共查询到20条相似文献,搜索用时 31 毫秒
1.
Joanne A. Labate Larry D. Robertson Feinan Wu Steven D. Tanksley Angela M. Baldo 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,118(5):1005-1014
Because cultivated tomato (Solanum lycopersicum L.) is low in genetic diversity, public, verified single nucleotide polymorphism (SNP) markers within the species are in
demand. To promote marker development we resequenced approximately 23 kb in a diverse set of 31 tomato lines including TA496.
Three classes of markers were sampled: (1) 26 expressed-sequence tag (EST), all of which were predicted to be polymorphic
based on TA496, (2) 14 conserved ortholog set II (COSII) or unigene, and (3) ten published sequences, composed of nine fruit
quality genes and one anonymous RFLP marker. The latter two types contained mostly noncoding DNA. In total, 154 SNPs and 34
indels were observed. The distributions of nucleotide diversity estimates among marker types were not significantly different
from each other. Ascertainment bias of SNPs was evaluated for the EST markers. Despite the fact that the EST markers were
developed using SNP prediction within a sample consisting of only one TA496 allele and one additional allele, the majority
of polymorphisms in the 26 EST markers were represented among the other 30 tomato lines. Fifteen EST markers with published
SNPs were more closely examined for bias. Mean SNP diversity observations were not significantly different between the original
discovery sample of two lines (53 SNPs) and the 31 line diversity panel (56 SNPs). Furthermore, TA496 shared its haplotype
with at least one other line at 11 of the 15 markers. These data demonstrate that public EST databases and noncoding regions
are a valuable source of unbiased SNP markers in tomato.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
The use of trade, firm, or corporation names in this publication is for the information and convenience of the reader. Such
use does not constitute an official endorsement or approval by the United States Department of Agriculture or the Agricultural
Research Service of any product or service to the exclusion of others that may be suitable. 相似文献
2.
3.
Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato 总被引:2,自引:0,他引:2
Robbins MD Sim SC Yang W Van Deynze A van der Knaap E Joobeur T Francis DM 《Journal of experimental botany》2011,62(6):1831-1845
The history of tomato (Solanum lycopersicum L.) improvement includes genetic bottlenecks, wild species introgressions, and divergence into distinct market classes. This history makes tomato an excellent model to investigate the effects of selection on genome variation. A combination of linkage mapping in two F(2) populations and physical mapping with emerging genome sequence data was used to position 434 PCR-based markers including SNPs. Three-hundred-and-forty markers were used to genotype 102 tomato lines representing wild species, landraces, vintage cultivars, and contemporary (fresh market and processing) varieties. Principal component analysis confirmed genetic divergence between market classes of cultivated tomato (P <0.0001). A genome-wide survey indicated that linkage disequilibrium (LD) decays over 6-8 cM when all cultivated tomatoes, including vintage and contemporary, were considered together. Within contemporary processing varieties, LD decayed over 6-14 cM, and decay was over 3-16 cM within fresh market varieties. Significant inter-chromosomal (gametic phase) LD was detected in both fresh market and processing varieties between chromosomes 2 and 3, and 2 and 4, but in distinct chromosomal locations for each market class. Additional LD was detected between chromosomes 3 and 4, 3 and 11, and 4 and 6 in fresh market varieties and chromosomes 3 and 12 in processing varieties. These results suggest that breeding practices for market specialization in tomato have led to a genetic divergence between fresh market and processing types. 相似文献
4.
