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Molecular breeding and the impacts of some important genes families on agronomic traits, a review

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Abstract

Gene identification and evolution and also their impacts on agronomical traits are important variations between related species which are often because of differences in the cumulative actions of multiple gene products. Understanding genetic variability for agronomic traits is important parameter of breeding programs for broadening the gene pool of different crops. The Short-Chain Dehydrogenase/Reductase (SDR) super-family is one of the largest known protein families and comprises thousands of members found in species ranging from bacteria to humans. SDR involvement has been demonstrated in a variety of primary and secondary metabolisms. Quantitative trait locus (QTL) mapping provides a starting point for dissecting complex traits into its component alleles which may help to quantify relative impacts of alleles on the traits and locates genomic regions responsible for marker-trait association, and provide a foundation of marker-assisted selection which expedites the breeding process given the proper estimation of position and the effects of QTLs. In this manuscript we have reviewed, molecular breeding and gene evolution and domestication in crops, and also survey some important reported genes which have notable impact on agronomical traits in various crops.

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References

  • Abbo S, Lev-Yadun S, Gopher A (2012) Plant domestication and crop evolution in the Near East: on events and processes. Crit Rev Plant Sci 31(3):241–257

    Google Scholar 

  • Abbo S, van-Oss RP, Gopher A, Saranga Y, Ofner I, Peleg Z (2014) Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes. Trends Plant Sci 19(6):351–360

    CAS  PubMed  Google Scholar 

  • Abbo S, Gopher A (2017) Near Eastern plant domestication: a history of thought. Trends Plant Sci 22(6):491–511

    CAS  PubMed  Google Scholar 

  • Abbo S, Gopher A, Lev-Yadun S (2017) The domestication of crop plants. Ency Appl Plant Sci (Second Edition) 3:50–54

    Google Scholar 

  • Adamski J, Jakob JF (2001) A guide to 17β-hydroxysteroid dehydrogenases. Mol Cell Endocrinol 171:1–4

    CAS  PubMed  Google Scholar 

  • Agrama HA (2006) Application of molecular markers in breeding for nitrogen use efficiency. J Crop Improv 15(2):175–211

    Google Scholar 

  • Ali MB (2015) Genetic linkage maps and homology study of backcross families of german faba bean (Vicia faba L.). J Crop Improv 29(4):474–490

    Google Scholar 

  • Allwright MR, Taylor G (2016) Molecular breeding for improved second generation bioenergy crops. Trends Plant Sci 21(1):43–54

    CAS  PubMed  Google Scholar 

  • Anderson JA, Vilgalys TP, Tung J (2020) Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation. Curr Opin Genet Dev 62:16–22

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ashikawa I, Abe F, Nakamura S (2013) DOG1-like genes in cereals: investigation of their function by means of ectopic expression in Arabidopsis. Plant Sci 208:1–9

    CAS  PubMed  Google Scholar 

  • Ashkani S, Rafii MY, Shabanimofrad M, Ghasemzadeh A, Ravanfar SA, Latif MA (2016) Molecular progress on the mapping and cloning of function genes for blast disease in rice (Oryza sativa L.): current status and future considerations. Crit Rev Biotechnol 36(2):353–367

    CAS  PubMed  Google Scholar 

  • Babb S, Muehlbauer GJ (2003) Genetic and morphological characterization of the barley uniculm2 (cul2) mutant. Theor Appl Genet 106:846–857

    CAS  PubMed  Google Scholar 

  • Baek M-H, Chung BY, Kim J-H, Wi SG, An BC, Kim J-S, Lee SS, Lee I-J (2008) Molecular cloning and characterization of the flavanone-3-hydroxylase gene from Korean black raspberry. J Hortic Sci Biotechnol 83(5):595–602

  • Bernardo R, Yu J (2007) Prospects for genomewide selection for quantitative traits in maize. Crop Sci 47:1082–1090

    Google Scholar 

  • Bhattacharya D, Qiu H, Lee J-M, Soon HS, Weber APM, Price DC (2018) When less is more: red algae as models for studying gene loss and genome evolution in eukaryotes. Crit Rev Plant Sci 37(1):81–99

    Google Scholar 

  • Bohra A, Mir RR, Jha R, Maurya AK, Varshney RK (2020) Chapter 9- Advances in genomics and molecular breeding for legume improvement. Adv Crop Improv Tech 2020:129–139

    Google Scholar 

  • Bouchez D, Hofte H (1998) Functional genomics in plants. Plant Physiol 118:725–732

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bouton JH (2007) Molecular breeding of switchgrass for use as a biofuel crop. Curr Opin Genet Dev 17(6):553–558

    CAS  PubMed  Google Scholar 

  • Brock A, Brandt W, Drager B (2008) The functional divergence of short-chain dehydrogenases involved in tropinone reduction. Plant J 54:388–401

    CAS  PubMed  Google Scholar 

  • Cao J, Li X, Lv Y (2017) Dynein light chain family genes in 15 plant species: identification, evolution and expression profiles. Plant Sci 254:70–81

    CAS  PubMed  Google Scholar 

  • Cardoso HG, Campos MD, Costa AR, Campos MC, Nothnagel T, Arnholdt-Schmitt A (2009) Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3. Physiol Plant 137:592–608

    CAS  Google Scholar 

  • Carrier G, Huang Y-F, Cunff LL, Fournier-Level A, Vialet S, Souqut J-M, Cheynier V, Terrier N, This P (2013) Selection of candidate genes for grape proanthocyanidin pathway by an integrative approach. Plant Physiol Biochem 72:87–95

    CAS  PubMed  Google Scholar 

  • Castren E, Kontkanen O (2002) Functional genomics in neuropsychiatric disorders and in neuropharmacology. Expert Opin Ther Targets 6(3):363–374

    PubMed  Google Scholar 

  • Cerda J, Bobe J, Babin PJ, Admon A, Lubzens E (2008) Functional genomics and proteomic approaches for the study of gamete formation and viability in farmed finish. Rev Fish Sci 16(Sup 1):56–72

    CAS  Google Scholar 

  • Chacon-Fuentes M, Bardehle L, Lizama M, Seguel I, Quiroz A (2019) Restoration of flavonolds and isoflavonoids in Ugni molinae subjected to a reciprocal transplant experiment in a domestication framework. Chem Ecol 35(2):115–127

    CAS  Google Scholar 

  • Chai Y, Zhao L, Liao Z, Sun X, Zuo K, Zhang L, Wang S, Tang K (2003) Molecular cloning of a potential Verticillium dahliae resistance gene SlVe1 with multi-site polyadenylation from Solanum licopersicoides. DNA Seq 14(5):375–384

    CAS  PubMed  Google Scholar 

  • Che G, Zhang X (2019) Molecular basis of cucumber fruit domestication. Curr Opin Plant Biol 47:38–46

    CAS  PubMed  Google Scholar 

  • Chen YH, Ruiz-Arocho J, von Wettberg EJB (2018) Crop domestication: anthropogenic effects on insect-plant interactions in agroecosystems. Curr Opin Insect Sci 29:56–63

