Skip to main content
SpringerLink
Log in

Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective

  • Review Article
  • Published:
Journal of Genetics Aims and scope Submit manuscript

Abstract

Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding, with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information on population dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Abbo S. and Gopher A. 2017 Near eastern plant domestication: a history of thought. Trends Plant Sci. 22, 491–511.

    Article  CAS  PubMed  Google Scholar 

  • Akbar W., Aslam M., Maqbool M. A., Ali M. and Arshad M. 2018 Inheritance pattern of mungbean yellow mosaic disease resistance and gene action for different traits in mungbean (Vigna radiata (L.) Wilczek) under protected and unprotected field conditions. Plant Breed. 137, 763–772.

    Article  CAS  Google Scholar 

  • Aliyu S., Massawe F. and Mayes S. 2014 Beyond landraces: developing improved germplasm resources for underutilized species – a case for Bambara groundnut. Biotechnol. Genet. Eng. Rev. 30, 127–141.

    Article  PubMed  Google Scholar 

  • Anhalt U. C. M., Heslop-Harrison P., Byrne S., Guillard A. and Barth S. 2008 Segregation distortion in Lolium: evidence for genetic effects. Theor. Appl. Genet. 117, 297–306.

    Article  CAS  PubMed  Google Scholar 

  • Annicchiarico P., Nazzicari N., Pecetti L., Romani M., Ferrari B., Wei Y. L. et al. 2017 GBS-Based genomic selection for pea grain yield under severe terminal drought. Plant Genome 10, 1–13.

    Article  CAS  Google Scholar 

  • Argyris J. M., Diaz A., Ruggieri V., Fernandez M., Jahrmann T., Gibon Y. et al. 2017 QTL analyses in multiple populations employed for the fine mapping and identification of candidate genes at a Locus affecting sugar accumulation in melon (Cucumis melo L.). Front. Plant Sci. 8, article ID 1679.

  • Arms E. M., Bloom A. J. and St Clair D. A. 2015 High-resolution mapping of a major effect QTL from wild tomato Solanum habrochaites that influences water relations under root chilling Theor. Appl. Genet. 128, 1713–1724.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arora H., Padmaja K. L., Paritosh K., Mukhi N., Tewari A. K., Mukhopadhyay A. et al. 2019 BjuWRR1, a CC-NB-LRR gene identified in Brassica juncea, confers resistance to white rust caused by Albugo candida. Theor. Appl. Genet. 32, 2223–2236.

    Article  CAS  Google Scholar 

  • Asadi A., Zebarjadi A., Abdollahi M. R. and Seguí-Simarro J. M. 2018 Assessment of different anther culture approaches to produce doubled haploids in cucumber (Cucumis sativus L.). Euphytica 214, 216.

    Article  CAS  Google Scholar 

  • Ashikari M. and Matsuoka M. 2006 Identification, isolation and pyramiding of quantitative trait loci for rice breeding. Trends Plant Sci. 11, 344–350.

    Article  CAS  PubMed  Google Scholar 

  • Ashrafi H., Kinkade M. and Foolad M. R. 2009 A new genetic linkage map of tomato based on a Solanum lycopersicum x S. pimpinellifolium RIL population displaying locations of candidate pathogen response genes. Genome 52, 935–956.

    Article  CAS  PubMed  Google Scholar 

  • Babu R., Nair S. K., Prasanna B. M. and Gupta H. S. 2004 Integrating marker-assisted selection in crop breeding - prospects and challenges. Curr. Sci. India 87, 607–619.

    CAS  Google Scholar 

  • Balconi C., Stevanato P., Motto M. and Biancardi E. 2012 Breeding for biotic stress resistance/tolerance in plants. In Crop production for agricultural improvement. (ed. M. Ashraf M., M. Öztürk M., M. S. A. Ahmad and A. Aksoy), pp. 57–114. Springer Netherlands, Dordrecht.

    Chapter  Google Scholar 

  • Baloch A. M., Baloch A. W., Liu S., Gao P., Baloch M. J., Wang X. Z. et al. 2016 Linkage map construction and Qtl analysis of fruit traits in melon (Cucumis Melo L.) based on caps. Markers Pak. J. Bot. 48, 1579–1584.

    CAS  Google Scholar 

  • Bandillo N., Raghavan C., Muyco P. A., Sevilla M. A. L., Lobina I. T., Dilla-Ermita C. J. et al. 2013 Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 6, 11.

    Article  PubMed  PubMed Central  Google Scholar 

  • Barabaschi D., Tondelli A., Desiderio F., Volante A., Vaccino P., Vale G. et al. 2016 Next generation breeding. Plant Sci. 242, 3–13.

    Article  CAS  PubMed  Google Scholar 

  • Baret P. V., Knott S. A. and Visscher P. M. 1998 On the use of linear regression and maximum likelihood for QTL mapping in half-sib designs. Genet. Res. 72, 149–158.

    Article  CAS  PubMed  Google Scholar 

  • Belyayev A. 2014 Bursts of transposable elements as an evolutionary driving force. J. Evol. Biol. 27, 2573–2584.

    Article  CAS  PubMed  Google Scholar 

  • Bhanu A. N., Singh M. N. and Srivastava K. 2019 Genetic analysis of gene-specific resistance to mungbean yellow mosaic virus in mungbean (Vigna radiata). Plant Breed. https://doi.org/10.1111/pbr.12675.

    Article  Google Scholar 

  • Bhatia R., Dey S. S., Parkash C., Sharma K., Sood S., Kumar R. 2018 Modification of important factors for efficient microspore embryogenesis and doubled haploid production in field grown white cabbage (Brassica oleracea var. capitata L.) genotypes in India. Sci. Hortic. 233,178–187.

    Article  Google Scholar 

  • Bhojwani S. S. and Razdan M. K. (ed.) 1996 Plant tissue culture : theory and practice, a revised edition. In Studies in plant science. p ix. Elsevier.

  • Bohanec B. 2009 Doubled haploids via gynogenesis. In Advances in haploid production in higher plants (ed. A. Touraev, B. P. Forster and S. M. Jain), pp. 35–46. Springer Netherlands, Dordrecht.

    Chapter  Google Scholar 

  • Branham S. E. and Farnham M. W. 2017 Genotyping-by-sequencing of waxy and glossy near-isogenic broccoli lines. Euphytica 213, 84.

    Article  CAS  Google Scholar 

  • Branham S. E. and Farnham M. W. 2019 Identification of heat tolerance loci in broccoli through bulked segregant analysis using whole genome resequencing. Euphytica 215, 34.

    Article  CAS  Google Scholar 

  • Branham S. E., Stansell Z. J., Couillard D. M. and Farnham M. W. 2017 Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing. Theor. Appl. Genet. 130, 529–538.

    Article  CAS  PubMed  Google Scholar 

  • Brinez B., Perseguini J., Rosa J. S., Bassi D., Goncalves J. G. R., Almeida C. et al. 2017 Mapping QTLs for drought tolerance in a SEA 5 x AND 277 common bean cross with SSRs and SNP markers. Genet. Mol. Biol. 40, 813–823.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Brisco E. I., Porch T. G., Cregan P. B. and Kelly J. D. 2014 Quantitative trait loci associated with resistance to Empoasca in common bean. Crop Sci. 54, 2509–2519.

    Article  CAS  Google Scholar 

  • Brog Y. M., Osorio S., Yichie Y., Alseekh S., Bensal E., Kochevenko A. et al. 2019 A Solanum neorickii introgression population providing a powerful complement to the extensively characterized Solanum pennellii population. Plant J. 97, 391–403.

