The document discusses a study on understanding the genetic basis of chapatti (Indian flat bread) making quality. Researchers analyzed samples from different wheat cultivars and identified genes associated with chapatti quality scores. Gene expression profiling identified differentially expressed genes between good and poor quality cultivars at different developmental stages. Upregulated genes in good quality cultivars were associated with storage proteins and nutrient reservoir activity, while downregulated genes were related to catalytic activity and starch biosynthesis.

1. 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.

9. Pinb-D1 Chapatti
Sample ID Character Hardness Pina-D1
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

10. Parameter/cultiva
C306 LOK1 WH291 SONALIKA
r
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
2*,17+18,
HMW-GS-ABD Null, 20, 2+12
2+12
2*,20, 2+12 2*,7+9, 2+12
PinaD1b, PinaD1b, PinaD1b, PinaD1a,
Puroindolines (5DS) PinbD1a PinbD1a PinbD1a PinbD1b

11. 7DAA 14DAA 21DAA 28DAA 35DAA
Fig. 1 Caryopsis at three developmental stages- 7, 14, 21, 28, & 35 days after
anthesis (DAA)
Affymetrix GeneChip® Wheat Genome Array
Expression profiling of 17,344 probe
sets at three developmental stages-
7DAA, 14DAA, 28DAA
11

12. Overview of experiment
RNA EXTRACTION
3’-IVT
Hybridization
Washing, Staining and scanning
File generation and Data analysis
AGCC-MAS5,RMA, GCRMA, PILER)
{GeneSpring, Array star,

15. Quality control of samples
 RIN calculation
Correlation coefficient (r)
Positive hybridization control

17. Summary

18. 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

19. Contd…. GO ANALYSIS:
Two fold regulation:
Functional annotation:
Molecular function: 43.6%
Up-regulating
Biological function: 34.0%
Catalytic subunit activity
Cellular function: 22.6%
Nutrient reservoir activity
DNA binding activity
Translational initiation factor activity
Down regulation:
Catalytic subunit activity
Magnesium ion binding activity

20. 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↓)

21. Contd…
Functional annotation: GO ANALYSIS:
Up-regulating Two fold regulation:
Response towards heat (HSP-16, 26) Molecular process: 33.3%
Lipid binding proteins and its transport Biological process: 66.6%
(LTP3)
Down regulation:
Catalase activity (Response towards
oxidative stress)
Starch biosynthesis activity (WGBSSI)

22. 1
2
3,4
5
30% - storage proteins
Major genes – No prior
30% -no prior information on gene
information on gene function.
function. Rest - Transcription
Rest - cytochrome C heme
factors, trypsin inhibitors,
attached protein, peroxidases.
metal binding, lipid transfer, cell
wall related proteins, etc.
starch synthesis, proteases
photosynthesis, regulatory genes

23. Differentially expressed genes (up and down)
Probe Set ID UniGen (DAA) Fold Function
S. e ID change
No.
1 Ta.24736.1.S1_at NA 7 +284.7 Predicted protein (Hordeum
vulgare )
2 Ta.27778.4.S1_x_at Ta.5420 7 +108.1 Pre-alpha-/beta-gliadin A-II
6
3 Ta.7158.1.S1_at Ta.7158 7 +105.9 Transcribed locus
4 Ta.6175.1.S1_at Ta.3546 7 +102.3 No significant similarity in non-
3 redundant (nr) protein
sequences database
5 Ta.24114.14.S1_x_ Ta.6588 7 +284.7 Triticum aestivum gamma-
at 1 gliadin gene
At the three development stages among two good and two poor chapatti varieties
23
Source-Dr. Joy K Roy

24. 6 Ta.6984.1.A1_at Ta.5710 7 -58.0 Predicted protein & also
0 similar with PHD zinc finger
protein-like [Oryza sativa
Japonica Group]
7 TaAffx.104444.1.S1 Ta.3578 7 -47.5 No significant similarity
_at 4
8 Ta.23013.3.S1_s_a NA 7 -31.5 B22EL8 [Hordeum vulgare]
t
9 Ta.14507.2.S1_at Ta.5418 7 -29.9 Predicted protein & also similar
6 with nucleotide-binding protein
1 [Zea mays]
10 Ta.4957.1.S1_at Ta.4957 7 -26.6
Triticum aestivum granule
bound starch synthase I (GbssI)
11 Ta.23366.2.S1_at 28 Triticum aestivum TaPrx-B
NA +59.96 mRNA for peroxidase, partial
cds
12 Ta.28744.1.S1_at Ta.2874 28 Transcribed locus, Triticum
+35.22
4 aestivum cDNA
13 Ta.14050.1.S1_at 28 Hordeum vulgare subsp.
Ta.1405 24
+37.26 vulgare mRNASource-Dr. Joy K Roy
for predicted

