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Molecular Breeding and Marker-Assisted Selection for Crop Improvement

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Plant Genomics for Sustainable Agriculture

Abstract

In an era of speedily increasing population and unpredictable incidence of climate changes, enhancing agricultural productivity has imposed a big challenge to the crop scientists. The situation becomes graver with the continuously shrinking land resources. To cope up with such an alarming situation, it will be quite beneficial to intervene the recent modern tools of genomics like molecular breeding and marker-assisted selection for crop improvement. Marker-assisted breeding involving trait introgression for biotic and abiotic resistance, breaking the genetic plateau and quality improvement will require a prior attention. In this chapter, we present an outline of the conventional breeding techniques, molecular breeding involving marker-assisted selection/breeding, DNA markers and mapping populations that have massive potential to perk up the effectiveness and accuracy of conventional plant breeding through marker-assisted selection (MAS), advantages of marker-assisted selection and its commonly used applications in plant breeding. Consideration is also given to genotyping methodologies and exploitation of genetic diversity. Finally, the approaches to study genotype-phenotype associations like QTL mapping, GWAS/Association mapping, transcriptomics and other techniques will also be discussed. Achieving a significant impact on crop improvement by MAS represents the great challenge as well as opportunity for agricultural scientists. The objective of this chapter is to present and describe the methods of molecular breeding and their genetic underpinnings.

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References

  • Acquaah G (2012) Principles of plant genetics and breeding. Wiley-Blackwell, Oxford

    Book  Google Scholar 

  • Ahmadi N, Albar L, Pressoir G, Pinel A, Fargette D, Ghesquière A (2001) Genetic basis and mapping of the resistance to rice yellow mottle virus. III. Analysis of QTL efficiency in introgressed progenies confirmed the hypothesis of complementary epistasis between two resistance QTLs. Theor Appl Genet 103:1084–1092

    Article  CAS  Google Scholar 

  • Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S, Uszynski G, Mohler V, Lehmensiek A, Kuchel H, Hayden MJ (2006) Diversity arrays technology (DArt) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420

    Article  CAS  PubMed  Google Scholar 

  • Allard RW (1960) Principles of plant breeding. Wiley, New York

    Google Scholar 

  • Babu R, Nair S, Prasanna BM, Gupta HS (2004) Integrating marker-assisted selection in crop breeding – prospects and challenges. Curr Sci 87:607–619

    CAS  Google Scholar 

  • Babu RSK, Nair A, Kumar S, Venkatesh JC, Sekhar NN, Singh G, Srinivasan HS, Gupta (2005). Two-generation marker-aided backcrossing for rapid conversion of normal maize lines to quality protein maize (QPM). Theor Appl Genet 111:888-897

    Google Scholar 

  • Banerjee S, Yandell BS, Yi N (2008) Bayesian quantitative trait loci mapping for multiple traits. Genetics 179:2275–2289

    Article  PubMed  PubMed Central  Google Scholar 

  • Belicuas PR, Guimaraes CT, Paiva LV, Duarte JM, Maluf WR, Paiva E (2007) Androgenetic Haploids and SSR markers as tools for the development of tropical maize hybrids. Euphytica 156(1–2):95–102

    Article  CAS  Google Scholar 

  • Bernacchi D-T, Beck-Bunn D, Emmatty Y, Eshed S, Inai J, Lopez V, Petiard H, Sayama J, Uhlig D, Zamir SD, Tanksley S (1998) Advanced backcross QTL analysis of tomato: II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild Qtl-alleles derived from Lycopersicon hirsutum and L.pimpinellifolium. Theor Appl Genet 97:170–180

    Article  CAS  Google Scholar 

  • Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last twenty years. Crop Sci 48:1649–1664

    Article  Google Scholar 

  • Bernardo R, Charcosset A (2006) Usefulness of gene information in marker assisted recurrent selection: a simulation appraisal. Crop Sci 46(2):614–621

    Article  Google Scholar 

  • Bernardo A, Wang SST, Amand P, Bai G (2015) Using next generation sequencing for multiplexed trait-linked markers in wheat. PLoS One 10(12):e0143890