Tomato (Solanum lycopersicum) is considered a model plant species for a group of economically important crops, such as potato, pepper, eggplant, since it exhibits a reduced genomic size (950 Mb), a short generation time, and routine transformation technologies. Moreover, it shares with the other Solanaceous plants the same haploid chromosome number and a high level of conserved genomic organization. Finally, many genomic and genetic resources are actually available for tomato, and the sequencing of its genome is in progress. These features make tomato an ideal species for theoretical studies and practical applications in the genomics field. The present review describes how structural genomics assist the selection of new varieties resistant to pathogens that cause damage to this crop. Many molecular markers highly linked to resistance genes and cloned resistance genes are available and could be used for a high-throughput screening of multiresistant varieties. Moreover, a new genomics-assisted breeding approach for improving fruit quality is presented and discussed. It relies on the identification of genetic mechanisms controlling the trait of interest through functional genomics tools. Following this approach, polymorphisms in major gene sequences responsible for variability in the expression of the trait under study are then exploited for tracking simultaneously favourable allele combinations in breeding programs using high-throughput genomic technologies. This aims at pyramiding in the genetic background of commercial cultivars alleles that increase their performances. In conclusion, tomato breeding strategies supported by advanced technologies are expected to target increased productivity and lower costs of improved genotypes even for complex traits.Key Words: Solanum lycopersicum, genetic and genomic resources, molecular markers, microarray, resistance to pathogens, fruit quality. 相似文献
5.
Santiago García-Martínez Lorella Andreani Marta Garcia-Gusano Filippo Geuna Juan J Ruiz 《Génome》2006,49(6):648-656
Cultivated tomato (Solanum lycopersicum L.) germplasm shows limited genetic variation. Many DNA marker systems have been used for genetic diversity studies in wild and cultivated tomatoes, but their usefulness for characterizing phenotypic differences among very closely related cultivars remains uncertain. We have used 19 selected simple sequence repeat (SSR) markers and 7 amplified fragment length polymorphism (AFLP) primer combinations to characterize 48 cultivars of tomato, mainly traditional cultivars from the south-east of Spain. The main types were Solanum lycopersicum L. 'Muchamiel', 'De la pera', and 'Moruno'. The robustness of the dendrograms and the discrimination power reached with each marker type were similar. Unique fingerprinting even of the most closely related tomato cultivars could be obtained using a combination of some SSR and AFLP markers. A better grouping of the 'Muchamiel' cultivars was observed with SSR markers, whereas the grouping of cultivars of 'De la pera' type was best achieved with AFLPs. However, both types of markers adequately grouped cultivars of the main types, confirming the utility of SSR and AFLP markers for the identification of traditional cultivars of tomato. 相似文献
6.
Hamid Ashrafi Matthew P. Kinkade Heather L. Merk Majid R. Foolad 《Molecular breeding : new strategies in plant improvement》2012,30(1):549-567
Epidemiological and clinical studies indicate that a steady dietary intake of bioavailable lycopene, a C40 carotenoid and potent natural antioxidant, may be associated with a decreased incidence of prostate cancer in humans. Since fresh tomatoes and processed tomato products represent approximately 85% of the average human??s dietary lycopene intake, the identification of novel genetic factors which regulate high fruit lycopene content in tomato is imperative for the improvement of nutritional quality in this commercially valuable specialty crop. To understand the genetic control of the extraordinarily high fruit lycopene content in an accession (LA2093) of the tomato wild species Solanum pimpinellifolium, a quantitative trait locus (QTL) mapping study was conducted using a recombinant inbred line (RIL) population of a cross between LA2093 and a cultivated tomato (S. lycopersicum) breeding line, NCEBR-1. The parental lines, F1 progeny, and F7-F10 RIL populations were grown in replicated field trials in four successive years and evaluated for lycopene content as well as several other traits, including fruit fresh weight, soluble solids content, pH of puree, and plant maturity. The lycopene content of ripe fruit was estimated using three methods: high-performance liquid chromatography (HPLC), spectrophotometry, and colorimetric assays. Based on these measurements, QTL were identified and compared across generations. Among the QTL identified for lycopene, two QTL, located on chromosomes 7 and 12, had very large effects and were consistent across generations. The genomic intervals in which these two QTL reside do not correspond to known map positions of carotenoid biosynthetic genes, indicating that these QTL may represent novel alleles with potentially important implications for tomato breeding as well as increased understanding of carotenoid accumulation in tomato. Several QTL were also identified for fruit weight, soluble solids content and plant maturity. The potential implications of these results for tomato crop improvement are discussed. 相似文献
7.
