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Functional Genomics for Plant Breeding

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (30 November 2020) | Viewed by 49839

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Dr. Fatemeh Maghuly

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Institute of Molecular Biotechnology, Department of Biotechnology, VIBT, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
Interests: plant functional genomics; plant breeding; plant physiology; population genetics; omic strategies and molecular biology
Special Issues, Collections and Topics in MDPI journals

Dr. Joanna Jankowicz-Cieślak

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Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division on Nuclear Techniques in Food and Agriculture, Department of Nuclear Applications, International Atomic Energy Agency, A-1400 Vienna, Austria
Interests: plant biotechnology; mutations; forward and reverse genetics; functional genomics; biotic and abiotic stresses; molecular breeding

Dr. Bradley John Till

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Guest Editor

Genomics Unit. CGNA, Temuco, Chile
Interests: reverse-genetics; TILLING; induced mutations; population genomics; comparative genomics; understudied crops; domestication; climate adaptation; bioinformatics

Dr. Beata Myśków

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Guest Editor

Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology in Szczecin (ZUT)), Szczecin, Poland
Interests: genetic mapping; crop breeding; quantitative traits loci (QTL); drought stress; earliness; pre-harvest sprouting

Dr. Ilona Czyczyło-Mysza

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Franciszek Górski Institute of Plant Physiology of the Polish Academy of Sciences, Department of Biotechnology, 30-239 Krakow, Poland
Interests: drought stress; phenotyping; quantitative traits loci (QTL); in vitro plant tissue cultures; double haploids of wheat and oat

Special Issue Information

Dear Colleagues,

Next-generation genome sequencing technology in plants has accelerated the generation of multiomic data at the DNA, RNA, protein, and metabolite levels, leading to a new era of "big data". This can provide us an integrative view, and opens up new possibilities to draw attention to the importance of recording and analyzing large-scale omics data obtained in different systems and their relationship to phenotypes, and also for understanding how the exploration of these relationships can be used for management intervention and agricultural innovation in breeding programs.

Large-scale sequence-based markers and precise phenotypic data provide a crucial basis for the application of GWAS and QTL-mapping analysis. Besides, genomic research has facilitated and accelerated the breeding process and offers applications for genetic improvement such as GS, MAS, and gene pyramiding.

On the other hand, it is not just the sequence of plant DNA that matters: how do some genes get activated, and why are others silenced? How can genomics facilitate the study of complex traits in plant breeding? These are questions of widespread interest, and genome editing has shown to be a crucial tool for functional genomic research that could be utilized as a precision-breeding approach for any programs seeking to improve traits of interest.

This Special Issue, “Functional Genomics for Plant Breeding”, will cover a selection of research topics and review articles regarding the recent development of genomics, epigenomics, and epitranscriptomics, that can enhance breeding strategies to shorten the time and efficiency of development of new crop cultivars.

Dr. Fatemeh Maghuly
Dr. Bradley John Till
Dr. Beata Myśków
Dr. Ilona Czyczyło-Mysza
Guest Editors

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Published Papers (11 papers)

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Editorial

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3 pages, 211 KiB

Open AccessEditorial

Functional Genomics for Plant Breeding

by Fatemeh Maghuly, Beata Myśków and Bradley J. Till

Int. J. Mol. Sci. 2021, 22(21), 11854; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222111854 - 01 Nov 2021

Cited by 3 | Viewed by 1637

Abstract

To face the rapidly growing world human population, an increase in agricultural productivity and production is necessary to overcome the enhanced food demand [...] Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding)

Research

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26 pages, 3385 KiB

Open AccessArticle

Apple Autotetraploids with Enhanced Resistance to Apple Scab (Venturia inaequalis) Due to Genome Duplication-Phenotypic and Genetic Evaluation

by Małgorzata Podwyszyńska, Monika Markiewicz, Agata Broniarek-Niemiec, Bożena Matysiak and Agnieszka Marasek-Ciolakowska

Int. J. Mol. Sci. 2021, 22(2), 527; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22020527 - 07 Jan 2021