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Borlaug NE, Dowswell CR (2005) Feeding a world of ten billion people a 21st century challenge. In: Tuberosa R, Phillips RL, Gale M (eds) Proceedings of the international congress in the wake of the double helix: from the green revolution to the gene revolution. 27–31 May 2003. Bologna Italy Avenue Media, Bologna, pp 3–23

    Google Scholar 

  • Bouchez A, Hospital F, Causse M et al (2002) Marker assisted introgression of favorable alleles at quantitative trait loci between maize elite lines. Genetics 162:1945–1959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE (2005a) The gene for fragrance in rice. Plant Biotech J 3:363–370

    Article  CAS  Google Scholar 

  • Bradbury LMT, Henry RJ, Jin Q, Reinke RF, Waters DLE (2005b) A perfect marker for fragrance genotyping in rice. Mol Breeding 16:279–283

    Article  CAS  Google Scholar 

  • Brennan JP, Martin PJ (2007) Returns to investment in new breeding technologies. Euphytica 157:337–349

    Article  Google Scholar 

  • Brinez B, Blair MW, Kilian A, Carbonell SAM, Chiorato AF, Rubiano LB (2012) A Whole genome dart assay to assess germplasm collection diversity in common beans. Mol Breed 30:181–193

    Article  CAS  Google Scholar 

  • Castro AJ, Capettini FLAVIO, Corey AE, Filichkina T, Hayes PM, Kleinhofs ANDRIS, Kudrna D, Richardson K, Sandoval-Islas S, Rossi C, Vivar H (2003) Mapping and pyramiding of qualitative and quantitative resistance to stripe rust in barley. Theor Appl Genet 107:922–930

    Article  CAS  PubMed  Google Scholar 

  • Collard BCY, Mackill DJ (2007) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 363(1491):557–572

    Article  PubMed Central  CAS  Google Scholar 

  • Collard BC, Mackill DJ (2008a) Marker assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc B 363:557–572

    Article  CAS  PubMed  Google Scholar 

  • Collard BCY, Mackill DJ (2008b) Marker-assisted selection : an approach for precision plant breeding in the twenty-first century. PhilosTrans R SocLond B Biol Sci 363:557–572

    Article  CAS  Google Scholar 

  • Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196

    Article  CAS  Google Scholar 

  • Concibido VC, La Vallee B, Mclaird P, Pineda N, Meyer J, Hummel L, Yang J, Wu K, Delannay X (2003) Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars. Theor Appl Genet 106:575–582

    Article  CAS  PubMed  Google Scholar 

  • Datta K, Baisakh TN, Tu KMJ, Datta S (2002) Pyramiding transgenes for multiple resistance in rice against bacterial blight, yellow stem borer and sheath blight. Theor Appl Genet 106:1–8

    Article  CAS  PubMed  Google Scholar 

  • Dhingani RM, Umrania VV, Tomar RS, Parakhia MV, Golakiya B (2015) Introduction to Qtl mapping in plants. Ann Plant Sci 4(04):1072–1079

    Google Scholar 

  • Dwivedi SL, Crouch JH, Mackill DJ, Xu Y, Blair MW, Ragot M, Upadhyaya HD, Oritiz R (2007) The molecularization of public sector crop breeding: progress, problems and prospects. Adv Agron 95:163–318

    Article  CAS  Google Scholar 

  • Eathington SR, Crosbie TM, Edwards MD, Reiter RS, Bull JK (2007) Molecular markers in a commercial breeding program. Crop Sci 47(Suppl. 3):S154–S163

    Article  Google Scholar 

  • Francia E, Tacconi G, Crosatti C, Barabaschi D, Bulgarelli D, Dall’Aglio E, Valè G (2005) Marker assisted selection in crop plants. Plant Cell Tissue Org 82(3):317–342

    Article  CAS  Google Scholar 

  • Fulton TM, Bucheli P, Voirol E, Lopez J, Peetiard V, Tanksley SD (2002) Quantitative trait loci (QTL) affecting sugars, organic acids and other biochemical properties possibly contributing to flavor, identified in four advanced backcross populations of tomato. Euphytica 127:163–177

