Deployment of Molecular Markers and Marker-assisted Selection in Tomato Breeding

In tomato, Lycopersi conesculentum Mill., currently there are >285 known morphological, physiological and disease resistance markers, 36 isozymes, and >1000 RFLPs, which have been mapped onto the 12 tomato chromosomes. In addition, currently there are >162,000 ESTs, of which ∼3.2% have been mapped. Several tomato genetic maps have been developed, mainly based on interspecific crosses between the cultivated tomato and its related wild species. The markers and maps have been used to locate and tag genes or QTLs for disease resistance and other horticultural characteristics. Such information can be used for various purposes, including marker-assisted selection (MAS) and map-based cloning of desirable genes or QTLs. Many seed companies have adopted using MAS for manipulating genes for a few simple morphological characteristics and several vertical disease resistance traits in tomato. However, MAS is not yet a routine procedure in seed companies for manipulating QTLs although it has been tried for a few complex disease resistance and fruit quality characteristics. In comparison, the use of MAS is less common in public tomato breeding programs, although attempts have been made to transfer QTLs for resistances to a few complex diseases. The potential benefits of marker deployment to plant breeding are undisputed, in particular for pyramiding disease resistance genes. It is expected that in the near future MAS will be routine in many breeding programs, taking advantage of high-resolution markers such as SNPs. For quantitative traits, QTLs must be sought for components of genetic variation before they are applicable to marker-assisted breeding. However, MAS will not be a “silver bullet” solution to every breeding problem or for every crop species.

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Tomato breeding for disease resistance

Multi-Science Journal ◽

10.33837/msj.v3i3.1287 ◽

2020 ◽

Vol 3 (3) ◽

pp. 8-16

Author(s):

Gabriella Queiroz De Almeida ◽

Juliana de Oliveira Silva ◽

Mariane Gonçalves Ferreira Copati ◽

Felipe de Oliveira Dias ◽

Manoel Coelho dos Santos

Keyword(s):

Disease Resistance ◽

Disease Management ◽

Late Blight ◽

Fruit Quality ◽

Genetic Resistance ◽

Black Spot ◽

Breeding Programs ◽

Tomato Production ◽

Genetic Breeding ◽

Tomato Breeding

In the genetic breeding of tomatoes, not only productivity, but also factors related to fruit quality and pest and disease management are taken into account. In this context, diseases stand out, since they are the main bottlenecks for successful cultivation. Currently, the search for more sustainable crops has demanded from producers’ alternatives to disease control to reduce the use of pesticides. Among the diseases that most reduce tomato production in Brazil, whether for table or industry, we can mention late blight, black spot, fusarium wilt, viruses, bacterial and nematode diseases. Genetic resistance, obtained by genetic breeding programs, is one of the best tools to deal with diseases to depend less on pesticides. Thus, this review aims to provide an overview of tomato breeding programs in terms of resistance to the main diseases that affect this crop.

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Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data

Genome ◽

10.1139/g06-151 ◽

2007 ◽

Vol 50 (4) ◽

pp. 373-384 ◽

Cited By ~ 23

Author(s):

M. Maccaferri ◽

S. Stefanelli ◽

F. Rotondo ◽

R. Tuberosa ◽

M.C. Sanguineti

Keyword(s):

Durum Wheat ◽

Genetic Relatedness ◽

Morphological Characteristics ◽

Morphological Data ◽

Phenotypic Traits ◽

Pedigree Data ◽

Crop Species ◽

Phenotypic Data ◽

Breeding Programs ◽

Triticum Durum Desf

The determination of genetic relatedness among elite materials of crop species allows for more efficient management of breeding programs and for the protection of breeders’ rights. Seventy simple sequence repeats (SSRs) and 234 amplified fragment length polymorphisms (AFLPs) were used to profile a collection of 58 durum wheat ( Triticum durum Desf.) accessions, representing the most important extant breeding programs. In addition, 42 phenotypic traits, including the morphological characteristics recommended for the official distinctness, uniformity, and stability tests, were recorded. The correlation between the genetic similarities obtained with the 2 marker classes was high (r = 0.81), whereas lower values were observed between molecular and phenotypic data (r = 0.46 and 0.56 for AFLPs and SSRs, respectively). Morphological data, even if sampled in high numbers, largely failed to describe the pattern of genetic similarity, according to known pedigree data and the indications provided by molecular markers.

