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      Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed down the Genomic Region Responsible for Leaf Shape in Endive ( Cichorium endivia L.)

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          Abstract

          The characterization of genetic diversity in elite breeding stocks is crucial for the registration and protection of new varieties. Moreover, experimental population structure analysis and information about the genetic distinctiveness of commercial materials are essential for crop breeding programs. The purpose of our research was to assess the genetic relationships of 32 endive ( Cichorium endivia L.) breeding lines, 18 from var. latifolium (escarole) and 14 from var. crispum (curly), using heterologous Cichorium intybus-derived simple sequence repeats (SSR) markers and single-nucleotide polymorphisms (SNP) markers. We found that 14 out of 29 SSR markers were successfully amplified, but only 8 of them were related to polymorphic loci. To overcome the limitation of the low number of informative SSR marker loci, an alternative SNP-based approach was employed. The 4621 SNPs produced by a restriction site-associated DNA marker sequencing approach were able to fully discriminate the 32 endive accessions; most importantly, as many as 50 marker loci were found to distinguish the curly group from the escarole group. Interestingly, 24 of the marker loci mapped within a peripheral segment of chromosome 8 of lettuce ( Lactuca sativa L.), spanning a chromosomal region of 49.6 Mb. Following Sanger sequencing-based validation, three genes were determined to carry nonsynonymous SNPs, and one of them matched a putative ortholog of AtELP1, subunit 1 of the Elongator complex. Considering that several previously characterized Elongator complex subunit mutants exhibited elongated and/or curly leaf phenotypes, this gene should be taken into consideration for a better understanding of the underlying mechanism controlling leaf shape in endive.

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          Most cited references53

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          Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

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            Microsatellite markers: an overview of the recent progress in plants

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              Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

              Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence.
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                Author and article information

                Journal
                Genes (Basel)
                Genes (Basel)
                genes
                Genes
                MDPI
                2073-4425
                23 April 2020
                April 2020
                : 11
                : 4
                : 462
                Affiliations
                Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro PD, Italy; alice.patella@ 123456phd.unipd.it (A.P.); fabio.palumbo@ 123456unipd.it (F.P.); samathmikaravi@ 123456gmail.com (S.R.); stevanato@ 123456unipd.it (P.S.)
                Author notes
                [†]

                These authors equally contributed.

                Author information
                https://orcid.org/0000-0001-7421-1837
                https://orcid.org/0000-0002-6577-6956
                https://orcid.org/0000-0001-7478-5048
                Article
                genes-11-00462
                10.3390/genes11040462
                7231076
                32340299
                b371c726-ed1c-4262-b92f-4e7ff2cc9c34
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 24 March 2020
                : 21 April 2020
                Categories
                Article

                rad-seq,ssr markers,snp markers,genetic diversity,elo2/atelp1,leaf shape,endive,breeding

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