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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

An overview of single trait QTL profiles of seed germination, seedling vigor and salt tolerance parameters under non-stress and 50 mM NaCl salt of 2010 and 2011 seed batches. (A) QTL hotspots (>8 significant QTLs) indicated by the number of significant QTLs plotted for 10 linkage groups (A01-A10). The dotted vertical lines separate the 10 linkage groups. (B) Single trait QTL profiles of flowering time, seed weight, seed germination, seedling vigor, and salt tolerance parameters. Seed germination includes five parameters: T10, T50, U7525, Gmax and AUC; seedling vigor includes root and shoot length at different DAGs, and root and shoot biomass measured under non-stress and 50 mM NaCl salt stress conditions. The different traits are on different rows along the y-axis, the 10 linkage groups on the x-axis, separated by dotted lines. QTLs that had a high phenotypic value for the YS143 allele are in light blue (for QTLs with LOD 2–3) and blue (for QTL with LOD >3) while QTLs with a high phenotypic value for the PC175 allele are indicated in yellow (for QTLs with LOD 2–3) and green (for QTLs with LOD > 3). The color mark on the QTL profile indicates the QTL peak position. The 26 QTL co-localization regions are indicated as Co-QTL followed by the number of the linkage group and a serial number within a linkage group, for example, Co-QTL1-2 indicates the second co-localization QTL region on A01. The red color of a trait label indicates the trait under 50 mM NaCl salt stress. The trait labels are described in Supplementary Table S1. LOD scores of QTLs shown in this figure are also presented in Supplementary Table S6.
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Figure 2: An overview of single trait QTL profiles of seed germination, seedling vigor and salt tolerance parameters under non-stress and 50 mM NaCl salt of 2010 and 2011 seed batches. (A) QTL hotspots (>8 significant QTLs) indicated by the number of significant QTLs plotted for 10 linkage groups (A01-A10). The dotted vertical lines separate the 10 linkage groups. (B) Single trait QTL profiles of flowering time, seed weight, seed germination, seedling vigor, and salt tolerance parameters. Seed germination includes five parameters: T10, T50, U7525, Gmax and AUC; seedling vigor includes root and shoot length at different DAGs, and root and shoot biomass measured under non-stress and 50 mM NaCl salt stress conditions. The different traits are on different rows along the y-axis, the 10 linkage groups on the x-axis, separated by dotted lines. QTLs that had a high phenotypic value for the YS143 allele are in light blue (for QTLs with LOD 2–3) and blue (for QTL with LOD >3) while QTLs with a high phenotypic value for the PC175 allele are indicated in yellow (for QTLs with LOD 2–3) and green (for QTLs with LOD > 3). The color mark on the QTL profile indicates the QTL peak position. The 26 QTL co-localization regions are indicated as Co-QTL followed by the number of the linkage group and a serial number within a linkage group, for example, Co-QTL1-2 indicates the second co-localization QTL region on A01. The red color of a trait label indicates the trait under 50 mM NaCl salt stress. The trait labels are described in Supplementary Table S1. LOD scores of QTLs shown in this figure are also presented in Supplementary Table S6.

Mentions: Over the two seed batches (2010 and 2011), two conditions (non-stress and salt stress) and five germination parameters, in total, 26 QTLs and 20 putative QTLs (LOD score between 2 and 3) were found (Figure 2B; Supplementary Table S3). For the significant QTLs, the explained variances ranged from 7.5 to 27.2%. On A02, QTLs were detected mainly for T10 and T50 (Supplementary Table S3), with the favorable effect coming from the yellow sarson allele. On A05, one QTL and three putative QTLs with explained variance from 6.5 to 11.1% were mapped for mainly uniformity under salt stress. On A10, 3 QTLs with explained variance from 10.3 to 15.4% were mapped mainly for T50 under both non-stress and salt stress conditions. For 1000-seed weight in 2010 and 2011 a single QTL was found on A05, with explained variance ranging from 8.3 to 16.1%.