    PubMed  Google Scholar 

  • Cheng W-H, Endo A, Zhou L, Penney J, Chen H-C, Arroyo A, Leon P, Nambara E, Asami T, Seo M, Koshiba T, Sheen J (2002) A unique short-chain dehydrogenase/reductase in Arabidopsis glucose signaling and abscisic acid biosynthesis and functions. Plant Cell 14:2723–2743

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chowrasia S, Panda AK, Rawal HC, Kaur H, Mondal TK (2018) Identification of jumonjiC domain containing gene family among the Oryza species and their expression analysis in FL478, a salt tolerant rice genotype. Plant Physiol Biochem 130:43–53

    CAS  PubMed  Google Scholar 

  • Clarke JW, Donoghue PCJ (2018) Whole-genome duplication and plant macroevolution. Trends Plant Sci 23(10):933–945

    Google Scholar 

  • Coelho CP, Huang P, Lee D-Y, Brutnell TP (2018) Making roots, shoots and seeds: IDD gene family diversification in plants. Trends Plant Sci 23(1):66–78

    CAS  PubMed  Google Scholar 

  • Cong B, Barrero LS, Tanksley SD (2008) Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat Genet 40:800–804

    CAS  PubMed  Google Scholar 

  • Costa A, Di Giacomo M, Massarelli I, De Palma M, Leone A, Grillo MS (2010) Isolation, characterization and expression of an elongation factor 1α gene in potato (Solanum tuberosum) cell cultures. Plant Biosyst 618–625

  • Dabbert T, Okagaki RJ, Cho S, Boddu J, Muehlbauer GJ (2009) The genetics of barley low-tillering mutants: absent lower laterals (als). Theor Appl Genet 118:1351–1360

    CAS  PubMed  Google Scholar 

  • Dabbert T, Okagaki RJ, Cho S, Heinen S, Boddu J, Muehlbauer GJ (2010) The genetic of barley low-tillering mutants: low number of tillers-1 (Int1). Theor Appl Genet 121:705–715

    CAS  PubMed  Google Scholar 

  • Di Gaspero G, Foria S (2015) Molecular grapevine breeding techniques. Grapevine Breeding Programs for the Wine Industry 2015:23–37

  • Dong Z, Alexander M, Chuck G (2019) Understanding grass domestication through maize mutants. Trends Genet 35(2):118–128

    CAS  PubMed  Google Scholar 

  • Dorn G, Hall J, Husken D, Lange J, Martin P, Natt F, Wishart WL, Weiler J (2003) A role for oligonucleotide-based RNA-knock down technologies in functional genomics. Necleosides, Necleotides Nucleic Acids 22:5–8

  • Duan P, Xu J, Zeng D, Zhang B, Geng M, Zhang G, Huang K, Huang L, Xu R, Ge S, Qian Q, Li Y (2017) Natural variation in the promoter of GSE5 contributes to grain size diversity in rice. Mol Plant 10:685–694

    CAS  PubMed  Google Scholar 

  • Dwivedi SL, Crouch JH, Nigam SN, Ferguson ME, Paterson AH (2003) Molecular breeding of groundnut for enhanced productivity and food security in the semi-arid tropics: opportunities and challenges. Adv Agron 80:153–221

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Ebert B, Kisiela M, Maser E (2016) Transcriptional regulation of human and murine short-chain dehydrogenase/reductases (SDRs)- an in silico approach. Drug Metab Rev 48(2):183–217

    PubMed  Google Scholar 

  • Eness J, Del Cardayre SB, Minshull J, Stemmer WPC (2001) Molecular breeding: the natural approach to protein design. Adv Protein Chem 55:261–292

    Google Scholar 

  • Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171

    CAS  PubMed  Google Scholar 

  • Fan Y, Guo H, Wei J, Zhang Y, Wu J, Zeng F (2020) Meiosis, the master driver of gene duplication in higher plants? Biochem Biophys Res Commun 514(3):756–758

    Google Scholar 

  • Fei J, Chai Y, Wang J, Lin J, Sun X, Sun C, Zuo K, Tang K (2004) cDNA cloning and characterization of the Ve homologue gene StVe from Solanum torvum Swartz. DNA Sequence 15(2):88–95

  • Feng L, Li G, He Z, Han W, Sun J, Huang F, Di J, Chen Y (2019) The ARF, GH3, and Aux/IAA gene families in castor bean (Ricinus communis L.): Genome-wide identification and expression profiles in high-stalk and dwarf strains. Ind Crops Prod 141:111804

    CAS  Google Scholar 

  • Feng D, Gao L, Zheng Y, Li D, Zhou P (2020) Molecular cloning and function characterization of a cytoplasmic fructose-1, 6-bisphosphate aldolase gene from coconut (Cocos nucifera L.). J Hortic Sci Biotechnol. https://doi.org/10.1080/14620316.2020.1749139

    Article  Google Scholar 

  • Ferreira MDG, Castro JA, Silva RJS, Micheli F (2019) HVA22 from citrus: a small gene family whose some members are involved in plant response to abiotic stress. Plant Physiol Biochem 142:395–404

    Google Scholar 

  • Fields S, Kohara Y, Lockhart DJ (1999) Functional genomics. Proc Natl Acad Sci 96:8825–8826

    CAS  PubMed  PubMed Central  Google Scholar 

  • Francki M, Appeles R (2002) Wheat functional genomics and engineering crop improvement. Genome Biol 3:1013.1-1013.5

  • Frary A, Nesbitt TC, Frary A, Grandillo S, van der Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB et al (2000) Fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88

    CAS  PubMed  Google Scholar 

  • Frenkel ZM, Trifonov EN (2012) Origin and evolution of genes and genomes. Crucial role of triplet expansions. J Biomol Struct Dyn 30(2):201–210

    CAS  PubMed  Google Scholar 

  • Fu Q, Zhang P, Tan L, Zhu Z, Ma D, Fu Y, Zhan X, Cai H, Sun C (2010) Analysis of QTLs for yield-related traits in Yuanjiang common wild rice (Oryza rufipogon Griff.). J Genet Genom 37(2):147–157

    CAS  Google Scholar 

  • Gao Y, Zhao H, Jin Y, Xu X, Han G-Z (2017) Extent and evolution of gene duplication in DNA viruses. Virus Res 240:161–165

    CAS  PubMed  Google Scholar 

  • Gebhardt C (2013) Bridging the gap between genome analysis and precision breeding in potato. Trends Genet 29(4):248–256

    CAS  PubMed  Google Scholar 

  • Gebre E, Hedden P, Kunert K, Schluter U (2013) Isolation, characterization, and expression of the rice sd-1 (GA20ox) gene ortholog in Eragrostis tef. J Improve 27(5):50–527

    Google Scholar 

  • Gepts P (2014) The contribution of genetic and genomic approaches to plant domestication studies. Curr Opin Plant Biol 18:51–59