    Article  CAS  PubMed  Google Scholar 

  • Broman K. W. 2005 The genomes of recombinant inbred lines. Genetics 169, 1133–1146.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bu Y., Zhang X., Wang C., Guo J., Zhang X., Li X. et al. 2018 Conditional and unconditional QTL analyses of seed hardness in vegetable soybean (Glycine max L. Merr.). Euphytica 214, 237.

    Article  CAS  Google Scholar 

  • Burr B. and Burr F. A. 1991 Recombinant inbreds for molecular mapping in maize - theoretical and practical considerations. Trends Genet. 7, 55–60.

    CAS  PubMed  Google Scholar 

  • Cao Y. C., Li S. G, Wang Z. L., Chang F. G., Kong J. J., Gai J. Y. et al. 2017 Identification of major quantitative trait Loci for seed oil content in soybeans by combining linkage and genome-wide association mapping. Front. Plant Sci. 8, 1222.

    Article  PubMed  PubMed Central  Google Scholar 

  • Cavanagh C., Morell M., Mackay I. and Powell W. 2008 From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr. Opin. Plant Biol. 11, 215–221.

    Article  PubMed  CAS  Google Scholar 

  • Ceamerarius R. J. 1694 Rudolphi Jacobi Camerarii ad Thessalum, D. Mich. Bernardum Valentini De sexu plantarum epistola [microform]. Tybingai: Typis Viduae Rommeili.

  • Celik I., Gurbuz N., Uncu A. T., Frary A. and Doganlar S. 2017 Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing. BMC Genomics 18, 1.

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen J., Pang W., Chen B., Zhang C. and Piao Z. 2016 Transcriptome analysis of Brassica rapa near-isogenic lines carrying clubroot-resistant and –susceptible alleles in response to Plasmodiophora brassicae during early infection. Front. Plant Sci. 6, 1183.

    PubMed  PubMed Central  Google Scholar 

  • Chen S. S., Han X. J., Fang J., Lu Z. C., Qiu W. M., Liu M. Y. et al. 2017 Sedum alfredii SaNramp6 metal transporter contributes to cadmium accumulation in transgenic Arabidopsis thaliana. Sci. Rep. 7, 13318.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Da F. S. Michelle, Möller M., Clough S. J. and Pinheiro J. B. 2018 Heritability of agronomic traits correlated with reduced stink bug damage in an F\(_{2:3}\) soybean population derived from IAC-100. J. Crop Improv. 32, 1–18.

    Article  Google Scholar 

  • De Beukelaer H., De Meyer G. and Fack V. 2015 Heuristic exploitation of genetic structure in marker-assisted gene pyramiding problems. BMC Genet. 16, 2.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Delaat A. M. M., Gohde W. and Vogelzang M. J. D. C. 1987 Determination of ploidy of single plants and plant-populations by flow-cytometry. Plant Breed. 99, 303–307.

    Article  Google Scholar 

  • Deokar A., Sagi M., Daba K. and Tar’an B. 2019 QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea. Plant Biotechnol. J. 17, 275–288.

    Article  CAS  PubMed  Google Scholar 

  • Descalsota G. I. L, Swamy B. P. M., Zaw H., Inabangan-Asilo M. A., Amparado A., Mauleon R. et al. 2018 Genome-wide association mapping in a Rice MAGIC plus population detects QTLs and genes useful for biofortification. Front. Plant Sci. 9, 1347.

    Article  PubMed  PubMed Central  Google Scholar 

  • Deschamps S., Llaca V. and May G. D. 2012 Genotyping-by-sequencing in plants. Biology 1, 460–483.

    Article  PubMed  PubMed Central  Google Scholar 

  • Dickson S. P., Wang K., Krantz I., Hakonarson H. and Goldstein D. B. 2010 Rare variants create synthetic genome-wide associations. PLoS Biol. 8, e1000294.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Diers B. W., Specht J., Rainey K. M., Cregan P., Song Q., Ramasubramanian V. et al. 2018 Genetic architecture of soybean yield and agronomic traits. G3 (Bethesda) 8, 3367–3375.

    Article  Google Scholar 

  • Ding Y., Mei J., Wu Q., Xiong Z., Li Y., Shao C. et al. 2019 Synchronous improvement of subgenomes in allopolyploid: a case of Sclerotinia resistance improvement in Brassica napus. Mol. Breed. 39, 10.

    Article  CAS  Google Scholar 

  • Doebley J. F., Gaut B. S. and Smith B. D. 2006 The molecular genetics of crop domestication. Cell 127, 1309–1321.

    Article  CAS  PubMed  Google Scholar 

  • Doerge R. W. 2002 Mapping and analysis of quantitative trait loci in experimental populations. Nat. Rev. Genet. 3, 43–52.

    Article  CAS  PubMed  Google Scholar 

  • Dole J. and Weber D. F. 2007 Detection of quantitative trait loci influencing recombination using recombinant inbred lines. Genetics 177, 2309–2319.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Draicchio F., Sharma R., Flavell A. J., Bull H., Thomas W. T. B., Maurer A. et al. 2018 Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding. J. Exp. Bot. 69, 3811–3822.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dwivedi S. L., Britt A. B., Tripathi L., Sharma S., Upadhyaya H. D. and Ortiz R. 2015 Haploids: constraints and opportunities in plant breeding. Biotechnol. Adv. 33, 812–829.

    Article  PubMed  Google Scholar 

  • Dwivedi S. L., Ceccarelli S., Blair M. W., Upadhyaya H. D., Are A. K. and Ortiz R. 2016 Lancrace Germplasm for improving yield and abiotic stress adaptation. Trends Plant Sci. 21, 31–42.

    Article  CAS  PubMed  Google Scholar 

  • Eathington S. R., Crosbie T. M., Edwards M. D., Reiter R., Bull J. K. 2007 Molecular markers in a commercial breeding program. Crop Sci. 47, S154–S163.

    Article  Google Scholar 

  • Ebrahimzadeh H., Soltanloo H., Shariatpanahi M. E., Eskandari A. and Ramezanpour S. S. 2018 Improved chromosome doubling of parthenogenetic haploid plants of cucumber (Cucumis sativus L.) using colchicine, trifluralin, and oryzalin. Plant Cell Tissue Organ Cult. 135, 407–417.

    Article  CAS  Google Scholar 

  • Elshire R. J., Glaubitz J. C., Sun Q., Poland J. A., Kawamoto K., Buckler E. S. et al. 2011 A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. https://doi.org/10.1371/journal.pone.0019379.

    Article  PubMed  PubMed Central  Google Scholar 

  • Eshed Y. and Zamir D. 1995 An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141, 1147–1162.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Esteras C., Gomez P., Monforte A. J., Blanca J., Vicente-Dolera N., Roig C. et al. 2012 High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping. BMC Genomics 13, 80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fall L. A., Perkins-Veazie P., Ma G. and McGregor C. 2019 QTLs associated with flesh quality traits in an elite \(\times \) elite watermelon population. Euphytica 215, 30.

    Article  CAS  Google Scholar 

  • FAO 2017 FAO statistical databases FAOSTAT. Food and Agricultural Organization. http://www.fao.org/faostat/en/#data. 2017.

  • Farre A., Sayers L., Leverington-Waite M., Goram R., Orford S, Wingen L. et al. 2016 Application of a library of near isogenic lines to understand context dependent expression of QTL for grain yield and adaptive traits in bread wheat. BMC Plant Biol. 16, 161–173.

    Article  PubMed  PubMed Central  Google Scholar 

  • Fattahi F., Fakheri B. A., Solouki M., Möllers C. and Rezaizad A. 2018 Mapping QTL controlling agronomic traits in a doubled haploid population of winter oilseed rape (Brassica napus L.). J. Genet. 97, 1389–1406.