    Article  CAS  Google Scholar 

  • George ML, Prasanna BM, Rathore RS, Setty TAS, Kasim F, Azrai M, Vasal S, Balla O, Hautea D, Canama A, Regalado E (2003) Identification of QTLs conferring resistance to downy mildews of maize in Asia. Theor Appl Genet 107(3):544–551

    Article  CAS  PubMed  Google Scholar 

  • Gopalakrishnan S, Sharma RK, Anand Rajkumar K, Joseph M, Singh VP, Singh AK, Bhat KV, Singh NK, Mohapatra T (2008) Integrating marker assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice. Plant Breed 127:131–139

    Article  CAS  Google Scholar 

  • Grzebelus D, Iorizzo M, Senalik D, Ellison S, Cavagnaro P, Macko-Podgorni A, Heller-Uszynska K, Kilian A, Nothnagel T, Allender C, Simon PW (2014) Diversity, genetic mapping and signatures of domestication in the carrot (Daucus carota L.) genome, As revealed by diversity arrays technology (Dart) markers. Mol Breed 33:625–637

    Article  CAS  PubMed  Google Scholar 

  • Guo H, Mendrikahy JN, Xie L, Deng J, Lu Z, Wu J, Li X, Shahid MQ, Liu X (2017) Transcriptome analysis of neo-tetraploid rice reveals specific differential gene expressions associated with fertility and heterosis. Sci Rep 7:40139

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gupta PK, Kulwal PL, Jaiswal V (2014) Association mapping in crop plants: opportunities and challenges. In: Friedmann T, Dunlap J, Goodwin S (eds) Advances in genetics, vol 85. Academic Elsevier, Waltham, MA, USA, pp 109–148

    Google Scholar 

  • Hackett CA (2002) Statistical methods for Qtl mapping in cereals. Plant Mol Biol 48(5–6):585–599

    Article  CAS  PubMed  Google Scholar 

  • Haley CS, Andersson LE (1997) Linkage mapping of quantitative trait loci in plants and animals. In: Dear PH (ed) Genome mapping: a practical approach. IRL Press, Oxford, pp 49–71

    Google Scholar 

  • Hittalmani S, Parco A, Mew TV, Zeigler RS, Huang N (2000) Fine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in rice. Theor Appl Genet 100:1121–1128

    Article  CAS  Google Scholar 

  • Hospital F, Charcosset A (1997) Marker-assisted introgression of quantitative trait loci. Genetics 147:1469–1485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang N, Angeles ER, Domingo J, Magpantay G, Singh S, Zhang G, Kumaravadivel N, Bennett J, Khush GS (1997) Pyramiding of bacterial blight resistance genes in rice: marker-assisted selection using RFLP and PCR. Theor Appl Genet 95(3):313–320

    Article  CAS  Google Scholar 

  • Ingvarsson PK, Street NR (2011) Association genetics of complex traits in plants. New Phytol 189:909–922

    Article  PubMed  Google Scholar 

  • Ishii T, Yonezawa K (2007) Optimization of the marker based procedures for pyramiding genes from multiple donor lines: I. Schedule of crossing between the donor lines. Crop Sci 47:537–546

    Article  Google Scholar 

  • Islam MN, Molla M, Rohman MM, Hasanuzzaman M, Islam SMN, Rahman L (2012) DNA fingerprinting and genotyping of cotton varieties using SSR markers. Not Bot Horti Agrobo 40:261–265

    Article  CAS  Google Scholar 

  • Jain HK, Kharkwal MC (2004) Plant breeding Mendelian to molecular approaches. Springer, Dordrecht

    Google Scholar 

  • Jannink JL, Walsh B (2002) Association mapping in plant populations. In: Kang MS (ed) Quantitative genetics, genomics and plant breeding. CAB International, Oxford, pp 59–68