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Gen dan QTL Pengendali Toleransi Tanaman terhadap Keracunan Aluminium dan Aplikasinya untuk Pemuliaan Tanaman di Indonesia

Jurnal AgroBiogen ◽

10.21082/jbio.v11n3.2015.p111-124 ◽

2016 ◽

Vol 11 (3) ◽

pp. 111

Author(s):

I Made Tasma

Keyword(s):

Dominant Gene ◽

Al Toxicity ◽

Breeding Program ◽

Genetic Maps ◽

Single Dominant Gene ◽

Breeding Methods ◽

Al Tolerance ◽

Crop Species ◽

Breeding Programs ◽

Genomic Technologies

Genetic knowledge of loci controlling Al toxicity tolerance is the key for a successful breeding program in developing Al tolerant cultivars. Tolerance level of crop plants to Al toxicity is genetically controlled. The gene inheritance pattern is mainly resulted from intensive studies of cereal crops, such as wheat, sorghum, maize, and rice. The trait can be controlled by a single dominant gene, a single dominant gene with many alleles, a pair of dominant genes, or by many genes (QTL). The majority of the Al tolerance genes identified so far belongs to two independent groups of gene families, i.e. aluminumactivated malate transporter (ALMT) and multidrug and toxic compound extrusion (MATE), both encoding transport proteins involved in Al-activated organic acid release, mainly citrate and malate. The variations in Al toxicity tolerance phenotypes are strongly correlated with the expressions of such genes in the root apical cells. Many Al tolerance QTLs have been mapped in the genomes of various crop species and were found to be colocated with the ALMT and MATE genes. The genetic maps of the Al tolerance genes and QTLs facilitate breeding programs for developing Al-tolerant cultivars through marker-assisted breeding methods. Al tolerance genes that have been isolated from genetically unrelated species can be used in genetic transformation studies of crop genotypes sexually incompatible to the gene source genotypes. The application of these molecular breeding methods expedites breeding programs to develop crop cultivars tolerance to Al toxicity and acid soils. Genomic technologies by using next-generation sequencing and high-throughput genotyping system accelerate Al toxicity tolerance gene and QTL discoveries of various crop species. The modern genomic technologies also facilitate more comprehensive PGR characterization and utilization to accelerate identification and isolation of the Al tolerance genes and QTLs to be used in a more comprehensive breeding program to support national food self sufficiency and food security programs.

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998 CLASSICAL AND MOLECULAR APPROACHES TO BREEDING FRUIT AND NUT CROPS FOR DISEASE RESISTANCE

HortScience ◽

10.21273/hortsci.29.5.572d ◽

1994 ◽

Vol 29 (5) ◽

pp. 572d-572

Author(s):

Shawn A. Mehlenbacher

Keyword(s):

Disease Resistance ◽

Cost Effective ◽

Genetic Maps ◽

Great Success ◽

Breeding Programs ◽

Bacterial Diseases ◽

Molecular Approaches ◽

Tree Fruits ◽

Segregating Population

Disease resistance is an objective of most breeding programs for small fruits, tree fruits, and nuts. Often a moderate level of resistance is adequate, and must be combined with many other desirable horticultural characteristics. Classical methods (a segregating population of the host plant is inoculated with a virulent isolate of the pathogen under environmental conditions appropriate for disease development) have been used with great success and have incorporated both horizontal and vertical resistance. Molecular approaches offer new opportunities and are likely to be appropriate and cost-effective in a few situations. Transformation is not yet routine in fruit and nut crops, and there is a shortage of useful genes. Genetic maps are being constructed using RFLP and RAPD markers in several species, allowing determination of number and location of important genes as well as indirect selection based on linked markers. This presentation will include examples of both classical and molecular approaches as they are used in the genetic improvement of fruit and nut crops with an emphasis on fungal and bacterial diseases.