    Article  CAS  PubMed  Google Scholar 

  • Feldman M. and Levy A. A. 2005 Allopolyploidy - a shaping force in the evolution of wheat genomes. Cytogenet. Genome Res. 109, 250–258.

    Article  CAS  PubMed  Google Scholar 

  • Ferreira A., Silva M. Fd, Silva LdCe and Cruz C. D. 2006 Estimating the effects of population size and type on the accuracy of genetic maps. Genet. Mol. Biol. 29, 187–192.

    Article  CAS  Google Scholar 

  • Filiz E., Uras M. E., Ozyigit., II, Sen U. and Gungor H. 2018 Genetic diversity and phylogenetic analyses of Turkish rice varieties revealed by Issr markers and chloroplast trnL-F Region. Fresenius Environ. Bull. 27, 8351–8358.

    CAS  Google Scholar 

  • Flannery K. V. 1969 Origins and ecological effects of early domestication in Iran and the near east. In The domestication and exploitation of plants and animals (ed. P. J. Ucko and G. W Dimbleby), pp. 73–100. Gerald Duckworth, London.

    Google Scholar 

  • Flint-Garcia S. A. 2013 Genetics and consequences of crop domestication. J. Agr. Food Chem. 61, 8267–8276.

    Article  CAS  Google Scholar 

  • Fragoso C. A., Moreno M., Wang Z., Heffelfinger C., Arbelaez L. J., Aguirre J. A. et al. 2017 Genetic architecture of a rice nested association mapping population. G3 (Bethesda) 7, 1913–1926.

    Article  Google Scholar 

  • Fulop D., Ranjan A., Ofner I., Covington M. F., Chitwood D. H., West D. et al. 2016 A new advanced backcross tomato population enables high resolution leaf QTL mapping and gene identification. G3 (Bethesda) 6, 3169–3184.

    Article  CAS  Google Scholar 

  • Gao L., Zhao S., Lu X., He N., Zhu H., Dou J. et al. 2018 Comparative transcriptome analysis reveals key genes potentially related to soluble sugar and organic acid accumulation in watermelon. PLoS One 13, e0190096.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • García-Fortea E., Gramazio P., Vilanova S., Fita A., Mangino G., Villanueva G. et al. 2019 First successful backcrossing towards eggplant (Solanum melongena) of a New World species, the silverleaf nightshade (S. elaeagnifolium), and characterization of interspecific hybrids and backcrosses. Sci. Hortic. 246, 563–573.

    Article  Google Scholar 

  • Garcia-Mas J., Benjak A., Sanseverino W., Bourgeois M., Mir G., Gonzalez V. M. et al. 2012 The genome of melon (Cucumis melo L.). Proc. Natl. Acad. Sci. USA 109, 11872–11877.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gepts P. 2014 Domestication of plants. In Encyclopedia of agriculture and food system (ed. N. V. Alfen), vol. 2, pp. 474–486. Elsevier, San Diego.

    Chapter  Google Scholar 

  • Gepts P. L. and Harlan S. 2012 Biodiversity in agriculture: domestication, evolution, and sustainability. Cambridge University Press, New York.

    Book  Google Scholar 

  • Gholizadeh A., Dehghani H. and Khodadadi M. 2019 Quantitative genetic analysis of water deficit tolerance in coriander through physiological traits. Plant Genet. Resour. 17, 255–264.

    Article  CAS  Google Scholar 

  • Gibson G. 2012 Rare and common variants: twenty arguments. Nat. Rev. Genet. 13, 135–145.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gramazio P., Prohens J., Plazas M., Mangino G., Herraiz F. J., Garcia-Fortea E. et al. 2018 Genomic tools for the enhancement of vegetable crops: a case in Eggplant. Not. Bot. Horti. Agrobo 46, 1–13.

    Article  CAS  Google Scholar 

  • Gregory T. R. 2009 Artificial selection and domestication: modern lessons from Darwin’s enduring analogy. Evol. Edu. Outreach 2, 5–27.

    Article  Google Scholar 

  • Guan H., Ali F. and Pan Q. 2017 Dissection of recombination attributes for multiple maize populations using a common SNP assay. Front. Plant Sci. 8, article ID 2063.

  • Guha S. and Maheshwari S. C. 1964 In vitro production of embryos from anthers of datura. Nature 204, 497–497.

    Article  Google Scholar 

  • Hallauer A. R. 2011 Evolution of plant breeding. Crop Breed. Appl. Biot. 11, 197–206.

    Article  Google Scholar 

  • Hamawaki R. L., Hamawaki O. T., Nogueira A. P. O., Juliatti F. C., Glasenapp J. S. and Hamawaki C. D. L 2019 New high-yielding conventional soybean adapted to the states of Goiás, Minas Gerais and Mato Grosso. Acta Sci. Agron. 41, e39913.

    Article  Google Scholar 

  • Han B. K., Rhee S. J., Jang Y. J., Sim T. Y., Kim Y. J., Park T. S. et al. 2016 Identification of a causal pathogen of watermelon powdery mildew in Korea and development of a genetic linkage marker for resistance in watermelon (Citrullus lanatus). Korean J. Hortic. Sci. 34, 912–923.

    CAS  Google Scholar 

  • Han K., Jang S., Lee J.-H., Lee D.-G., Kwon J.-K., Kang B.-C. 2019 A MYB transcription factor is a candidate to control pungency in Capsicum annuum. Theor. Appl. Genet. 132, 1235–1246.

    Article  CAS  PubMed  Google Scholar 

  • Hasan M. M., Rafii M. Y., Ismail M. R., Mahmood M., Rahim H. A., Alam M. A. et al. 2015 Marker-assisted backcrossing: a useful method for rice improvement. Biotechnol. Biotechnol. Equip. 29, 237–254.

    Article  PubMed  PubMed Central  Google Scholar 

  • Hasan Y., Briggs W., Matschegewski C., Ordon F., Stutzel H., Zetzsche H. et al. 2016 Quantitative trait loci controlling leaf appearance and curd initiation of cauliflower in relation to temperature. Theor. Appl. Genet. 129, 1273–1288.

    Article  CAS  PubMed  Google Scholar 

  • Hayat I., Ahmad A., Masud T., Ahmed A. and Bashir S. 2014 Nutritional and health perspectives of beans (Phaseolus vulgaris L.): an overview. Crit. Rev. Food Sci. 54, 580–592.

    Article  CAS  Google Scholar 

  • Hedrick P. W. 2005 A standardized genetic differentiation measure. Evolution 59, 1633–1638.

    Article  CAS  PubMed  Google Scholar 

  • Hedrick P. W. 2011 Genetics of populations, 4th edition. Jones and Bartlett, Sudbury.

    Google Scholar 

  • Heino M. 2014 Quantitative traits. In Stock identification methods (ed. S. X. Cadrin, L. A. Kerr and S. Mariani), pp. 59–76. Academic Press, San Diego.

    Chapter  Google Scholar 

  • Hoyos-Villegas V., Song Q. J., Wright E. M., Beebe S. E. and Kelly J. D. 2016 Joint linkage QTL mapping for yield and agronomic traits in a composite map of three common bean RIL populations. Crop Sci. 56, 2546–2563.

    Article  Google Scholar 

  • Huang B. E., Raghavan C., Mauleon R., Broman K. W. and Leung H. 2014 Efficient imputation of missing markers in low-coverage genotyping-by-sequencing data from multiparental crosses Genetics 197, 401–404.

    Article  PubMed  PubMed Central  Google Scholar 

  • Huang B. E., Verbyla K. L., Verbyla A. P., Raghavan C., Singh V. K., Gaur P. et al. 2015 MAGIC populations in crops: current status and future prospects. Theor. Appl. Genet. 128, 999–1017.

    Article  PubMed  Google Scholar 

  • Hung H. Y., Browne C., Guill K., Coles N., Eller M., Garcia A. et al. 2012 The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population. Heredity 108, 490–499.

