Towards understanding genetic basis of chapatti (Indian flat bread) making quality M. GARG, S. ARORA, R.P. Singh*, A. SINGH, J.K. ROY National Agri-Food Biotechnology Institute *Deptt. Of Plant Breeding and Genetics Punjab Agricultural University, Ludhiana.
60
Embed
Towards understanding genetic basis of chapatti (Indian flat bread) making quality
International Gluten Workshop, 11th; Beijing (China); 12-15 Aug 2012
Welcome message from author
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Towards understanding genetic basis of chapatti (Indian flat bread) making quality
M. GARG, S. ARORA, R.P. Singh*, A. SINGH, J.K. ROY
National Agri-Food Biotechnology Institute
*Deptt. Of Plant Breeding and Genetics
Punjab Agricultural University, Ludhiana.
Sample ID Character Hardness Pina-D1 Pinb-D1
Chapatti
Score
CHINESE SPRING Check 48.66 a a -
PBW 343 Check 86.26 b a 7.5
WH 291 Chapatti 60.81 b a 5
SONALIKA Chapatti 66.88 a b 6
C 306 Chapatti 94.64 b a 9
LOK 1 Chapatti 67.51 b a 7
Parameter/cultivar
C306 LOK1 WH291 SONALIKA
Chapatti score Very Good Good Poor Medium Poor
Grain hardness (g) Hard Med Soft Med hard Med Soft
Seed size Med Med Small Large
Color White Brown Brown Brown
Water absorption High Med Med Med
Protein content Med Med High Med
Gluten Medium Medium High Low
Starch gelatinisation Medium High Medium High
RVA Breakdown High High Low Medium
HMW-GS-ABD Null, 20, 2+12 2*,17+18,
2+12 2*,20, 2+12 2*,7+9, 2+12
Puroindolines (5DS) PinaD1b, PinbD1a
PinaD1b, PinbD1a
PinaD1b, PinbD1a
PinaD1a, PinbD1b
11
Affymetrix GeneChip® Wheat Genome Array
7DAA 14DAA 21DAA 28DAA 35DAA Fig. 1 Caryopsis at three developmental stages- 7, 14, 21, 28, & 35 days after
anthesis (DAA)
Expression profiling of 17,344 probe
sets at three developmental stages-
7DAA, 14DAA, 28DAA
RNA EXTRACTION
3’-IVT
Hybridization
Washing, Staining and scanning
File generation and Data analysis
AGCC-MAS5,RMA, GCRMA, PILER)
{GeneSpring, Array star,
Overview of experiment
Quality control of samples RIN calculation
Correlation coefficient (r)
Positive hybridization control
Summary
Data analysis of7DAA Good vs. Poor
61,290 (Total probe sets)
Normalized & filter by percentile
37,277 (Probe sets)
Statistical data analysis
2,989 (Probe sets)
Fold change analysis
59
1027 137
Functional annotation:
Up-regulating
Catalytic subunit activity
Nutrient reservoir activity
DNA binding activity
Translational initiation factor activity
Down regulation:
Catalytic subunit activity
Magnesium ion binding activity
GO ANALYSIS:
Two fold regulation:
Molecular function: 43.6%
Biological function: 34.0%
Cellular function: 22.6%
Contd….
Data analysis of28DAA Good vs.Poor
61,290 (Total probe sets)
Normalized & filter by percentile
33,083 (Probe sets)
Statistical data analysis
527 (Probe sets)
Fold change analysis
• 194 (113↑, 81↓)
• 72 (33↑, 26↓)
• 19 (9↑, 10↓)
Functional annotation:
Up-regulating
Response towards heat (HSP-16, 26)
Lipid binding proteins and its transport (LTP3)
Down regulation:
Catalase activity (Response towards oxidative stress)
Starch biosynthesis activity (WGBSSI)
GO ANALYSIS:
Two fold regulation: Molecular process: 33.3%
Biological process: 66.6%
Contd…
30% - storage proteins
30% -no prior information on gene
function. Rest - Transcription
factors, trypsin inhibitors,
metal binding, lipid transfer, cell
wall related proteins, etc.
photosynthesis, regulatory genes
Major genes – No prior
information on gene function.
Rest - cytochrome C heme
attached protein, peroxidases.
starch synthesis, proteases
1 2
3,4 5
23
S.
No.
Probe Set ID UniGen
e ID
(DAA) Fold
change
Function
1 Ta.24736.1.S1_at NA 7 +284.7 Predicted protein (Hordeum
vulgare )
2 Ta.27778.4.S1_x_at Ta.5420
6
7 +108.1 Pre-alpha-/beta-gliadin A-II
3 Ta.7158.1.S1_at Ta.7158 7 +105.9 Transcribed locus
4 Ta.6175.1.S1_at Ta.3546
3
7 +102.3 No significant similarity in non-
redundant (nr) protein
sequences database
5 Ta.24114.14.S1_x_
at
Ta.6588
1
7 +284.7 Triticum aestivum gamma-
gliadin gene
Differentially expressed genes (up and down)
At the three development stages among two good and two poor chapatti varieties Source-Dr. Joy K Roy
10 HI977 A 5+10 b 11 HI1563 A 2+12 b 12 HD2987 A 5+10 b 13 HD2236 A 2+12 b 14 HD2385 A 2+12 b 15 WH416 A 2+12 b 16 JWS17 A 2+12 b 17 K8434 A 2+12 b 18 HD2307 A 2+12 b 19 HD2380 A 2+12 a
20 TAWA267 A 2+12 b
53
1 Poor PBW343 P 5+10 b
2 Poor PBW621 P 2+12 b
3 Poor SONALIKA P 2+12 a
4 Poor WH291 P 2+12 b
5 Soft IITR67 P 2+12 a
6 Soft NAPHAL P A a
7 HUW629 P 5+10 b
8 UAS305 P 5+10 b
9 DHT5 P 2+12 LIGHT b
10 CPAN4202 P 2+12 b
11 UTKALIKA P 5+10 b
12 DWR39 P 2+12 b
54
• Batey et al., 1997. Cereal Chem. 74(4):497–50
3 6 9 12 15
500
1000
1500
2000
Rapid visco
analyzer’s graph
Influenced of RVA breakdown on chapatti making quality
Variety Breakdown (cP)
Final Viscosity (cP)
Set back (cP)
Peak time (min)
Pasting temp (˚C)
C306 648.7 1580.7 828.3 5.7 69.7
LOK1 752.3 1821.0 842.0 5.9 85.2
WH291 374.3 1393.0 697.7 5.4 65.8
Sonalika 504.0 1923.0 935.7 6.0 87.7
Commercial
C306
Sonalika
Lok1
WH291
High RVA breakdown in good chapatti variety (C306, Lok1)
Low RVA breakdown in poor chapatti variety (WH291)
Medium RVA breakdown in poor chapatti variety (Sonalika)
•The analysis will be repeated on the above samples and to be conducted on a larger samples to calculate correlation between RVA breakdown and good chapatti