    Chapter  Google Scholar 

  • Jansen RC (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136:1447–1455

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jefferies SP, King BJ, Barr AR, Warner P, Logue SJ, Langridge P (2003) Marker-assisted backcross introgression of the Yd2 gene conferring resistance to barley yellow dwarf virus in barley. Plant Breed 122:52–56

    Article  CAS  Google Scholar 

  • Jiang GL (2013) Molecular markers and marker-assisted breeding in plants. In: Andersen SB (ed) Plant breeding from laboratories to fields. Rijeka Intech, pp 45–83

    Google Scholar 

  • Joseph M, Sharma RK, Anand Rajkumar K et al (2004) Combining bacterial blight resistance and Basmati quality characteristics by phenotypic and marker assisted selection in rice. Mol Breed 13:377–387

    Article  CAS  Google Scholar 

  • Kao CH, Zeng ZB, Teasdale RD (1999) Multiple interval mapping. Genetics 152:1203–1216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khush GS, Virmani SS (1996) Haploids in plant breeding. In: Jain SM, Sopory SK, Veilleux RE (eds) In vitro haploid production in higher plants, Current plant science and biotechnology in agriculture. Springer, Dordrecht, pp 11–33

    Chapter  Google Scholar 

  • Kraakman AT, Martinez F, Mussiraliev B, Van Eeuwijk FA, Niks RE (2006) Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Mol Breed 7(1):41–58

    Article  CAS  Google Scholar 

  • Kulshreshtha K, Parihar A, Parihar P (2020) Next generation based transcriptome analysis for nematode resistance in three different species of tomato (S. lycopersicum, S. habrochaites & S. arcanum). Plant Gene 24:100255

    Article  CAS  Google Scholar 

  • Kunzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154(1):397–412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lande R, Thompson R (1990) Efficiency of marker assisted selection in the improvement of quantitative traits. Genetics 124:743–756

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lawson DM, Lunde CF, Mutschler MA (1997) Marker assisted transfer of acylsugar-mediated resistance from the wild tomato, Lycopersicon pennellii to the cultivated tomato, Lycopersicon esculentum. Mol Breed 3:307–317

    Article  CAS  Google Scholar 

  • Lecomte L, Duffe P, Buret M, Servin B, Causse M (2004) Marker-assisted introgression of five QTLs controlling fruit quality traits into three tomato lines revealed interactions between QTLs and genetic backgrounds. Theor Appl Genet 109:658–668

    Article  CAS  PubMed  Google Scholar 

  • Leng PF, Lübberstedt T, Xu ML (2017) Genomics assisted breeding – a revolutionary strategy for crop improvement. J Integr Agric 16(12):2674–2685

    Article  Google Scholar 

  • Li YH, Xiao H, Zhang CQ, Hu GC (1999) Genetic variation of main parents of hybrid rice in china was revealed with simple sequence repeat markers. Zhiwuxue Tongbao 41:1061–1066

    CAS  Google Scholar 

  • Li X, Shahid MQ, Xia J (2017) Analysis of small RNAs revealed differential expressions during pollen and embryo sac development in auto tetraploid rice. BMC Genomics 18(1):129

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liu J, Liu D, Tao W, Li W, Wang S, Chen P, Cheng S, Gao D (2000) Molecular marker-facilitated pyramiding of different genes for powdery mildew resistance in wheat. Plant Breed 119:21–24

    Article  CAS  Google Scholar 

  • Luo Y, Sangha JS, Wang S, Li Z, YangJ YZ (2012) Marker assisted breeding of Xa4, Xa21 And Xa27. In the restorer lines of hybrid rice for broad-spectrum and enhanced disease resistance to bacterial blight. Mol Breed 30(4):1601–1610

    Article  CAS  Google Scholar 

  • Mariya ZS, Jadeja GC, Akarsh P, Ankita P (2017) Comparative analysis for seed protein profiling and SSR markers in Rice cultivars (Oryza sativa L.) Res. J Biotechnol 12(5):12–19

    Google Scholar 

  • Melchinger AE, Winter M, Mi X, Piepho HP, Schipprack W, Mirdita V (2015) Controlling misclassification rates in identification of haploid seeds from induction crosses in maize with high-oil inducers. Crop Sci 55(3):1076–1086