    Article  CAS  PubMed  Google Scholar 

  • Huynh B.-L., Ehlers J. D., Huang B. E., Muñoz-Amatriaín M., Lonardi S., Santos J. R. P. et al. 2018 A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.). Plant J. 93, 1129–1142.

    Article  CAS  PubMed  Google Scholar 

  • Huynh B. L., Matthews W. C., Ehlers J. D., Lucas M. R., Santos J. R. P., Ndeve A. et al. 2016 A major QTL corresponding to the Rk locus for resistance to root-knot nematodes in cowpea (Vigna unguiculata L. Walp.). Theor. Appl. Genet. 129, 87–95.

    Article  CAS  PubMed  Google Scholar 

  • Jat G. S., Das Munshi A., Behera T. K., Choudhary H., Dash P., Ravindran A. et al. 2019 Genetics and molecular mapping of gynoecious (F) locus in cucumber (Cucumis sativus L). J. Hortic. Sci. Biotech. 94, 24–32.

    Article  CAS  Google Scholar 

  • Jeong H. S., Jang S., Han K., Kwon J. K. and Kang B. C. 2015 Marker-assisted backcross breeding for development of pepper varieties (Capsicum annuum) containing capsinoids. Mol. Breed. 35, 266–275.

    Article  CAS  Google Scholar 

  • Ji J., Cao W., Dong X., Liu Z., Fang Z., Zhuang M. et al. 2018 A 252-bp insertion in BoCER1 is responsible for the glossy phenotype in cabbage (Brassica oleracea L. var. capitata) Mol. Breed. 38, 128.

    Article  CAS  Google Scholar 

  • Jiang H., Tian H., Yan C., Jia L., Wang Y., Wang M. et al. 2019 RNA-seq analysis of watermelon (Citrullus lanatus) to identify genes involved in fruit cracking. Sci. Hortic. 248, 248–255.

    Article  CAS  Google Scholar 

  • Jordan K. W., Wang S., He F., Chao S., Lun Y., Paux E. et al. 2018 The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. Plant J. 95, 1039–1054.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jost L. 2008 GST and its relatives do not measure differentiation. Mol. Ecol. 17, 4015–4026.

    Article  PubMed  Google Scholar 

  • Kamfwa K., Beaver J. S., Cichy K. A. and Kelly J. D. 2018 QTL mapping of resistance to bean Weevil in common bean. Crop Sci. 58, 2370–2378.

    Article  CAS  Google Scholar 

  • Kamfwa K., Cichy K. A. and Kelly J. D. 2019 Identification of quantitative trait loci for symbiotic nitrogen fixation in common bean. Theor. Appl. Genet. 132, 1375–1387.

    Article  CAS  PubMed  Google Scholar 

  • Kang Y. J., Ahn Y. K., Kim K. T. and Jun T. H. 2016 Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance. BMC Plant Biol. 16, 235.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kasha K. J. and Kao K. N. 1970 High frequency haploid production in barley (Hordeum vulgare L). Nature 225, 874–876.

    Article  CAS  PubMed  Google Scholar 

  • Keurentjes J. J. B., Bentsink L., Alonso-Blanco C., Hanhart C. J., Vries H. B. D., Effgen S. et al. 2007 Development of a near-isogenic line population of Arabidopsis thaliana and comparison of mapping power with a recombinant inbred line population. Genetics 175, 891–905.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Keurentjes J. J. B., Willems G., van Eeuwijk F., Nordborg M. and Koornneef M. 2011 A comparison of population types used for QTL mapping in Arabidopsis thaliana. Plant Genet. Resour. 9, 185–188.

    Article  CAS  Google Scholar 

  • Khan M. A., Tong F., Wang W., He J., Zhao T. and Gai J. 2018 Analysis of QTL–allele system conferring drought tolerance at seedling stage in a nested association mapping population of soybean (Glycine max (L.) Merr.) using a novel GWAS procedure. Planta 248, 947–962.

    Article  CAS  PubMed  Google Scholar 

  • Kooke R., Wijnker E. and Keurentjes J. J. 2012a Backcross populations and near isogenic lines. Methods Mol. Biol. 871, 3–16.

    Article  CAS  PubMed  Google Scholar 

  • Kooke R., Wijnker E. and Keurentjes J. J. B. 2012b Quantitative trait Loci (QTL): methods and protocols. In Quantitative trait loci (QTL) (ed. S. A. Rifkin), vol. 871, pp. XI, 331. Humana Press, Totowa.

  • Korte A. and Farlow A. 2013 The advantages and limitations of trait analysis with GWAS: a review. Plant Methods 9, 29–29.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kover P. X., Valdar W., Trakalo J., Scarcelli N., Ehrenreich I. M., Purugganan M. D. et al. 2009 A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet. 5, e1000551.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kumar A., Tiwari K. L., Datta D. and Singh M. 2014 Marker assisted gene pyramiding for enhanced Tomato leaf curl virus disease resistance in tomato cultivars. Biol. Plant. 58, 792–797.

    Article  CAS  Google Scholar 

  • Kumar A., Ranjan T., Kumar R. R., Rajani K., Kishore C. and Kumar J. 2018 Development of mapping populations. In Plant biotechnology (ed. B. Prasad, S. Sahni, P. Kumar and M. Siddiqui), vol. 1. Apple Academic Press, New York.

    Google Scholar 

  • Kumari M., Clarke H. J., Small I. and Siddique K. H. M. 2009 Albinism in plants: a major bottleneck in wide hybridization, androgenesis and doubled haploid culture. Crit. Rev. Plant Sci. 28, 393–409.

    Article  CAS  Google Scholar 

  • Kump K. L., Bradbury P. J., Wisser R. J., Buckler E. S., Belcher A. R., Oropeza-Rosas M. A. et al. 2011 Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat. Genet. 43, 163.

    Article  CAS  PubMed  Google Scholar 

  • Ladejobi O., Elderfield J., Gardner K. A., Gaynor R. C., Hickey J., Hibberd J. M. et al. 2016 Maximizing the potential of multi-parental crop populations. Appl. Trans. Genom. 11, 9–17.

    Google Scholar 

  • Lander E. S. and Botstein D. 1989 Mapping mendelian factors underlying quantitative traits using Rflp linkage maps. Genetics 121, 185–199.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lavaud C., Lesne A., Piriou C., Le Roy G., Boutet G., Moussart A. et al. 2015 Validation of QTL for resistance to Aphanomyces euteiches in different pea genetic backgrounds using near-isogenic lines. Theor. Appl. Genet. 128, 2273–2288.

    Article  CAS  PubMed  Google Scholar 

  • Li H., Li X. N., Xuan Y. H., Jiang J., Wei Y. D. and Piao Z. Y. 2018a Genome wide identification and expression profiling of SWEET genes family reveals its role during Plasmodiophora brassicae-ınduced formation of clubroot in Brassica rapa. Front. Plant Sci. 9, 207.

    Article  PubMed  PubMed Central  Google Scholar 

  • Li H. H., Rasheed A., Hickey L. T. and He Z. H. 2018b Fast-forwarding genetic gain. Trends Plant Sci. 23, 184–186.

    Article  CAS  PubMed  Google Scholar 

  • Li R., Jeong K., Davis J. T., Kim S., Lee S., Michelmore R. W. et al. 2018c Integrated QTL and eQTL Mapping provides insights and candidate genes for fatty acid composition, flowering time, and growth traits in a \(\text{F}_2\) population of a novel synthetic allopolyploid Brassica napus. Front. Plant Sci. 9, 1632

    Article  PubMed  PubMed Central  Google Scholar 

  • Li S., Cao Y., He J., Zhao T. and Gai J. 2017 Detecting the QTL-allele system conferring flowering date in a nested association mapping population of soybean using a novel procedure. Theor. Appl. Genet. 130, 2297–2314.