Feinan Wu Nancy T. Eannetta Yimin Xu Richard Durrett Michael Mazourek Molly M. Jahn Steven D. Tanksley 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,118(7):1279-1293
We report herein the development of a pepper genetic linkage map which comprises 299 orthologous markers between the pepper
and tomato genomes (including 263 conserved ortholog set II or COSII markers). The expected position of additional 288 COSII
markers was inferred in the pepper map via pepper–tomato synteny, bringing the total orthologous markers in the pepper genome
to 587. While pepper maps have been previously reported, this is the first complete map in the sense that all markers could
be placed in 12 linkage groups corresponding to the 12 chromosomes. The map presented herein is relevant to the genomes of
cultivated C. annuum and wild C. annuum (as well as related Capsicum species) which differ by a reciprocal chromosome translocation. This map is also unique in that it is largely based on COSII
markers, which permits the inference of a detailed syntenic relationship between the pepper and tomato genomes—shedding new
light on chromosome evolution in the Solanaceae. Since divergence from their last common ancestor is approximately 20 million
years ago, the two genomes have become differentiated by a minimum number of 19 inversions and 6 chromosome translocations,
as well as numerous putative single gene transpositions. Nevertheless, the two genomes share 35 conserved syntenic segments
(CSSs) within which gene/marker order is well preserved. The high resolution COSII synteny map described herein provides a
platform for cross-reference of genetic and genomic information (including the tomato genome sequence) between pepper and
tomato and therefore will facilitate both applied and basic research in pepper.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
8.
Adriana Sacco Valentino Ruggieri Mario Parisi Giovanna Festa Maria Manuela Rigano Maurizio Enea Picarella Andrea Mazzucato Amalia Barone 《PloS one》2015,10(9)
During its evolution and domestication Solanum lycopersicum has undergone various genetic ‘bottlenecks’ and extreme inbreeding of limited genotypes. In Europe the tomato found a secondary centre for diversification, which resulted in a wide array of fruit shape variation given rise to a range of landraces that have been cultivated for centuries. Landraces represent a reservoir of genetic diversity especially for traits such as abiotic stress resistance and high fruit quality. Information about the variation present among tomato landrace populations is still limited. A collection of 123 genotypes from different geographical areas was established with the aim of capturing a wide diversity. Eighteen morphological traits were evaluated, mainly related to the fruit. About 45% of morphological variation was attributed to fruit shape, as estimated by the principal component analysis, and the dendrogram of relatedness divided the population in subgroups mainly on the basis of fruit weight and locule number. Genotyping was carried out using the tomato array platform SolCAP able to interrogate 7,720 SNPs. In the whole collection 87.1% markers were polymorphic but they decreased to 44–54% when considering groups of genotypes with different origin. The neighbour-joining tree analysis clustered the 123 genotypes into two main branches. The STRUCTURE analysis with K = 3 also divided the population on the basis of fruit size. A genomic-wide association strategy revealed 36 novel markers associated to the variation of 15 traits. The markers were mapped on the tomato chromosomes together with 98 candidate genes for the traits analyzed. Six regions were evidenced in which candidate genes co-localized with 19 associated SNPs. In addition, 17 associated SNPs were localized in genomic regions lacking candidate genes. The identification of these markers demonstrated that novel variability was captured in our germoplasm collection. They might also provide a viable indirect selection tool in future practical breeding programs. 相似文献
9.
Development of intron targeting (IT) markers for potato and cross-species amplification in Solanum nigrum (Solanaceae) 总被引:1,自引:0,他引:1
Poczai P Cernák I Gorji AM Nagy S Taller J Polgár Z 《American journal of botany》2010,97(12):e142-e145
? Premise of the study: Intron Targeting (IT) primers were developed for potato using expressed sequence tags (EST) and NCBI database records to study genetic diversity. ? Methods and Results: Twenty-nine polymorphic intron targeting (IT) markers were generated and characterized from 30 samples of potato and 22 samples of Solanum nigrum to detect polymorphism. The number of alleles (A) per locus ranged from 2 to 7 in the analyzed populations, and the observed heterozygosity (H(O)) and expected heterozygosity (H(E)) from 0 to 0.833 and 0.750, respectively. All of the primers also amplified in the related species S. nigrum. ? Conclusions: The developed markers will provide valuable tools for genetic diversity analysis, genetic mapping, and marker-assisted breeding of potato and related Solanum species. 相似文献
10.
