South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Electronic Theses and Dissertations 2019 Validation of Candidate Loci for Maize Regrowability and Selection of Near Isogenic Lines for the Loci Tajbir Raihan South Dakota State University Follow this and additional works at: https://openprairie.sdstate.edu/etd Part of the Biology Commons, Plant Biology Commons, and the Plant Breeding and Genetics Commons Recommended Citation Raihan, Tajbir, "Validation of Candidate Loci for Maize Regrowability and Selection of Near Isogenic Lines for the Loci" (2019). Electronic Theses and Dissertations. 3521. https://openprairie.sdstate.edu/etd/3521 This Thesis - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. VALIDATION OF CANDIDATE LOCI FOR MAIZE REGROWABILITY AND SELECTION OF NEAR ISOGENIC LINES FOR THE LOCI BY TAJBIR RAIHAN A thesis submitted in partial fulfillment of the requirements for the Master of Science Major in Biological Sciences Specialization in Biology South Dakota State University 2019 iii ACKNOWLEDGEMENTS In the beginning, I would like to express my sincere thanks and gratitude to my advisor Dr. Yang Yen for his supervision, support, and care for the last three years. I also would thank my other committee members: Dr. Yajun Wu, Dr. Donald Auger, and Dr. Padmanaban Krishnan for their critical evaluation and suggestion in case of designing and execution of my experiments, data analysis, and manuscript preparation. I am also thankful to my current lab mate Bimal Paudel and Ex lab mates Subha Dahal, Anjun Ma for their help with the lab work and helpful discussions. Most importantly, I would like to show my gratitude to my beloved parents, especially to my mother; even after her death, the memory of her love and care encourages me to get over my distress and keep me on the road of success. iv TABLE OF CONTENTS LIST OF TABLES ...............................................................................................................v LIST OF FIGURES ........................................................................................................... vi ABBREVIATIONS .......................................................................................................... vii ABSTRACT ..................................................................................................................... viii 1 CHAPTER 1: LITERATURE REVIEW ......................................................................1 1.1 Introduction .......................................................................................................1 1.2 Perennialism in woody perennials. ....................................................................3 1.3 Types of perennating structures in herbs and grasses. .......................................6 1.4 Progress in overall perennialism research in various crops .............................15 1.5 Summary and concluding remarks: .................................................................24 References ..........................................................................................................................26 2 CHAPTER 2: VALIDATION OF CANDIDATE LOCI FOR REGROWABILITY AND SELECTION OF THEIR NEAR ISOGENIC LINES IN MAIZE. .........................37 2.1 Introduction .....................................................................................................37 2.2 Materials and methods .....................................................................................39 2.2.1 Formation of the population for marker study .............................................39 2.2.2 DNA extraction ............................................................................................39 2.2.3 PCR assay ....................................................................................................39 2.3 Results and discussions ...................................................................................40 2.3.1 The study of gt1, id1, and tb1 for their contribution to regrowability .........40 2.3.2. Validation of the candidate SNPs by genotyping the F2 population ............42 2.3.3 Genes found in peak locations .....................................................................43 2.3.4 Selection of the Near Isogenic lines for reg1 and reg2 ...............................44 2.4 Prospects and future direction of maize perennialism research ......................45 References ..........................................................................................................................47 v LIST OF TABLES Table 1. List of primers used in this study ....................................................................... 49 Table 2. The phenotype for regrowability and marker genotypes .................................... 51 Table 3. Detection of polymorphic marker between Z. diploperennis and B73 parent .... 56 Table 4. Result of chi square test of independent segregation .......................................... 57 Table 5. Genes located around peak position ................................................................... 58 Table 6. The results of F3 screening using allele-specific markers for reg1 and reg2 ..... 59 Table 7. The results of F4 screening using allele-specific markers for reg1 and reg2 ..... 60 vi LIST OF FIGURES Figure 1. Satellite image of the Gulf of Mexico ................................................................61 Figure 2. Perennial Wild Maize .........................................................................................62 Figure 3. Z. diploperennis, Mo17- Z F1 and B73- Z F1 ....................................................63 Figure 4. Loci in maize inbred B73 genome that are related to regrowth .........................64 Figure 5. Process of designing allele specific primers .......................................................65 Figure 6. Results of genotyping the B73-Zd F2s using S2 primers. ..................................66 Figure 7. Results of genotyping the B73-Zd F2s using S7 primers ...................................68 Figure 9. The polypeptide sequence of “Chromatin remodeling protein 24” gene ..........70 Figure 9. The coding sequence of “Chromatin remodeling protein 24” gene ..................71 Figure 10. The polypeptide sequence of “Flocculation protein FLO11” gene ................73 Figure 11. The coding sequence of “Flocculation protein FLO11” gene ........................74 Figure 12. F4 NIL screening using both chromosome 2 and 7 primers ...........................76 vii ABBREVIATIONS AS-PCR Allele-specific polymerase chain reaction bp Base pair CO CONSTANS CTAB Cetyl trimethylammonium bromide DNA Deoxyribonucleic acid FT FLOWERING LOCUS T GBS Genotype-by-sequencing gt1 grassy tiller 1 IAA Indole acetic acid id1 Indeterminate 1 LOD Logarithm of odds ng Nanogram NIL Near-isogenic line PCR Polymerase chain reaction pe Perennialism QTL Quantitative trait loci SNP Single-nucleotide-polymorphism SOC1 SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 SSR Simple-sequencing-repeat tb1 teosinte branched 1 TNT Tiller number at tasseling stage viii ABSTRACT VALIDATION OF CANDIDATE LOCI FOR MAIZE REGROWABILITY AND SELECTION OF NEAR ISOGENIC LINES FOR THE LOCI TAJBIR RAIHAN 2019 Developing perennial grain crops is an effective way for sustainable agriculture and it can be a tool for the betterment of the overall ecosystem. To understand how perenniality works in perennial species, we made a cross between Zea diploperennis and maize (Z. mays) inbred line B73. F1 hybrids produced from this cross were selfed to get the F2 population and later the F2 population underwent Genotyping-By- Sequencing (GBS) analysis. Based on the candidate loci identified on chromosome 2 and chromosome 7 from GBS, SNP-specific markers were developed from the 2 candidate locus interval and used to genotype the F2 population. test for independence showed that the tested SNPs are associated with regrowth. Additionally, gene-specific markers (gt1, tb1, id1) were also used to genotype the F2 population and the 2 test result indicates that none of these genes is significantly associated with regrowth. This result is inconsistent with the previous works conducted on these genes. Later the SNP-specific markers were used to select near-isogenic lines for the two regrowth loci. Key words: maize, perennialism, GBS, SNP, chi-square test, near isogenic lines. 1 1 CHAPTER 1: LITERATURE REVIEW 1.1 Introduction In a wider sense, perennialism refers to the phenomenon of a plant to live for more than two years (Ma et al. 2019). However, in the narrow sense, perennialism is the ability of a plant to regrow on the same body after reproduction and senescence (Ma et al. 2019). Most of the domesticated crops are annuals that reproduce, senesce and die during the same growing season, and they only have one cycle of growth and reproduction. Perennial crops are capable to overwinter or over-summer (depending on the locations) and stay alive for several consecutive years. The key to this long life is their ability to maintain some juvenile meristematic tissues even after their senescence which allow them to regrow