Since the 1980s, agriculture and plant breeding have changed with the development of molecular marker technology. In recent decades, different types of molecular markers have been used for different purposes: mapping, marker-assisted selection, characterization of genetic resources, etc. These have produced effective genotyping, but the results have been costly and time-consuming, due to the small number of markers that could be tested simultaneously. Recent advances in molecular marker technologies such as the development of high-throughput genotyping platforms, genotyping by sequencing, and the release of the genome sequences of major crop plants open new possibilities for advancing crop improvement. This Special Issue collects sixteen research studies, including the application of molecular markers in eleven crop species, from the generation of linkage maps and diversity studies to the application of marker-assisted selection and genomic prediction.info:eu-repo/semantics/publishedVersio

Soriano, Jose Miguel

Agronomy

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agronomyEditorialMolecular Marker Technology for Crop ImprovementJose Miguel SorianoSustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology),25198 Lleida, Spain; josemiguel.soriano@irta.catReceived: 3 September 2020; Accepted: 23 September 2020; Published: 24 September 2020 Abstract: Since the 1980s, agriculture and plant breeding have changed with the development ofmolecular marker technology. In recent decades, different types of molecular markers have been usedfor different purposes: mapping, marker-assisted selection, characterization of genetic resources, etc.These have produced effective genotyping, but the results have been costly and time-consuming,due to the small number of markers that could be tested simultaneously. Recent advances in molecularmarker technologies such as the development of high-throughput genotyping platforms, genotypingby sequencing, and the release of the genome sequences of major crop plants open new possibilitiesfor advancing crop improvement. This Special Issue collects sixteen research studies, including theapplication of molecular markers in eleven crop species, from the generation of linkage maps anddiversity studies to the application of marker-assisted selection and genomic prediction.Keywords: crop breeding; genetic maps; QTL mapping; GWAS; marker assisted selection; genomicselection; DNA sequencing1. IntroductionClassical breeding was the main approach used by breeders to increase crop productivity duringthe 20th century. It implies the selection of cultivars with the desired characteristics for the target trait,usually morphological or visual characteristics. The best genotypes were selected and used as parentsin a backcross scheme with a recurrent parent to dilute the irrelevant or undesired traits [1]. However,the long time to get a commercial cultivar and limitations related to traits highly dependent onthe environment or with low heritability make necessary the use of complementary approaches toassist the breeding process. The development of molecular biology made possible the appearanceof a new type of marker based on polymorphisms in the DNA sequence, the molecular markers,which broaden the possibilities for new challenges in plant breeding. Molecular markers are widelydistributed in the genome, they are not affected by the environment, and they can be identified in anytissue and developmental stage. From their development, their use in agriculture increased throughthe construction of genetic maps in crop species, the association between molecular markers andimportant agronomic traits, the dissection of quantitative traits, and the positional cloning of genesof interest. Besides the estimation of genetic distances and molecular cloning, molecular markersprovide the most suitable tool for the evaluation of genetic diversity, allowing for the selection ofthe most suitable parental lines in breeding programs, the management of germplasm collections,and varietal identification [2].Once the association between a marker and a trait is detected, it can be deployed into abreeding program through marker-assisted selection (MAS). The success of this technique relies onthe identification of markers tightly linked with the genome region of a target trait. MAS improvesthe efficiency of the selection of Mendelian traits, facilitating the introgression of single genes withthe desired alleles into elite cultivars and removing the undesirable genome of the donor parent ina backcrossing program, and allows for the identification and protection of commercial cultivarsAgronomy 2020, 10, 1462; doi:10.3390/agronomy10101462 www.mdpi.com/journal/agronomyAgronomy 2020, 10, 1462 2 of 5through fingerprinting [3]. Although MAS has been effectively used before for Mendelian traits orthose regulated by a low number of genes, many of the