Bean: Bean gene-based models dataset
In ZeBook: Working with Dynamic Models for Agriculture and Environment
Description
Usage
Format
Source
Examples
Description
Genetic data for the common bean (Phaseolus vulgaris L) that was based on a population
created by C. E. Vallejos (personal communication; also see Bhakta et al., 2015, 2017)
by crossing two widely-differing cultivars of bean (Calima, an Andean type, with Jamapa,
a Mesoamerican type).
Bean$marker : Bean Marker Data
Bean$MET : Weather data on 5 Locations
Bean$QTL : QTL Data
Bean$modelpar : Dynamic Model parameters
Usage
1
Format
a List including 4 data.frame Bean$marker, Bean$MET, Bean$QTL, Bean$modelpar.
Source
C. E. Vallejos (personal communication) and Bhakta et al. (2015, 2017).
Bhakta, M. S., V. A. Jones, C. E. Vallejos. 2015. Punctuated distribution of recombination hotspots and demarcation of pericentromeric regions in Phaseolus vulgaris L. PLoS ONE 10(1): https://doi.org/10.1371/journal.pone.0116822
Bhakta, M. S., S. A. Gezan, J. A. Clavijo Michelangeli, M. Carvalho, L. Zhang, J. W. Jones, K. J. Boote, M. J. Correll, J. Beaver, J. M. Osorno, R. Colbert, I. Rao, S. Beebe, A. Gonzalez, J. Ricaurte, and C. E.do Vallejos, 2017. A predictive model for time-to-flower in the common bean based on QTL and environmental variables. G3: Genes, Genomes, Genetics 7(12) 3901-3912. https://doi.org/10.1534/g3.117.300229.
Examples
1
2
3
4
5
6
7
8
9
Example output
Linked.Marker.data DiM_1.1 DiM_1.2 Bng195 DiM_1.3 DiM_1.4 DiM_1.5 DiM_1.6
2 JAM B B B B B B B
3 CAL A A A A A A A
4 RIJC001 B B B B B B B
5 RIJC002 A A A A A A A
6 RIJC003 B B B B A A A
7 RIJC004 A B B B B B B
8 RIJC005 A A A A A A A
DiM_1.7 DiM_1.8
2 B B
3 A A
4 B B
5 A A
6 A A
7 B B
8 A A
Genotype SITE TF.obs Srad Day Tmax Tmin
1 RIJC001 CIT 47 20.3 12.84 29.42 14.31
2 RIJC002 CIT 47 20.3 12.84 29.42 14.31
3 RIJC003 CIT 33 20.3 12.84 29.42 14.31
4 RIJC004 CIT 44 20.3 12.84 29.42 14.31
5 RIJC005 CIT 39 20.3 12.84 29.42 14.31
6 RIJC006 CIT 33 20.3 12.84 29.42 14.31
Linked.Marker DiM_1.13 Fin DiM_1.28 DiM_1.34 DiM_3.22 DiM_3.27 DiM_4.13
4 Calima 1 1 1 1 1 1 1
5 Jamapa -1 -1 -1 -1 -1 -1 -1
6 RIJC001 -1 -1 -1 1 -1 -1 -1
7 RIJC002 1 -1 1 1 1 -1 -1
8 RIJC003 1 1 1 1 1 1 -1
9 RIJC004 -1 -1 -1 -1 1 1 -1
10 RIJC005 1 1 1 -1 1 -1 -1
DiM_6.23 DiM_7.4
4 1 1
5 -1 -1
6 -1 1
7 -1 -1
8 1 -1
9 1 1
10 -1 -1
GSP.Effect Parameter QTL Value Std..Error Significance
1 a, Multiplier a0 n/a 0.0383385 0.0003531 ***
2 a, Multiplier a1 Tfi,1 0.0020454 0.0003151 ***
3 a, Multiplier a2 Tfi,2 0.0022676 0.0003588 ***
4 a, Multiplier a3 Tfi,3 -0.0001572 0.0004158 <NA>
5 a, Multiplier a4 Tfi,4 0.0007003 0.0003687 .