    Article  CAS  PubMed  Google Scholar 

  • Liang D., Hu Q., Xu Q., Qi X., Zhou F. and Chen X. 2015 Genetic inheritance analysis of melon aphid (Aphis gossypii Glover) resistance in cucumber (Cucumis sativus L.). Euphytica 205, 361–367.

    Article  CAS  Google Scholar 

  • Liang Z., Qiu Y. and Schnable J. 2019 Distinct characteristics of genes associated with phenome-wide variation in maize (Zea mays). (in press).

  • Liu G., Zhao T., You X., Jiang J., Li J. and Xu X. 2019 Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum). BMC Plant Biol. 19, 15.

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu X., Han F. Q., Kong C. C., Fang Z. Y., Yang L. M., Zhang Y. Y. et al. 2017 Rapid introgression of the Fusarium wilt resistance gene into an elite cabbage line through the combined application of a microspore culture, genome back ground analysis, and disease resistance-Sspecific marker assisted fore ground selection. Front. Plant Sci. 8. 354.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lv H. H, Wang Q. B., Liu X., Han F. Q., Fang Z. Y., Yang L. M. et al. 2016 Whole-genome mapping reveals novel QTL clusters associated with main agronomic traits of cabbage (Brassica oleracea var. capitata L.). Front. Plant Sci. 7, 989.

    PubMed  PubMed Central  Google Scholar 

  • Ma L., Ji Y. J. and Zhang D. X. 2015 Statistical measures of genetic differentiation of populations: rationales, history and current states. Curr. Zool. 61, 886–897.

    Article  Google Scholar 

  • Mackay T. F. C. 2001 The genetic architecture of quantitative traits. Annu. Rev. Genet. 35, 303–339.

    Article  CAS  PubMed  Google Scholar 

  • Madhusudhana R. 2015 Linkage mapping. In Sorghum molecular breeding (ed. R. Madhusudhana, P. Rajendrakumar and J. V. Patil), pp. 47–70. Springer India, New Delhi.

    Chapter  Google Scholar 

  • Mang X. L., Su Y. B., Liu Y. M., Fang Z. Y., Yang L. M., Zhuang M. et al. 2016 Genetic analysis and QTL mapping of traits related to head shape in cabbage (Brassica oleracea var. capitata L.). Sci. Hortic. 207, 82–88.

    Article  CAS  Google Scholar 

  • Mazoyer M. and Roudart L. 2006 Centers of origin of neolithic agriculture. In A history of world agriculture, pp. 74. Earthscan, London.

  • McMullen M. D., Kresovich S., Villeda H. S., Bradbury P., Li H., Sun Q. et al. 2009 Genetic properties of the Maize nested association mapping population. Science 325, 737–740.

    Article  CAS  PubMed  Google Scholar 

  • Meijer D., Viquez-Zamora M., van Eck H. J., Hutten R. C. B., Su Y., Rothengatter R. et al. 2018 QTL mapping in diploid potato by using selfed progenies of the cross S. tuberosum \(\times \) S. chacoense. Euphytica 214, 121.

  • Melchinger A. E., Technow F. and Dhillon B. S. 2011 Gene stacking strategies with doubled haploids derived from biparental crosses: theory and simulations assuming a finite number of loci. Theor. Appl. Genet. 123, 1269–1279.

    Article  PubMed  Google Scholar 

  • Mercati F., Riccardi P., Harkess A., Sala T., Abenavoli M. R., Leebens-Mack J. et al. 2015 Single nucleotide polymorphism-based parentage analysis and population structure in garden asparagus, a worldwide genetic stock classification. Mol. Breed. 35, 59–70.

    Article  Google Scholar 

  • Milla R., Osborne C. P., Turcotte M. M. and Violle C. 2015 Plant domestication through an ecological lens. Trends Ecol. Evol. 30, 463–469.

    Article  PubMed  Google Scholar 

  • Miyatake K., Saito T., Negoro S., Yamaguchi H., Nunome T., Ohyama A. et al. 2012 Development of selective markers linked to a major QTL for parthenocarpy in eggplant (Solanum melongena L.). Theor. Appl. Genet. 124, 1403–1413.

    Article  PubMed  Google Scholar 

  • Morgan C. 2015 Is it intensification yet? Current archaeological perspectives on the evolution of hunter-gatherer economies. J. Archaeol. Res. 23, 169.

    Article  Google Scholar 

  • Muylle H., Baert J., Van Bockstaele E., Pertijs J. and Roldan-Ruiz I. 2005 Four QTLs determine crown rust (Puccinia coronata f. sp lolii) resistance in a perennial ryegrass (Lolium perenne) population. Heredity 95, 348–357.

    Article  CAS  PubMed  Google Scholar 

  • Nadeem M. A., Nawaz M. A., Shahid M. Q., Doğan Y., Comertpay G., Yıldız M. et al. 2018 DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol. Biotech. Eq. 32, 261–285.

    Article  CAS  Google Scholar 

  • Nadeem S. M., Naveed M., Zahir Z. A. and Asghar H. N. 2013 Plant–microbe interactions for sustainable agriculture: fundamentals and recent advances. In Plant microbe symbiosis: fundamentals and advances (ed. N. K. Arora), pp. 51–103. , Springer India, New Delhi.

    Chapter  Google Scholar 

  • Nakedde T., Ibarra-Perez F. J., Mukankusi C., Waines J. G. and Kelly J. D. 2016 Mapping of QTL associated with Fusarium root rot resistance and root architecture traits in black beans. Euphytica 212, 51–63.

    Article  CAS  Google Scholar 

  • Naresh P., Lin S.-W., Lin C-Y., Wang Y-W., Schafleitner R., Kilian A. et al. 2018 Molecular markers associated to two non-allelic genic male sterility genes in peppers (Capsicum annuum L.). Front. Plant Sci. 9,1343.

    Article  PubMed  PubMed Central  Google Scholar 

  • Nei M. 1973 Analysis of gene diversity in subdivided populations. Proc. Natl. Acad Sci. USA 70, 3321–3323.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nguyen T. C. T., Abrams S. R., Friedt W. and Snowdon R. J. 2018 Quantitative trait locus analysis of seed germination, seedling vigour and seedling-regulated hormones in Brassica napus. Plant Breed. 137, 388–401.

    Article  CAS  Google Scholar 

  • Niu L., Shi F., Feng H. and Zhang Y. 2019 Efficient doubled haploid production in microspore culture of Zengcheng flowering Chinese cabbage (Brassica campestris L. ssp. chinensis [L.] Makino var. utilis Tsen et Lee). Sci. Hortic. 245, 57–64.

    Article  CAS  Google Scholar 

  • Nogue F., Mara K., Collonnier C. and Casacuberta J. M. 2016 Genome engineering and plant breeding: impact on trait discovery and development. Plant Cell Rep. 35, 1475–1486.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Obi VI., Barriuso J. J., Usall J. and Gogorcena Y. 2019 Breeding strategies for identifying superior peach genotypes resistant to brown rot. Sci. Hortic. 246, 1028–1036.

    Article  Google Scholar 

  • Omoigui L. O., Danmaigona C. C., Kamara A. Y., Ekefan E. J. and Timko M. P. 2018 Genetic analysis of Fusarium wilt resistance in cowpea (Vigna unguiculata Walp.). Plant Breed. 137, 773–781.

    Article  CAS  Google Scholar 

  • Parker T. A., Berny Mier y Teran J. C., Palkovic A., Jernstedt J. and Gepts P. 2019 Genetic control of pod dehiscence in domesticated common bean: associations with range expansion and local aridity conditions. (bioRxiv 517516).