We describe the isolation and characterization of 31 polymorphic di- and trinucleotide microsatellite marker loci for Carolina hemlock (Tsuga caroliniana Englem.). In addition, primer pairs for 16 loci amplified scoreable alleles in six other Tsuga species. In eastern North America, both Carolina hemlock and eastern hemlock (Tsuga canadensis [L.] Carr.) populations are declining due to infestation by hemlock woolly adelgid, Adelges tsugae. The markers described here should enhance population genetic studies of hemlocks, providing valuable information for conserving and restoring these important forest tree species. 相似文献
11.
ABSTRACT: BACKGROUND: Many beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. RESULTS: Each marker was mapped with high confidence (e < 1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 plus or minus 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. CONCLUSION: Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help inform conservation and utilization of crop germplasm diversity, for example, facilitating the purging of undesirable linkage drag or the exploitation of novel, favorable alleles. 相似文献
12.
RAPD markers for constructing intraspecific tomato genetic maps 总被引:8,自引:0,他引:8
The existing molecular genetic maps of the tomato, Lycopersicon spp, are constructed based on isozyme and RFLP polymorphisms between tomato species. These maps are useful for certain applications but have few markers that exhibit sufficient polymorphisms for intraspecific analysis and manipulations within the cultivated tomato. The purpose of this study was to investigate the relative potential of RAPD technology, as compared to isozymes and RFLPs, to generate polymorphic DNA markers within cultivated tomatoes. Sixteen isozymes and 25 RFLP clones that were known to detect polymorphism between L. esculentum and L. pennellii, and 313 random oligonucleotide primers were examined. None of the isozymes and only four of the RFLP clones (i.e., 16%) revealed polymorphism between the cultivated varieties whereas up to 63% of the RAPD primers detected one or more polymorphic DNA fragments between these varieties. All RAPD primers detected polymorphism between L. esculentum and L. pennellii genotypes. These results clearly indicate that RAPD technology can generate sufficient genetic markers exploiting sequence differences within cultivated tomatoes to facilitate construction of intraspecific genetic maps.Abbreviations RFLP
restriction fragments length polymorphism
- RAPD
random amplified polymorphic DNA
- PCR
polymerase chain reaction
- QTLs
quantitative trait loci 相似文献
13.
Feinan Wu Nancy T. Eannetta Yimin Xu Jörg Plieske Martin Ganal Carlo Pozzi Nicolas Bakaher Steven D. Tanksley 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2010,120(4):809-827
Using single-copy conserved ortholog set (COSII) and simple sequence repeat (SSR) markers, we have constructed two genetic
maps for diploid Nicotiana species, N. tomentosiformis and N. acuminata, respectively. N. acuminata is phylogenetically closer to N. sylvestris than to N. tomentosiformis, the latter two of which are thought to contribute the S-genome and T-genome, respectively, to the allotetraploid tobacco
(N. tabacum L., 2n = 48). A comparison of the two maps revealed a minimum of seven inversions and one translocation subsequent to the divergence
of these two diploid species. Further, comparing the diploid maps with a dense tobacco map revealed that the tobacco genome
experienced chromosomal rearrangements more frequently than its diploid relatives, supporting the notion of accelerated genome
evolution in allotetraploids. Mapped COSII markers permitted the investigation of Nicotiana–tomato syntenic relationships. A minimum of 3 (and up to 10) inversions and 11 reciprocal translocations differentiate the
tomato genome from that of the last common ancestor of N. tomentosiformis and N. acuminata. Nevertheless, the marker/gene order is well preserved in 25 conserved syntenic segments. Molecular dating based on COSII
sequences suggested that tobacco was formed 1.0MYA or later. In conclusion, these COSII and SSR markers link the cultivated
tobacco map to those of wild diploid Nicotiana species and tomato, thus providing a platform for cross-reference of genetic and genomic information among them as well as
other solanaceous species including potato, eggplant, pepper and the closely allied coffee (Rubiaceae). Therefore they will
facilitate genetic research in the genus Nicotiana. 相似文献
14.