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)

An overview of single trait QTL profiles of seed germination, seedling vigor and salt tolerance parameters under non-stress and 50 mM NaCl salt of 2010 and 2011 seed batches. (A) QTL hotspots (>8 significant QTLs) indicated by the number of significant QTLs plotted for 10 linkage groups (A01-A10). The dotted vertical lines separate the 10 linkage groups. (B) Single trait QTL profiles of flowering time, seed weight, seed germination, seedling vigor, and salt tolerance parameters. Seed germination includes five parameters: T10, T50, U7525, Gmax and AUC; seedling vigor includes root and shoot length at different DAGs, and root and shoot biomass measured under non-stress and 50 mM NaCl salt stress conditions. The different traits are on different rows along the y-axis, the 10 linkage groups on the x-axis, separated by dotted lines. QTLs that had a high phenotypic value for the YS143 allele are in light blue (for QTLs with LOD 2–3) and blue (for QTL with LOD >3) while QTLs with a high phenotypic value for the PC175 allele are indicated in yellow (for QTLs with LOD 2–3) and green (for QTLs with LOD > 3). The color mark on the QTL profile indicates the QTL peak position. The 26 QTL co-localization regions are indicated as Co-QTL followed by the number of the linkage group and a serial number within a linkage group, for example, Co-QTL1-2 indicates the second co-localization QTL region on A01. The red color of a trait label indicates the trait under 50 mM NaCl salt stress. The trait labels are described in Supplementary Table S1. LOD scores of QTLs shown in this figure are also presented in Supplementary Table S6.
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Related In: Results  -  Collection

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Figure 2: An overview of single trait QTL profiles of seed germination, seedling vigor and salt tolerance parameters under non-stress and 50 mM NaCl salt of 2010 and 2011 seed batches. (A) QTL hotspots (>8 significant QTLs) indicated by the number of significant QTLs plotted for 10 linkage groups (A01-A10). The dotted vertical lines separate the 10 linkage groups. (B) Single trait QTL profiles of flowering time, seed weight, seed germination, seedling vigor, and salt tolerance parameters. Seed germination includes five parameters: T10, T50, U7525, Gmax and AUC; seedling vigor includes root and shoot length at different DAGs, and root and shoot biomass measured under non-stress and 50 mM NaCl salt stress conditions. The different traits are on different rows along the y-axis, the 10 linkage groups on the x-axis, separated by dotted lines. QTLs that had a high phenotypic value for the YS143 allele are in light blue (for QTLs with LOD 2–3) and blue (for QTL with LOD >3) while QTLs with a high phenotypic value for the PC175 allele are indicated in yellow (for QTLs with LOD 2–3) and green (for QTLs with LOD > 3). The color mark on the QTL profile indicates the QTL peak position. The 26 QTL co-localization regions are indicated as Co-QTL followed by the number of the linkage group and a serial number within a linkage group, for example, Co-QTL1-2 indicates the second co-localization QTL region on A01. The red color of a trait label indicates the trait under 50 mM NaCl salt stress. The trait labels are described in Supplementary Table S1. LOD scores of QTLs shown in this figure are also presented in Supplementary Table S6.
Mentions: Over the two seed batches (2010 and 2011), two conditions (non-stress and salt stress) and five germination parameters, in total, 26 QTLs and 20 putative QTLs (LOD score between 2 and 3) were found (Figure 2B; Supplementary Table S3). For the significant QTLs, the explained variances ranged from 7.5 to 27.2%. On A02, QTLs were detected mainly for T10 and T50 (Supplementary Table S3), with the favorable effect coming from the yellow sarson allele. On A05, one QTL and three putative QTLs with explained variance from 6.5 to 11.1% were mapped for mainly uniformity under salt stress. On A10, 3 QTLs with explained variance from 10.3 to 15.4% were mapped mainly for T50 under both non-stress and salt stress conditions. For 1000-seed weight in 2010 and 2011 a single QTL was found on A05, with explained variance ranging from 8.3 to 16.1%.

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