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Chenopodium Quinoa Willd.) Brigham Young University BYU ScholarsArchive Theses and Dissertations 2006-07-19 Simple Sequence Repeat Development, Polymorphism and Genetic Mapping in Quinoa (Chenopodium quinoa Willd.) David Jarvis Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Animal Sciences Commons BYU ScholarsArchive Citation Jarvis, David, "Simple Sequence Repeat Development, Polymorphism and Genetic Mapping in Quinoa (Chenopodium quinoa Willd.)" (2006). Theses and Dissertations. 504. https://scholarsarchive.byu.edu/etd/504 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. SIMPLE SEQUNCE REPEAT DEVELOPMENT, POLYMORPHISM AND GENETIC MAPPING IN QUINOA (CHENOPODIUM QUINOA WILLD.) by David E. Jarvis A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the degree requirements for Master of Science Department of Plant and Animal Sciences Brigham Young University August 2006 BRIGHAM YOUNG UNIVERSITY GRADUATE COMMITTEE APPROVAL of a thesis submitted by David E. Jarvis This thesis has been read by each member of the following graduate committee and by majority vote has been found to be satisfactory. ______________________________ ____________________________________ Date Eric N. Jellen, Chair ______________________________ ____________________________________ Date P. Jeffrey Maughan ______________________________ ____________________________________ Date R. Paul Evans BRIGHAM YOUNG UNIVERSITY As chair of the candidate’s graduate committee, I have read the thesis of David E. Jarvis in its final form and have found that (1) its format, citations, and bibliographical style are consistent and acceptable and fulfill university and departmental style requirements; (2) its illustrative material including figures, tables, and charts are in place; and (3) the final manuscript is satisfactory to the graduate committee and is ready for submission to the university library. ______________________________ _________________________________ Date Eric N. Jellen Chair, Graduate Committee Accepted for the Department _________________________________ Von D. Jolley Graduate Coordinator Accepted for the College _________________________________ Rodney J. Brown Dean, College of Biology and Agriculture ABSTRACT SIMPLE SEQUNCE REPEAT DEVELOPMENT, POLYMORPHISM AND GENETIC MAPPING IN QUINOA (CHENOPODIUM QUINOA WILLD.) David E. Jarvis Department of Plant and Animal Sciences Master of Science Quinoa is an important, highly nutritional grain crop in the Andean region of South America. DNA markers and linkage maps are important tools for the improvement of underdeveloped crops such as quinoa. The objectives of this study were to (i) develop a new set of SSR markers to augment the number of SSR markers available in quinoa, and (ii) construct a new genetic linkage map of quinoa based on SSRs using multiple recombinant-inbred line (RIL) populations. Here we report the development of 216 new polymorphic SSR markers from libraries enriched for GA, CAA, and AAT repeats, as well as 6 SSR markers developed from BAC-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranged from 0.12 to 0.90, with an average value of 0.56. These new SSR and BES-SSR markers were analyzed on two RIL mapping populations (designated Population 1 and Population 40), each obtained by crossing Altiplano and coastal ecotypes of quinoa. Additional markers, including AFLPs, two 11S seed storage protein loci, a SNP, and the nucleolar organizing region (NOR), were also analyzed on one or both populations. Linkage maps were constructed for both populations. The Population 1 map contains 275 markers, including 200 SSR and 70 AFLP markers, as well as five additional markers. The map consists of 41 linkage groups (LGs) covering 913 cM. The Population 40 map contains 68 markers, including 62 SSR and six BES-SSR markers, and consists of 20 LGs covering 353 cM. Thirty-nine anchor markers common between both maps were used to combine 15 Population 1 LGs with 13 Population 40 LGs. The resulting integrated map consists of 13 LGs containing 140 SSR, 48 AFLP, four BES-SSR, one SNP, and one NOR marker spanning a total of 606 cM. A high level of segregation distortion was observed in both populations, indicating possible chromosomal regions associated with gametophytic factors or QTLs conferring a selective advantage under the particular growing conditions. As these maps are based primarily on easily-transferable SSR markers, they are particularly suitable for applications in the underdeveloped Andean regions where quinoa is grown. ACKNOWLEDGMENTS Many thanks are owed to my committee chair, Dr. Eric N. Jellen, and my committee