Cited by 16 | Viewed by 2968

Abstract

Among the fungal diseases of apple trees, serious yield losses are due to an apple scab caused by Venturia inaequalis. Protection against this disease is based mainly on chemical treatments, which are currently very limited. Therefore, it is extremely important to introduce cultivars with reduced susceptibility to this pathogen. One of the important sources of variability for breeding is the process of polyploidization. Newly obtained polyploids may acquire new features, including increased resistance to diseases. In our earlier studies, numerous tetraploids have been obtained for several apple cultivars with ‘Free Redstar’ tetraploids manifesting enhanced resistance to apple scab. In the present study, tetraploids of ‘Free Redstar’ were assessed in terms of phenotype and genotype with particular emphasis on the genetic background of their increased resistance to apple scab. Compared to diploid plants, tetraploids (own-rooted plants) were characterized with poor growth, especially during first growing season. They had considerably shorter shoots, fewer branches, smaller stem diameter, and reshaped leaves. In contrast to own-rooted plants, in M9-grafted three-year old trees, no significant differences between diplo- and tetraploids were observed, either in morphological or physiological parameters, with the exceptions of the increased leaf thickness and chlorophyll content recorded in tetraploids. Significant differences between sibling tetraploid clones were recorded, particularly in leaf shape and some physiological parameters. The amplified fragment length polymorphism (AFLP) analysis confirmed genetic polymorphism of tetraploid clones. Methylation-sensitive amplification polymorphism (MSAP) analysis showed that the level of DNA methylation was twice as high in young tetraploid plants as in a diploid donor tree, which may explain the weaker vigour of neotetraploids in the early period of their growth in the juvenile phase. Molecular analysis showed that ‘Free Redstar’ cultivar and their tetraploids bear six Rvi genes (Rvi5, Rvi6, Rvi8, Rvi11, Rvi14 and Rvi17). Transcriptome analysis confirmed enhanced resistance to apple scab of ‘Free Redstar’ tetraploids since the expression levels of genes related to resistance were strongly enhanced in tetraploids compared to their diploid counterparts. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding)

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12 pages, 2002 KiB

Open AccessArticle

Al-Tolerant Barley Mutant hvatr.g Shows the ATR-Regulated DNA Damage Response to Maleic Acid Hydrazide

by Joanna Jaskowiak, Jolanta Kwasniewska, Miriam Szurman-Zubrzycka, Magdalena Rojek-Jelonek, Paul B. Larsen and Iwona Szarejko

Int. J. Mol. Sci. 2020, 21(22), 8500; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21228500 - 12 Nov 2020

Cited by 6 | Viewed by 2099

Abstract

ATR, a DNA damage signaling kinase, is required for cell cycle checkpoint regulation and detecting DNA damage caused by genotoxic factors including Al³⁺ ions. We analyzed the function of the HvATR gene in response to chemical clastogen-maleic acid hydrazide (MH). For this purpose, the Al-tolerant barley TILLING mutant hvatr.g was used. We described the effects of MH on the nuclear genome of hvatr.g mutant and its WT parent cv. “Sebastian”, showing that the genotoxic effect measured by TUNEL test and frequency of cells with micronuclei was much stronger in hvatr.g than in WT. MH caused a significant decrease in the mitotic activity of root cells in both genotypes, however this effect was significantly stronger in “Sebastian”. The impact of MH on the roots cell cycle, analyzed using flow cytometry, showed no differences between the mutant and WT. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding)

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26 pages, 6576 KiB

Open AccessArticle

Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.

by Stephanie Schaarschmidt, Axel Fischer, Lovely Mae F. Lawas, Rejbana Alam, Endang M. Septiningsih, Julia Bailey-Serres, S. V. Krishna Jagadish, Bruno Huettel, Dirk K. Hincha and Ellen Zuther

Int. J. Mol. Sci. 2020, 21(21), 8148; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21218148 - 31 Oct 2020

Cited by 25 | Viewed by 6793

Abstract

The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant aus cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding)

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23 pages, 2792 KiB

Open AccessArticle

How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data

by Magdalena Góralska, Jan Bińkowski, Natalia Lenarczyk, Anna Bienias, Agnieszka Grądzielewska, Ilona Czyczyło-Mysza, Kamila Kapłoniak, Stefan Stojałowski and Beata Myśków

Int. J. Mol. Sci. 2020, 21(20), 7501; https://doi.org/10.3390/ijms21207501 - 12 Oct 2020

Cited by 3 | Viewed by 2555

Abstract

The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F₂ population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding)

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20 pages, 4132 KiB

Open AccessArticle

Silencing of HvGSK1.1—A GSK3/SHAGGY-Like Kinase–Enhances Barley (Hordeum vulgare L.) Growth in Normal and in Salt Stress Conditions

by Yuliya Kloc, Marta Dmochowska-Boguta, Andrzej Zielezinski, Anna Nadolska-Orczyk, Wojciech M. Karlowski and Waclaw Orczyk

Int. J. Mol. Sci. 2020, 21(18), 6616; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21186616 - 10 Sep 2020

