1. Fall 2014 HORT6033 Molecular plant breeding
Instructor: Ainong Shi

2. Molecular Plant Breeding
Fall 2014 HORT6033
Molecular Plant Breeding
Lecture 1 (08/25/2014)
Class Overview (5 min)
Class Estimation Questions and Answers (15 min)
SSR Marker and Tools (25 min)
Homework (3 min)
Questions (2 min)

3. Molecular Plant Breeding
Fall 2014 HORT6033
Molecular Plant Breeding
Instructor: Dr. Ainong Shi
Phone: (o), (c)
Office: PTSC 321
Office Hours: Please to Ainong Shi at to set up an appointment. But feel free to call or stop by.
Class Hours: MWF 9:40 – 10:30 am, August 25 – December 19, 2014
Classroom: UAF campus AGRI 0301A
Lab Location: PTSC 322, open: 7 days a week
Lab Assistant: Dr. Jianbing Ma
Guest Instructor: Dr. John R. Clark, Dr. Pengyin Chen, Dr. Richard Esten Mason, Dr. Andy Pereira, Dr. Subodh Srivastava, and
Dr. Weiguo Lu ………..

4. Student Info Register Name Major Email Marlovi Andrea Acuna Galindo
CSES
Abeer Muhammedali Jasim Al-Nasrawi
CEMB
FNU Anuj Kumar
Jessica L Chitwood
HORT
Marcos Paulo Da Silva
Mirta Beatriz Dalzotto
Terrence James Frett
PLSC
Clinton Philip Greub
Ashley Elizabeth Humphreys
ENTO
Avjinder Singh Kaler
Mariola Klepadlo
Laura Melissa Lara Santisteban
Jennifer Anne Lewter
Cindy Massiel Lopez Ramirez
Dennis Nicuh Bulusan Lozada
Reiofeli Algodon Salas
Shilpa Singh
Vijay Singh
Brant Michael Smith
PLPA
Janithri S. Wickramanayake
Name
Jianbing Ma
Weiguo Lu
Haizheng Xiong
Jun Qin
Long Yan
Maria Nelly Arguello Blanco
Liliana Florez-Palacios
Register

5. Molecular Plant Breeding
Fall 2014 HORT6033
Molecular Plant Breeding
Lecture
Lab
Project
Tools, Homework, Reading, and Research

6. Syllabus of Molecular Plant Breeding
Fall 2014 HORT6033
Syllabus of Molecular Plant Breeding
Course Description
Course Objective and Outcome
Grading
Class Schedule
Software and Tools Download and Installation
Quiz and Examination (30%)
Assignment (homework, computer tools, and reading) (30% + 5% bonus)
Lab, Project, Report, Presentation, and Article Reading (30% + 10% bonus)
Reading Materials
Download Syllabus at
Course Web:

7. Molecular Plant Breeding
Fall 2014 HORT6033
Molecular Plant Breeding
Lecture 1 (08/25/2014)
II. Class Estimation Questions and Answers
1. Quiz
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
2. Quiz discussion

8. III. SSR Marker and Tools
SSR is repeating sequences of 2-5 (most of them) base pairs of DNA
such as (AT)n, (CTC)n, (GAGT)n, (CTCGA)n
SSR is called Microsatellites
SSR usually is co-dominant
SSR can be used:
Fingerprinting
Genetic diversity
Genetic mapping
Association mapping
Marker-assisted selection
Genome-wide selection etc.
Left Figure:
Allele #1: (CA)11 [SSR motif (CA) repeat 11 times]
Allele #2: (CA)13
Allele #3: (CA)16
After PCR, the DNA sample with Allele #1, #2, #3
showing different size DNA fragment and the
different combination of allele #1, #2, and #3
With different pattern with co-dominant.
(image from

9. Example for SSR (AT)

10. 1. SSRLocator
SSR discovery for large DNA sequences, and also for primer design and PCR simulation (Maia et al Int J Plant Genomics. 2008:412696)[PDF]
Tools: from Plant Genomics and Breeding Center - Federal University of Pelotas – Brazil ( ufpel.edu.br ).
Example: cowpea_EST_1_0693.fasta (linked)

11. 1. SSRLocator - running
Install SSRLocator in C: as showing C:\SSRLocatorI
Copy your data file with fasta format (.fasta) into the SSRLocatorI folder such as “cowpea_EST_1_0693.fasta”.
Open SSRLocatorI.exe
Format file to SSRLocator Standart in the “Create File” button. Save a new file called “cowpea_EST_1_0693format.fasta”
And more …….

12. 1. SSRLocator - Output
The SSR motif (AT) creates various repeats from 12 to 20 among the five cowpea samples (below Loci in the Table). Primer pairs are designed and expected PCR size are estimated ranged 211 to 381 bp. The polymorphism can be used as marker – SSR marker !
Contig
Loci
Start_SSR1
End_SSR1
FG938745_UCRVU09_UCR_707
(AT)20
239
278
FG908248_UCRVU08_CCNS5607_IT97K-461-4
(AT)13
204
229
FG875445_UCRVU07_CCNP10713_UCR_779
(AT)12
205
228
FG850994_UCRVU05_CCNN17188_IT84S-2049
(AT)19
200
237
FG815463_UCRVU04_CCNI2988_524B
(AT)15
216
245
Contig
Foward TM
Reverse
Product
Size
FG938745
AACAGCTTAGAGCGTGAAAG
55.1
TTTCGATGTGTGAGAAATGA
381
FG908248
CAGCTGTTAAACCACACAAA
54.9
213
FG875445
211
FG850994
224
FG815463
216

13. 2. MEGA and BioEdit
MEGA 6 and BioEdit can be used to view SSR motifs among DNA samples (above from MEGA 6 and the bottom from BioEdit)

14. 3. BatchPrimer3 BatchPrimer3 is the tool for primer design including
Primers for SSRs.
It can be used for SSR discovery as well.
Tool website:
Web tool:
An example cowpea_EST_1_0693.fasta”.

15. Molecular Plant Breeding
Fall 2014 HORT6033
Molecular Plant Breeding
Lecture 1 (08/25/2014)
IV. Homework
Download cowpea ESTs from GenBank
Download and Install software SSRLocator
Read SSRlocator manual and SSR articles
Download MEGA 6, BioEdit and manuals

16. Molecular Plant Breeding
Fall 2014 HORT6033
Molecular Plant Breeding
Lecture 1 (08/25/2014)
V. Homework
Download cowpea ESTs from GenBank

17. 2. Download and Install software SSRLocator
V. Homework
2. Download and Install software SSRLocator
Download the tools from Plant Genomics and Breeding Center - Federal University of Pelotas – Brazil ( ufpel.edu.br ). The tools for Windows Seven 32 bits should still work for Windows You should download FireBird (database for store SSR data) and SSRLocator. The In the web page, you can see the link for Install Instruction and User Guide. You should also download or view the instruction for FireBird and SSRLocator, and also for User Guide!

18. V. Homework
3. Read SSR locator manual and SSR articles Manual download! SSR article:

19. Thanks! Dear Students: Please read and download homework and quiz at!
Thanks!