Detection of major loci associated with the variation of 18 important agronomic traits between Solanum pimpinellifolium and cultivated tomatoes
下载免费PDF全文
![点击此处可从《The Plant journal : for cell and molecular biology》网站下载免费的PDF全文](/ch/ext_images/free.gif)
Shuaibin Zhang Hong Yu Ketao Wang Zheng Zheng Lei Liu Meng Xu Zhicheng Jiao Ren Li Xiyan Liu Jiayang Li Xia Cui 《The Plant journal : for cell and molecular biology》2018,95(2):312-323
Wild species can be used to improve various agronomic traits in cultivars; however, a limited understanding of the genetic basis underlying the morphological differences between wild and cultivated species hinders the integration of beneficial traits from wild species. In the present study, we generated and sequenced recombinant inbred lines (RILs, 201 F10 lines) derived from a cross between Solanum pimpinellifolium and Solanum lycopersicum tomatoes. Based on a high‐resolution recombination bin map to uncover major loci determining the phenotypic variance between wild and cultivated tomatoes, 104 significantly associated loci were identified for 18 agronomic traits. On average, these loci explained ~39% of the phenotypic variance of the RILs. We further generated near‐isogenic lines (NILs) for four identified loci, and the lines exhibited significant differences for the associated traits. We found that two loci could improve the flower number and inflorescence architecture in the cultivar following introgression of the wild‐species alleles. These findings allowed us to construct a trait–locus network to help explain the correlations among different traits based on the pleiotropic or linked loci. Our results provide insights into the morphological changes between wild and cultivated tomatoes, and will help to identify key genes governing important agronomic traits for the molecular selection of elite tomato varieties. 相似文献
15.
The transition from self-incompatibility to self-compatibility is a common transition in angiosperms often reported in populations at the edge of species range limits. Geographically distinct populations of wild tomato species (Solanum section Lycopersicon (Solanaceae)) have been described as polymorphic for mating system with both self-incompatible and self-compatible populations. Using controlled pollinations and sequencing of the S-RNase mating system gene, we test the compatibility status of a population of S. peruvianum located near its southern range limit. Pollinations among plants of known genotypes revealed strong self-incompatibility; fruit set following compatible pollinations was significantly higher than following incompatible pollinations for all tested individuals. Sequencing of the S-RNase gene in parents and progeny arrays was also as predicted under self-incompatibility. Molecular variation at the S-RNase locus revealed a diverse set of alleles, and heterozygosity in over 500 genotyped individuals. We used controlled crosses to test the specificity of sequences recovered in this study; in all cases, results were consistent with a unique allelic specificity for each tested sequence, including two alleles sharing 92% amino-acid similarity. Site-specific patterns of selection at the S-RNase gene indicate positive selection in regions of the gene associated with allelic specificity determination and purifying selection in previously characterized conserved regions. Further, there is broad convergence between the present and previous studies in specific amino-acid positions inferred to be evolving under positive selection. 相似文献
16.
Kenta Shirasawa Erika Asamizu Hiroyuki Fukuoka Akio Ohyama Shusei Sato Yasukazu Nakamura Satoshi Tabata Shigemi Sasamoto Tsuyuko Wada Yoshie Kishida Hisano Tsuruoka Tsunakazu Fujishiro Manabu Yamada Sachiko Isobe 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2010,121(4):731-739
Despite the collection and availability of abundant tomato genome sequences, PCR-based markers adapted to large scale analysis have not been developed in tomato species. Therefore, using public genome sequence data in tomato, we developed three types of DNA markers: expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers (TES markers), genome-derived SSR markers (TGS markers) and EST-derived intronic polymorphism markers (TEI markers). A total of 2,047 TES, 3,510 TGS and 674 TEI markers were established and used in the polymorphic analysis of a cultivated tomato (Solanum lycopersicum) ‘LA925’ and its wild relative Solanum pennellii ‘LA716’, parents of the Tomato-EXPEN 2000 mapping population. The polymorphic ratios between parents revealed by the TES, TGS and TEI markers were 37.3, 22.6 and 80.0%, respectively. Those showing polymorphisms were used to genotype the Tomato-EXPEN 2000 mapping population, and a high-density genetic linkage map composed of 1,433 new and 683 existing marker loci was constructed on 12 chromosomes, covering 1,503.1 cM. In the present map, 48% of the mapped TGS loci were located within heterochromatic regions, while 18 and 21% of TES and TEI loci, respectively, were located in heterochromatin. The large number of SSR and SNP markers developed in this study provide easily handling genomic tools for molecular breeding in tomato. Information on the DNA markers developed in this study is available at http://www.kazusa.or.jp/tomato/. 相似文献
17.
