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Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals QTL Hotspots and Epistatic Interactions.

Basnet RK, Duwal A, Tiwari DN, Xiao D, Monakhos S, Bucher J, Visser RG, Groot SP, Bonnema G, Maliepaard C - Front Plant Sci (2015)

Bottom Line: The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species.We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustrating the polygenic nature of these traits.These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding.

View Article: PubMed Central - PubMed

Affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen University Wageningen, Netherlands ; Centre for BioSystems Genomics Wageningen, Netherlands.

ABSTRACT
The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (QTL) of seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 mapped at the B. rapa Flowering Locus C (BrFLC2). Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa Fatty acid desaturase 2 (BrFAD2) locus. Epistatic interactions were observed between QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding.

No MeSH data available.


Related in: MedlinePlus

eQTL profiles for BrFLC2 (a Brassica homolog of FLC2 of A. thaliana) and BrFAD2 (a Brassica homolog of FAD2 of A. thaliana) measured in developing B. rapa seeds (28 days after pollination) across 10 linkage groups. The y-axis represents the LOD score, the x-axis represents the 10 linkage groups separated by dotted lines; the QTL significance threshold is indicated by a red colored solid line at LOD score 3.
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Figure 4: eQTL profiles for BrFLC2 (a Brassica homolog of FLC2 of A. thaliana) and BrFAD2 (a Brassica homolog of FAD2 of A. thaliana) measured in developing B. rapa seeds (28 days after pollination) across 10 linkage groups. The y-axis represents the LOD score, the x-axis represents the 10 linkage groups separated by dotted lines; the QTL significance threshold is indicated by a red colored solid line at LOD score 3.

Mentions: For BrFLC2, a cis-eQTL was mapped over the Co-QTL2-1 and -2 hotspots on A02 with LOD scores 5.4 and 3.7 that explained 20.8 and 14.0% of the total variation in transcript abundance, respectively. For BrFAD2, a cis-eQTL co-located with the Co-QTL5-1 and -2 regions with LOD score 7.1 and 22.0% explained variance while another trans-eQTL mapped at the Co-QTL9-2 region on A09 with LOD score 3.6 and 10.5% explained variance (Figure 4; Table 5).


Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals QTL Hotspots and Epistatic Interactions.

Basnet RK, Duwal A, Tiwari DN, Xiao D, Monakhos S, Bucher J, Visser RG, Groot SP, Bonnema G, Maliepaard C - Front Plant Sci (2015)

eQTL profiles for BrFLC2 (a Brassica homolog of FLC2 of A. thaliana) and BrFAD2 (a Brassica homolog of FAD2 of A. thaliana) measured in developing B. rapa seeds (28 days after pollination) across 10 linkage groups. The y-axis represents the LOD score, the x-axis represents the 10 linkage groups separated by dotted lines; the QTL significance threshold is indicated by a red colored solid line at LOD score 3.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664704&req=5

Figure 4: eQTL profiles for BrFLC2 (a Brassica homolog of FLC2 of A. thaliana) and BrFAD2 (a Brassica homolog of FAD2 of A. thaliana) measured in developing B. rapa seeds (28 days after pollination) across 10 linkage groups. The y-axis represents the LOD score, the x-axis represents the 10 linkage groups separated by dotted lines; the QTL significance threshold is indicated by a red colored solid line at LOD score 3.
Mentions: For BrFLC2, a cis-eQTL was mapped over the Co-QTL2-1 and -2 hotspots on A02 with LOD scores 5.4 and 3.7 that explained 20.8 and 14.0% of the total variation in transcript abundance, respectively. For BrFAD2, a cis-eQTL co-located with the Co-QTL5-1 and -2 regions with LOD score 7.1 and 22.0% explained variance while another trans-eQTL mapped at the Co-QTL9-2 region on A09 with LOD score 3.6 and 10.5% explained variance (Figure 4; Table 5).

Bottom Line: The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species.We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustrating the polygenic nature of these traits.These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding.

View Article: PubMed Central - PubMed

Affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen University Wageningen, Netherlands ; Centre for BioSystems Genomics Wageningen, Netherlands.

ABSTRACT
The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (QTL) of seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 mapped at the B. rapa Flowering Locus C (BrFLC2). Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa Fatty acid desaturase 2 (BrFAD2) locus. Epistatic interactions were observed between QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding.

No MeSH data available.


Related in: MedlinePlus