25. 14 TaAffx.91902.1.A1 28
_at Ta.4769 Transcribed locus, Triticum
+32.62
5 aestivum cDNA
15 Ta.23366.2.S1_x_at 28 Triticum aestivum TaPrx-B
NA +28.88 mRNA for peroxidase, partial
cds
16 Ta.2025.1.S1_at 28 -1727.4 Transcribed locus_Hordeum
Ta.2025 vulgare subsp. vulgare cDNA
clone: FLbaf53o13
17 Ta.24114.7.A1_at Ta.3098 28 -92.767 Triticum aestivum granule
9 bound starch synthase I (GbssI)
18 TaAffx.80118.1.S1_ Ta.4855 28 -32.63 Transcribed locus
at 8
19 Ta.14489.1.S1_at 28 -28.99 S.cereale acclimation
NA protein/Triticum aestivum cold-
responsive protein (Wlt10)
20 Ta.27445.1.S1_at Ta.2744 28 -28.62 Medicago sativa FtsH protease
5 (FtsH) mRNA/Triticum aestivum
clone wlp1c.pk007.f6:fis 25
Source-Dr. Joy K Roy

26. 26

28. DAY
NIGHT
zEEMAN et al. Biochem. J. (2007) 401 (13–28

29. Nagai Y S et al. Plant Cell Physiol 2009;50:635-643
© The Author 2009. Published by Oxford University Press on behalf of Japanese Society of Plant
Physiologists. All rights reserved. For permissions, please email:
journals.permissions@oxfordjournals.org

32. ©2009 by National Academy of Sciences Tian Z et al. PNAS 2009;106:21760-21765

34. GBSS genes
GBSS genes
GC rich rich
GC
11 EXONS 10 INTRONS
11 EXONS 10 INTRONS
GBSS A1 gene
2781bp
GBSS B1 gene
2794bp
GBSS D1 gene
2862bp

36. Saito et al., JARQ 44 (2), 109–115 (2010)

37. Low amylose content
(27-28% compared to 29%
22-23% compared to 25%)
Amylopectin matrix in
starch granule can swell
better
Good starch swelling properties-
Good for Udon noodles

38. Indian Chapatti Softness Japanese Udon
38

39. 39

40. Null GBSS A1 gene
Deletion mutation -19bp
2762bp (2781bp wild type)

41. Null GBSS A1 gene
Insertion mutation from Turkey
(Transposable element)
2854bp (2781bp wild type)
IR IR 12bp
Transp.elemt
Target site duplication 8bp

42. Null GBSS B1 gene
Absence (2794bp wild type)

43. Null GBSS D1 gene
Deletion mutation 2850bp (2862bp
wild type)

44. GBSS D1 gene
Allele GBSS-D1e
Yanagisawa et al EUPHYTICA, 121-3, 209-214

45. Waxy
Waxy
Normal
Nakamura et al. Plant physiology

46. Nakamura et al. Plant physiology

49. 49
49

50. 50

51. Chapatti 5+10/
S.No Cultivar GBSS 4A1 PINa-D1
Quality 2+12
1 Good PBW550 A 5+10 b
2 Good C306 A 2+12 b
3 Good LOK1 A 2+12 b
4 Good PBW175 A 2+12 b
5 Good HI1563 A 2+12 b
6 Good K8027 A 5+10 b
7 Good HD2888 A 2+12 b
8 Good HI1500 A 2+12 b
9 Good PBW175 A 2+12 b
51

52. 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
52

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+12LIGHT b
10 CPAN4202 P 2+12 b
11 UTKALIKA P 5+10 b
12 DWR39 P 2+12 b
53

54. 2000
1500
1000
500
3 6 9 12 15
54
• Batey et al., 1997. Cereal Chem. 74(4):497–50

55. Influenced of RVA breakdown on chapatti making quality
Medium RVA
breakdown in poor
chapatti variety
(Sonalika) Commercial
High RVA C306
breakdown in good Sonalika
chapatti variety Lok1
(C306, Lok1) WH291
Low RVA breakdown
in poor chapatti
variety (WH291) Rapid visco
analyzer’s graph
Variety Breakdown Final Viscosity Set back Peak time Pasting temp
(cP) (cP) (cP) (min) (˚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
• 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

56. GBSSB1
778 bp
668 bp
GBSSB1null 500 bp
250 bp

57. F1
1st Year
BC1
MAs
BC2
2nd Year MAS
BC3
BC3F2 BC4

58. 58

59. 59

60. 60