Carson C. Keever Christal Nieman Larissa Ramsay Carol E. Ritland Leah S. Bauer D. Barry Lyons Jenny S. Cory 《Biological invasions》2013,15(7):1537-1559
The emerald ash borer (EAB) (Agrilus planipennis Fairmaire) (Coleoptera; Buprestidae), is an invasive wood-boring beetle native to northeast Asia. This species was first detected in Michigan USA in 2002, and is a significant threat to native and ornamental ash tree species (Fraxinus spp.) throughout North America. We characterized seven polymorphic microsatellite markers for EAB and used these to investigate EAB population structure in the early invasive populations within North America and in comparison with Asia. We found 2–9 alleles per microsatellite locus, no evidence of linkage disequilibrium, and no association with known coding sequences, suggesting that these markers are suitable for population genetic analysis. Microsatellite population genetic structure was examined in 48 EAB populations sampled between 2003 and 2008 from five regions, three in the introduced range, Michigan (US) and Ontario and Quebec (Canada) and two Asian regions, China and South Korea, where EAB is native. We found significant genetic variation geographically but not temporally in EAB populations. Bayesian clustering analyses of individual microsatellite genotypes showed strong clustering among multiple North American populations and populations in both China and South Korea. Finally, allelic richness and expected heterozygosity were higher in the native range of EAB, but there was no difference in observed heterozygosity, suggesting a significant loss of alleles upon introduction but no significant change in the distribution of alleles within and among individuals. 相似文献
18.
Akio Ohyama Kenta Shirasawa Hiroshi Matsunaga Satomi Negoro Koji Miyatake Hirotaka Yamaguchi Tsukasa Nunome Hiroyoshi Iwata Hiroyuki Fukuoka Takeshi Hayashi 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2017,130(8):1601-1616
Key message
Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato.Abstract
So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F2 population derived from a cross between two commercial F1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.19.
Christophe Rothan Isidore Diouf Mathilde Causse 《The Plant journal : for cell and molecular biology》2019,97(1):73-90
Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato. 相似文献
20.
Xiao Cheng Zhu Harsh Raman Hanwen Wu Deirdre Lemerle Geoffrey E. Burrows Rex Stanton 《Plant Molecular Biology Reporter》2013,31(1):248-254
Silverleaf nightshade (2n?=?2x?=?24) is a serious weed in the Solanaceae, for which no specific molecular markers are currently available. In order to investigate the extent and distribution of genetic diversity among accessions of silverleaf nightshade, we developed 23 simple sequence repeat (SSR) markers from publicly available nucleotide and EST databases for silverleaf nightshade. Eleven of them were single-locus polymorphic markers. The number of alleles among these loci ranged from 2 to 4. The observed and expected heterozygosity ranged from 0 to 0.97 and 0.07 to 0.64, respectively. Fourteen SSR markers enabled to amplify alleles in morphologically similar species quena. These results proved that the SSR markers that we developed could be useful for (1) determining genetic diversity and structure among natural populations of silverleaf nightshade and (2) identifying silverleaf nightshade and quena ecotypes. This is the first set of species-specific SSR markers identified in silverleaf nightshade, which could contribute to the better understanding of genetic diversity of silverleaf nightshade and related species. 相似文献