BỘ GIÁO DỤC VÀ ĐÀO TẠO
TRƢỜNG ĐẠI HỌC NÔNG LÂM TP. HỒ CHÍ MINH
BỘ MÔN CÔNG NGHỆ SINH HỌC
***000*** TRẦN NGUYỄN MINH ĐĂNG XÂY DỰNG CƠ SỞ DỮ LIỆU SSRs (SIMPLE
SEQUENCE REPEATS) TỪ ESTs (EXPRESSED
SEQUENCE TAGS) CỦA CÂY DỨA (Ananas comosus)



/2006
MINISTRY OF EDUCATION AND TRAINING
NONG LAM UNIVERSITY, HCMC
DEPARTMENT OF BIOTECHNOLOGY
***000***

BUILDING SSRs (SIMPLE SEQUENCE REPEATS)
DATABASE FROM ESTs (EXPRESSED SEQUENCE
TAGS) OF PINEAPPLE (Ananas comosus)
Graduation thesis
Major: Biotechnology

Professor Student
PhD. Tran Thi Dung TRAN NGUYEN MINH DANG

điều kiện và động viên con trong suốt quá trình học tập tại trƣờng.

Tháng 08 năm 2006

Trần Nguyễn Minh Đăng

v
TÓM TẮT KHOÁ LUẬN

TRẦN NGUYỄN MINH ĐĂNG, đại học Nông Lâm TP. Hồ Chí Minh, tháng
08/2006. “XÂY DỰNG CƠ SỞ DỮ LIỆU SSRs (SIMPLE SEQUENCE
REPEATS) TỪ ESTs (EXPRESSED SEQUENCE TAGS) CỦA CÂY DỨA
(Ananas comosus)”

 
 
              





 


 Ananas comosus 


 


 ................................................................................................................. 5
2.1.3.4. Hoa ............................................................................................................... 5
 ............................................................................................................... 6
 ................................................................................................................ 6
 .................................................................................................... 6
2.1.4 .............................................................................................. 6
 ............................................................................................... 6
 ............................................................................................. 7
 .......................................................................................... 7
 .......................................................................................................... 8
 ............................................................................................. 8
 ................................................................................................ 9
 .............................................................................................. 9

vii
 ........................................................................................... 10
 ....................................................................... 11
 ........................................ 11
2.2. Các Marker phân tử ............................................................................................ 12
2.2.1. Isozymes .................................................................................................................... 12
2.2.2. ALP ............................................................................................................................ 12
2.2.3. AFLP .......................................................................................................................... 12
2.2.4. RAPD ......................................................................................................................... 13
2.2.5. SSCP .......................................................................................................................... 14
2.2.6. SNP ............................................................................................................................ 14
2.2.7. SSR ............................................................................................................................. 15
2.2.8.   .................................................................................. 15
2.2.9. RFLP .......................................................................................................................... 15
2.3. Chi tiết về microsatellite ..................................................................................... 16
 ................................................................................................................. 16

 .............................................................................. 28
2.7. Ngôn ngữ lập trình Perl và Javascript .............................................................. 28
 ........................................................................................................... 28
2.7.1.1. T ........................................................................... 28
.................................................................................................... 29
 .......................................... 29
................................................................................................. 30
 ................................................................................. 31
 ............................................................................ 31
 .............................................................. 31
2.8. Cơ sở dữ liệu sinh học ......................................................................................... 32
2.8.1. NCBI .......................................................................................................................... 32
 ......................................................................................... 32
 ............................................................... 33
 ....................................................................... 33
Phần 3. Phƣơng pháp và chƣơng trình sử dụng ....................................................... 35
3.1. Các chƣơng trình và ngôn ngữ lập trình đƣợc sử dụng .................................. 35
 ............................................................................................................. 35
  ....................................................................... 35
 .................................................... 35
 BLAST ....................... 36
 ............................................................. 36
3.1.2.4. Apache web Server .................................................................................... 37
3.2. Thu nhận trình tự SSRs ...................................................................................... 38
 ................................................................................... 40

ix
3 ............................................................................................. 41
3.3. Xây dựng CSDL, công cụ để giúp ngƣời dùng có thể khai thác tốt dữ liệu. .. 44
 ............................................................................................ 44