agronomic traits show a quantitative natureand are influenced by the environment [4]. In the last decade, the development of high-throughputgenotyping platforms has allowed for the screening of whole genomes for the selection of desired traits.In addition, novel statistical approaches for the use of large amounts of genetic and phenotypic datahave been developed. Altogether, this has allowed for the development of new selection strategies,such as the genomic prediction or selection (GS), which attempts to skip the limitations of MAS [5].Coupled with the rapid development of high-throughput genotypic technology, the next DNAsequencing technologies and their applications in genetic and physical mapping have made significantprogress in accelerating plant breeding with a lower cost.2. Overview of the Special IssueThis special issue of Agronomy with the title “Molecular marker technology for crop improvement”publishes 16 articles providing insights into the different applications of molecular markers inplant breeding. Eleven crop species were analyzed with six different approaches.Although the development of linkage maps is the first step for gene identification and many mapshave been developed in several crop species, novel marker approaches involving high-throughputgenotyping are evolving for the construction of highly saturated maps. A high-density single nucleotidepolymorphism (SNP) linkage map in potato was developed using a recently developed strategy for thediscovery of SNPs, the specific length amplified fragment sequencing (SLAF-seq) approach [6].Biparental quantitative trait loci (QTL) mapping is a classical approach to identify multi-genic traits.The success of detecting a QTL depends on several factors: (1) marker density, (2) population size,and (3) trait heritability. As a classical approach in crop breeding, within the Special Issue it was appliedfor the identification of the loci controlling milling yield in rice [7], resistance to Striga hermonthicain maize [8], and leaf rust and stem rust resistance in wheat [9]. These studies identified new locifor important traits in breeding and will be the starting point for a deeper analysis of candidategene identification.Genome-wide association studies (GWASs) have become a valuable tool in recent years as acomplementary approach to biparental mapping, providing broader allelic coverage and highermapping resolution. In this issue, GWASs were performed for the analysis of seminal roots in landracesof wheat and durum wheat from the Mediterranean basin [10,11], agronomic and quality traits in elitedurum wheat [12], and for flowering time in maize inbred lines [13]. The studies of Roselló et al. [10]and Rufo et al. [11] pointed out the usefulness of the old germplasm to be used as genetic resourcesfor improving drought-related traits in the breeding programs to broaden the genetic variability.Merida-García et al. [12] combined a GWAS with a candidate gene approach to successfully identifygene clusters involved in important traits for wheat breeding. The study of Maldonado et al. [13]revealed that the use of a GWAS based on haplotype blocks was more efficient than the standardapproach to identify major effect loci, and the network-assisted gene prioritization used identified fourgenes influencing flowering time in tropical maize.Genetic diversity is crucial for crop improvement, as it allow breeders to identify appropriateparents to be included in breeding programs for broadening genetic variability. Within this Special Issue,the genetic diversity of wheat, avocado, and raspberry was assessed by high-resolution melting (HRM),and insertion site-based polymorphism (ISBP) markers, simple sequence repeats (SSR) developed fromsingle-molecule long-read sequences, and SSRs from flavonoid biosynthesis genes, respectively [14–16].Merida-Garcia et al. [14] developed ISBP markers for the wheat genome as an alternative to SSRsand SNPs. The authors concluded that these HRM-ISBPs are a cost-effective and efficient markerapproach for wheat breeding programs, being also useful for gene tagging. The studies of Ge et al. [15]and Lebedev et al. [16] demonstrated the power of SSR markers. Although they were developed threedecades ago [17], they are still commonly used because of their codominant and multi-allelic natureand high reproducibility.Agronomy 2020, 10, 1462 3 of 5The abovementioned studies in this Special Issue have taken into account the use of molecularmarkers for the development of linkage maps, the analysis of genetic diversity, and the mappingof quantitative traits, by means of the classic biparental QTL mapping or GWASs. The rest of thestudies represent direct applications of molecular markers after these previous steps of development,location in a linkage map, and genotype–phenotype association: MAS and GS.Marker-assisted selection was applied in four studies for (1) the selection of