  • Pascual L., Desplat N., Huang B. E., Desgroux A., Bruguier L., Bouchet J. P. et al. 2015 Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotechnol. J. 13, 565–577.

    Article  CAS  PubMed  Google Scholar 

  • Pathirana R. 2011 Plant mutation breeding in agriculture. CAB Rev.: Perspect. Agric., Vet. Sci., Nutr. Nat. Resou. 6, 1–20.

    Article  CAS  Google Scholar 

  • Pen S., Nath U. K., Song S., Goswami G., Lee J.-H. and Jung H.-J. et al. 2018 Developmental stage and shape of embryo determine the efficacy of embryo rescue in introgressing orange/yellow color and anthocyanin genes of Brassica species. Plants 7, 99.

    Article  PubMed Central  Google Scholar 

  • Peng T., Sun X. and Mumm R. H. 2014 Optimized breeding strategies for multiple trait integration: I. Minimizing linkage drag in single event introgression molecular breeding : new strategies in plant improvement. Mol. Breed. 33, 89–104.

    Article  PubMed  Google Scholar 

  • Pereira L., Ruggieri V., Pérez S., Alexiou K. G., Fernández M., Jahrmann T. et al. 2018 QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map. BMC Plant Biol. 18, 324.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Popovsky-Sarid S., Borovsky Y., Faigenboim A., Parsons E. P., Lohrey G. T., Alkalai-Tuvia S. et al. 2017 Genetic and biochemical analysis reveals linked QTLs determining natural variation for fruit post-harvest water loss in pepper (Capsicum). Theor. Appl. Genet. 130, 445–459.

    Article  CAS  PubMed  Google Scholar 

  • Pradhan D., Mathew D., Mathew S. K. and Nazeem P. A. 2018 Identifying the markers and tagging a leucine-rich repeat receptor-like kinase gene for resistance to anthracnose disease in vegetable cowpea (Vigna unguiculata (L.) Walp.). J. Hortic. Sci. Biotech. 93, 225–231.

    Article  CAS  Google Scholar 

  • Qaim M. 2016 Plant breeding and agricultural Development. In Genetically modified crops and agricultural development, pp. 15–38. Palgrave Macmillan US, New York.

    Chapter  Google Scholar 

  • Qian W., Fan G. Y., Liu D. D., Zhang H. L., Wang X. W., Wu J. et al. 2017 Construction of a high-density genetic map and the X/Y sex-determining gene mapping in spinach based on large-scale markers developed by specific-locus amplified fragment sequencing (SLAF-seq). BMC Genomics 18, 276.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rambla J. L., Medina A., Fernandez-del-Carmen A., Barrantes W., Grandillo S., Cammareri M. et al. 2017 Identification, introgression, and validation of fruit volatile QTLs from a red-fruited wild tomato species. J. Exp. Bot. 68, 429–442.

    CAS  PubMed  Google Scholar 

  • Ravi M. and Chan S. W. L. 2010 Haploid plants produced by centromere-mediated genome elimination. Nature 464, 615.

    Article  CAS  PubMed  Google Scholar 

  • Ren J. J., Wu P. H., Trampe B., Tian X. L., Lubberstedt T., Chen S. J. 2017 Novel technologies in doubled haploid line development. Plant Biotechnol. J. 15, 1361–1370.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ripoll J., Urban L. and Bertin N. 2016 The potential of the MAGIC TOM parental accessions to explore the genetic variability in Tomato Acclimation to Repeated cycles of water deficit and recovery. Front Plant Sci. 6, 1172.

    Article  PubMed  PubMed Central  Google Scholar 

  • Rong F., Chen F., Huang L., Zhang J., Zhang C., Hou D. et al. 2019 A mutation in class III homeodomain-leucine zipper (HD-ZIP III) transcription factor results in curly leaf (cul) in cucumber (Cucumis sativus L.). Theor. Appl. Genet. 132, 113–123.

    Article  CAS  PubMed  Google Scholar 

  • Rubinstein M., Katzenellenbogen M., Eshed R., Rozen A., Katzir N., Colle M. et al. 2015 Ultrahigh-Density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array. PLoS One 10, e0124101.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Saba Rahim M., Sharma H., Parveen A. and Roy J. K. 2018 Trait mapping approaches through association analysis in plants. In Plant Genetics and Molecular Biology (ed. R. K. Varshney, M. K. Pandey and A. Chitikineni), pp. 83–108. Springer International Publishing, Cham.

    Chapter  Google Scholar 

  • Sai C. B., Nagarajan P., Raveendran M., Rabindran R., Bapu J. R. K. and Senthil N. 2017 Understanding the inheritance of mungbean yellow mosaic virus (MYMV) resistance in mungbean (Vigna radiata L. Wilczek). Mol. Breed. 37, 63.

    Article  CAS  Google Scholar 

  • Sallam A. and Martsch R. 2015 Association mapping for frost tolerance using multi-parent advanced generation inter-cross (MAGIC) population in faba bean (Vicia faba L.). Genetica 143, 501–514.

    Article  PubMed  Google Scholar 

  • Sanetomo R., Habe I. and Hosaka K. 2019 Sexual introgression of the late blight resistance gene Rpi-blb3 from a Mexican wild diploid species Solanum pinnatisectum Dunal into potato varieties. Mol. Breed. 39, 13.

    Article  CAS  Google Scholar 

  • Sannemann W., Lisker A., Maurer A., Léon J., Kazman E., Cöster H. et al. 2018 Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800. BMC Genomics 19, 559.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Santamaria L., Ernest E. G., Gregory N. F. and Evans T. A. 2018 Inheritance of resistance in Lima Bean to Phytophthora phaseoli, the causal agent of downy mildew of lima bean. Hort. Sci. 53, 777–781.

    Article  Google Scholar 

  • Sapkota S., Chen L.-L., Yang S., Hyma K. E., Cadle-Davidson L. and Hwang C.-F. 2019 Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis-derived ‘Norton’. Theor. Appl. Genet. 132, 137–147.

    Article  CAS  PubMed  Google Scholar 

  • Schneider K. 2005 Mapping populations and principles of genetic mapping. In The handbook of plant genome mapping (ed. K. Meksem and G. Kahl). Wiley-VCH Verlag, Weinheim.

    Google Scholar 

  • Scott K., Balk C., Veney D., McHale L. K. and Dorrance A. E. 2019 Quantitative disease resistance loci towards Phytophthora sojae and three species of pythium in six soybean nested association mapping populations. Crop Sci. S9, 605–623.

    Article  Google Scholar 

  • Segui-Simarro J. M. 2015 Doubled haploidy in model and recalcitrant species. Front. Plant Sci. 6. 1175.

    Article  PubMed  PubMed Central  Google Scholar 

  • Semagn K., Bjornstad A. and Ndjiondjop M. N. 2006 Principles, requirements and prospects of genetic mapping in plants. Afr. J. Biotechnol. 5, 2569–2587.

    CAS  Google Scholar 

  • Seo J.-H., Kim K.-S., Ko J.-M., Choi M.-S., Kang B.-K., Kwon S.-W. et al. 2019 Quantitative trait locus analysis for soybean (Glycine max) seed protein and oil concentrations using selected breeding populations. Plant Breed. 138, 95–104.

    Article  CAS  Google Scholar 

  • Seymour D. K., Filiault D. L., Henry I. M., Monson-Miller J., Ravi M., Pang A. D. et al. 2012 Rapid creation of Arabidopsis doubled haploid lines for quantitative trait locus mapping. Proc. Natl. Acad. Sci. USA 109, 4227–4232.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shivakumar M., Gireesh C. and Talukdar A. 2016 Efficiency and utility of pollination without emasculation (PWE) method in intra- and inter-specific hybridization in soybean. Indian J. Genet. Plant Breed. 76, 98–100.