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Combining metabolomic and transcriptomic approaches to assess and improve crop quality traits

CABI Agriculture and Bioscience ◽

10.1186/s43170-020-00021-8 ◽

2021 ◽

Vol 2 (1) ◽

Author(s):

Delphine M. Pott ◽

Sara Durán-Soria ◽

Sonia Osorio ◽

José G. Vallarino

Keyword(s):

Quality Trait ◽

Quality Traits ◽

Crop Species ◽

Breeding Programs ◽

Crop Quality ◽

Crop Varieties ◽

New Genes ◽

Technical Advances ◽

Health Promoting ◽

Selection Of

AbstractPlant quality trait improvement has become a global necessity due to the world overpopulation. In particular, producing crop species with enhanced nutrients and health-promoting compounds is one of the main aims of current breeding programs. However, breeders traditionally focused on characteristics such as yield or pest resistance, while breeding for crop quality, which largely depends on the presence and accumulation of highly valuable metabolites in the plant edible parts, was left out due to the complexity of plant metabolome and the impossibility to properly phenotype it. Recent technical advances in high throughput metabolomic, transcriptomic and genomic platforms have provided efficient approaches to identify new genes and pathways responsible for the extremely diverse plant metabolome. In addition, they allow to establish correlation between genotype and metabolite composition, and to clarify the genetic architecture of complex biochemical pathways, such as the accumulation of secondary metabolites in plants, many of them being highly valuable for the human diet. In this review, we focus on how the combination of metabolomic, transcriptomic and genomic approaches is a useful tool for the selection of crop varieties with improved nutritional value and quality traits.

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Mapping QTL for spike fertility and related traits in two doubled haploid wheat (Triticum aestivum L.) populations

BMC Plant Biology ◽

10.1186/s12870-021-03061-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Nicole Pretini ◽

Leonardo S. Vanzetti ◽

Ignacio I. Terrile ◽

Guillermo Donaire ◽

Fernanda G. González

Keyword(s):

Doubled Haploid ◽

Marker Assisted Selection ◽

Triticum Aestivum L ◽

Physiological Model ◽

Yield Potential ◽

Breeding Programs ◽

Per Se ◽

Genomic Regions ◽

Fertility Traits ◽

Selection Of

Abstract Background In breeding programs, the selection of cultivars with the highest yield potential consisted in the selection of the yield per se, which resulted in cultivars with higher grains per spike (GN) and occasionally increased grain weight (GW) (main numerical components of the yield). In this study, quantitative trait loci (QTL) for GW, GN and spike fertility traits related to GN determination were mapped using two doubled haploid (DH) populations (Baguette Premium 11 × BioINTA 2002 and Baguette 19 × BioINTA 2002). Results In total 305 QTL were identified for 14 traits, out of which 12 QTL were identified in more than three environments and explained more than 10% of the phenotypic variation in at least one environment. Eight hotspot regions were detected on chromosomes 1A, 2B, 3A, 5A, 5B, 7A and 7B in which at least two major and stable QTL sheared confidence intervals. QTL on two of these regions (R5A.1 and R5A.2) have previously been described, but the other six regions are novel. Conclusions Based on the pleiotropic analysis within a robust physiological model we conclude that two hotspot genomic regions (R5A.1 and R5A.2) together with the QGW.perg-6B are of high relevance to be used in marker assisted selection in order to improve the spike yield potential. All the QTL identified for the spike related traits are the first step to search for their candidate genes, which will allow their better manipulation in the future.

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Wheat, Barley, and Oat Breeding for Health Benefit Components in Grain

Plants ◽

10.3390/plants10010086 ◽

2021 ◽

Vol 10 (1) ◽

pp. 86

Author(s):

Igor G. Loskutov ◽

Elena K. Khlestkina

Keyword(s):

