A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation

Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. Informative, saturated linkage maps associated with well characterized populations segregating for anthocyanin pigmentation have not been developed. To investigate the genetic architecture conditioning anthocyanin pigmentation we scored root color visually, quantified root anthocyanin pigments by high performance liquid chromatography in segregating F2, F3 and F4 generations of a mapping population, mapped quantitative trait loci (QTL) onto a dense gene-derived single nucleotide polymorphism (SNP)-based linkage map, and performed comparative trait mapping with two unrelated populations. Results: Root pigmentation, scored visually as presence or absence of purple coloration, segregated in a pattern consistent with a two gene model in an F2, and progeny testing of F3-F4 families confirmed the proposed genetic model. Purple petiole pigmentation was conditioned by a single dominant gene that co-segregates with one of the genes conditioning root pigmentation. Root total pigment estimate (RTPE) was scored as the percentage of the root with purple color. Conclusions: This study generated the first high resolution gene-derived SNP-based linkage map in the Apiaceae. Two regions of chromosome 3 with co-localized QTL for all anthocyanin pigments and for RTPE, largely condition anthocyanin accumulation in carrot roots and leaves. Loci controlling root and petiole anthocyanin pigmentation differ across diverse carrot genetic backgrounds.Fil: Cavagnaro, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. University of Wisconsin; Estados Unidos. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; ArgentinaFil: Iorizzo, Massimo. University of Wisconsin; Estados UnidosFil: Yildiz, Mehtap. Yuzuncu Yil University; TurquíaFil: Senalik, Douglas. University of Wisconsin; Estados UnidosFil: Parsons, Joshua. University of Wisconsin; Estados UnidosFil: Ellison, Shelby. University of Wisconsin; Estados UnidosFil: Simon, Philipp W.. University of Wisconsin; Estados Unido

Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers

Carrot is one of the most economically important vegetables worldwide, but genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to develop a saturated genetic linkage map of carrot. We analyzed a set of 900 DArT markers in a collection of plant materials comprising 94 cultivated and 65 wild carrot accessions. The accessions were attributed to three separate groups: wild, Eastern cultivated and Western cultivated. Twenty-seven markers showing signatures for selection were identified. They showed a directional shift in frequency from the wild to the cultivated, likely reflecting diversifying selection imposed in the course of domestication. A genetic linkage map constructed using 188 F2 plants comprised 431 markers with an average distance of 1.1 cM, divided into nine linkage groups. Using previously anchored single nucleotide polymorphisms, the linkage groups were physically attributed to the nine carrot chromosomes. A cluster of markers mapping to chromosome 8 showed significant segregation distortion. Two of the 27 DArT markers with signatures for selection were segregating in the mapping population and were localized on chromosomes 2 and 6. Chromosome 2 was previously shown to carry the Vrn1 gene governing the biennial growth habit essential for cultivated carrot. The results reported here provide background for further research on the history of carrot domestication and identify genomic regions potentially important for modern carrot breeding

Genetic and Transcription Profile Analysis of Tissue-Specific Anthocyanin Pigmentation in Carrot Root Phloem

In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNA-seq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F2 population (3242) and the inbred B7262. Genetic mapping of ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP.EEA MendozaFil: Bannoud, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Carvajal, Sofía. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Ellison, Shelby. University of Wisconsin. Department of Horticulture; Estados Unidos.Fil: Senalik, Douglas A. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados UnidosFil: Gomez Talquenca, Gonzalo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Iorizzo, Massimo. North Carolina State University. Plants for Human Health Institute; Estados UnidosFil: Iorizzo, Massimo. North Carolina State University. Department of Horticultural Science; Estados UnidosFil: Simon, Philipp. University of Wisconsin. Department of Horticulture; Estados Unidos.Fil: Simon, Philipp. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados UnidosFil: Cavagnaro, Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria La Consulta; ArgentinaFil: Cavagnaro, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Cavagnaro, Pablo. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Horticultura; Argentina

Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem

In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNAseq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F2 population (3242) and the inbred B7262. Genetic mapping of ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP.Fil: Bannoud, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Carvajal, Sofia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Ellison, Shelby. University of Wisconsin; Estados UnidosFil: Senalik, Douglas A.. United States Department of Agriculture. Agriculture Research Service; Estados Unidos. University of Wisconsin; Estados UnidosFil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Iorizzo, Massimo. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute.; Estados UnidosFil: Simon, Philipp W.. University of Wisconsin; Estados UnidosFil: Cavagnaro, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Departamento de Producción Agropecuaria. Cátedra de Horticultura y Floricultura; Argentin

An Automated Image Analysis Pipeline Enables Genetic Studies of Shoot and Root Morphology in Carrot (Daucus carota L.)

