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Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping.

Rebolledo MC, Dingkuhn M, Courtois B, Gibon Y, Clément-Vidal A, Cruz DF, Duitama J, Lorieux M, Luquet D - J. Exp. Bot. (2015)

Bottom Line: Associations for NSC and model parameters revealed new regions related to early vigour that had greater significance than morphological traits, providing additional information on the genetic control of early vigour.Twelve associations were related to loci for cloned genes, with nine related to organogenesis, plant height, cell size or cell number.The potential use of these associations as markers for breeding is discussed.

View Article: PubMed Central - PubMed

Affiliation: CIAT, Agrobiodiversity, AA 6713, Cali, Colombia m.c.rebolledo@cgiar.org.

No MeSH data available.


QQ plots and Manhattan plots for traits associated to markers with the highest level of significance: FRU, PLASTO, DEV_PLASTO_MGR, SDW, NBL, DR. In the Manhattan plots the red line indicates the threshold for significant SNP association (P <1×10–4) and the blue line indicates the threshold for suggestive SNP association (P <5×10–4).
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Figure 3: QQ plots and Manhattan plots for traits associated to markers with the highest level of significance: FRU, PLASTO, DEV_PLASTO_MGR, SDW, NBL, DR. In the Manhattan plots the red line indicates the threshold for significant SNP association (P <1×10–4) and the blue line indicates the threshold for suggestive SNP association (P <5×10–4).

Mentions: Figure 3 presents Quantile–Quantile (QQ) plots and Manhattan plots for the traits with the most significant detection levels (FRU, PLASTO, DEV_PLASTO_MGR, SDW, NBL, DR). Supplementary Fig. S2 at JXB online shows QQ plots and Manhattan plots for the other traits. A total of 23 QTL were identified that were significantly associated with either morphological traits, sugar-related traits or model parameters at P <1×10–4. For approximately two-thirds of the significant associations, the P-values corresponded to q-values below 0.10 (Table 2). Five QTL were significantly associated with morphological variables, eight with model parameters and seven with metabolic traits, the latter mainly on chromosome (chr) 11 and related to FRU and GLU in source leaves.


Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping.

Rebolledo MC, Dingkuhn M, Courtois B, Gibon Y, Clément-Vidal A, Cruz DF, Duitama J, Lorieux M, Luquet D - J. Exp. Bot. (2015)

QQ plots and Manhattan plots for traits associated to markers with the highest level of significance: FRU, PLASTO, DEV_PLASTO_MGR, SDW, NBL, DR. In the Manhattan plots the red line indicates the threshold for significant SNP association (P <1×10–4) and the blue line indicates the threshold for suggestive SNP association (P <5×10–4).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4585419&req=5

Figure 3: QQ plots and Manhattan plots for traits associated to markers with the highest level of significance: FRU, PLASTO, DEV_PLASTO_MGR, SDW, NBL, DR. In the Manhattan plots the red line indicates the threshold for significant SNP association (P <1×10–4) and the blue line indicates the threshold for suggestive SNP association (P <5×10–4).
Mentions: Figure 3 presents Quantile–Quantile (QQ) plots and Manhattan plots for the traits with the most significant detection levels (FRU, PLASTO, DEV_PLASTO_MGR, SDW, NBL, DR). Supplementary Fig. S2 at JXB online shows QQ plots and Manhattan plots for the other traits. A total of 23 QTL were identified that were significantly associated with either morphological traits, sugar-related traits or model parameters at P <1×10–4. For approximately two-thirds of the significant associations, the P-values corresponded to q-values below 0.10 (Table 2). Five QTL were significantly associated with morphological variables, eight with model parameters and seven with metabolic traits, the latter mainly on chromosome (chr) 11 and related to FRU and GLU in source leaves.

Bottom Line: Associations for NSC and model parameters revealed new regions related to early vigour that had greater significance than morphological traits, providing additional information on the genetic control of early vigour.Twelve associations were related to loci for cloned genes, with nine related to organogenesis, plant height, cell size or cell number.The potential use of these associations as markers for breeding is discussed.

View Article: PubMed Central - PubMed

Affiliation: CIAT, Agrobiodiversity, AA 6713, Cali, Colombia m.c.rebolledo@cgiar.org.

No MeSH data available.