    Article  Google Scholar 

  • Sidhu G. K., Warzecha T. and Pawlowski W. P. 2017 Evolution of meiotic recombination genes in maize and teosinte. BMC Genomics 18, 106.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Singh R. K., Rai N., Lima J. M., Singh M., Singh S. N. and Kumar S. 2015 Genetic and molecular characterisations of Tomato leaf curl virus resistance in tomato (Solanum lycopersicum L). J. Hortic. Sci. Biotech. 90, 503–510.

    Article  CAS  Google Scholar 

  • Singh S., Bhatia R., Kumar R., Sharma K., Dash S. and Dey S. S. 2018 Cytoplasmic male sterile and doubled haploid lines with desirable combining ability enhances the concentration of important antioxidant attributes in Brassica oleracea. Euphytica 214, 207.

    Article  CAS  Google Scholar 

  • Slavin J. L. and Lloyd B. 2012 Health benefits of fruits and vegetables. Adv. Nut. 3, 506–516.

    Article  CAS  Google Scholar 

  • Sleper J. A. and Bernardo R. 2016 Recombination and genetic variance among maize doubled haploids induced from F-1 and F-2 plants. Theor. Appl. Genet. 129, 2429–2436.

    Article  CAS  PubMed  Google Scholar 

  • Soltis D. E. and Soltis P. S. 1999 Polyploidy: recurrent formation and genome evolution. Trends Ecol. Evol. 14, 348–352.

    Article  CAS  PubMed  Google Scholar 

  • Stadlmeier M., Hartl L. and Mohler V. 2018 Usefulness of a multiparent advanced generation intercross population with a greatly reduced mating design for genetic studies in winter Wheat. Front. Plant Sci. 9, 1825–1825.

    Article  PubMed  PubMed Central  Google Scholar 

  • Strobbe S., De Lepeleire J. and Van Der Straeten D. 2018 From in planta function to vitamin-rich food crops: the ace of biofortification. Front. Plant Sci. 9, 1862.

    Article  PubMed  PubMed Central  Google Scholar 

  • Sugita T., Semi Y., Sawada H., Utoyama Y., Hosomi Y., Yoshimoto E. et al. 2013 Development of simple sequence repeat markers and construction of a high-density linkage map of Capsicum annuum. Mol. Breed. 31, 909–920.

    Article  CAS  Google Scholar 

  • Sun X.-R., Liu L., Zhi X.-N., Bai J.-R., Cui Y.-N., Shu J.-S. et al. 2019 Genetic analysis of tomato internode length via mixed major gene plus polygene inheritance model. Sci. Hortic. 246, 759–764.

    Article  Google Scholar 

  • Sun X., Luo S., Luo L., Wang X., Chen X., Lu Y. et al. 2018 Genetic analysis of Chinese cabbage reveals correlation between rosette leaf and leafy head variation. Front. Plant Sci. 9, 1455.

    Article  PubMed  PubMed Central  Google Scholar 

  • Swarm S. A., Sun L., Wang X., Wang W., Brown P. J., Ma J. et al. 2019 Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations. Theor. Appl. Genet. 135,1195–1209.

    Article  CAS  Google Scholar 

  • Szała L., Cegielska-Taras T., Adamska E. and Kaczmarek Z. 2018 Assessment of genetic effects on important breeding traits in reciprocal DH populations of winter oilseed rape (Brassica napus L.). J. Integr. Agri. 17, 76–85.

    Article  Google Scholar 

  • Taiz L. 2013 Agriculture, plant physiology, and human population growth: past, present, and future. Theor. Exp. Plant Phys. 25, 167–181.

    Google Scholar 

  • Takuno S., Terauchi R. and Innan H. 2012 The Power of QTL mapping with RILs. PLoS One 7, 46545.

    Article  CAS  Google Scholar 

  • Tanhuanpaa P., Kalendar R., Schulman A. H. and Kiviharju E. 2008 The first doubled haploid linkage map for cultivated oat. Genome 51, 560–569.

    Article  CAS  PubMed  Google Scholar 

  • Thakur H., Jindal S. K., Sharma A. and Dhaliwal M. S. 2019 A. monogenic dominant resistance for leaf curl virus disease in chilli pepper (Capsicum annuum L.). Crop Prot. 116, 115–120.

    Article  Google Scholar 

  • Toppino L., Barchi L., Lo Scalzo R., Palazzolo E., Francese G. and Fibiani M. et al. 2016 Mapping quantitative trait loci affecting biochemical and morphological fruit properties in eggplant (Solanum melongena L.). Front. Plant Sci. 7, article ID 256.

  • Torkamaneh D., Boyle B. and Belzile F. 2018 Efficient genome-wide genotyping strategies and data integration in crop plants. Theor. Appl. Genet. 131, 499–511.

    Article  CAS  PubMed  Google Scholar 

  • Turcotte M. M., Araki H., Karp D. S., Poveda K. and Whitehead S. R. 2017 The eco-evolutionary impacts of domestication and agricultural practices on wild species. Philos. Trans R. Soc. London, B Biol. Sci. 372, pii: 20160033.

    Article  Google Scholar 

  • Vallarino J. G., Pott D. M., Cruz-Rus E., Miranda L., Medina-Minguez J. J., Valpuesta V. et al. 2019 Identification of quantitative trait loci and candidate genes for primary metabolite content in strawberry fruit. Hortic. Res. 6, 4.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • van Berloo R. and Stam P. 1998 Marker-assisted selection in autogamous RIL populations: a simulation study. Theor. Appl. Genet. 96, 147–154.

    Article  Google Scholar 

  • van de Wouw M., Kik C., van Hintum T., van Treuren R. and Visser B. 2010 Genetic erosion in crops: concept, research results and challenges. Plant Genet. Resour. C 8, 1–15.

    Article  Google Scholar 

  • Varshney R. K., Terauchi R. and McCouch S. R. 2014 Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol. 12, e1001883.

    Article  PubMed  PubMed Central  Google Scholar 

  • Velmurugan J., Milbourne D., Connolly V., Heslop-Harrison J. S., Anhalt U. C. M., Lynch M. B. et al. 2018 An immortalized genetic mapping population for perennial ryegrass: a resource for phenotyping and complex trait mapping. Front. Plant Sci. 9, 717.

    Article  PubMed  PubMed Central  Google Scholar 

  • Wada T., Oku K., Nagano S., Isobe S., Suzuki H., Mori M. et al. 2017 Development and characterization of a strawberry MAGIC population derived from crosses with six strawberry cultivars. Breed. Sci. 67, 370–381.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wahid A., Gelani S., Ashraf M. and Foolad M. R. 2007 Heat tolerance in plants: an overview. Environ. Exp. Bot. 61, 199–223.

    Article  Google Scholar 

  • Wang C., Li H., Li Y., Meng Q., Xie F., Xu Y et al. 2019 Genetic characterization and fine mapping BrCER4 in involved cuticular wax formation in purple cai-tai (Brassica rapa L. var. purpurea). Mol. Breed. 39, 12.

    Article  CAS  Google Scholar 

  • Wang P. Y., Wang L. R., Guo J. J., Yang W. C. and Shen H. L. 2016 Molecular mapping of a gene conferring resistance to Phytophthora capsici Leonian race 2 in pepper line PI201234 (Capsicum annuum L.). Mol. Breed. 36, 66.

    Article  CAS  Google Scholar 

  • Wang Y., Zhou Q., Zhu G., Wang S., Ma Y., Miao H. et al. 2018 Genetic analysis and identification of a candidate gene associated with in vitro regeneration ability of cucumber. Theor. Appl. Genet. 131, 2663–2675.

