both narrow and wide fibers exist in G. hirsutum cv. Deltapine 90, which may impact the quality of our most abundant renewable textile material. More efficient cellular phenotyping methods are needed to empower future research efforts. Methods We developed semi‐automated imaging methods for young cotton fibers and a novel machine learning algorithm for the rapid detection of tapered (narrow) or hemisphere (wide) fibers in homogeneous or mixed populations. Results The new methods were accurate for diverse accessions of G. hirsutum and G. barbadense and at least eight times more efficient than manual methods. Narrow fibers dominated in the three G. barbadense accessions analyzed, whereas the three G. hirsutum accessions showed a mixture of tapered and hemisphere fibers in varying proportions. Discussion The use or adaptation of these improved methods will facilitate experiments with higher throughput to understand the biological factors controlling the variable shapes of young cotton fibers or other elongating single cells. This research also enables the exploration of links between early cell shape and mature cotton fiber quality in diverse field‐grown cotton accessions.

The sugarcane ratooning ability (RA) is the most important target trait for breeders seeking to enhance the profitability of sugarcane production by reducing the planting cost. Understanding the genetics governing the RA could help breeders by identifying molecular markers that could be used for genomics-assisted breeding (GAB). A replicated field trial was conducted for three crop cycles (plant cane, first ratoon, and second ratoon) using 432 sugarcane clones and used for conducting genome-wide association and genomic prediction of five sugar and yield component traits of the RA. The RA traits for economic index (EI), stalk population (SP), stalk weight (SW), tonns of cane per hectare (TCH), and tonns of sucrose per hectare (TSH) were estimated from the yield and sugar data. A total of six putative quantitative trait loci and eight nonredundant single-nucleotide polymorphism (SNP) markers were associated with all five tested RA traits and appear to be unique. Seven putative candidate genes were colocated with significant SNPs associated with the five RA traits. The genomic prediction accuracies for those tested traits were moderate and ranged from 0.21 to 0.36. However, the models fitting fixed effects for the most significant associated markers for each respective trait did not give any advantages over the standard models without fixed effects. As a result of this study, more robust markers could be used in the future for clone selection in sugarcane, potentially helping resolve the genetic control of the RA in sugarcane.

Background Muscadine grape ( Vitis rotundifolia ) is resistant to many of the pathogens that negatively impact the production of common grape ( V. vinifera ), including the bacterial pathogen Xylella fastidiosa subsp. fastidiosa ( Xfsf ), which causes Pierce’s Disease (PD). Previous studies in common grape have indicated Xfsf delays host immune response with a complex O-chain antigen produced by the wzy gene. Muscadine cultivars range from tolerant to completely resistant to Xfsf , but the mechanism is unknown. Results We assembled and annotated a new, long-read genome assembly for ‘Carlos’, a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We used these resources to construct an initial pan-genome for three cultivars of muscadine and one cultivar of common grape. This pan-genome contains a total of 34,970 synteny-constrained entries containing genes of similar structure. Comparison of resistance gene content between the ‘Carlos’ and common grape genomes indicates an expansion of resistance (R) genes in ‘Carlos.’ We further identified genes involved in Xfsf response by transcriptome sequencing ‘Carlos’ plants inoculated with Xfsf . We observed 234 differentially expressed genes with functions related to lipid catabolism, oxidation-reduction signaling, and abscisic acid (ABA) signaling as well as seven R genes. Leveraging public data from previous experiments of common grape inoculated with Xfsf , we determined that most differentially expressed genes in the muscadine response were not found in common grape, and three of the R genes identified as differentially expressed in muscadine do not have an ortholog in the common grape genome. Conclusions Our results support the utility of a pan-genome approach to identify candidate genes for traits of interest, particularly disease resistance to Xfsf , within and between muscadine and common grape.