Genetic association between microsatellite loci and phenotypic traits of weedy rice.
Kethuvarni Veeranmuthu, 23039213
Part 3A.
Title: Genetic association between microsatellite loci and phenotypic traits of weedy rice.
Objective:
The main aim of this practical was to determine the whether there is association between markers and phenotypes of weedy rice plants (seed awn and pericarp colour).Besides, this practical was aimed to understand chi-square analysis to test the genetic association. Understanding the concept of linkage disequilibrium was also one of the objectives of this practical.
Chi-square statistical analysis was used to identify the association between markers and phenotypes of weedy rice plants tested.
Results:
For Awn and Awnless:
Table 1.0: Chi-square calculation of phenotype I (awn-awnless) and genotype (RM106) correlation.
Genotype
Phenotype
Row total (p)
Awn
Awnless
Observed number (O1)
Expected number (E1)
Chi square,X2
(O1-E1)2 / E1
Observed number (O2)
Expected number (E2)
Chi square,X2
(O2-E2)2 / E2
RM106_a
0
0.58
0.58
1
0.42
0.80
1
RM106_b
2
3.50
0.64
4
2.50
0.90
6
RM106_c
6
3.50
1.79
0
2.50
2.50
6
RM106_d
3
2.33
0.19
1
1.67
0.27
4
RM106_e
3
4.08
0.29
4
2.91
0.41
7
Column Total
14
-
3.49
10
-
4.88
24
Chi-square, X2 total
8.37
H0: The phenotype of awn/awnless is not associated with RM106
Ha: The phenotype of awn/awnless is associate with RM106
Df = 4 X0.052 = 9.49
Since X2 < X0.052, the Ho is not rejected. RM106 was not associated with awn phenotype.
Table 1.1: Chi-square calculation of phenotype I (awn-awnless) and genotype (RM345) correlation.
Genotype
Phenotype
Row total (p)
Awn
Awnless
Observed number (O1)
Expected number (E1)
Chi square,X2
(O1-E1)2 / E1
Observed number (O2)
Expected number (E2)
Chi square,X2
(O2-E2)2 / E2
RM345_a
14
13.4
0.03
9
9.58
0.04
23
RM345_b
0
0.58
0.30
1
0.42
0.80
1
Column Total
14
-
0.33
10
-
0.84
24
Chi-square, X2 total
1.17
H0: The
Part 3A.
Title: Genetic association between microsatellite loci and phenotypic traits of weedy rice.
Objective:
The main aim of this practical was to determine the whether there is association between markers and phenotypes of weedy rice plants (seed awn and pericarp colour).Besides, this practical was aimed to understand chi-square analysis to test the genetic association. Understanding the concept of linkage disequilibrium was also one of the objectives of this practical.
Chi-square statistical analysis was used to identify the association between markers and phenotypes of weedy rice plants tested.
Results:
For Awn and Awnless:
Table 1.0: Chi-square calculation of phenotype I (awn-awnless) and genotype (RM106) correlation.
Genotype
Phenotype
Row total (p)
Awn
Awnless
Observed number (O1)
Expected number (E1)
Chi square,X2
(O1-E1)2 / E1
Observed number (O2)
Expected number (E2)
Chi square,X2
(O2-E2)2 / E2
RM106_a
0
0.58
0.58
1
0.42
0.80
1
RM106_b
2
3.50
0.64
4
2.50
0.90
6
RM106_c
6
3.50
1.79
0
2.50
2.50
6
RM106_d
3
2.33
0.19
1
1.67
0.27
4
RM106_e
3
4.08
0.29
4
2.91
0.41
7
Column Total
14
-
3.49
10
-
4.88
24
Chi-square, X2 total
8.37
H0: The phenotype of awn/awnless is not associated with RM106
Ha: The phenotype of awn/awnless is associate with RM106
Df = 4 X0.052 = 9.49
Since X2 < X0.052, the Ho is not rejected. RM106 was not associated with awn phenotype.
Table 1.1: Chi-square calculation of phenotype I (awn-awnless) and genotype (RM345) correlation.
Genotype
Phenotype
Row total (p)
Awn
Awnless
Observed number (O1)
Expected number (E1)
Chi square,X2
(O1-E1)2 / E1
Observed number (O2)
Expected number (E2)
Chi square,X2
(O2-E2)2 / E2
RM345_a
14
13.4
0.03
9
9.58
0.04
23
RM345_b
0
0.58
0.30
1
0.42
0.80
1
Column Total
14
-
0.33
10
-
0.84
24
Chi-square, X2 total
1.17
H0: The
References: Liu, K., M.M. Goodman, S. Muse, J.S.C. Smith, E.S. Buckler, and J. Doebley, 2003.Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165: 2117-2128.