Summary Harnessing stem carbohydrate dynamics in grasses offers an opportunity to help meet future demands for plant‐based food, fiber and fuel production, but requires a greater understanding of the genetic controls that govern the synthesis, interconversion and transport of such energy reserves.We map out a blueprint of the genetic architecture of rice (Oryza sativa) stem nonstructural carbohydrates (NSC) at two critical developmental time‐points using a subpopulation‐specific genome‐wide association approach on two diverse germplasm panels followed by quantitative trait loci (QTL) mapping in a biparental population.Overall, 26 QTL are identified; three are detected in multiple panels and are associated with starch‐at‐maturity, sucrose‐at‐maturity and NSC‐at‐heading. They tag OsHXK6 (rice hexokinase), ISA2 (rice isoamylase) and a tandem array of sugar transporters.This study provides the foundation for more in‐depth molecular investigation to validate candidate genes underlying rice stem NSC and informs future comparative studies in other agronomically vital grass species.

Whole oat has been described as an important healthy food for humans due to its beneficial nutritional components. The positive health benefits of consuming oats as a whole-grain food are attributed in part to b-glucan, which has outstanding functional and nutritional properties. Near infrared reflectance spectroscopy is a powerful, fast, accurate and non-destructive analytical tool that can be substituted for some traditional chemical analysis. A total of 1728 single intact groats of six different oat varieties were scanned by near infrared spectroscopy to develop non-destructive predictions for (1,3;1,4)-b-D-glucan (b-glucan), protein and oil content in groats. Prediction models for single kernels were developed using partial least squares regression. Regression parameters between the chemical values, determined by wet-lab reference methods, and the predicted values determined from near infrared spectra, were veriEed by cross-validation and against data from a set of independent samples. The cross-validation correlation coefficients (R 2 CV) for b-glucan, protein and oil were 0.83, 0.72 and 0.92, respectively, the root-mean-square error ranged from 0.25% to 0.60% for all compounds. Independent validation data had r 2 values ranging from 0.69 to 0.95; root-mean-square error of prediction values (RMSEP) values were equal to or less than 0.52%, 0.62% and 0.27% for b-glucan, protein and oil, respectively. The data indicated that non-destructive screening of b-glucan, protein and oil contents in single kernels of dehulled oat grains from their near infrared spectra could be successfully used in breeding programs.

Understanding the basis of hybrid vigor remains a key question in crop breeding and improvement, especially for rootstock development where F1 hybrids are extensively utilized. Full-sibling UCB-1 F1 seedling rootstocks are widely planted in commercial pistachio orchards that are generated by crossing two highly heterozygous outbreeding parental trees of Pistacia atlantica (female) and P. integerrima (male). This results in extensive phenotypic variability, prompting costly removal of low-yielding small trees. To identify the genetic basis of this variability, we assembled chromosome-scale genome assemblies of the parental trees of UCB-1. We genotyped 960 UCB-1 trees in an experimental orchard for which we also collected multi-year phenotypes. We genotyped an additional 1,358 rootstocks in six commercial pistachio orchards and collected single-year tree size data. Genome-wide single marker association tests identified loci associated with tree size and shape, sex, and precocity. In the experimental orchard, we identified multiple trait-associated loci and a strong candidate for ZZ/ZW sex chromosomes. We found significant marker associations unique to different traits and to early vs. late phenotypic measures of the same trait. We detected two loci strongly associated with rootstock size in commercial orchards. Pseudo-testcross classification of markers demonstrated that the trait-associated alleles for each locus were segregating in the gametes of opposite parents. These two loci interact epistatically to generate the bimodal distribution of tree size with undesirable small trees observed by growers. We identified candidate genes within these regions. These findings provide a foundational resource for marker development and genetic selection of vigorous pistachio UCB-1 rootstock.

Tipburn is an important physiological disorder of lettuce, Lactuca sativa L., related to calcium deficiency that can result in leaf necrosis and unmarketable crops. The major quantitative trait locus, qTPB5.2, can account for up to 70% of the phenotypic variance for tipburn incidence in the field. This quantitative trait locus was genetically dissected to identify candidate genes for tipburn by creating lines with recombination events within the quantitative trait locus and assessing their resistance to tipburn. By comparing lines with contrasting haplotypes, the genetic region was narrowed down to ∼877 Kb that was associated with a reduction of tipburn by ∼60%. Analysis of the lettuce reference genome sequence revealed 12 genes in this region, one of which is a calcium transporter with a single nucleotide polymorphism in an exon between haplotypes with contrasting phenotypes. RNA-seq analysis of recombinants revealed two genes that were differentially expressed between contrasting haplotypes consistent with the tipburn phenotype. One encodes a Teosinte branched1/Cycloidea/Proliferating Cell factor transcription factor; however, differential expression of the calcium transporter was not detected. The phenotypic data indicated that there is a second region outside of the ∼877 Kb region but within the quantitative trait locus, at which a haplotype from the susceptible parent decreased tipburn by 10 to 20%. A recombinant line was identified with beneficial haplotypes in each region from both parents that showed greater tipburn resistance than the resistant parent; this line could be used as the foundation for breeding cultivars with more resistance than is currently available.

Key message A population of lettuce that segregated for photoperiod sensitivity was planted under long-day and short-day conditions. Genetic mapping revealed two distinct sets of QTLs controlling daylength-independent and photoperiod-sensitive flowering time. Abstract The molecular mechanism of flowering time regulation in lettuce is of interest to both geneticists and breeders because of the extensive impact of this trait on agricultural production. Lettuce is a facultative long-day plant which changes in flowering time in response to photoperiod. Variations exist in both flowering time and the degree of photoperiod sensitivity among accessions of wild (Lactuca serriola) and cultivated (L. sativa) lettuce. An F6 population of 236 recombinant inbred lines (RILs) was previously developed from a cross between a late-flowering, photoperiod-sensitive L. serriola accession and an early-flowering, photoperiod-insensitive L. sativa accession. This population was planted under long-day (LD) and short-day (SD) conditions in a total of four field and screenhouse trials; the developmental phenotype was scored weekly in each trial. Using genotyping-by-sequencing (GBS) data of the RILs, quantitative trait loci (QTL) mapping revealed five flowering time QTLs that together explained more than 20% of the variation in flowering time under LD conditions. Using two independent statistical models to extract the photoperiod sensitivity phenotype from the LD and SD flowering time data, we identified an additional five QTLs that together explained more than 30% of the variation in photoperiod sensitivity in the population. Orthology and sequence analysis of genes within the nine QTLs revealed potential functional equivalents in the lettuce genome to the key regulators of flowering time and photoperiodism, FD and CONSTANS, respectively, in Arabidopsis.