 ...................................................... 2
 ................................................... 3
- Red Spanish  Cayenne ................................ 11
 .............................................................. 22
 ............................... 25
-DBI-DBD- ...................................... 30
 ..... 32
 ......... 38
 ................................. 39
............................. 40
 .............................. 41
........................ 42
......................................................... 42
 .................................................... 43
 ..................................................... 44
 ........................................................... 47
 .................................................. 48
 ....................................... 50
 .................................................................... 57
 ....................................................................... 59
 ................................................... 60
Ananas comosus .............................................. 61
 ESTs ............................................................................. 61
 .................................................................... 62
 ............ 63
 .................................................. 64 xi
DANH SÁCH CÁC BẢNG

HTTP Hypertext Transfer Protocol
JSP Java Server Page
NCBI the National Center for Biotechnology Information
NIG the National Institute of Genetics
NIH the National Institutes of Health
NLM the Nation Library of Medicine
Perl Practical Extraction and Report Language
PHP Hypertext Preprocessior
RAPD Random Amplififed Polymorphic DNA
RDBMS Relational Database Management System
RFLP Restriction Fragment Length Polymorphism
SNP Single Nucleotide Polymorphism
SSCP Single- Strand Conformation Polymorphism
SSR Simple Sequence Repeats
STS Sequence Tagged Site

1

Phần 1
MỞ ĐẦU

1.1. Đặt vấn đề
1.1.1. Sơ lƣợc về sinh – tin học
 
.214.
 SWISS-
 

 


 

  
X 
 citric, men bromelin...
 
 

1.1.3. Sơ lƣợc về phƣơng pháp Microsatellite (SSR)
ng c c li quyt vn  nh danh
v pht hiy b ng thi cng nh gi 


TOÁN HỌC
KHOA HỌC MÁY TÍNH
THỐNG KÊ
SINH HỌC
HÓA HỌC
VẬT LÝ

Bioinformatics

3 Hình 1. 2. Tìm hiểu nguồn gốc dựa vào Microsatellite
1.2. Mục tiêu của khóa luận




 : 
2.1.2. Nguồn gốc và phân bố
 
          



o

o
, kinh

o

o

(Claude, 1963)
            

 




 
 


5



6






2.1.3.5. Quả
- 
     


 

2.3.1.6. Hạt




2.1.4. Đặc điểm trồng trọt
2.1.4.1. Yếu tố khí hậu


o
C  31
o

o



 




2.1.4.3. Yếu tố sinh vật
              

Dysmicocus Pseudoeocus brevipes).
Adoretus chinensis 

             

          Phytophthora
cinnamonic  Phytophthora palmisora    Erwinia
chrysanthemi

2.1.5. Giá trị kinh tế và sử dụng


        



Vitamin A.
8

Vitamin C.







 (Wilt).

2.1.6.2. Nhóm Queen





 Cayenne.






 
 


2.1.6.3. Nhóm Spanish (Tây Ban Nha)






 
 
11 Hình 2. 1. Các giống dứa Natal Queen - Red Spanish – Cayenne
(
2.1.6.5. Các giống trồng trong nƣớc
 

 Na hoa (Nam phi Queen): Paris, Yellow Mauritius

 

 K
  
 
 Canning, Alexandra, Mac-
 
2.1.7. Tình hình phát triển của cây dứa trong và ngoài nƣớc
             


 




 
.

 

 .
.
13

2.2.4. RAPD (Random Amplififed Polymorphic DNA)







  
             

 


ra AP-PCR (Arbitrary Primer- PCR).
Trong AP-
             

 
 

0

