Characterization of a Genomic Region under Selection in Cultivated Carrot (Daucus carota subsp. sativus) Reveals a Candidate Domestication Gene

Abstract

Carrot is one of the most important vegetables worldwide, owing to its capability to develop fleshy, highly nutritious storage roots. It was domesticated ca. 1,100 years ago in Central Asia. No systematic knowledge about the molecular mechanisms involved in the domestication syndrome in carrot are available, however, the ability to form a storage root is undoubtedly the essential transition from the wild Daucus carota to the cultivated carrot. Here, we expand on the results of a previous study which identified a polymorphism showing a significant signature for selection upon domestication. We mapped the region under selection to the distal portion of the long arm of carrot chromosome 2, confirmed that it had been selected, as reflected in both the lower nucleotide diversity in the cultivated gene pool, as compared to the wild (πw/πc = 7.4 vs. 1.06 for the whole genome), and the high FST (0.52 vs. 0.12 for the whole genome). We delimited the region to ca. 37 kb in length and identified a candidate domestication syndrome gene carrying three non-synonymous single nucleotide polymorphisms and one indel systematically differentiating the wild and the cultivated accessions. This gene, DcAHLc1, belongs to the AT-hook motif nuclear localized (AHL) family of plant regulatory genes which are involved in the regulation of organ development, including root tissue patterning. AHL genes work through direct interactions with other AHL family proteins and a range of other proteins that require intercellular protein movement. Based on QTL data on root thickening we speculate that DcAHLc1 might be involved in the development of the carrot storage root, as the localization of the gene overlapped with one of the QTLs. According to haplotype information we propose that the ‘cultivated’ variant of DcAHLc1 has been selected from wild Central Asian carrot populations upon domestication and it is highly predominant in the western cultivated carrot gene pool. However, some primitive eastern landraces and the derived B7262 purple inbred line still carry the ‘wild’ variant, reflecting a likely complexity of the genetic determination of the formation of carrot storage roots.

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

“…QTL for image measurements tended to overlap with QTL for manual measurements, providing confirmation that this pipeline can be used reliably for genetic studies of shoot and root morphology in carrot. Notably, QTL for several traits in this study had various amounts of overlap with previously identified QTL for root swelling on chromosomes 2, 3, 4, and 5 ( Macko-Podgórni et al, 2017 ).…”

“…Carrot is a globally important crop that originated in Central Asia ( Vavilov , 1992 ; Iorizzo et al, 2013 ) with a secondary center of diversity in Asia Minor ( Banga, 1957 ). A hallmark of carrot domestication is the capacity to develop a thickened storage root ( Macko-Podgórni et al, 2017 ). Selective breeding has since improved taproot size, shape, and uniformity, resulting in forms that have served as the primary delimiter of variety classification since the 1600s ( Simon et al, 2008 ).…”

“…To date, the majority of genetic studies in carrot have focused on storage root pigmentation, specifically anthocyanin content ( Yildiz et al, 2013 ; Cavagnaro et al, 2014 ) and carotenoid accumulation ( Buishand and Gabelman, 1979 ; Bradeen and Simon, 1998 ; Just et al, 2007 , 2009 ; Iorizzo et al, 2016 ; Ellison et al, 2017 ). More recently, two potential domestication loci that influence carrot morphology were identified on chromosome 2 for early flowering ( Vrn1 ; Alessandro et al, 2013 ) and storage root development ( DcAHLc1 , Macko-Podgórni et al, 2014 , 2017 ). Additionally, the observation of a linear relationship between the logarithms of shoot biomass and storage root biomass in carrot ( Hole et al, 1983 ; Turner et al, 2018 ) suggests potential genetic relationships, but the causal genetic loci, the extent of polygenic control, and the influence of pleiotropy on shoot and root architecture in carrot have not yet been investigated.…”

Cytological and transcriptome analyses reveal abrupt gene expression for meiosis and saccharide metabolisms that associated with pollen abortion in autotetraploid rice

“…RNA transcript technology (RNA-seq) is a helpful tool for understanding of differentially expressed genes and the expression patterns of stage-specific genes in plants. RNA-seq has been applied to detect differentially expressed genes under abiotic stresses in diploid rice (Jin et al 2013 ; Fu et al 2017 ). In addition, RNA-seq has also been applied to identify differentially expressed genes in autotetraploid rice compared to diploid rice during pollen development (Wu et al 2014 ).…”

The Expected and Unexpected Roles of Nitrate Transporters in Plant Abiotic Stress Resistance and Their Regulation

“…ABA is a phytohormone involved in the regulation of plant development and plant adaptation to adverse stress conditions [ 78 ]. Several ABC (ATP-binding cassette) transporters were identified to transport ABA using mutant analysis and biochemical characterization [ 79 ].…”