Bioactive Compounds ◽

Plant Genetic Resources ◽

Health Benefit ◽

Cultivated Plants ◽

Crop Species ◽

Breeding Programs ◽

Cereal Grain ◽

Staple Foods ◽

Functional Components ◽

Oat Breeding

Cereal grains provide half of the calories consumed by humans. In addition, they contain important compounds beneficial for health. During the last years, a broad spectrum of new cereal grain-derived products for dietary purposes emerged on the global food market. Special breeding programs aimed at cultivars utilizable for these new products have been launched for both the main sources of staple foods (such as rice, wheat, and maize) and other cereal crops (oat, barley, sorghum, millet, etc.). The breeding paradigm has been switched from traditional grain quality indicators (for example, high breadmaking quality and protein content for common wheat or content of protein, lysine, and starch for barley and oat) to more specialized ones (high content of bioactive compounds, vitamins, dietary fibers, and oils, etc.). To enrich cereal grain with functional components while growing plants in contrast to the post-harvesting improvement of staple foods with natural and synthetic additives, the new breeding programs need a source of genes for the improvement of the content of health benefit components in grain. The current review aims to consider current trends and achievements in wheat, barley, and oat breeding for health-benefiting components. The sources of these valuable genes are plant genetic resources deposited in genebanks: landraces, rare crop species, or even wild relatives of cultivated plants. Traditional plant breeding approaches supplemented with marker-assisted selection and genetic editing, as well as high-throughput chemotyping techniques, are exploited to speed up the breeding for the desired genotуpes. Biochemical and genetic bases for the enrichment of the grain of modern cereal crop cultivars with micronutrients, oils, phenolics, and other compounds are discussed, and certain cases of contributions to special health-improving diets are summarized. Correlations between the content of certain bioactive compounds and the resistance to diseases or tolerance to certain abiotic stressors suggest that breeding programs aimed at raising the levels of health-benefiting components in cereal grain might at the same time match the task of developing cultivars adapted to unfavorable environmental conditions.

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Evolution of a Complex Disease Resistance Gene Cluster in Diploid Phaseolus and Tetraploid Glycine

PLANT PHYSIOLOGY ◽

10.1104/pp.112.195040 ◽

2012 ◽

Vol 159 (1) ◽

pp. 336-354 ◽

Cited By ~ 29

Author(s):

Tom Ashfield ◽

Ashley N. Egan ◽

Bernard E. Pfeil ◽

Nicolas W.G. Chen ◽

Ram Podicheti ◽

...

Keyword(s):

Disease Resistance ◽

Gene Cluster ◽

Resistance Gene ◽

Complex Disease ◽

Disease Resistance Gene ◽

Resistance Gene Cluster

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Relatedness severely impacts accuracy of marker-assisted selection for disease resistance in hybrid wheat

Heredity ◽

10.1038/hdy.2013.139 ◽

2013 ◽

Vol 112 (5) ◽

pp. 552-561 ◽

Cited By ~ 40

Author(s):

M Gowda ◽

Y Zhao ◽

T Würschum ◽

C FH Longin ◽

T Miedaner ◽

...

Keyword(s):

Disease Resistance ◽

Marker Assisted Selection ◽

Hybrid Wheat ◽

Selection For

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MORPHOLOGICAL AND PRODUCTIVE CHARACTERIZATION OF FORAGE CACTUS VARIETIES

Revista Caatinga ◽

10.1590/1983-21252015v28n326rc ◽

2015 ◽

Vol 28 (3) ◽

pp. 230-238 ◽

Cited By ~ 2

Author(s):

PHILIPE LIMA DE AMORIM ◽

JANAINA AZEVEDO MARTUSCELLO ◽

JOSÉ TEODORICO DE ARAÚJO FILHO ◽

DANIEL DE NORONHA FIGUEIREDO VIEIRA DA CUNHA ◽

LIANA JANK

Keyword(s):

Block Design ◽

Morphological Characteristics ◽

Correlation Coefficients ◽

Dry Mass ◽

Negative Effects ◽

Breeding Programs ◽

Area Index ◽

Promising Alternative ◽

Randomized Block Design ◽

Use Efficiency

ABSTRACT: Cultivars of the genus Nopalea are known in Brazil for being tolerant to cochineal carmine attacks, thus making the cultivation of this genus a promising alternative for mitigating the negative effects of this insect on the production of biomass. With the objectives of characterizing morphologically spineless forage cactus varieties and identify morphological characteristics that may be the focus in spineless forage cactus breeding programs, an experiment was conducted in a completely randomized block design with 11 treatments and four replications. The variety Alagoas showed the highest values of weight, area and volume of cladodes. The varieties Negro Michoacan F7 and V7, Tamazunchale V12 showed the highest values of the cladode area index, the total volume of cladodes and total fresh mass production. The varieties Negro Michoacan V7 and F7 presented the highest water use efficiency and dry mass yield. Cladode volume showed the highest correlation coefficients with the fresh weight of cladodes. Aiming the release of varieties for biomass production, varieties Negro Michoacan F7, V7 and Tamazunchale V12 may substitute the Miúda variety. The number and cladode area index may be used as criteria for selection of superior varieties in breeding programs.

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