SNP Discovery and Linkage Map Construction in Cultivated Tomato

Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single nucleotide polymorphisms (SNPs), the most abundant source of genomic variation, are the most promising source of polymorphisms for the construction of linkage maps for closely related intraspecific lines. In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato. Out of the 5607 SNP positions detected through in silico analysis, 1536 were selected for high-throughput genotyping of two mapping populations derived from crosses between ‘Micro-Tom’ and either ‘Ailsa Craig’ or ‘M82’. A total of 1137 markers, including 793 out of the 1338 successfully genotyped SNPs, along with 344 simple sequence repeat and intronic polymorphism markers, were mapped onto two linkage maps, which covered 1467.8 and 1422.7 cM, respectively. The SNP markers developed were then screened against cultivated tomato lines in order to estimate the transferability of these SNPs to other breeding materials. The molecular markers and linkage maps represent a milestone in the genomics and genetics, and are the first step toward molecular breeding of cultivated tomato. Information on the DNA markers, linkage maps, and SNP genotypes for these tomato lines is available at http://www.kazusa.or.jp/tomato/

An EST-SSR Linkage Map of Raphanus sativus and Comparative Genomics of the Brassicaceae†

Raphanus sativus (2n = 2x = 18) is a widely cultivated member of the family Brassicaceae, for which genomic resources are available only to a limited extent in comparison to many other members of the family. To promote more genetic and genomic studies and to enhance breeding programmes of R. sativus, we have prepared genetic resources such as complementary DNA libraries, expressed sequences tags (ESTs), simple sequence repeat (SSR) markers and a genetic linkage map. A total of 26 606 ESTs have been collected from seedlings, roots, leaves, and flowers, and clustered into 10 381 unigenes. Similarities were observed between the expression patterns of transcripts from R. sativus and those from representative members of the genera Arabidopsis and Brassica, indicating their functional relatedness. The EST sequence data were used to design 3800 SSR markers and consequently 630 polymorphic SSR loci and 213 reported marker loci have been mapped onto nine linkage groups, covering 1129.2 cM with an average distance of 1.3 cM between loci. Comparison of the mapped EST-SSR marker positions in R. sativus with the genome sequence of A. thaliana indicated that the Brassicaceae members have evolved from a common ancestor. It appears that genomic fragments corresponding to those of A. thaliana have been doubled and tripled in R. sativus. The genetic map developed here is expected to provide a standard map for the genetics, genomics, and molecular breeding of R. sativus as well as of related species. The resources are available at http://marker.kazusa.or.jp/Daikon

Altered Energy Homeostasis and Resistance to Diet-Induced Obesity in KRAP-Deficient Mice

Obesity and related metabolic disorders have become leading causes of adult morbidity and mortality. KRAP (Ki-ras-induced actin-interacting protein) is a cytoskeleton-associated protein and a ubiquitous protein among tissues, originally identified as a cancer-related molecule, however, its physiological roles remain unknown. Here we demonstrate that KRAP-deficient (KRAP−/−) mice show enhanced metabolic rate, decreased adiposity, improved glucose tolerance, hypoinsulinemia and hypoleptinemia. KRAP−/− mice are also protected against high-fat diet-induced obesity and insulin resistance despite of hyperphagia. Notably, glucose uptake in the brown adipose tissue (BAT) in KRAP−/− mice is enhanced in an insulin-independent manner, suggesting that BAT is involved in altered energy homeostasis in KRAP−/− mice, although UCP (Uncoupling protein) expressions are not altered. Of interest is the down-regulation of fatty acid metabolism-related molecules, including acetyl-CoA carboxylase (ACC)-1, ACC-2 and fatty acid synthase in the liver of KRAP−/− mice, which could in part account for the metabolic phenotype in KRAP−/− mice. Thus, KRAP is a novel regulator in whole-body energy homeostasis and may be a therapeutic target in obesity and related diseases

High Potential of a Transposon mPing as a Marker System in japonica × japonica Cross in Rice

Although quantitative traits loci (QTL) analysis has been widely performed to isolate agronomically important genes, it has been difficult to obtain molecular markers between individuals with similar phenotypes (assortative mating). Recently, the miniature inverted-repeat transposable element mPing was shown to be active in the japonica strain Gimbozu EG4 where it had accumulated more than 1000 copies. In contrast, most other japonicas, including Nipponbare, have 50 or fewer mPing insertions in their genome. In this study we have exploited the polymorphism of mPing insertion sites to generate 150 PCR markers in a cross between the closely related japonicas, Nipponbare × Gimbozu (EG4). These new markers were distributed in genic regions of the whole genome and showed significantly higher polymorphism (150 of 183) than all other molecular markers tested including short sequence repeat markers (46 of 661). In addition, we performed QTL analysis with these markers using recombinant inbred lines derived from Nipponbare × Gimbozu EG4, and successfully mapped a locus involved in heading date on the short arm of chromosome 6. Moreover, we could easily map two novel loci involved in the culm length on the short arms of chromosomes 3 and 10

Extensive Chromosome Homoeology among Brassiceae Species Were Revealed by Comparative Genetic Mapping with High-Density EST-Based SNP Markers in Radish (Raphanus sativus L.)‡

A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction–mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another

Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion

In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it. Fortunately, the emergence of genome editing technologies based on programmable nucleases, and especially the arrival of a multipurpose RNA-guided Cas9 endonuclease system, has made it possible to reconsider this challenge. For such purpose, a particular type of transposons referred to as miniature inverted-repeat transposable elements (MITEs) has shown a series of interesting characteristics for designing functional drivers. Here, recent insights into MITE elements and versatile RNA-guided CRISPR/Cas9 genome engineering system are given to understand how to deploy the potential of TEs for control of the host transcriptional activity.Fil: Vaschetto, Luis Maria Benjamin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Cátedra de Diversidad Animal I; Argentin

Location of chlorogenic acid biosynthesis pathway and polyphenol oxidase genes in a new interspecific anchored linkage map of eggplant

© Gramazio et al.; licensee BioMed Central. 2014. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated

QTL mapping for late leaf spot and rust resistance using an improved genetic map and extensive phenotypic data on a recombinant inbred line population in peanut (Arachis hypogaea L.)