    PubMed  Google Scholar 

  • Guindo D, Teme N, Vaksmann M, Doumbia M, Vilmus I, Guitton B, Sissoko A, Mestres C, Davrieux F, Fliedel G, Kouressy M, Courtois B, Rami J-F (2019) Quantitative trait loci for sorghum grain morphology and quality traits: toward breeding for a traditional food preparation of West-Africa. J Cereal Sci 85:256–272

    Google Scholar 

  • Gutterson NC (1993) Molecular breeding for color, flavor and fragrance. Sci Hortic 55(1–2):141–160

    CAS  Google Scholar 

  • Ha JH, Jang HA, Moon L-B, Baek KH, Choi GJ, Choi D, Cho HS, Kwon SY, Jeon J-H, Oh S-K, Kim H-S (2017) Nicotiana benthamiana Matrix Metalloprotease 1 (NMMP1) gene confers disease resistance to Phytophthora infestans in tobacco and potato plants. J Plant Physiol 218:189–195

  • Haley B, Roudnicky F (2020) Functional genomics for cancer drug target discovery. Cancer Cell 38(1):31–43

    CAS  PubMed  Google Scholar 

  • Harrison PW, Wright AE, Mank JE (2012) The evolution of gene expression and the transcriptome-phenotype relationship. Semin Cell Dev Biol 23(2):222–229

    CAS  PubMed  Google Scholar 

  • Hayes B, He J, Moen T, Bennewitz J (2006) Use of molecular markers to maximize diversity of founder populations for aquaculture breeding programs. Aquaculture 255(1–4):573–578

    CAS  Google Scholar 

  • Hoffmann F, Maser E (2007) Carbonyl reductases and pluripotent hydroxysteroid dehydrogenases of the short-chain dehydrogenase/reductase superfamily. Drug Metab Rev 39(1):87–144

    CAS  PubMed  Google Scholar 

  • Holtorf H, Guitton M-C, Reski R (2002) Plant functional genomics. Naturwissenschaften 89:235–249

    CAS  PubMed  Google Scholar 

  • Hu K, Cao J, Zhang J, Xia F, Ke Y, Zhang H, Xie W, Liu H, Cui Y, Cao Y, Sun X, Xiao J, Li X, Zhang Q, Wang S (2017) Improvement of multiple agronomic traits by a disease resistance gene via cell wall reinforcement. Nature Plants 17(3):17009

    Google Scholar 

  • Huang B, Liu X, Wang X, Pi Y, Zeng H, Lin J, Fei J, Sun X, Tan K (2005) Genomic cloning and characterization of a Pto-like gene SsPto-2 from Solanum surattense. DNA Seq 16(4):277–287

    CAS  PubMed  Google Scholar 

  • Huang K, Wang D, Duan P, Zhang B, Xu R, Li N, Li Y (2017) WIDE AND THICK GRAIN 1, which encodes an otubain-like protease with deubiquitination activity, influences grain size and shape in rice. Plant J 91:849–860

    CAS  PubMed  Google Scholar 

  • Huang J-F, Li L, Mao X-G, Wang J-Y, Liu H-M, Li C-N, Jing R-L (2020) dCAPS markers developed for nitrate transporter genes TaNRT2L12s associating with 1000-grain weight in wheat. J Integr Agric 19(6): 1543–1553

  • Housman G, Gilad Y (2020) Prime time for primate functional genomics. Curr Opin Genet Dev 62:1–7

    CAS  PubMed  PubMed Central  Google Scholar 

  • Huang J-J (2013) Knowledge diffusion models-perspectives of gene evolution and population dynamics. Knowl Manag Res Pract 11(3):313–322

    Google Scholar 

  • Huminiecki L, Horbanczuk J, Atanasov AG (2017) The functional genomics studies of curcumin. Semin Cancer Biol 46:107–118

    CAS  PubMed  Google Scholar 

  • Ishikawa S (2020) Mechanisms of cadmium accumulation in rice grains and molecular breeding for its reduction. Soil Sci Plant Nutr 66(1):28–33

    CAS  Google Scholar 

  • Jacob P, Avni A, Bendahmane A (2018) Translational research: Exploring and creating genetic diversity. Trends Plant Sci 23(1):42–52

    CAS  PubMed  Google Scholar 

  • Jain A, Roorkiwal M, Kale S, Garg V, Yadala R, Varshney RK (2019) InDel markers: An extended marker resource for molecular breeding in chickpea. PLoS ONE 14(3):e0213999

    CAS  PubMed  PubMed Central  Google Scholar 

  • Janila P, Pandey MK, Shasidhar Y, Variath M, Sriswathi M, Khera P, Manohar SS, Nagesh P, Vishwakarma MK, Mishra GP, Radhakrishnan T, Manivannan N, Dobariya KL, Vasanthi RP, Varshney RK (2016) Molecular breeding for introgression of fatty acid desaturase mutant alleles (ahFAD2A and ahFAD2B) enhances oil quality in high and low oil containing peanut genotypes. Plant Sci 242:203–213

    CAS  PubMed  Google Scholar 

  • Jares P (2006) DNA microarray applications in functional genomics. Ultrastruct Pathol 30(3):209–219

    PubMed  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

    CAS  Google Scholar 

  • Jia T, Bin Z, Shu-Ping L, Xiu-gen L, Bin W, Jiang L (2016) Cloning, localization and expression analysis of two fw2.2-like genes in small- and large-fruited pear species. J Integr Agric 15(2):282–294

    Google Scholar 

  • Jia S, Xiong Y, Ziao P, Wang X, Yao J (2019) OsNF-YC10, a seed preferentially expressed gene regulates grain width by affecting cell proliferation in rice. Plant Sci 280:219–227

    CAS  PubMed  Google Scholar 

  • Jiang Y, Cai Z, Xie W, Long T, Yu H, Zhang Q (2012) Rice functional genomics research: progress and implications for crop genetic improvement. Biotechnol Adv 30(5):1059–1070

    CAS  PubMed  Google Scholar 

  • Jiang L, Liu X, Xiong G, Liu H, Chen F, Wang L, Meng X, Liu G, Yu H, Yuan Y, Yi W, Zhao L, Ma H, He Y, Wu Z, Melcher K, Qian Q, Xu HE, Wang Y, Li J (2013) DWARF 53 acts as a repressor of strigolactone signaling in rice. Nature 504:401–405

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang W, Geng Y, Liu Y, Chen S, Cao S, Li W, Chen H, Ma D, Yin J (2020) Genome-wide identification and characterization of SRO gene family in wheat: molecular evolution and expression profiles during different stresses. Plant Physiol Biochem 154:590–611

    CAS  PubMed  Google Scholar 

  • Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42:541–544

    CAS  PubMed  Google Scholar 

  • Jin S, Nasim Z, Susila H, Ahn JH (2020) Evolution and functional diversification of Flowering Locus T/Terminal Flower 1 family genes in plants. Semin Cell Dev Biol. DOI:https://doi.org/10.1016/j.semcdb.2020.05.007