6 a, Multiplier a5 Tfi,5 0.0003044 0.0003862 <NA>
7 a, Multiplier a6 Tfi,6 0.0014344 0.0003849 ***
8 a, Multiplier a7 Tfi,7 -0.0004395 0.0002769 <NA>
9 a, Multiplier a8 Tfi,8 0.0007758 0.0002958 **
10 a, Multiplier a9 Tfi,9 -0.0005678 0.0002646 *
11 a, Multiplier a10 Tfi,10 -0.0003708 0.0002774 <NA>
12 a, Multiplier a11 Tfi,11 0.0020583 0.0003704 ***
13 a, Multiplier a12 Tfi,12 -0.0016888 0.0003758 ***
14 Topt, f(T) b0 n/a 28.2731522 0.1901096 ***
15 Topt, f(T) b1 Tfi,1 0.1620477 0.1735334 <NA>
16 Topt, f(T) b2 Tfi,2 -0.0332905 0.1944726 <NA>
17 Topt, f(T) b3 Tfi,3 -0.5332828 0.2164413 *
18 Topt, f(T) b4 Tfi,4 0.1519428 0.1900266 <NA>
19 Topt, f(T) b5 Tfi,5 0.1782697 0.2172405 <NA>
20 Topt, f(T) b6 Tfi,6 0.2515454 0.2127882 <NA>
21 Topt, f(T) b7 Tfi,7 -0.2348149 0.1536186 <NA>
22 Topt, f(T) b8 Tfi,8 0.4434925 0.1611772 **
23 Topt, f(T) b9 Tfi,9 -0.0057060 0.1483663 <NA>
24 Topt, f(T) b10 Tfi,10 0.0752517 0.1525530 <NA>
25 Topt, f(T) b11 Tfi,11 0.6252024 0.1976438 **
26 Topt, f(T) b12 Tfi,12 -0.9259222 0.2025129 ***
27 Beta, f(D) c0 n/a 0.0559803 0.0015134 ***
28 Beta, f(D) c1 Tfi,1 0.0017637 0.0016613 <NA>
29 Beta, f(D) c2 Tfi,2 -0.0011211 0.0019928 <NA>
30 Beta, f(D) c3 Tfi,3 0.0240581 0.0024992 ***
31 Beta, f(D) c4 Tfi,4 0.0009699 0.0021564 <NA>
32 Beta, f(D) c5 Tfi,5 0.0021426 0.0019912 <NA>
33 Beta, f(D) c6 Tfi,6 -0.0023279 0.0019625 <NA>
34 Beta, f(D) c7 Tfi,7 0.0093435 0.0014220 ***
35 Beta, f(D) c8 Tfi,8 0.0027584 0.0014618 .
36 Beta, f(D) c9 Tfi,9 -0.0010933 0.0014028 <NA>
37 Beta, f(D) c10 Tfi,10 -0.0012584 0.0014343 <NA>
38 Beta, f(D) c11 Tfi,11 0.0033323 0.0022207 <NA>
39 Beta, f(D) c12 Tfi,12 0.0046893 0.0021667 *
ZeBook documentation built on May 1, 2019, 9:48 p.m.
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Description Usage Format Source Examples
Description
Genetic data for the common bean (Phaseolus vulgaris L) that was based on a population created by C. E. Vallejos (personal communication; also see Bhakta et al., 2015, 2017) by crossing two widely-differing cultivars of bean (Calima, an Andean type, with Jamapa, a Mesoamerican type). Bean$marker : Bean Marker Data Bean$MET : Weather data on 5 Locations Bean$QTL : QTL Data Bean$modelpar : Dynamic Model parameters
Usage
1 |
Format
a List including 4 data.frame Bean$marker, Bean$MET, Bean$QTL, Bean$modelpar.
Source
C. E. Vallejos (personal communication) and Bhakta et al. (2015, 2017). Bhakta, M. S., V. A. Jones, C. E. Vallejos. 2015. Punctuated distribution of recombination hotspots and demarcation of pericentromeric regions in Phaseolus vulgaris L. PLoS ONE 10(1): https://doi.org/10.1371/journal.pone.0116822 Bhakta, M. S., S. A. Gezan, J. A. Clavijo Michelangeli, M. Carvalho, L. Zhang, J. W. Jones, K. J. Boote, M. J. Correll, J. Beaver, J. M. Osorno, R. Colbert, I. Rao, S. Beebe, A. Gonzalez, J. Ricaurte, and C. E.do Vallejos, 2017. A predictive model for time-to-flower in the common bean based on QTL and environmental variables. G3: Genes, Genomes, Genetics 7(12) 3901-3912. https://doi.org/10.1534/g3.117.300229.