    Article  Google Scholar 

  • Min J, Chunyu Z, Khalid H, Nan L, Quan S, Qing M, Suwen W, Feng L (2012) Pyramiding resistance genes to northern leaf blight and head smut in maize. Int J Agric Biol 14:430–434

    Google Scholar 

  • Muthusamy V, Hossain F, Thirunavukkarasu N, Choudhary M, Saha S, Bhat JS, Prasanna BM, Gupta HS (2014) Development of β-carotene rich maize hybrids through marker assisted introgression of β-carotene hydroxylase allele. PLoS One 9:e113583. https://doi.org/10.1371/journal.pone.0113583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Naeem M, Ghouri F, Shahid MQ, Iqbal M, Baloch FS, Chen L, Allah S, Babar M, Rana M (2015) Genetic diversity in mutated and non-mutated rice varieties. Genet Mol Res 14(4):17109–17123

    Article  CAS  PubMed  Google Scholar 

  • Nawaz MA, Baloch FS, Rehman HM, Le B, Akther F, Yang SH, Gyuhwa C (2016) Development of a competent and trouble free DNA isolation protocol or downstream genetic analysis in glycine species. Turk J Agri Food Sci Tech 4(8):700–705

    Google Scholar 

  • Neeraja C, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BC, Septiningsih EM, Vergara G, Sanchez D, Xu K, Ismail AM, Mackill DJ (2007) A marker assisted backcross approach for developing submergence-tolerance rice cultivars. Theor Appl Genet 115:767–776

    Article  CAS  PubMed  Google Scholar 

  • Nelson RR (1978) Genetics of horizontal resistance to plant diseases. Annu Rev Phytopathol 16:359–378

    Article  Google Scholar 

  • Ogbonnaya FC, Subrahmanyam NC, Moullet O, De Majnik J, Eagles HA, Brown JS, Eastwood RF, Kollmorgen J, Appels R, Lagudah ES (2001) Diagnostic DNA markers for cereal cyst nematode resistance in bread wheat. Crop Pasture Sci 52(12):1367–1374

    Article  CAS  Google Scholar 

  • Okada Y, Kanatani R, Arai S, Ito K (2004) Interaction between barley yellow mosaic disease-resistance genes Rym1 And Rym5, In the response to BaYMVstrains. Breed Sci 54:319–325

    Article  CAS  Google Scholar 

  • Parihar A, Pathak AR, Parihar P (2010) Identification of RAPD marker for the White Backed Plant Hopper (WBPH) resistant gene in rice. Afr J Biotechnol 9(10):1423–1426

    Article  CAS  Google Scholar 

  • Randhawa HS, Mutti JS, Kidwell K, Morris CF, Chen X, Gill KS (2009) Rapid and targeted introgression of genes into popular wheat cultivars using marker-assisted background selection. PLoS One 4:e5752. https://doi.org/10.1371/journal.pone.0005752

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ribaut JM, de Vicente MC, Delannay X (2010) Molecular breeding in developing countries: challenges and perspectives. Curr Opin Plant Biol 13:213–218

    Article  PubMed  Google Scholar 

  • Sanchez AC, Brar DS, Huang N, Li Z, Khush GS (2000) Sequence tagged site marker-assisted selection for three bacterial blight resistance genes in rice. Crop Sci 40:792–797

    Article  CAS  Google Scholar 

  • Satgopan JM, Yandell BS, Newton MA, Osborn TC (1996) A Bayesian approach to detect quantitative trait locus Markov chain Monte Carlo. Genetics 144:805–816

    Article  Google Scholar 

  • Schmierer DA, Kandemir N, Kudrna DA, Jones BL, Ullrich SE, Kleinhofs A (2004) Molecular marker-assisted selection for enhanced yield in malting Barley. Mol Breed 14:463–473

    Article  CAS  Google Scholar 

  • Sebolt AM, Shoemaker RC, Diers BW (2000) Analysis of a quantitative trait locus allele from wild soybean that increases seed protein concentration in soybean. Crop Sci 40:1438–1444