    Article  PubMed  Google Scholar 

  • Jones DM, Vandepoele K (2020) Identification and evolution of gene regulatory networks: insights from comparative studies in plants. Curr Opin Plant Biol 54:42–48

    CAS  PubMed  Google Scholar 

  • Jornvall H, Persson B, Krook M, Atrian S, Gonzalez-Duarte R, Jeffery J, Ghosh D (1995) Short-chain dehydrogenases/reductases (SDR). Biochemistry 34(18):6003–6013

    CAS  PubMed  Google Scholar 

  • Kallberg Y, Oppermann U, Jornvall H, Persson B (2002) Short-chain dehydrogenases/reductases (SDRs). Eur J Biochem 269(18):4409–4417

    CAS  PubMed  Google Scholar 

  • Kaushik S, Kaushik S, Sharma D (2019) Functional genomics. Ency Bioinform Comput Biol 2:118–133

    Google Scholar 

  • Keller B, Volkmann A, Wilckens T, Moeller G, Adamski J (2006) Bioinformatic identification and characterization of new members of short-chain dehydrogenase/reductase superfamily. Mol Cell Endocrinol 248(1–2):56–60

    CAS  PubMed  Google Scholar 

  • Khalil F, Yueyu X, Naiyan X, Di L, Tayyab M, Hengbo W, Islam W, Rauf S, Pinghua C (2018) Genome characterization of sugarcane yellow leaf virus with special reference to RNAi based molecular breeding. Microb Pathog 120:187–197

    CAS  PubMed  Google Scholar 

  • Khuman A, Arora S, Makkar H, Patel A, Chaudhary B (2020) Extensive intragenic divergences amongst ancient WRKY transcription factor gene family is largely associated with their functional diversity in plants. Plant Gene 22:100222

    CAS  Google Scholar 

  • Klee HJ, Resende MFR (2020) Plant domestication: Reconstructing the route to modern tomatoes. Current Biol 30(8):R359–R361

    CAS  Google Scholar 

  • Kobayashi S, Fukuta Y, Yagi T, Sato T, Osaki M, Khush GS (2004) Identification and characterization of quantitative trait loci affecting spikelet number per panicle in rice (Oryza sativa L.). Field Crops Res 89(2–3):253–262

    Google Scholar 

  • Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, Stein N, Graner A, Wicker T, Tagiri A et al (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper l-class homeobox gene. Proc Natl Acad Sci USA. 104: 1424–1429

  • Koppolu R, Anwar N, Sakuma S, Tagiri A, Lundqvist U, Pourkheirandish M, Rutten T, Seiler C, Himmelbach A, Ariyadasa R, Youssef HM, Stein N, Sreenivasulu N, Komatsuda T, Schnurbusch T (2013) Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley. Proc Natl Acad Sci USA 110(32):13198–13203

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kouprina N, Larionov V (2019) TAR cloning: Perspectives for functional genomics, biomedicine, and biotechnology. Mol Ther Meth Clin Develop 14:16–26

    CAS  Google Scholar 

  • Langridge P (2005) Molecular breeding of wheat and barley, in In the Wake of Double Helix. In: Tuberosa R, Phillips RL, Gale M (eds) From the green revolution to the gene revolution. Avenue Media, Bologna, pp 279–286

    Google Scholar 

  • Lata C, Gupta S, Prasad M (2013) Foxtain millet: a model crop for genetic and genomic studies in bioenergy grasses. Crit Rev Biotechnol 33(3):328–343

    PubMed  Google Scholar 

  • Lei M, Li Z-Y, Wang J-B, Fu Y-L, Xu L (2019) Ectopic expression of the Aechmea fasciata APETALA2 gene AfAP2-2 reduces seed size and delays flowering in Arabidopsis. Plant Physiol Biochem 139:642–650

    CAS  PubMed  Google Scholar 

  • Lenser T, TheiBen G (2013) Molecular mechanisms involved in convergent crop domestication. Trends Plant Sci 18(12):704–714

    CAS  PubMed  Google Scholar 

  • Lema M (2018) PMarker assisted selection in comparison to conventional plant breeding: Review article. Agric Res Technol Open Access J 14(2):555914

    Google Scholar 

  • Li X, Qian Q, Fu Z, Wang Y, Xiong G, Zeng D, Wang X, Liu X, Teng S, Hiroshi F et al (2003) Control of tillering in rice. Nature 422:618–621

    CAS  PubMed  Google Scholar 

  • Li H, Yang X, Lu M, Chen J, Shi T (2020) Gene expression and evolution of Family-1 UDP-glycosyltransferases-insights from an aquatic flowering plant (sacred lotus). Aquat Bot 166:103270

    Google Scholar 

  • Lichman BR, Godden G, Buell CR (2020) Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae. Curr Opin Plant Biol 55:74–83

    CAS  PubMed  Google Scholar 

  • Lin Q, Wang D, Dong H, Gu S, Cheng Z, Gong J, Qin R, Jiang L, Li G, Wang JL et al (2012) Rice APC/CTE controls tillering by mediating the degradation of MONOCULM1. Nat Commun 3:752

    PubMed  Google Scholar 

  • Liu Q, Chen Y-Q (2010) A new mechanism in plant engineering: the potential roles of microRNAs in molecular breeding for crop improvement. Biotechnol Adv 28(3):301–307

    CAS  PubMed  Google Scholar 

  • Liu YB, Wei W, Ma KP, Darmency H (2010) Backcrosses to Brassica napus of hybrids between B. juncea and B. napus as a source of herbicide-resistant volunteer-like feral populations. Plant Sci 179:459–465

    CAS  PubMed  Google Scholar 

  • Liu Z, Li H, Fan X, Huang W, Yang J, Wen Z, Li Y, Guan R, Guo Y, Chang R, Wang D, Chen P, Wang S, Qiu L-J (2017a) Phenotypic characterization and genetic dissection of nine agronomic traits in Tokachi nagaha and its derived cultivars in soybean (Glycine max (L.) Merr.). Plant Sci 256:72–86

    CAS  PubMed  Google Scholar 

  • Liu J, Chen J, Zheng X, Wu F, Lin Q, Heng Y, Tian P, Cheng Z, Yu X, Zhou K, Zhang X, Guo X, Wang J, Wang H, Wan J (2017b) GW5 acts in the brassinosteroid signaling pathway to regulate grain width and weight in rice. Nat Plants 3:17043

    CAS  PubMed  Google Scholar 

  • Liu Q, Han R, Wu K, Zhang J, Ye Y, Wang S, Chen J, Pan Y, Li Q, Xu X, Zhou J, Tao D, Wu Y, Fu X (2018) G-protein betagamma subunits determine grain size through interaction with MADS-domain transcription factors in rice. Nat Commun 9:852

    PubMed  PubMed Central  Google Scholar 

  • Liu H, Liu H, Zhou L, Lin Z (2019) Genetic architecture of domestication-and improvement-related traits using a population derived from Sorghum virgatum and Sorghum bicolor. Plant Sci 283:135–146