    Article  CAS  PubMed  Google Scholar 

  • Wei Y., Li F., Zhang S., Zhang S., Zhang H. and Sun R. 2018 Characterization of ınterspecific hybrids between flowering Chinese cabbage and Chinese kale. Agronomy 8, 258.

    Article  Google Scholar 

  • Welsh C. E. and McMillan L. 2012 Accelerating the inbreeding of multi-parental recombinant inbred lines generated by sibling matings. Genes Genomes Genet. 2, 191–198.

    Google Scholar 

  • Whitlock M. C and Guillaume F. 2009 Testing for spatially divergent selection: comparing Q(ST) to F-ST. Genetics 183, 1055–1063.

    Article  PubMed  PubMed Central  Google Scholar 

  • Win K. T., Zhang C., Silva R. R., Lee J. H., Kim Y.-C. and Lee S. 2019 Identification of quantitative trait loci governing subgynoecy in cucumber. Theor. Appl. Genet. 132, 1505–1521.

    Article  CAS  PubMed  Google Scholar 

  • Win K. T., Zhang C., Song K., Lee J. H. and Lee S. 2015 Development and characterization of a co-dominant molecular marker via sequence analysis of a genomic region containing the Female (F) locus in cucumber (Cucumis sativus L.). Mol. Breed. 35, 229–238.

    Article  CAS  Google Scholar 

  • Wright S. I. 2005 The effects of artificial selection on the maize genome. Science 310, 54–54.

    Article  Google Scholar 

  • Wu X., Li G., Wang B., Hu Y., Wu X., Wang Y et al. 2018 Fine mapping Ruv2, a new rust resistance gene in cowpea (Vigna unguiculata), to a 193-kb region enriched with NBS-type genes. Theor. Appl. Genet. 131, 2709–2718.

    Article  CAS  PubMed  Google Scholar 

  • Xia N., Wu D. P., Zhan Y. H., Liu Y., Sun M. Y., Zhao X. et al. 2017 Dissection of genetic architecture for oil content in soybean seed using two backcross populations. Plant Breed. 136, 365–371.

    Article  CAS  Google Scholar 

  • Xiao D., Shen H.-R., Zhao J.-J., Wei Y.-P., Liu D.-R., Hou X.-L. et al. 2019 Genetic dissection of flowering time in Brassica rapa responses to temperature and photoperiod. Plant Sci. 280, 110–119.

    Article  CAS  PubMed  Google Scholar 

  • Xu Y., Guo S. R., Shu S., Ren Y. and Sun J. 2017 Construction of a genetic linkage map of rootstock-used pumpkin using SSR markers and QTL analysis for cold tolerance. Sci. Hortic. 220, 107–113.

    Article  CAS  Google Scholar 

  • Yan G. J., Liu H., Wang H. B., Lu Z. Y., Wang Y. X., Mullan D. et al. 2017 Accelerated generation of selfed pure Lline plants for gene identification and Crop Breeding. Front. Plant Sci. 8, 1786.

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang H. Y. and Zhou C. 1982 In vitro induction of haploid plants from unpollinated ovaries and ovules. Theor. Appl. Genet. 63, 97–104.

    Article  CAS  PubMed  Google Scholar 

  • Yang S., Chen S., Zhang K., Li L., Yin Y., Gill R. A. et al. 2018 A high-density genetic map of an Allohexaploid brassica doubled haploid population reveals quantitative trait loci for pollen viability and fertility. Front. Plant Sci. 9, 1161.

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang Y., Lv H. and Liao H. 2019 Identification and mapping of two independent recessive loci for the root hairless mutant phenotype in soybean. Theor. Appl. Genet. 132, 301– 312.

    Article  CAS  PubMed  Google Scholar 

  • Yano M., Harushima Y., Nagamura Y., Kurata N., Minobe Y. and Sasaki T. 1997 Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map. Theor. Appl. Genet. 95, 1025– 1032.

    Article  CAS  Google Scholar 

  • Yu H. F., Wang J. S., Zhao Z. Q., Sheng X. G., Shen Y. S., Branca F. et al. 2019 Construction of a high-density genetic map and identification of loci related to hollow stem trait in broccoli (Brassic oleracea L. italica). Front. Plant Sci. 10, 00045.

    Article  Google Scholar 

  • Yu J. M., Holland J. B., McMullen M. D. and Buckler E. S. 2008 Genetic design and statistical power of nested association mapping in maize. Genetics 178, 539–551.

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang M., Montooth K. L., Wells M. T., Clark A. G. and Zhang D. 2005 Mapping multiple quantitative trait loci by Bayesian classification. Genetics 169, 2305–2318.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang S., Yu H., Wang K., Zheng Z., Liu L., Xu M. et al. 2018 Detection of major loci associated with the variation of 18 important agronomic traits between Solanum pimpinellifolium and cultivated tomatoes. The Plant J. 95, 312–323.

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y.-M. 2012 F2 Designs for QTL analysis. In Quantitative trait loci (QTL): methods and protocols (ed. S. A. Rifkin), pp. 17–29. Humana Press, Totowa.

    Chapter  Google Scholar 

  • Zhang Y. M. and Xu S. 2004 Mapping quantitative trait loci in F2 incorporating phenotypes of F3 progeny. Genetics 166, 1981–1993.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao B., Wang B., Li Z., Guo T., Zhao J. and Guan Z. et al. 2019 Identification and characterization of a new dwarf locus DS-4 encoding an Aux/IAA7 protein in Brassica napus. Theor. Appl. Genet. 132, 1435–1449.

    Article  CAS  PubMed  Google Scholar 

  • Zhao Z. D., Gu H. H., Sheng X. G., Yu H. F., Wang J. S., Huang L. et al. 2016 Genome-wide single-nucleotide polymorphisms discovery and high-density genetic map construction in cauliflower using specific-locus amplified fragment sequencing. Front. Plant Sci. 7, 334.

    PubMed  PubMed Central  Google Scholar 

  • Zhong Y. J., Zhou Y. Y., Li J. X., Yu T., Wu T. Q., Luo J. N. et al. 2017 A high-density linkage map and QTL mapping of fruit-related traits in pumpkin (Cucurbita moschata Duch). Sci. Rep. 7, 12785.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhu C., Huang J and Zhang Y. M. 2007 Mapping binary trait loci in the F-2 : 3 design. J. Hered. 98, 337–344.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Faculty of Agriculture, Department of Field Crops and Horticulture, Kyrgyz-Turkish Manas University, Bishkek, 720038, Kyrgyzstan

    Hasan Can & Mustafa Paksoy

  2. Applied Science School of Kadirli, Department of Organic Farming Management, Osmaniye Korkut Ata University, Osmaniye, 80000, Turkey

    Unal Kal

  3. Faculty of Science and Arts, Department of Biology, Marmara University, Goztepe, 34722, Istanbul, Turkey

    Ibrahim Ilker Ozyigit

  4. Faculty of Science, Department of Biology, Kyrgyz-Turkish Manas University, Bishkek, 720038, Kyrgyzstan

    Ibrahim Ilker Ozyigit

  5. Faculty of Agriculture, Department of Horticulture, Selcuk University, Konya, 42130, Turkey

    Mustafa Paksoy & Onder Turkmen

Authors
  1. Hasan Can
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Unal Kal
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ibrahim Ilker Ozyigit
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mustafa Paksoy
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Onder Turkmen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Hasan Can or Onder Turkmen.

Additional information

Corresponding Editor: Manoj Prasad

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Can, H., Kal, U., Ozyigit, I.I. et al. Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective. J Genet 98, 86 (2019). https://doi.org/10.1007/s12041-019-1129-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12041-019-1129-7

Keywords

Search

Navigation