    Article  CAS  Google Scholar 

  • Semagn K, Bjørnstad A, Ndjiondjop MN (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 2540:25–68

    Google Scholar 

  • Shahid MQ, Chen FY, Li HY, Wang SZ, Chen PF, Lin SQ, Liu XD, Lu YG (2013) Double-neutral genes, and for pollen fertility in rice to overcome × hybrid sterility. Crop Sci 53(1):164–176

    Article  CAS  Google Scholar 

  • Shen LB, Courtois B, McNally KL, Robin S, Li Z (2001) Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection. Theor Appl Genet 103:75–83

    Article  CAS  Google Scholar 

  • Simmonds NW (1993) Introgression and incorporation. Strategies for the use of crop genetic resources. Biol Rev 68(4):539–562

    Article  Google Scholar 

  • Singh BD (2012) Plant breeding, principles and methods, 9th edn. Kalyani Publishers, New Delhi

    Google Scholar 

  • Singh S (2015) Mapping population, marker-assisted plant breeding: principles and practices. Springer. https://doi.org/10.1007/978-81-322-2316-0

    Book  Google Scholar 

  • Singh N, Choudhury DR, Tiwari G, Singh AK, Kumar S, Srinivasan K, Tyagi RK, Sharma AD, Singh NK, Singh R (2016) Genetic diversity trend in Indian rice varieties: an analysis using SSR markers. BMC Genet 17:127

    Article  PubMed  PubMed Central  Google Scholar 

  • Soller M, Brody T (1976) On the power of experimental designs for the detection on linkage between marker loci and quantitative loci in crosses between inbred lines. Theor Appl Genet 47:35–39

    Article  CAS  PubMed  Google Scholar 

  • Steele KA, Price AH, Shahsidhar HE, Witcombe JR (2006) Marker assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety. Theor Appl Genet 112:208–221

    Article  CAS  PubMed  Google Scholar 

  • Stuber CW, Polacco M, Senior ML (1999) Synergy of empirical breeding, marker-assisted selection and genomics to increase crop yield potential. Crop Sci 39:1571–1583

    Article  Google Scholar 

  • Sundaram RM, Vishnupriya MR, Biradar SK, Laha GS, Reddy GA, Rani NS, Sarma NP, Sonti RV (2008) Marker assisted introgression of bacterial blight resistance in Samba Mahsuri, an elite Indica rice variety. Euphytica 160:411–422

    Article  Google Scholar 

  • Tang F, Tao Y, Zhao T, Wang G (2006) In vitro production of haploid and doubled haploid plants from pollinated ovaries of maize (Zea Mays). Plant Cell Tissue Organ Cult 84(2):233–237

    Article  Google Scholar 

  • Tanksley SD (1983) Molecular markers in plant breeding. Plant Mol Biol Rep 1:3–8

    Article  CAS  Google Scholar 

  • Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27(1):205–233

    Article  CAS  PubMed  Google Scholar 

  • Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203

    Article  CAS  PubMed  Google Scholar 

  • Tanksley SD, Young ND, Patterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Biotechnology 7:257–263

    CAS  Google Scholar 

  • Tiwari JK, SinghBP GJ, Poonam P, Patil VU (2013) Molecular characterization of the Indian andigena potato core collection using microsatellite markers. Afr J Biotechnol 12(10):1025–1033

    CAS  Google Scholar 

  • Walunjkar BC, Parihar A, Singh NK, Parmar LD (2015) Genetic diversity of wild and c.ultivated genotypes of pigeonpea through RAPD and SSR markers. J Environ Biol 36(2):461–466

    CAS  PubMed  Google Scholar 

  • Wang B, Chee PW (2010) Application of advanced backcross quantitative trait locus (Qtl) analysis in crop improvement. J Plant Breed Crop Sci 2:221–232

    CAS  Google Scholar 

  • Wang FG, Zhao JR, Guo JL, Liu LZ (2003) Series of research on establishing DNA fingerprinting pool of Chinese new maize cultivars in the establishment of a standard SSR system fitting for maize cultivars’ identification. Yumi Kexue 11:3–6