  • Liu F-H, Yang F (2020) Male sterility induction and evolution of cytoplasmic male sterility related atp9 gene from Boehmeria nivea (L.) Gaudich. Ind Crops Prod 156:112861

    CAS  Google Scholar 

  • Liu J, Fernie AR, Yan K (2020) The part, present, and future of maize improvement: domestication, genomics and functional genomics routes toward crop enhancement. Plant Commun 1:100010

    PubMed  Google Scholar 

  • Long Y, Liang F, Zhang J, Xue M, Zhang T, Pei X (2020) Identification of drought response genes by digital gene expression (DGE) analysis in Caragana korshinskii Kom. Gene 725:144170

    CAS  PubMed  Google Scholar 

  • Luo J, Liu H, Zhou T, Gu B, Huang X, Shangguan Y, Zhu J, Li Y, Zhao Y, Wang Y et al (2013) An-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice. Plant Cell 25:3360–3376

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ma Y, Lu S (2012) T-DNA tagging: a promising tool for functional genomics in medicinal plants. Single Cell Biol 1:e106

    Google Scholar 

  • Mahalakshmi V, Ortiz R (2001) Plant genomics and agriculture: From model organisms to crops, the role of data mining for gene discovery. EJB Electron J Biotechnol 4(3):169–178

    Google Scholar 

  • Makhzoum A, Yousefzadi M, Malik S, Gantet P, Tremouillaux-Guiller J (2017) Strigolactone biology: genes, functional genomics, epigenetics and applications. Crit Rev Biotechnol 37(2):151–162

    CAS  PubMed  Google Scholar 

  • Manzoor MA, Cheng X, Li G, Su X, Abdullah M, Cai Y (2020) Gene structure, evolution and expression analysis of the P-ATPase gene family in Chinese pear (Pyrus bretschneideri). Comput Biol Chem 88:107346

    CAS  PubMed  Google Scholar 

  • Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA 107:19579–19584

    CAS  PubMed  PubMed Central  Google Scholar 

  • Martinez-Romero E, Aguirre-Noyola JL, Taco-Taype N, Martinez-Romero J, Zuniga-Davila D (2020) Plant microbiota modified by plant domestication. Syst Appl Microbiol 43(5):126106

    CAS  PubMed  Google Scholar 

  • Mathan J, Bhattacharya J, Ranjan A (2016) Enhancing crop yield by optimizing plant developmental features. Development 143:3283–3294

    CAS  PubMed  Google Scholar 

  • Matsunaga T, Endo S, Maeda S, Ishikura S, Tajima K, Tanaka N, Nakamura KT, Imamura Y, Hara A (2008) Characterization of human DHRS4: an inducible short-chain dehydrogenase/reductase enzyme with 3β-hydroxysteroid dehydrogenase activity. Archives Arch Biochem Biophys 477(2):339–347

    CAS  Google Scholar 

  • Mehta BK, Muthusamy V, Zunjare RU, Baveja A, Chauhan HS, Chhabra R, Singh AK, Hossain F (2020) Biofortification of sweet corn hybrids for provitamin-A, lysine and tryptophan using molecular breeding. J Cereal Sci. https://doi.org/10.1016/j.jcs.2020.103093

    Article  Google Scholar 

  • Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value genome-wide dense marker maps. Genetics 157:1819–1829

    CAS  PubMed  PubMed Central  Google Scholar 

  • Micallef MC, Austin S, Bingham ET (1995) Improvement of transgenic alfalfa by backcrossing. In Vitro Cell Dev Biol 31:187–192

    CAS  Google Scholar 

  • Milla R, Osborne CP, Turcotte MM, Violle C (2015) Plant domestication through an ecological lens. Trends Ecol Evol 30(8):463–469

    PubMed  Google Scholar 

  • Minshull J, Stemmer PCW (1999) Protein evolution by molecular breeding. Curr Opin Chem Biol 3(3):284–290

    CAS  PubMed  Google Scholar 

  • Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M (2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet 42:545–549

    CAS  PubMed  Google Scholar 

  • Mizuno H, Kasuga S, Kawahigashi H (2016) The sorghum SWEET gene family: stem sucrose accumulation as revealed through transcriptome profiling. Biotechnol Biofuels 9:127

    PubMed  PubMed Central  Google Scholar 

  • Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255–264

    CAS  PubMed  Google Scholar 

  • Mosse SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969–977

    Google Scholar 

  • Moummou H, Kallberg Y, Tonfack LB, Persson B, van der Rest B (2012) The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns. BMC Plant Biol 12:219

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nakazawa M, Ichikawa T, Ishikawa A, Kobayashi H, Tsuhara Y et al (2003) Activation tagging, a novel tool to dissect the functions of gene family. Plant J 34:741–750

    CAS  PubMed  Google Scholar 

  • Narayanan NN, Baisakh N, Vera Cruz CM, Gnanamanickam SS, Datta K, Datta SK (2002) Molecular breeding for the development of blast and bacterial blight resistance in rice cv. IR50. Crop Sci 42:2072–2079

    CAS  Google Scholar 

  • Nimisha S, Kherwar D, Ajay KM, Singh B, Usha K (2013) Molecular breeding to improve guava (Psidium guajava L.): current status and future prospective. Scientia Hortic 164:578–588

    Google Scholar 

  • Niu X, Luo D, Gao S, Ren G, Chang L, Zhou Y, Luo X, Li Y, Hou P, Tang W, Lu B-R, Liu Y (2010) A conserved unusual posttranscriptional processing mediated by short, direct repeated (SDR) sequences in plants. J Genet Genomics 37(1):85–99

    CAS  PubMed  Google Scholar 

  • Noulas C, Tziouvalekas M, Vlachostergios D, Baxevanos D, Karyotis T, Iliadis C (2017) Adaptation, agronomic potential and current perspectives of quinoa under Mediterranean conditions: case studies from the lowlands of central Greece. Commun Soil Sci Plant Anal 48(22):2612–2629

    CAS  Google Scholar 

  • Ordonio R, Ito Y, Morinaka Y, Sazuka T, Matsuoka M (2016) Chapter five- molecular breeding of Sorghum bicolor, a novel energy crop. Int Rev Cell Mol Biol 321:221–257

    CAS  PubMed  Google Scholar 

  • Palfreyman MG (1998) Functional genomics conference: From identifying proteins to faster drug discovery. Expert Opin Invetig Drugs 7(7):1201–1207

  • Pang Y, Liu C, Wang D, Amand PSt, Bernardo A, Li W, He F, Li L, Wang L, Yuan X, Dong L, Su Y, Zhang H, Zhao M, Liang Y, Jia H, Shen X, Liu S (2020) High-resolution genome-wide association study identifies genomic regions and candidate genes for important agronomic traits in wheat. Mol Plant 13(9):1311–1327

    CAS  PubMed  Google Scholar 

  • Paul S, Ali N, Gayen D, Datta SK, Datta K (2012) Molecular breeding of Osfer2 gene to increase iron nutrition in rice grain. GM Crops Food 3(4):310–316

