Genetic Analysis and Molecular Markers of Root vigor of Canola
Mukhlesur Rahman and Arif-Uz-Zaman North Dakota State University Fargo, ND, USA
Why vigorous root system is important Strong root system can uptake more water and nutrient. It helps crop for good stand. Root vigor is prerequisite for optimal plant growth, that boost the yield (Marschner, 1998). In canola, few studies describe the importance of root traits for nutrient acquisition (Solaiman et al. 2007; Duan et al., 2009).
Canola Root System
Spring canola roots in 4Ë? pot
Winter canola roots in 4Ë? pot
Spring canola roots
Winter canola roots
Rahman and McClean (2013): Crop Sci. 53:141–147
Canola Root System
Genetic analysis of root vigor
Plant materials • Parents: –
Winter: Lorenz, Lagoda, and ARC97018
–
Spring: Legend and Regent
• Crosses and Reciprocal Crosses –
Lorenz × Legend
–
Legend x Lorenz
–
Lagoda × Regent
–
Regent x Lagoda
–
ARC97018 x Regent
–
Regent x ARC97018
Roots in F1 generation
Winter - Parent
F1 (Win x Spring)
F1 (Spring x Win)
Spring - Parent
Rahman and McClean (2013): Crop Sci. 53:141–147
Segregation of ROOT VIGOR in F2 population
Score-1
Score-2
Score-3
Score-4
Score-5
Root score-1: plants with weak bottom & surface roots those observed in spring parents. Root score-2: more bottom and surface roots. Root score-3: intermediate bottom and surface roots. Root score-4: strong bottom and surface roots. Root score-5: strongest bottom and surface roots those observed in winter parents. Rahman and McClean (2013): Crop Sci. 53:141–147
Segregation of ROOT VIGOR in F2 population
F2 Population
Total Plants
Lorenz × Legend 179 Legend × Lorenz 179 Lagoda × Regent 179 Regent × Lagoda 180 Regent x ARC97018 176 ARC97018 x Regent 165 Total χ2 (pooled data) 1058 Homogeneity χ2 (total – polled)
Vigorous Weak roots Roots (score 2-5) (score-1) 174 178 176 179 172 160
5 1 3 1 4 5
1039
19
Segregation ratio 15:1 63:1 χ2 3.65 9.89 6.39 9.96 4.75 2.92 37.56 35.82 1.74
df
P
χ2
1 0.060 1.76 1 0.002 1.73 1 0.010 0.02 1 0.002 1.19 1 0.066 0.58 1 0.090 2.31 6 >0.001 7.59 1 >0.001 0.38 5 0.88 7.21
df
P
1 1 1 1 1 1 6 1 5
0.18 0.19 0.89 0.28 0.46 0.14 0.18 0.55 0.30
Flowering Time
Spring types ďƒ˜ Vernalization not required
Winter types ďƒ˜ Vernalization required (4oC)
Flowering Time Flowering No flowering without vernalization
P1 (Winter)
F1 (WinxSp)
P2 (Spring)
Flowering Time
F2 Population Lorenz × Legend Legend × Lorenz Lagoda × Regent Regent × Lagoda ARC97018 x Regent Regent x ARC97018 Favorite x Legend Legend x Favorite Vision x Topas Topas x Vision χ2 (pooled data)
Total Plants Flowered 142 151 180 180 76 57 75 78 77 78 1094
103 103 140 145 60 49 54 60 62 63 839
Not Flowered 39 48 40 35 16 8 21 18 15 15 255
Segregation ratio 3:1 χ2
P
0.46 3.02 0.74 2.96 0.63 3.66 0.36 0.15 1.25 1.38 1.67
0.5 0.08 0.39 0.09 0.43 0.06 0.06 0.51 0.27 0.25 0.2
Molecular marker for root vigor Root traits are complex in nature Root phenotyping is difficult, time & labor intensive Molecular marker may help us for early selection of desired root traits
GENOTYPING DNA extraction and marker analysis: ď ą 92 F2 plants from Regent and Lagoda crosses ď ą GBS data obtained from the Institute of Genomic Diversity, Cornell University, Ithaca, NY.
LINKAGE MAPPING 25,942 Initial SNPs Discard Monomorphic Parental missing data Parental heterozygosity
6,657 SNPs
Genotype missing data >50% Chi-Sq (p>0.05)
4,570 SNPs Framework mapping in CARTHAGENE with LOD threshold 3 Final SNPs= 1,025. Total LGs= 23; Map Length= 4,290
QTL ANALYSIS Composite Interval Mapping method was used in Qgene (Joehanes & Nelson, 2008) A QTL was defined as the region on chromosome that has a LOD ≥ 3.
QTL ANALYSIS Putative R-square Chromos
Trait
QTL
LOD
Root Vigor
NRV-1
3.56
22.2
A01
Days to Flower
NFT-1
4.48
17.3
C08_1
Root Vigor QTL
Days to flowering QTL
Blast Analysis Table : Identified QTL for root vigor and days to flowering with putative candidate genes from BLAST against Brassicaceae family gene model Trait
QTL
Root Vigor
NRV-1
QTL Position in LG (cM) Flanking Markers 132
A01_20479286 (L)
Position in Position in Chromosome Chromosome LG (cM) (Mbp) 127.1
20.47
At GR5 (20.54 Mbp)
20.85
GIP1 GBFinteracting protein (20.65 Mbp)
A01
Days to Flower
NFT-1
36
A01_20857091 (R)
141.7
C08_8399161 (L)
32
C08_8399213(R)
42.6
A08
Candidate genes with Positions
83.99 83.99
Ath AGAMOUS like 65 (84.14 Mbp)
At GR5
Growth regulating factor that encodes transcription activator. It expressed in root, shoot and flower.
GIP1 GBF-interacting protein
Encodes a protein that binds to G-box binding transcription factors. It expressed predominantly in the root.
At AGAMOUS like 65
AGAMOUS is a large group of gene family which encodes MADs-BOX transcription factors for different flowering traits. AGAMOUS like 65 is related to flower development.
Future study on Root traits We have developed double haploid lines of some winter and spring parents. We will make new crosses between DH parents. We will also develop new F1 derived DH and F2 populations to study the genetics of root trait morphology – and will validate the QTL in the new populations. Association mapping with 367 genetically diverged germplasm
Acknowledgements
Funding:
National Institute of Food and Agriculture (NIFA) Northern Canola Growers’ Association
Genotyping:
Institute of Genomic Diversity, Cornell University, Ithaca, NY
Data Analysis:
Phil McClean Sujan Mamidi
Thank you