The linkage map for the recombinant inbred line (RIL) mapping population derived from late leaf spot (LLS) and rust disease susceptible (TAG 24) and resistant (GPBD 4) varieties of peanut was improved by adding 139 new SSR and transposable element (TE) markers. The improved map now has 289 mapped loci with a total map distance of 1730.8 cM and average inter-marker distance of 6.0 cM across 20 linkage groups. Quantitative trait loci (QTL) analysis using improved genetic map with 289 markers and comprehensive phenotypic data for LLS and rust from 11 seasons could identify a region on linkage group AhXV (B03 linkage group of B genome) which contributed significantly towards LLS and rust resistance. Of the five QTL mapped in this region, three showed high phenotypic variance explained (PVE) for both LLS and rust, and two QTL showed high PVE for only rust. The QTL flanked by GM2009-IPAHM103 had very high PVE of 44.5 % and 53.7 %, respectively for LLS and rust response. Another genomic region on AhXII (B10 linkage group of B genome) contained a QTL flanked by GM1839-GM1009 which had a PVE of 14.1–35.2 % for LLS resistance. A new QTL with marker interval GM1989-AhTE0839 on AhV (A05 linkage group of A genome) showed a PVE of 10.2 % for rust resistance. The new markers, AhTE0498 and AhTE0928 linked to rust resistance were validated using another RIL population of TG 26 × GPBD 4. The marker AhTE0498 showed 49.3–52.3 % PVE, indicating a strong marker validation in the new population. The improved map, QTL and markers for LLS and rust resistance reported in this study will be of immense utility in peanut molecular breeding

Resequencing

[ES] La revolución que supone la secuenciación de próxima generación está permitiendo la resecuenciación del genoma completo (WGRS) de cientos o incluso miles de ejemplares de cultivos básicos y especies modelo. Con el lanzamiento de su genoma de referencia, progresivamente se están emprendiendo proyectos WGRS también para otras especies de plantas en una amplia variedad de estudios. En berenjena común (Solanum melongena L.), aunque se ha publicado un primer borrador de la secuencia del genoma de referencia, hasta el momento no se han realizado estudios de resecuenciación. En este capítulo presentamos los primeros resultados de la resecuenciación de ocho accesiones, siete de berenjena común y una del pariente silvestre S. incanum L., que corresponden a los progenitores de un cruce multiparental de generación avanzada (MAGIC) población que se encuentra actualmente en desarrollo utilizando la secuencia del genoma de la berenjena recién desarrollada que se presenta en el Cap. 7 de este libro. Se identificaron más de diez millones de polimorfismos entre las accesiones, el 90% de ellos en el S. incanum silvestre relacionado, lo que confirma la erosión genética de la berenjena común cultivada. Entre los progenitores de la población MAGIC, el patrón de distribución de polimorfismos comunes a lo largo de los cromosomas ha revelado posibles huellas de introgresión ancestral de cruces interespecíficos. El conjunto de polimorfismos se ha anotado extensamente y actualmente se está utilizando para análisis adicionales con el fin de genotipar eficientemente la población MAGIC en curso y diseccionar rasgos agronómicos y morfológicos importantes. La información proporcionada en este primer estudio de resecuenciación en berenjena será extremadamente útil para ayudar al fitomejoramiento a desarrollar nuevas variedades mejoradas y resistentes para enfrentar futuras amenazas y desafíos.[EN] The next-generation sequencing revolution is allowing the whole-genome resequencing (WGRS) of hundreds or even thousands of accessions for staple crops and model species. With the release of their reference genome, progressively also other plants, species are undertaking WGRS projects for a broad variety of studies. In common eggplant (Solanum melongena L.), although a first draft of the reference genome sequence has been published, no resequencing studies have been performed so far. In this chapter, we present the first results of the resequencing of eight accessions, seven of common eggplant and one of the wild relative S. incanum L., that correspond to the parents of a multi-parent advanced generation inter-cross (MAGIC) population that is currently under develop- ment using the newly developed eggplant genome sequence presented in Chap. 7 of this book. Over ten million polymorphisms were identified among the accessions, 90% of them in the wild related S. incanum, confirming the genetic erosion of the cultivated common eggplant. Among the MAGIC population parents, the common polymorphism distribu- tion pattern along the chromosomes has revealed possible footprints of ancestral intro- gression from interspecific crosses. The set of polymorphisms has been extensively anno- tated and currently is being used for further analyses in order to efficiently genotype the ongoing MAGIC population and to dissect important agronomic and morphological traits. The information provided in this first resequencing study in eggplant will be extremely helpful to assist plant breeding to develop new improved and resilient varieties to face future threats and challenges.This work has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and from Spanish Ministerio de Economía, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER).Prohens Tomás, J.; Vilanova Navarro, S.; Gramazio, P. (2019). Resequencing. En The Eggplant Genome. Springer. 81-89. http://hdl.handle.net/10251/181875S818