    CAS  Google Scholar 

  • Wang YH, Liu SJ, Ji SL, Zhang WW, Wang CM, Jiang L, Wan JM (2005) Fine mapping and Marker Assisted Selection (MAS) of a low glutelin content genein rice. Cell Res 15(8):622–630

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Shahid MQ, Ghouri F, Baloch FS, Wang Y, Huang H (2015) Evaluation of the geographical pattern of genetic diversity of glycine soja and glycine max based on four single copy nuclear gene loci: for conservation of soybean germplasm. Biochem Syst Ecol 62:229–235

    Article  CAS  Google Scholar 

  • Wang Y, Ghouri F, Shahid MQ, Naeem M, Baloch FS (2017) The genetic diversity and population structure of wild soybean evaluated by chloroplast and nuclear gene sequences. Biochem Syst Ecol 71:170–178

    Article  CAS  Google Scholar 

  • Wu JW, Hu CY, Shahid MQ, Guo HB, Zeng YX, Liu XD, Lu YG (2013) Analysis on genetic diversification and heterosis in autotetraploid rice. Springer Plus 2(1):439

    Article  PubMed  PubMed Central  Google Scholar 

  • Wu J, Shahid MQ, Chen L, Chen Z, Wang L, LiuX LY (2015) Polyploidy enhances f1pollen sterility loci interactions that increase meiosis abnormalities and pollen sterility in autotetraploid rice. Plant Physiol 169(4):2700–2717

    CAS  PubMed  PubMed Central  Google Scholar 

  • Xie F, He Z, Esguerra MQ, Qiu F, Ramanathan V (2014) Determination of heterotic groups for tropical Indica hybrid rice germplasm. Theor Appl Genet. https://doi.org/10.1007/s00122-013-2227-1

  • Xu Y (2010). Molecular plant breeding CAB International

    Google Scholar 

  • Young ND (1999) A cautiously optimistic vision for marker-assisted breeding. Mol Breed 5:505–510

    Article  Google Scholar 

  • Young ND, Tanksley SD (1989) RFLP analysis of the size of chromosomal segments retained around theTm-2 locus of tomato during backcross breeding. Theor Appl Genet 77:353–359

    Article  CAS  PubMed  Google Scholar 

  • You-Xin Y, Yan-Hong L, Jing-Fei T (2012) Wide-compatibility gene exploited by functional molecular markers and its effect on fertility of intersubspecific rice hybrids. Crop Sci 52(2):669–675

    Article  CAS  Google Scholar 

  • Yu J, Holland JB, McMullen MD et al (2008) Genetic design and statistical power of nested association. Genetics 178:539–551

    Article  PubMed  PubMed Central  Google Scholar 

  • Zeng Z-B (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang P, Zhong KM, Shahid Q, Tong H (2016a) Association analysis in rice: from application to utilization. Front Plant Sci 7:1202

    PubMed  PubMed Central  Google Scholar 

  • Zhang P, Zhong KH, Tong H, Shahid MQ, Li J (2016b) Association mapping for aluminum tolerance in a core collection of rice landraces. Front Plant Sci 7:1415

    PubMed  PubMed Central  Google Scholar 

  • Zhao X, Tan G, Xing Y, Wei L, Chao Q, Zuo W, Lübberstedt T, Xu M (2012) Marker-assisted introgression of qHSR1to improve maize resistance to head smut. Mol Breeding. https://doi.org/10.1007/s11032-011-9694-3

  • Zou F (2009) QTL mapping in intercross and backcross populations. In: DiPitrello K (ed) Cardiovascular genomics, methods and protocols. Humana Press (Springer Science + Business Media), LLC, New York, pp 157–173

    Chapter  Google Scholar 

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Parihar, A., Shiwani (2022). Molecular Breeding and Marker-Assisted Selection for Crop Improvement. In: Singh, R.L., Mondal, S., Parihar, A., Singh, P.K. (eds) Plant Genomics for Sustainable Agriculture. Springer, Singapore. https://doi.org/10.1007/978-981-16-6974-3_6

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