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This study investigated the genetic basis of carrot root shape traits using composite interval mapping in two biparental populations (n = 119 and n = 128). The roots of carrot F2:3 progenies were grown over 2 years and analyzed using a digital imaging pipeline to extract root phenotypes that compose market class. Broad-sense heritability on an entry-mean basis ranged from 0.46 to 0.80 for root traits. Reproducible quantitative trait loci (QTL) were identified on chromosomes 2 and 6 on both populations. Colocalization of QTLs for phenotypically correlated root traits was also observed and coincided with previously identified QTLs in published association and linkage mapping studies. Individual QTLs explained between 14 and 27% of total phenotypic variance across traits, while four QTLs for length-to-width ratio collectively accounted for up to 73% of variation. Predicted genes associated with the OFP-TRM (OVATE Family Proteins—TONNEAU1 Recruiting Motif) and IQD (IQ67 domain) pathway were identified within QTL support intervals. This observation raises the possibility of extending the current regulon model of fruit shape to include carrot storage roots. Nevertheless, the precise molecular mechanisms through which this pathway operates in roots characterized by secondary growth originating from cambium layers remain unknown. [ABSTRACT FROM AUTHOR]

Summary: The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions 'Rush' and 'Winkler'. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for 'Rush' and 'Winkler', respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. 'Rush' has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while 'Winkler' had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana, as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana, C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus. [ABSTRACT FROM AUTHOR]

The necrotrophic fungus Rhizoctonia solani Kühn is a major concern for table beet (Beta vulgaris L. ssp. vulgaris) producers across the United States causing upward of 75% losses in severe instances. Thus far, there have been minimal efforts to incorporate host resistance to R. solani in table beet germplasm. To investigate the genetic control of R. solani resistance in table beet, we developed two mapping populations. Parents of the two populations were a Rhizoctonia‐susceptible table beet inbred W357A and a resistant sugar beet germplasm FC709‐2 (sugar beet resistance population, SBRP) and a Rhizoctonia‐resistant table beet inbred W364B and a susceptible sugar beet inbred FC901/C817 (table beet resistance population, TBRP). In Spring 2020, F2:3 families were evaluated for response to artificial inoculation with R. solani AG 2‐2 IIIB isolate R1 in replicated greenhouse experiments. This work also represents the first use of the W357B table beet reference genome, utilized here to align genotyping‐by‐sequencing reads to identify polymorphic markers. Using interval linkage mapping, we identified one quantitative trait locus (QTL) in each of the two populations, each accounting for 30% of the phenotypic variation. The QTL in both the SBRP and TBRP were found on chromosome 2 and contained several putative resistance genes in annotations of the Beta vulgaris and Arabidopsis thaliana genomes. This is the first report of a QTL on chromosome 2 for resistance to R. solani in B. vulgaris ssp. vulgaris and the first identification of QTL for disease resistance in table beet. The newly developed table beet reference genome and markers identified in this study may be of value for marker‐assisted selection in breeding for resistance to R. solani in both sugar beet and table beet breeding programs. Core Ideas: Table beets resistant to Rhizoctonia solani have not been identified, but sugar beet has resistance.We used two populations developed from crosses between sugar beet and table beet and identified two new QTL.These QTL were both located on chromosome 2 in a new table beet reference genome. [ABSTRACT FROM AUTHOR]

Root shape in carrot (Daucus carota subsp. sativus), which ranges from long and tapered to short and blunt, has been used for at least several centuries to classify carrot cultivars. The subjectivity involved in determining market class hinders the establishment of metric-based standards and is ill-suited to dissecting the genetic basis of such quantitative phenotypes. Advances in digital image acquisition and analysis has enabled new methods for quantifying sizes of plant structures and shapes, but in order to dissect the genetic control of the shape features that define market class in carrot, a tool is required that quantifies the specific shape features used by humans in distinguishing between classes. This study reports the construction and demonstration of the first such platform, which facilitates rapid phenotyping of traits that are measurable by hand, such as length and width, as well as principal component analysis (PCA) of the root contour and its curvature. This latter approach is of particular interest, as it enabled the detection of a novel and significant quantitative trait, defined here as root fill, which accounts for 85% of the variation in root shape. Curvature analysis was demonstrated to be an effective method for precise measurement of the broadness of the carrot shoulder, and degree of tip fill; the first principal component of the respective curvature profiles captured 87% and 84% of the total variance. This platform's performance was validated in two experimental panels. First, a diverse, global collection of germplasm was used to assess its capacity to identify market classes through clustering analysis. Second, a diallel mating design between inbred breeding lines of differing market classes was used to estimate the heritability of the key phenotypes that define market class, which revealed significant variation in the narrow-sense heritability of size and shape traits, ranging from 0.14 for total root size, to 0.84 for aspect ratio. These results demonstrate the value of high-throughput digital phenotyping in characterizing the genetic control of complex quantitative phenotypes. [ABSTRACT FROM AUTHOR]