    PubMed  Google Scholar 

  • Pavy N, Pelgas B, Laroche J, Rigault P, Isabel N, Bousquet J (2012) A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers. BMC Biol 10:84

    CAS  PubMed  PubMed Central  Google Scholar 

  • Persson B, Kallberg Y (2013) Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs). Chem Biol Interact 202(1–3):111–115

    CAS  PubMed  Google Scholar 

  • Poursarebani N, Trautewig C, Melzer M, Nussbaumer T, Lundqvist U, Rutten T, Schmutzer T, Brandt R, Himmelbach A, Altschmied L, Koppolu R, Youssef HM, Sibout R, Dalmais M, Bendahmane A, Stein N, Xin Z, Schnurbusch T (2020) COMPOSITUM1 contributes to the architectural simplification of barley inflorescence via meristem identity signals. Nat Commun 11(1):5138

    CAS  PubMed  PubMed Central  Google Scholar 

  • Qian Y, Huang S-SC (2020) Improving plant gene regulatory network inference by integrative analysis of multi-omics and high resolution data sets. Curr Opin Syst Biol. https://doi.org/10.1016/j.coisb.2020.07.010

    Article  Google Scholar 

  • Qiu Z, Fang C, Gao Q, Bao J (2020) A short-chain dehydrogenase plays a key wolrd in cellulosic D-lactic acid fermentability of Pediococcus acidilactici. Bioresour Technol 297:122473

    CAS  PubMed  Google Scholar 

  • Oppermann U, Filling C, Hult M, Shafqat N, Wu X, Lindh M, Shafqat J, Nordling E, Kallberg Y, Persson B, Jornvall H (2003) Short-chain dehydrogenases/reductases (SDR): the 2002 update. Chemico-Biol Interact 143–144:247–253

    Google Scholar 

  • Ozseyhan ME, Kang J, Mu X, Lu C (2018) Mutagenesis of the FAE1 genes significantly changes fatty acid composition in seeds of Camelina sativa. Plant Physiol Biochem 123:1–7

    CAS  PubMed  Google Scholar 

  • Rai A, Yamazaki M, Saito K (2019) A new era in plant functional genomics. Curr Opin Syst Biol 15:58–67

    Google Scholar 

  • Ranade SA, Farooqui N, Bhattacharya E, Verma A (2001) Gene tagging with random amplified polymorhphic DNA (RAPD) markers for molecular breeding in plants. Crit Rev Plant Sci 20(3):251–275

    CAS  Google Scholar 

  • Rensing SA (2014) Gene duplication as a driver of plant morphogenetic evolution. Curr Opin Plant Biol 17:43–48

    CAS  PubMed  Google Scholar 

  • Rezan T, Contreras JA, Rozman D (2007) Functional genomics approaches to studies of the cytochrome P450 superfamily. Drug Metab Rev 39(2–3):389–399

    Google Scholar 

  • Roy S, Banerjee A, Tarafdar J, Senapati BK, Dasgupta I (2011) Transfer of transgenes for resistance to rice tungro disease into high-yielding rice cultivars through genebased marker-assisted selection. J Agric Sci 150:610–618

    Google Scholar 

  • Roy S, Banerjee A, Tarafdar J, Senapati BK (2012) Detection of probable marker-free transgene-positive rice plants resistant to rice tungro disease from backcross progenies of transgenic Pusa Basmati 1. J Gene 91:213–218

    Google Scholar 

  • Rusanov K, Kovacheva N, Atanassov A, Atanassov I (2009) Rosa Damascena-Genetics of a complex allotetraploid species and perspectives for molecular breeding. Biotechnol Biotechnol Equip 23(Sup1):594–596

    Google Scholar 

  • Salaria N, Siddappa S, Thakur K, Tomar M, Goutam U, Sharma N, Sood S, Bhardwaj V, Singh B (2020) Solanum tuberosum (CYCLING DOF FACTOR) CDF1.2 allele: A candidate gene for developing earliness in potato. S Afr J Bot 132:242–248

    CAS  Google Scholar 

  • Schiessl S-V, Katche E, Ihien E, Chawla HS, Mason AS (2019) The role of genomic structural variation in the genetic improvement of polyploidy crops. Crop J 7:127–140

    Google Scholar 

  • Shelef O, Guy O, Solowey E, Kam M, Degen AA, Rachmilevitch S (2016) Domestication of plants for sustainable agriculture in drylands: experience from the Negec desert. Arid Res Manag 30(2):209–228

    Google Scholar 

  • Sigmon B, Vollbrecht E (2010) Evidence of selection at the ramosa1 locus during maize domestication. Mol Ecol 19:1296–1311

    CAS  PubMed  Google Scholar 

  • Signor SA, Nuzhdin SV (2018) The evolution of gene expression in cis and trans. Trends in Genetics 34(7):532–544

  • Singh S, Sidhu JS, Huang N, Vikal Y, Li Z, Brar DS, Dhaliwal H, Khush GS (2001) Pyramiding three bacterial blight resistance genes (xa-5, xa-13 and Xa21) using marker-assisted selection into indica rice cultivar RP106. Theor Appl Genet 102:1011–1015

  • Singh J, Zhao J, Vallejos CE (2018) Differential transcriptome patterns associated with early seedling development in a wild and a domesticated common bean (Phaseolus vulgaris L.) accession. Plant Sci 274:153–162

    CAS  PubMed  Google Scholar 

  • Soltis P, Marchant DB, Peer YVD, Soltis DE (2015) Polyploidy and genome evolution in plants. Curr Opin Genet Dev 35:119–125

    CAS  PubMed  Google Scholar 

  • Sonawane PD, Heinig U, Panda S, Gilboa NS, Yona M, Kumar P, Alkan N, Unger T, Bocobza S, Pliner M, Malitsky, Tkachev M, Meir S, Rogachev I, Aharoni A (2018) Short-chain dehydrogenase/reductase governs steroidal specialized metabolites structural diversity and toxicity in the genus Solanum. Proc Natl Acad Sci USA 115(23):E5419–E5428

    CAS  PubMed  PubMed Central  Google Scholar 

  • Springer PS (2000) Gene traps: tools for plant development and genomics. Plant Cell 12:1007–1020

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stemmer WPC (2002) Molecular breeding of genes, pathways and genomes by DNA shuffling. J Mol Catal B: Enzym 19–20:3–12

    Google Scholar 

  • Sun F, Zhang W, Xiong G, Yan M, Qian Q, Li J, Wang Y (2010) Identification and functional analysis of the MOC1 interacting protein 1. J Genet Genomics 37(1):69–77

    CAS  PubMed  Google Scholar 

  • Sun Y, Li Y, Huang G, Wu Q, Wang L (2017) Application of the yeast one-hybrid technique to plant functional genomics studies. Biotechnol Biotechnol Equip 31(6):1087–1092