members, Dr. P. Jeff Maughan and Dr. R. Paul Evans. Their doors and email inboxes have always been open, and they have been always willing to answer questions or give advice. Dr. Mikel Stevens and Dr. Craig Coleman have also been helpful and enjoyable to work with. Thanks to all the quinoa team for making such a unique environment in which students can learn and grow together. I am indebted to the countless undergrads that have helped me with the tedious tasks of pouring and loading gels; there are too many to mention them all. Dr. Olga Kopp and her team, especially Melanie Mallory, did excellent work on the SSR development. Thanks to Aaron Towers for his help on AFLPs, Kristin Andelin for her help on SNP mapping, and Jenny N. Thornton for her help on 11S mapping. I am also grateful to the McKnight Foundation and the Holmes Family Foundation, whose financial support made my project possible. Most of all, a very special thanks to my patient and beautiful wife, Stephanie, for her constant love and support. TABLE OF CONTENTS Graduate Committee Approval ii Final Reading Approval and Acceptance iii Abstract iv Acknowledgments vi List of Figures ix List of Tables x Chapter 1: Simple Sequence Repeat Development, Polymorphism, and Genetic Mapping in Quinoa (Chenopodium quinoa Willd.) 1 Introduction 2 Materials and Methods 4 Results and Discussion 10 Conclusions 20 References 23 Chapter 2: Tables and Figures 30 Chapter 3: Literature Review 51 Introduction 52 History 53 Taxonomy 54 Breeding 55 Biotic and Abiotic Stresses 57 Molecular Studies in Quinoa 58 vii Molecular Markers 60 Simple Sequence Repeats 62 Mapping 63 Conclusion 64 References 65 Appendix: Scoring Data 75 viii LIST OF FIGURES Figure 1. Number of clones sequenced and primers developed for each library. 39 (A) Total number of sequenced clones, including those containing unique microsatellites, redundant sequences, and those not used for primer design. 39 (B) Total number of primers designed, including polymorphic and monomorphic primers, polymorphic primers with high molecular weight amplicons, those polymorphic only between C. berlandieri and quinoa, and primers with poor or no amplification. 39 Figure 2. Histogram showing number and heterozygosity (H) values of polymorphic markers by repeat length. 40 Figure 3. Linkage maps. 44 (A) Population 1. 44 (B) Population 40. 45 (C) Integrated map. 46 Figure 4. Comparison of loci linked to the BSP locus (BSPL) (Ricks 2005) in LG 11 of the Maughan et al. (2004) map and linkage group (LG) 1 of the integrated map reported herein. 49 ix LIST OF TABLES Table 1. Quinoa microsatellite marker name, primary motif, complexity, type, primer sequences, expected PCR product size (PRO), observed number of alleles (ONA), and heterozygosity value (H). 31 Table 2. Significant database sequence homologies to microsatellite-containing clones for which primers were designed, including E-value, nucleotide and/or protein homology match, organism match, and GenBank accession number, as identified through BLASTN and BLASTX searches. 41 Table 3. Skewed markers scored and mapped in Populations 1 and 40. 47 (A) Name and parental direction of skewed markers scored in Populations 1 and 40. 47 (B) Number, linkage group location, and parental direction of skewed markers for Populations 1 and Population 40 . 48 Table 4. Potentially homoeologous loci and linkage groups (LG) in the Population 1, Population 40 and inegrated map, as indicated by a single primer set amplifying two segregating loci. 50 x Chapter 1: SIMPLE SEQUNCE REPEAT DEVELOPMENT, POLYMORPHISM AND GENETIC MAPPING IN QUINOA (CHENOPODIUM QUINOA WILLD.) 1 Introduction Quinoa (Chenopodium quinoa Willd.) is an allotetraploid (2n = 4x= 36) that shows amphidiploid inheritance for most qualitative traits (Simmonds 1971; Risi and Galwey 1984; Ward 2000). It is an important South American cereal crop that recently has gained international attention for the high nutritional value of its grain. Grown primarily in the Altiplano regions of Bolivia, Ecuador, Chile, and Peru, quinoa has served as an important staple crop for subsistence farmers for thousands of years (Pearsall 1992; Wilson 1988, Maughan et al. 2004). It is well-suited as a staple crop in the Altiplano due to its high protein content (7.5-22.1%) (Tapia et al. 1979) as well as its ability to grow in the harsh environments that characterize much of the Altiplano, specifically high altitudes (up to 4000 m), frequent frosts, and saline soils (Risi and Galwey 1984; Vacher 1998; Prado et al. 2000; Jacobsen et al. 2003; Maughan et al. 2004). Despite its many desirable nutritional characteristics,
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