Examples
1 2 3 4 5 6 7 8 9 |
Example output
Linked.Marker.data DiM_1.1 DiM_1.2 Bng195 DiM_1.3 DiM_1.4 DiM_1.5 DiM_1.6
2 JAM B B B B B B B
3 CAL A A A A A A A
4 RIJC001 B B B B B B B
5 RIJC002 A A A A A A A
6 RIJC003 B B B B A A A
7 RIJC004 A B B B B B B
8 RIJC005 A A A A A A A
DiM_1.7 DiM_1.8
2 B B
3 A A
4 B B
5 A A
6 A A
7 B B
8 A A
Genotype SITE TF.obs Srad Day Tmax Tmin
1 RIJC001 CIT 47 20.3 12.84 29.42 14.31
2 RIJC002 CIT 47 20.3 12.84 29.42 14.31
3 RIJC003 CIT 33 20.3 12.84 29.42 14.31
4 RIJC004 CIT 44 20.3 12.84 29.42 14.31
5 RIJC005 CIT 39 20.3 12.84 29.42 14.31
6 RIJC006 CIT 33 20.3 12.84 29.42 14.31
Linked.Marker DiM_1.13 Fin DiM_1.28 DiM_1.34 DiM_3.22 DiM_3.27 DiM_4.13
4 Calima 1 1 1 1 1 1 1
5 Jamapa -1 -1 -1 -1 -1 -1 -1
6 RIJC001 -1 -1 -1 1 -1 -1 -1
7 RIJC002 1 -1 1 1 1 -1 -1
8 RIJC003 1 1 1 1 1 1 -1
9 RIJC004 -1 -1 -1 -1 1 1 -1
10 RIJC005 1 1 1 -1 1 -1 -1
DiM_6.23 DiM_7.4
4 1 1
5 -1 -1
6 -1 1
7 -1 -1
8 1 -1
9 1 1
10 -1 -1
GSP.Effect Parameter QTL Value Std..Error Significance
1 a, Multiplier a0 n/a 0.0383385 0.0003531 ***
2 a, Multiplier a1 Tfi,1 0.0020454 0.0003151 ***
3 a, Multiplier a2 Tfi,2 0.0022676 0.0003588 ***
4 a, Multiplier a3 Tfi,3 -0.0001572 0.0004158 <NA>
5 a, Multiplier a4 Tfi,4 0.0007003 0.0003687 .
6 a, Multiplier a5 Tfi,5 0.0003044 0.0003862 <NA>
7 a, Multiplier a6 Tfi,6 0.0014344 0.0003849 ***
8 a, Multiplier a7 Tfi,7 -0.0004395 0.0002769 <NA>
9 a, Multiplier a8 Tfi,8 0.0007758 0.0002958 **
10 a, Multiplier a9 Tfi,9 -0.0005678 0.0002646 *
11 a, Multiplier a10 Tfi,10 -0.0003708 0.0002774 <NA>
12 a, Multiplier a11 Tfi,11 0.0020583 0.0003704 ***
13 a, Multiplier a12 Tfi,12 -0.0016888 0.0003758 ***
14 Topt, f(T) b0 n/a 28.2731522 0.1901096 ***
15 Topt, f(T) b1 Tfi,1 0.1620477 0.1735334 <NA>
16 Topt, f(T) b2 Tfi,2 -0.0332905 0.1944726 <NA>
17 Topt, f(T) b3 Tfi,3 -0.5332828 0.2164413 *
18 Topt, f(T) b4 Tfi,4 0.1519428 0.1900266 <NA>
19 Topt, f(T) b5 Tfi,5 0.1782697 0.2172405 <NA>
20 Topt, f(T) b6 Tfi,6 0.2515454 0.2127882 <NA>
21 Topt, f(T) b7 Tfi,7 -0.2348149 0.1536186 <NA>
22 Topt, f(T) b8 Tfi,8 0.4434925 0.1611772 **
23 Topt, f(T) b9 Tfi,9 -0.0057060 0.1483663 <NA>
24 Topt, f(T) b10 Tfi,10 0.0752517 0.1525530 <NA>
25 Topt, f(T) b11 Tfi,11 0.6252024 0.1976438 **
26 Topt, f(T) b12 Tfi,12 -0.9259222 0.2025129 ***
27 Beta, f(D) c0 n/a 0.0559803 0.0015134 ***
28 Beta, f(D) c1 Tfi,1 0.0017637 0.0016613 <NA>
29 Beta, f(D) c2 Tfi,2 -0.0011211 0.0019928 <NA>
30 Beta, f(D) c3 Tfi,3 0.0240581 0.0024992 ***
31 Beta, f(D) c4 Tfi,4 0.0009699 0.0021564 <NA>
32 Beta, f(D) c5 Tfi,5 0.0021426 0.0019912 <NA>
33 Beta, f(D) c6 Tfi,6 -0.0023279 0.0019625 <NA>
34 Beta, f(D) c7 Tfi,7 0.0093435 0.0014220 ***
35 Beta, f(D) c8 Tfi,8 0.0027584 0.0014618 .
36 Beta, f(D) c9 Tfi,9 -0.0010933 0.0014028 <NA>
37 Beta, f(D) c10 Tfi,10 -0.0012584 0.0014343 <NA>
38 Beta, f(D) c11 Tfi,11 0.0033323 0.0022207 <NA>
39 Beta, f(D) c12 Tfi,12 0.0046893 0.0021667 *
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