    CAS  Google Scholar 

  • Swamy BPM, Descalsota GIL, Nha CT, Amparado A, Inabangan-Asilo MA, Manito C et al (2018) Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice. PLOS ONE 13(8):e0201756

    PubMed  PubMed Central  Google Scholar 

  • Swinnen G, Goossens A, Pauwels L (2016) Lessons from domestication: Targeting cis-regulatory elements for crop improvement. Trends in Plant Sci 21(6):506–515

    CAS  Google Scholar 

  • Tabbita F, Pearce S, Barneix AJ (2017) Breeding for increased grain protein and micronutrient content in wheat: Ten years of the GPC-B1 gene. J Cereal Sci 73:183–191

    CAS  Google Scholar 

  • Taketa S, Amano S, Tsujino Y, Sato T, Saisho D, Kakeda K, Nomura M, Suzuki T, Matsumoto T, Sato K et al (2008) Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway. Proc Natl Acad Sci USA 105:4062–4067

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tavakol E, Okagaki R, Verderio G, Shariati JV, Hussein A, Bilgic H, Scanlon MJ, Todt NR, Close TJ, Druka A et al (2015) The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning. Plant Physiol 168:164–174

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tian Y, Zhang M, Hu X, Wang L, Dai J, Xu Y, Chen F (2016) Over-expression of CYP78A98, a cytochrome P450 gene from Jatropha curcas L., increases seed size of transgenic tobacco. Electron J Biotechnol 19:15–22

    Google Scholar 

  • Toenniessen GH, O,Toole JC, DeVries J (2003). Advances in plant biotechnology and its adoption in developing countries. Curr Opin Plant Biol 6:191–198

    PubMed  Google Scholar 

  • Tonfack LB, Moummou H, Latche A, Youmbi E, Benichou M, Pech JC et al (2011) The plant SDR superfamily: involvement in primary and secondary metabolism. Curr Top Plant Biol 12:41–53

    CAS  Google Scholar 

  • Tong H, Jin Y, Liu W, Li F, Fang J, Yin Y, Qian Q, Zhu L, Chu C (2009) DWARF and low-tillering, a new member of the GRAS family, plays positive roles in brassinosteroid signaling in rice. Plant J 58:803–816

    CAS  PubMed  Google Scholar 

  • Toojinda T, Tragoonrung S, Vanavichit A, Siangliw JL, Pa-In N, Jantaboon J, Siangliw M, Fukai S (2005) Molecular breeding for rainfed lowland rice in Mekong region. Plant Prod Sci 8(3):330–333

    CAS  Google Scholar 

  • Van Esse GW, Walla A, Finke A, Koornneef M, Pecinka A, von Korff M (2017) Six-rowed spike3 (VRS3), is a histone demethylase that controls lateral spikelet development in barley. Plant Physiol 174(4):2397–2408

    PubMed  PubMed Central  Google Scholar 

  • Varshney RK, Langridge P, Graner A (2007) Application of genomics to molecular breeding of wheat and barley. Adv Genet 58:121–155

    CAS  PubMed  Google Scholar 

  • Venkanna D, Sudfeld C, Baier T, Homburg SV, Patel AV, Wobbe L, Kruse O (2017) Knock-down of the IFR1 protein perturbs the homeostasis of reactive electrophile species and boosts photosynthetic hydrogen production in Chlamydomonas reinhardtii. Front Plant Sci 8:1347

    PubMed  PubMed Central  Google Scholar 

  • Verdeprado H, Kretzschmar T, Begum H, Raghavan C, Joyce P, Lakshmanan P, Cobb JN, Collard BCY (2018) Association mapping in rice: basic concepts and perspectives for molecular breeding. Plant Product Sci 21(3):159–176

    CAS  Google Scholar 

  • Wang X-M, Liang Y-Y, Li L, Gong C-W, Wang H-P, Huang X-X, Li S-C, Deng Q-M, Zhu J, Zheng A-P, Li P, Wang S-Q (2015) Identification and cloning of tillering-related genes OsMAX1 in rice. Rice Sci 22(6):255–263

    Google Scholar 

  • Wang S, Wu K, Qian Q, Liu Q, Li Q, Pan Y, Ye Y, Liu X, Wang J, Zhang J, Li S, Wu Y, Fu X (2017) Non-canonical regulation of SPL transcription factors by a human OTUB1-like deubiquitinase defines a new plant type rice associated with higher grain yield. Cell Res 27:1142–1156

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang H, Ni X, Harris-Shultz K (2019a) Molecular evolution of the plant ECERIFERUM1 and ECERIFERUM3 genes involved in aliphatic hydrocarbon production. Comput Biol Chem 80:1–9

    PubMed  Google Scholar 

  • Wang YL, Ye H, Liu L, Wu JH, Ru WM, Sun GL (2019b) Molecular insights on domestication of barley (Hordeum vulgare L.). Crit Rev Plant Sci 38(4):280–294

    CAS  Google Scholar 

  • Wang J, Zhang Z, Wu J, Han X, Wang-Pruski G, Zhang Z (2020a) Genome-wide identification, characterization, and expression analysis related to autotoxicity of the GST gene family in Cucumis melo L. Plant Physiol Biochem 155:59–69

    CAS  PubMed  Google Scholar 

  • Wang Y, Wan S, Fan H, Yan M, Li W, Guan R (2020b) A sulfotransferase gene BnSOT-like1 has a minor genetic effect on seed glucosinolate content in Brassica napus. Crop J. https://doi.org/10.1016/j.cj.2020b.07.003

    Article  Google Scholar 

  • Wang Y, Sun J, Ali SS, Gao L, Ni X, Li X, Wu Y, Jiang J (2020c) Identification and expression analysis of Sorghum bicolor gibberellins oxidase genes with varied gibberellins levels involved in regulation of stem biomass. Ind Crops Prod 145:111951

    CAS  Google Scholar 

  • Warren JM, Solan DB (2020) Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria. Mitochondrion 52:144–156

    CAS  PubMed  Google Scholar 

  • Wijerathna YMAM (2019) Marker assisted selection: Biotechnology tool for rice molecular breeding. J Biotechnol Phytochem 3(1)

  • Wu Z, Yang Y, Huang G, Lin J, Xia Y, Zhu Y (2017) Cotton functional genomics reveals global insight into genome evolution and fiber development. J Genet Genomics 44(11):511–518

    PubMed  Google Scholar 

  • Xiong D, Wang H, Chen M, Xue C, Li Z, Bian Y, Bao D (2014) Application of mating type genes in molecular marker-assisted breeding of the edible straw mushroom Volvariella volvacea. Scientia Hortic 180:59–62

    Google Scholar 

  • Xu C, Wang Y, Yu Y, Duan J, Liao Z, Xiong G, Meng X, Liu G, Qian Q, Li J (2012) Degradation of MONOCULM1 by APC/C(TAD1) regulates rice tillering. Nat Commun 3:750

    PubMed  Google Scholar 

  • Xue Y, Li J, Xu Z (2003) Recent highlights of the China rice functional genomics program. Trends Genet 19(7):390–394