Cited by 11 | Viewed by 2522

Abstract

Glycogen synthase kinase 3 (GSK3) is a highly conserved kinase present in all eukaryotes and functions as a key regulator of a wide range of physiological and developmental processes. The kinase, known in land plants as GSK3/SHAGGY-like kinase (GSK), is a key player in the brassinosteroid (BR) signaling pathway. The GSK genes, through the BRs, affect diverse developmental processes and modulate responses to environmental factors. In this work, we describe functional analysis of HvGSK1.1, which is one of the GSK3/SHAGGY-like orthologs in barley. The RNAi-mediated silencing of the target HvGSK1.1 gene was associated with modified expression of its paralogs HvGSK1.2, HvGSK2.1, HvGSK3.1, and HvGSK4.1 in plants grown in normal and in salt stress conditions. Low nucleotide similarity between the silencing fragment and barley GSK genes and the presence of BR-dependent transcription factors’ binding sites in promoter regions of barley and rice GSK genes imply an innate mechanism responsible for co-regulation of the genes. The results of the leaf inclination assay indicated that silencing of HvGSK1.1 and the changes of GSK paralogs enhanced the BR-dependent signaling in the plants. The strongest phenotype of transgenic lines with downregulated HvGSK1.1 and GSK paralogs had greater biomass of the seedlings grown in normal conditions and salt stress as well as elevated kernel weight of plants grown in normal conditions. Both traits showed a strong negative correlation with the transcript level of the target gene and the paralogs. The characteristics of barley lines with silenced expression of HvGSK1.1 are compatible with the expected phenotypes of plants with enhanced BR signaling. The results show that manipulation of the GSK-encoding genes provides data to explore their biological functions and confirm it as a feasible strategy to generate plants with improved agricultural traits. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding)

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18 pages, 2991 KiB

Open AccessArticle

Combination of Linkage Mapping, GWAS, and GP to Dissect the Genetic Basis of Common Rust Resistance in Tropical Maize Germplasm

by Maguta Kibe, Christine Nyaga, Sudha K. Nair, Yoseph Beyene, Biswanath Das, Suresh L. M, Jumbo M. Bright, Dan Makumbi, Johnson Kinyua, Michael S. Olsen, Boddupalli M. Prasanna and Manje Gowda

Int. J. Mol. Sci. 2020, 21(18), 6518; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21186518 - 06 Sep 2020

Cited by 15 | Viewed by 4644

Abstract

Common rust (CR) caused by Puccina sorghi is one of the destructive fungal foliar diseases of maize and has been reported to cause moderate to high yield losses. Providing CR resistant germplasm has the potential to increase yields. To dissect the genetic architecture of CR resistance in maize, association mapping, in conjunction with linkage mapping, joint linkage association mapping (JLAM), and genomic prediction (GP) was conducted on an association-mapping panel and five F₃ biparental populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). Analysis of variance for the biparental populations and the association panel showed significant genotypic and genotype x environment (GXE) interaction variances except for GXE of Pop4. Heritability (h²) estimates were moderate with 0.37–0.45 for the individual F₃ populations, 0.45 across five populations and 0.65 for the association panel. Genome-wide association study (GWAS) analyses revealed 14 significant marker-trait associations which individually explained 6–10% of the total phenotypic variances. Individual population-based linkage analysis revealed 26 QTLs associated with CR resistance and together explained 14–40% of the total phenotypic variances. Linkage mapping revealed seven QTLs in pop1, nine QTL in pop2, four QTL in pop3, five QTL in pop4, and one QTL in pop5, distributed on all chromosomes except chromosome 10. JLAM for the 921 F3 families from five populations detected 18 QTLs distributed in all chromosomes except on chromosome 8. These QTLs individually explained 0.3 to 3.1% and together explained 45% of the total phenotypic variance. Among the 18 QTL detected through JLAM, six QTLs, qCR1-78, qCR1-227, qCR3-172, qCR3-186, qCR4-171, and qCR7-137 were also detected in linkage mapping. GP within population revealed low to moderate correlations with a range from 0.19 to 0.51. Prediction correlation was high with r = 0.78 for combined analysis of the five F₃ populations. Prediction of biparental populations by using association panel as training set reveals positive correlations ranging from 0.05 to 0.22, which encourages to develop an independent but related population as a training set which can be used to predict diverse but related populations. The findings of this study provide valuable information on understanding the genetic basis of CR resistance and the obtained information can be used for developing functional molecular markers for marker-assisted selection and for implementing GP to improve CR resistance in tropical maize. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding)

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16 pages, 1448 KiB

Open AccessArticle

Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root

by Alicja Macko-Podgórni, Katarzyna Stelmach, Kornelia Kwolek, Gabriela Machaj, Shelby Ellison, Douglas A. Senalik, Philipp W. Simon and Dariusz Grzebelus

Int. J. Mol. Sci. 2020, 21(12), 4263; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21124263 - 15 Jun 2020