Carrot is a globally important crop, yet efficient and accurate methods for quantifying its most important agronomic traits are lacking. To address this problem, we developed an automated image analysis platform that extracts components of size and shape for carrot shoots and roots, which are necessary to advance carrot breeding and genetics. This method reliably measured variation in shoot size and shape, petiole number, petiole length, and petiole width as evidenced by high correlations with hundreds of manual measurements. Similarly, root length and biomass were accurately measured from the images. This platform also quantified shoot and root shapes in terms of principal components, which do not have traditional, manually measurable equivalents. We applied the pipeline in a study of a six-parent diallel population and an F2 mapping population consisting of 316 individuals. We found high levels of repeatability within a growing environment, with low to moderate repeatability across environments. We also observed co-localization of quantitative trait loci for shoot and root characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage and/or pleiotropy. By increasing the number of individuals and phenotypes that can be reliably quantified, the development of a rapid, automated image analysis pipeline to measure carrot shoot and root morphology will expand the scope and scale of breeding and genetic studies

Different Fertility Approaches in Organic Hemp (Cannabis sativa L.) Production Alter Floral Biomass Yield but Not CBD:THC Ratio

Industrial hemp is once again legal in the United States but agronomic practices are not well characterized, especially for organic production systems. Many producers are concerned that while increased fertility may increase biomass yield it will also disproportionally increase that rate of total tetrahydrocannabinol (THC) accumulation, making their crop more likely to be noncompliant at harvest. We measured the effect of four organic fertility treatments: (1) no fertility (NA); (2) manure-based compost (CM); (3) an industry-standard organic fertilizer blend (ST); and (4) an intensive fertility treatment designed for cannabis production (BQ), on biomass yield and cannabinoid accumulation over multiple timepoints and two years. We found that higher fertility (ST and BQ) led to increased biomass but did not influence the ratio of cannabidiol (CBD) to THC over time. We also found the ST treatment yielded the most consistently across years, whereas CM and BQ were less predictable and more costly, respectively. Our results show that fertility recommendations can be made to increase biomass yield without increasing the chance of noncompliance. Additional research addressing specific fertility requirements in organic cropping systems for hemp will be needed to meet consumer demand while remaining profitable and sustainable for growers

Different Fertility Approaches in Organic Hemp (<i>Cannabis sativa</i> L.) Production Alter Floral Biomass Yield but Not CBD:THC Ratio

Industrial hemp is once again legal in the United States but agronomic practices are not well characterized, especially for organic production systems. Many producers are concerned that while increased fertility may increase biomass yield it will also disproportionally increase that rate of total tetrahydrocannabinol (THC) accumulation, making their crop more likely to be noncompliant at harvest. We measured the effect of four organic fertility treatments: (1) no fertility (NA); (2) manure-based compost (CM); (3) an industry-standard organic fertilizer blend (ST); and (4) an intensive fertility treatment designed for cannabis production (BQ), on biomass yield and cannabinoid accumulation over multiple timepoints and two years. We found that higher fertility (ST and BQ) led to increased biomass but did not influence the ratio of cannabidiol (CBD) to THC over time. We also found the ST treatment yielded the most consistently across years, whereas CM and BQ were less predictable and more costly, respectively. Our results show that fertility recommendations can be made to increase biomass yield without increasing the chance of noncompliance. Additional research addressing specific fertility requirements in organic cropping systems for hemp will be needed to meet consumer demand while remaining profitable and sustainable for growers

Fine Mapping, Transcriptome Analysis, and Marker Development for Y2, the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.)

Domesticated carrots, Daucus carota subsp. sativus, are the richest source of β-carotene in the US diet, which, when consumed, is converted into vitamin A, an essential component of eye health and immunity. The Y2 locus plays a significant role in beta-carotene accumulation in carrot roots, but a candidate gene has not been identified. To advance our understanding of this locus, the genetic basis of β-carotene accumulation was explored by utilizing an advanced mapping population, transcriptome analysis, and nucleotide diversity in diverse carrot accessions with varying levels of β-carotene. A single large effect Quantitative Trait Locus (QTL) on the distal arm of chromosome 7 overlapped with the previously identified β-carotene accumulation QTL, Y2. Fine mapping efforts reduced the genomic region of interest to 650 kb including 72 genes. Transcriptome analysis within this fine mapped region identified four genes differentially expressed at two developmental time points, and 13 genes differentially expressed at one time point. These differentially expressed genes included transcription factors and genes involved in light signaling and carotenoid flux, including a member of the Di19 gene family involved in Arabidopsis photomorphogenesis, and a homolog of the bHLH36 transcription factor involved in maize carotenoid metabolism. Analysis of nucleotide diversity in 25 resequenced carrot accessions revealed a drastic decrease in diversity of this fine-mapped region in orange cultivated accessions as compared to white and yellow cultivated and to white wild samples. The results presented in this study provide a foundation to identify and characterize the gene underlying β-carotene accumulation in carrot

Additional file 1 Table S1

Additional file 1: Table S1. The 162 accessions of Daucus, and two accessions of related genera characterized in this study, improvement status, locality information and new identification