    CAS  PubMed  Google Scholar 

  • Xue Y, Jiang J, Yang X, Jiang H, Du Y, Liu X, Xie R, Chai Y (2020) Genome-wide mining and comparative analysis of fatty acid elongase gene family in Brassica napus and its progenitors. Gene 747:144674

    CAS  PubMed  Google Scholar 

  • Yagi M, Shirasawa K, Hirakawa H, Isobe S, Matsuno J, Uno Y, Tanase K, Onozaki T, Yamaguchi H (2020) QTL analysis for flowering time in carnation (Dianthus caryophyllus L.). Scientia Hortic 262:109053

    CAS  Google Scholar 

  • Yan SM, McCoy R (2020) Archaic hominin genomics provides a window into gene expression evolution. 2020. Curr Opin Genet Dev 62:44–49

  • Yang X, Leebens-Mack J, Chen F, Yin Y (2015) Plant comparative and functional genomics. Int J Genomics Article ID 924369:2 pages

    Google Scholar 

  • Yang M-Y, Chen J-Q, Tian H-Y, Ni C-Y, Xiao K (2019) TaARR1, a cytokinin response regulator gene in Triticum aestivum, is essential in plant N starvation tolerance via regulating the N acquisition and N assimilation. J Integr Agric 18(12):2691–2702

    Google Scholar 

  • Yang W, Chen S, Chen Y, Zhang N, Ma Y, Wang W, Tian H, Li Y, Hussain S, Wang S (2020) Cell wall/vacuolar inhibitor of fructosidase 1 regulates ABA response and salt tolerance in Arabidopsis. Plant Signal Behav 15(4):1744293

    PubMed  PubMed Central  Google Scholar 

  • Yin H, Chen CJ, Yang J, Weston DJ, Chen J-G, Muchero W, Ye N, Tschaplinski TJ, Wullschleger SD, Cheng Z-M, Tuskan GA, Yang X (2014) Functional genomics of drought tolerance in bioenergy crops. Crit Rev Plant Sci 33(2–3):205–224

    Google Scholar 

  • Youssef HM, Eggert K, Koppolu R, Alqudah AM, Poursarebani N, Fazeli A, Sakuma S, Tagiri A, Rutten T, Govind G, Lundqvist U, Graner A, Komatsuda T, Sreenivasulu N, Schnurbusch T (2017) VRS2 regulates hormone-mediated inflorescence patterning in barley. Nat Genet 49(1):157–161

    CAS  PubMed  Google Scholar 

  • Yu J, Miao J, Zhang Z, Xiong H, Zhu X, Sun X, Pan Y, Liang Y, Zhang Q, Rashid MAR, Li J, Zhang H, Li Z (2018) Alternative splicing of OsLF3b controls grain length and yield in japonica rice. Plant Biotechnol J 16:1667–1678

    CAS  PubMed Central  Google Scholar 

  • Yuan H, Qin P, Hu L, Zhan S, Wang S, Gao P, Li J, Jin M, Xu Z, Gao Q, Du A, Tu B, Chen W, Ma B, Wang Y, Li S (2019) OsSPL18 controls grain weight and grain number in rice. J Genet Genom 46:41–51

    Google Scholar 

  • Yuan L, Dai H, Zheng S, Huan R, Tong H-R (2020) Genome-wide identification of the HDAC family proteins and functional characterization of CsHD2C, a HD2-type histone deacetylase gene in tea plant (Camellia sinensis L. O. Kuntze). Plant Physiol Biochem. https://doi.org/10.1016/j.plaphy.2020.07.047

    Article  PubMed  Google Scholar 

  • Yue GH, Sun F, Liu P (2013) Status of molecular breeding for improving Jatropha curcas and biodiesel. Renew Susta Energ Rev 26:332–343

    CAS  Google Scholar 

  • Zeng Z-Q, Lin T-Z, Zhao J-Y, Zheng T-H, Xu L-F, Wang Y-H, Liu L-L, Jiang L, Chen S-H, Wan J-M (2020) OsHemA gene, encoding glutamyl-tRNA reductase (GlutTR) is essential for chlorophyll biosynthesis in rice (Oryza sativa). J Integr Agric 19(3):612–623

    CAS  Google Scholar 

  • Zhang Y, Yu H, Yang X, Li Q, Ling J, Wang H, Gu X, Huang S, Jiang W (2016) CsWRKY46, a WRKY transcription factor from cucumber, confers cold resistance in transgenic-plant by regulating a set of cold-stress responsive genes in an ABA-dependent manner. Plant Physiol Biochem 108:478–487

    CAS  PubMed  Google Scholar 

  • Zhang H, Zhang J, Lang Z, Botella JR, Zhu JK (2017) Genome editing- Principles and applications for functional genomics, research and crop improvement. Crit Rev Plant Sci 36(4):291–309

    Google Scholar 

  • Zhang L, Kong H, Ma H, Yang J (2018) Phylogenomic detection and functional prediction of genes potentially important for plant meiosis. Gene 643:83–97

    CAS  PubMed  Google Scholar 

  • Zhang Z, Feng X, Wang Y, Xu W, Huang K, Hu M, Zhang C, Yuan H (2019) Advances in research on functional genes of tea plant. Gene 711:143940

    CAS  PubMed  Google Scholar 

  • Zhao H-B, Jia H-M, Wang Y, Wang G-Y, Zhou C-C, Jia H-J, Gao Z-S (2019) Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit development and ripening in red bayberry (Morella rubra). Gene 717:144045

    CAS  PubMed  Google Scholar 

  • Zhou F, Lin Q, Zhu L, Ren Y, Zhou K, Shabek N, Wu F, Mao H, Dong W, Gan L (2013) D14-SCFD3-dependent degradation of D53 regulates strigolactone signaling. Nature 504:406–410

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou B, Lin JZ, Peng D, Yang YZ, Guo M, Tang DY, Tan X, Liu XM (2017) Plant architecture and grain yield are regulated by the novel DHHC-type zinc finger protein genes in rice (Oryza sativa L.). Plant Sci 254:12–21

    CAS  PubMed  Google Scholar 

  • Zhu H, Lv J, Zhao L, Tong X, Zhou B, Zhang T, Guo W (2012) Molecular evolution and phylogenetic analysis of geens related to cotton fibers development from wild and domesticated cotton species in Gossypium. Mol Phylogenet Evol 63(3):589–597

    PubMed  Google Scholar 

  • Zhu T, Xin F, Wei S-W, Liu Y, Han Y-C, Xie J, Ding Q, Ma L (2019) Genome-wide identification, phylogeny and expression profiling of class II peroxidases gene family in Brachypodium distachyon. Gene 700:149–162

    CAS  PubMed  Google Scholar 

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Shahrajabian, M.H., Sun, W. & Cheng, Q. Molecular breeding and the impacts of some important genes families on agronomic traits, a review. Genet Resour Crop Evol 68, 1709–1730 (2021). https://doi.org/10.1007/s10722-021-01148-x

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