parental germplasmin sugarcane breeding programs [18], (2) improving blast resistance and salt tolerance in rice [19],(3) the selection of the pollination constant non-astringent (PCNA) type in Spanish germplasms ofpersimmon [20], and (4) the selection of resistance to plum pox virus (PPV) in apricot by allele-specificPCR [21]. Wu et al. [18] identified two groups among the 150 most widely used sugarcane parental clones.Based on these results, the authors could identify the most appropriate cultivars to broaden the geneticbase of breeding germplasm. Thanasilungura et al. [19] improved the rice cultivar RD6 for salt tolerancewith the QTL “Saltol” and blast resistance with four different QTLs by marker-assisted backcrossingand phenotypic selection. The authors found that one of the introgression lines showed superiorsalt tolerance and blast resistance, maintaining higher quality and agronomic performance than RD6.In the study of the selection of the PCNA type of persimmon, Blasco et al. [20] identified in the Spanishgermplasm of persimmon the previously developed markers DlSx-AF4, linked to the productionof male flowers, and AST, linked to fruit astringency. The screening of these markers in differentprogenies of backcrosses demonstrated a very low rate of selection of both traits together and is thus avaluable tool in a breeding program. The last example of MAS in this Special Issue corresponds to theselection of PPV resistance in the apricot breeding program at IVIA (Valencia, Spain) [21]. In this study,the authors present a high-throughput method for a rapid test of PPV resistance, thus improving theefficiency of apricot breeding programs at a low cost. MAS is of special interest in fruit trees due to thelong time needed to obtain a new generation.Finally, GS was used to estimate the breeding values for grain composition in sorghum [22].Although GS was developed initially for animal breeding, its use in plant breeding has been extendedin recent years. GS emerged as a valuable tool for improving complex traits controlled by QTLs withsmall effects. Together with high-throughput phenotyping techniques, it has brought a revolution inbreeding by enhancing the accuracy level of selection. Sapkota et al. [22] report the use of GS for graincompositional traits. The authors found that the prediction accuracy for single trait prediction wasmoderate to high in respect to the phenotypic measurements obtained from near infra-red spectroscopy(NIRS) prediction.3. Concluding RemarksThe Special Issue covers the use of different types of molecular markers, from SSR markersdeveloped in 1989 to the newest high-throughput marker technology, as well as different approachesfor genetic mapping and the use of molecular markers to assist crop breeding as a single marker withMAS or at genome level with GS.To meet the needs of a growing world population, crop yields must be increased under the climatechange scenario predicted for the coming decades and the threat of the emergence of new pathogens.However, the information obtained by genome sequencing and its availability at low cost, the continuousdevelopment of new molecular markers, the implementation of high-throughput phenotyping tools,and speed breeding techniques will make it possible to face these new challenges. Although notdirectly related with the molecular marker technology of this Special Issue, the new systems based ongene editing will play an important role in the future of agriculture.Funding: This research received no external funding.Conflicts of Interest: The author declares no conflict of interest.Agronomy 2020, 10, 1462 4 of 5References1. Hou, H.; Atlihan, N.; Lu, Z.X. New biotechnology enhances the application of cisgenesis in plant breeding.Front. Plant Sci. 2014, 5, 389. [CrossRef]2. Phougat, D.; Panwar, I.; Puina, M.; Sethi, S. Microsatellite markers based characterization in advance breedinglines and cultivars of bread wheat. J. Environ. Biol. 2018, 39, 339–346. [CrossRef]3. Shimelis, H.; Laing, M. Timelines in conventional crop improvement: Pre-breeding and breeding procedures.Aust. J. Crop Sci. 2012, 6, 1542–1549.4. Goutam, U.; Kukreja, S.; Tiwari, R.; Chaudhury, A.; Gupta, R.K.; Dholakia, B.B.; Yadav, R. Biotechnologicalapproaches for grain quality improvement in wheat: Present status and future possibilities. Aust. J. Crop Sci.2013, 7, 469–483.5. Talukder, S.K.; Saha, M.C. Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses.Front. Plant Sci. 2017, 8, 1317. [CrossRef]6. Yu, X.; Zhang, M.; Yu, Z.; Yang, D.; Li, J.; Wu, G.; Li, J. An SNP-Based High-Density Genetic Linkage Map forTetraploid Potato Using Specific Length Amplified Fragment Sequencing (SLAF-Seq) Technology. Agronomy2020, 10, 114. [CrossRef]7. Zhang, H.; Zhu, Y.J.; Zhu, A.D.; Fan, Y.Y.; Huang, T.X.; Zhang, J.F.; Xie, H.A.; Zhuang, J.Y. Identification andVerification of Quantitative Trait Loci Affecting Milling Yield of Rice. Agronomy 2020, 10, 75. [CrossRef]8. Badu-Apraku, B.; Adewale, S.; Paterne, A.; Gedil, M.; Asiedu, R. Identification of QTLs ControllingResistance/Tolerance to Striga hermonthica in an Extra-Early Maturing Yellow Maize Population. Agronomy2020, 10, 1168. [CrossRef]9. Genievskaya, Y.; Abugalieva, S.; Rsaliyev, A.; Yskakova, G.; Turuspekov, Y. QTL Mapping for Seedling andAdult Plant Resistance to Leaf and Stem Rusts in Pamyati Azieva × Paragon Mapping Population of BreadWheat. Agronomy 2020, 10, 1285. [CrossRef]10. Roselló, M.; Royo, C.; Sanchez-Garcia, M.; Soriano, J.M. Genetic Dissection of the Seminal Root SystemArchitecture in Mediterranean Durum Wheat Landraces by Genome-Wide Association Study. Agronomy2019, 9, 364. [CrossRef]11. Rufo, R.; Salvi, S.; Royo, C.; Soriano, J.M. Exploring the Genetic Architecture of Root-Related Traits inMediterranean Bread Wheat Landraces by Genome-Wide Association Analysis. Agronomy 2020, 10, 613.12. Mérida-García, R.; Bentley, A.R.; Gálvez, S.; Dorado, G.; Solís, I.; Ammar, K.; Hernandez, P. MappingAgronomic and Quality Traits in Elite Durum Wheat Lines under Differing Water Regimes. Agronomy 2020,10, 144.13. Maldonado, C.; Mora, F.; Bertagna, F.A.B.; Kuki, M.C.; Scapim, C.A. SNP- and Haplotype-Based GWAS ofFlowering-Related Traits in Maize with Network-Assisted Gene Prioritization. Agronomy 2019, 9, 725.14. Mérida-García, R.; Gálvez, S.; Paux, E.; Dorado, G.; Pascual, L.; Giraldo, P.; Hernandez, P. High ResolutionMelting and Insertion Site-Based Polymorphism Markers for Wheat Variability Analysis and CandidateGenes Selection at Drought and Heat MQTL Loci. Agronomy 2020, 10, 1294.15. Ge, Y.; Zang, X.; Tan, L.; Wang, J.; Liu, Y.; Li, Y.; Wang, N.; Chen, D.; Zhan, R.; Ma, W. Single-MoleculeLong-Read Sequencing of Avocado Generates Microsatellite Markers for Analyzing the Genetic Diversity inAvocado Germplasm. Agronomy 2019, 9, 512.16. Lebedev, V.G.; Subbotina, N.M.; Maluchenko, O.P.; Krutovsky, K.V.; Shestibratov, K.A. Assessment of GeneticDiversity in Differently Colored Raspberry Cultivars Using SSR Markers Located in Flavonoid BiosynthesisGenes. Agronomy 2019, 9, 518.17. Tautz, D. Hypervariability of simple sequences as a general source for polymorphic DNA markers.Nucleic Acids Res. 1989, 17, 6463–6471.18. Wu, J.; Wang, Q.; Xie, J.; Pan, Y.-B.; Zhou, F.; Guo, Y.; Chang, H.; Xu, H.; Zhang, W.; Zhang, C.; et al. SSRMarker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) BreedingPrograms. Agronomy 2019, 9, 449.19. Thanasilungura, K.; Kranto, S.; Monkham, T.; Chankaew, S.; Sanitchon, J. Improvement of a RD6 Rice Varietyfor Blast Resistance and Salt Tolerance through Marker-Assisted Backcrossing. Agronomy 2020, 10, 1118.20. Blasco, M.; Gil-Muñoz, F.; Naval, M.M.; Badenes, M.L. Molecular Assisted Selection for Pollination-Constantand Non-Astringent Type without Male Flowers in Spanish Germplasm for Persimmon Breeding. Agronomy2020, 10, 1172.Agronomy 2020, 10, 1462 5 of 521. Polo-Oltra, Á.; Romero, C.; López, I.; Badenes, M.L.; Zuriaga, E. Cost-Effective and Time-Efficient MolecularAssisted Selection for Ppv Resistance in Apricot Based on ParPMC2 Allele-Specific PCR. Agronomy 2020,10, 1292. [CrossRef]22. Sapkota, S.; Boatwright, J.L.; Jordan, K.; Boyles, R.; Kresovich, S. Multi-Trait Regressor Stacking IncreasedGenomic Prediction Accuracy of Sorghum Grain Composition. Agronomy 2020, 10, 1221. [CrossRef]© 2020 by the author. Licensee MDPI, Basel, Switzerland. This article is an open accessarticle distributed under the terms and conditions of the Creative Commons Attribution(CC BY) license (http://creativecommons.org/licenses/by/4.0/).

Molecular Marker Technology for Crop Improvement

Since the 1980s, agriculture and plant breeding have changed with the development of molecular marker technology. In recent decades, different types of molecular markers have been used for different purposes: mapping, marker-assisted selection, characterization of genetic resources, etc. These have produced effective genotyping, but the results have been costly and time-consuming, due to the small number of markers that could be tested simultaneously. Recent advances in molecular marker technologies such as the development of high-throughput genotyping platforms, genotyping by sequencing, and the release of the genome sequences of major crop plants open new possibilities for advancing crop improvement. This Special Issue collects sixteen research studies, including the application of molecular markers in eleven crop species, from the generation of linkage maps and diversity studies to the application of marker-assisted selection and genomic prediction

Jose Miguel Soriano

Multidisciplinary Digital Publishing Institute

https://repositori.irta.cat/bitstream/20.500.12327/1213/1/Soriano_Molecular_2020.pdf

Molecular Marker Technology for Crop Improvement

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