1. Fall 2016 - HORT6033 Molecular Plant Breeding Instructor: Ainong Shi

2. Lecture 1 (08/22/2016) I.Class Overview II. Molecular Breeding Overview III.Class Estimation Questions IV.Homework V.Questions Fall 2016 - HORT6033 Molecular Plant Breeding

3. Instructor: Dr. Ainong Shi Phone: 479-575-2670 (o), 479-879-0159 (c) Email: ashi@uark.edu Office: PTSC 321 Office Hours: Please email to Ainong Shi at ashi@uark.edu to set up an appointment. But feel free to call or stop by. Class Hours: MWF 9:40 – 10:30 am, August 22 – December 16, 2016 Classroom: UAF campus Pest Control building- ROSE Room 110 Lab Location: PTSC 322, open: 7 days a week Teaching and Lab Assistant: Avjinder Kaler (askaler@email.uark.edu), Yuejin Weng (yw018@uark.edu), Wei Yang (wxy008@uark.edu), and Gehendra Bhattarai (gb005@email.uark.edu). Fall 2016 - HORT6033 Molecular Plant Breeding

4. Student Info NameEmailMajor Bazzer,Sumandeep Kaurskbazzer@uark.eduCSES Bhattarai,Gehendragb005@uark.eduCEMB Dwiningsih,Yheniydwining@uark.eduCSES Holder,Amanda L.alholder@uark.eduCSES Hummer,Wade Stileswshummer@uark.eduCSES Jamison,Daniel Reeddjamison@uark.eduCSES Moseley,David Octordomosele@uark.eduCSES Najjar,Joseph Edwardjenajjar@uark.eduCSES Mishra,Akshitaam068@uark.edu CSES Pathak,Bhuvanbppathak@uark.eduCEMB Pruett,Eliott Emeryexp009@uark.eduCEMB Ravelombola,Second Waltramwravelom@uark.eduCEMB Rice,Adam Davidadamrice@uark.eduCSES Rudolf,Xeniya Valeriivnaxrudolf@uark.eduCEMB Yang,Weiwxy008@uark.eduPLSC Yin,Melinda H.mhyin@uark.eduHORT Jamie Lynn Underwoodjunderwo@uark.edu CSES

5. Teaching Philosophy – a triangle diagram consisted of ‘Class’, ‘Teacher’, and ‘Student’ (Fig. 1). Simple said, as a teacher, who must have ability to teach, know how to teach, like to teach and love students. As a student, who would like to attend the class, enjoy the class, and learn from the class, and like the teacher. As a ‘class’, which should be content and interesting, readable, listenable, and viewable. Fall 2016 - HORT6033 Molecular Plant Breeding

6. Project Lecture Lab Tools, Homework, Reading, and Research Fall 2016 - HORT6033 Molecular Plant Breeding

7. I.Course Description II.Course Objective and Outcome III.Grading IV. Class Schedule V.Software and Tools Download and Installation VI. Quiz and Examination (30%) VII. Assignment (homework, computer tools, and reading) (30% + 5% bonus) VIII. Lab, Project, Report, Presentation, and Article Reading (30% + 10% bonus) Download Syllabus at http://comp.uark.edu/~ashi/MB/HORT6033Syllabus.pdfhttp://comp.uark.edu/~ashi/MB/HORT6033Syllabus.pdf Course Web: http://comp.uark.edu/~ashi/MBhttp://comp.uark.edu/~ashi/MB Fall 2016 - HORT6033 Molecular Plant Breeding

8. Plant Breeding Approach Classic Breeding Main Street Molecular breeding Abiotic and biotic resistance breeding (disease/pest resistance, drought and salt tolerance) Parent selection and progeny testing Marker-assisted selection (MAS) Genome-wide selection (GWS) Marker-assisted backcross breeding (MABB) QTL-based and genome-wide predictive breeding P 1 x P 2 F1F1 F 8-10 F 6-7 F 4-5 F3F3 F2F2 Cultivar variety Release Parent selection Predictive breeding True/false, self testing MAS for simple traits Preliminary Final Yield Test P1P1 x BC 1 F 1 Backcross breeding MAS for quantitative traits Genotyping by sequencing (GBS) RAD-seq and RNA-seq SNP discovery and validation QTL mapping and association analysis Candidate gene identified and clone

9. SSR is repeating sequences of 2-5 (most of them) base pairs of DNA such as (AT)n, (CTC)n, (GAGT)n, (CTCGA)n Tool: SSRLocator, BatchPrimer3, MEGA6, BioEdit SNP is a single nucleotide (A, T, C or G) mutation, and can be discovered from PCR, Next generation sequencing (NGS) such as RNA-Seq, RAD-Seq, GBS. Tool: BioEdit, DNASTAR, SAMtools, SOAPsnp, or GATK Marker Discovery (SNP, SSR) Genetic Diversity Analysis Linkage/QTL Mapping Genome-wide Selection Marker-assisted Selection Association Analysis Genetic Map Construction Molecular Plant Breeding Approach Marker Identification (SNP, SSR Markers) Molecular Breeding Genetic diversity Genetic Map QTL mapping Association analysis SNP markers MAS/GWS SNP Add effect Dom effect LOD R^2 (%) CoP930721_82-0.123-0.1224.4636.1 CoP930934_82-0.0760.2742.8073.9

10. Class Estimation Questions and Answers This is just an estimation to test which level each student has before the class, in order to divide students into groups. Download the questions at 1. Quiz 2. Quiz discussion http://comp.uark.edu/~ashi/MB/HORT6033_Estimation_question.pdf Fall 2016 - HORT6033 Molecular Plant Breeding

11. Homework 1 1. Read manuals related to PCR and PCR primer design: (1)BatchPrimer3: http://probes.pw.usda.gov/batchprimer3/http://probes.pw.usda.gov/batchprimer3/ (2)Primer-Blast: http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHomehttp://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome 2.Read articles related to PCR and molecular marker discovery For example 1: Shi et al. 2011. Molecular Markers for Tm-2 Alleles of Tomato Mosaic Virus Resistance in Tomato American Journal of Plant Sciences 2:180-189 [ pdf ] pdf http://www.scirp.org/Journal/PaperInformation.aspx?paperID=5712

12. Fall 2016 - HORT6033 Molecular Plant Breeding DateTopics, Tool, Activity, and Lab 8/22/2016Mon Topics: Molecular breeding overview Course estimation questions and overview 8/24/2016Wed Topics: PCR and primer design Tool: Primer-Blast, BatchPrimer3 8/26/2016Fri Topics: SSR discovery from genome sequences and ESTs Tool: GMATO Activity: SSR discovery Week 1

13. Dear Students: Please read and download homework and quiz at http://comp.uark.edu/~ashi/MB/molecularBreeding_homework.htmlhttp://comp.uark.edu/~ashi/MB/molecularBreeding_homework.html ! THANKS!