Cited by 7 | Viewed by 3087

Abstract

Background: Diverse groups of carrot cultivars have been developed to meet consumer demands and industry needs. Varietal groups of the cultivated carrot are defined based on the shape of roots. However, little is known about the genetic basis of root shape determination. Methods: Here, we used 307 carrot plants from 103 open-pollinated cultivars for a genome wide association study to identify genomic regions associated with the storage root morphology. Results: A 180 kb-long region on carrot chromosome 1 explained 10% of the total observed phenotypic variance in the shoulder diameter. Within that region, DcDCAF1 and DcBTAF1 genes were proposed as candidates controlling secondary growth of the carrot storage root. Their expression profiles differed between the cultivated and the wild carrots, likely indicating that their elevated expression was required for the development of edible roots. They also showed higher expression at the secondary root growth stage in cultivars producing thick roots, as compared to those developing thin roots. Conclusions: We provided evidence for a likely involvement of DcDCAF1 and/or DcBTAF1 in the development of the carrot storage root and developed a genotyping assay facilitating the identification of variants in the region on carrot chromosome 1 associated with secondary growth of the carrot root. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding)

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Review

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41 pages, 1584 KiB

Open AccessReview

Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects

by Hymavathi Salava, Sravankumar Thula, Vijee Mohan, Rahul Kumar and Fatemeh Maghuly

Int. J. Mol. Sci. 2021, 22(2), 682; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22020682 - 12 Jan 2021

Cited by 27 | Viewed by 9025

Abstract

Plants regularly face the changing climatic conditions that cause biotic and abiotic stress responses. The abiotic stresses are the primary constraints affecting crop yield and nutritional quality in many crop plants. The advances in genome sequencing and high-throughput approaches have enabled the researchers to use genome editing tools for the functional characterization of many genes useful for crop improvement. The present review focuses on the genome editing tools for improving many traits such as disease resistance, abiotic stress tolerance, yield, quality, and nutritional aspects of tomato. Many candidate genes conferring tolerance to abiotic stresses such as heat, cold, drought, and salinity stress have been successfully manipulated by gene modification and editing techniques such as RNA interference, insertional mutagenesis, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9). In this regard, the genome editing tools such as CRISPR/Cas9, which is a fast and efficient technology that can be exploited to explore the genetic resources for the improvement of tomato and other crop plants in terms of stress tolerance and nutritional quality. The review presents examples of gene editing responsible for conferring both biotic and abiotic stresses in tomato simultaneously. The literature on using this powerful technology to improve fruit quality, yield, and nutritional aspects in tomato is highlighted. Finally, the prospects and challenges of genome editing, public and political acceptance in tomato are discussed. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding)

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22 pages, 1451 KiB

Open AccessReview

Genomics-Assisted Breeding for Quantitative Disease Resistances in Small-Grain Cereals and Maize

by Thomas Miedaner, Ana Luisa Galiano-Carneiro Boeven, David Sewodor Gaikpa, Maria Belén Kistner and Cathérine Pauline Grote

Int. J. Mol. Sci. 2020, 21(24), 9717; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21249717 - 19 Dec 2020

Cited by 25 | Viewed by 5937

Abstract

Generating genomics-driven knowledge opens a way to accelerate the resistance breeding process by family or population mapping and genomic selection. Important prerequisites are large populations that are genomically analyzed by medium- to high-density marker arrays and extensive phenotyping across locations and years of the same populations. The latter is important to train a genomic model that is used to predict genomic estimated breeding values of phenotypically untested genotypes. After reviewing the specific features of quantitative resistances and the basic genomic techniques, the possibilities for genomics-assisted breeding are evaluated for six pathosystems with hemi-biotrophic fungi: Small-grain cereals/Fusarium head blight (FHB), wheat/Septoria tritici blotch (STB) and Septoria nodorum blotch (SNB), maize/Gibberella ear rot (GER) and Fusarium ear rot (FER), maize/Northern corn leaf blight (NCLB). Typically, all quantitative disease resistances are caused by hundreds of QTL scattered across the whole genome, but often available in hotspots as exemplified for NCLB resistance in maize. Because all crops are suffering from many diseases, multi-disease resistance (MDR) is an attractive aim that can be selected by specific MDR QTL. Finally, the integration of genomic data in the breeding process for introgression of genetic resources and for the improvement within elite materials is discussed. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding)

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32 pages, 1606 KiB

Open AccessReview

Functional Markers for Precision Plant Breeding

by Romesh K. Salgotra and C. Neal Stewart, Jr.

Int. J. Mol. Sci. 2020, 21(13), 4792; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21134792 - 06 Jul 2020

Cited by 58 | Viewed by 7292

Abstract

Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding)

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