Genomic selection in rubber tree breeding: A comparison of models and methods for managing G×E interactions

Several genomic prediction models combining genotype × environment (G×E) interactions have recently been developed and used for genomic selection (GS) in plant breeding programs. G×E interactions reduce selection accuracy and limit genetic gains in plant breeding. Two data sets were used to compare the prediction abilities of multienvironment G×E genomic models and two kernel methods. Specifically, a linear kernel, or GB (genomic best linear unbiased predictor [GBLUP]), and a nonlinear kernel, or Gaussian kernel (GK), were used to compare the prediction accuracies (PAs) of four genomic prediction models: 1) a single-environment, main genotypic effect model (SM); 2) a multienvironment, main genotypic effect model (MM); 3) a multienvironment, single-variance G×E deviation model (MDs); and 4) a multienvironment, environment-specific variance G×E deviation model (MDe). We evaluated the utility of genomic selection (GS) for 435 individual rubber trees at two sites and genotyped the individuals via genotyping-by-sequencing (GBS) of single-nucleotide polymorphisms (SNPs). Prediction models were used to estimate stem circumference (SC) during the first 4 years of tree development in conjunction with a broad-sense heritability (H2) of 0.60. Applying the model (SM, MM, MDs, and MDe) and kernel method (GB and GK) combinations to the rubber tree data revealed that the multienvironment models were superior to the single-environment genomic models, regardless of the kernel (GB or GK) used, suggesting that introducing interactions between markers and environmental conditions increases the proportion of variance explained by the model and, more importantly, the PA. Compared with the classic breeding method (CBM), methods in which GS is incorporated resulted in a 5-fold increase in response to selection for SC with multienvironment GS (MM, MDe, or MDs). Furthermore, GS resulted in a more balanced selection response for SC and contributed to a reduction in selection time when used in conjunction with traditional genetic breeding programs. Given the rapid advances in genotyping methods and their declining costs and given the overall costs of large-scale progeny testing and shortened breeding cycles, we expect GS to be implemented in rubber tree breeding programs

Quantitative unique continuation for real-valued solutions to second order elliptic equations in the plane

In this article, we study a quantitative form of the Landis conjecture on exponential decay for real-valued solutions to second order elliptic equations with variable coefficients in the plane. In particular, we prove the following qualitative form of Landis conjecture, for $W_1, W_2 \in L^{\infty}(\mathbb R^2;\mathbb R^2)$, $V \in L^{\infty}(\mathbb R^2;\mathbb R)$ and $u \in H_{\mathrm{loc}}^{1}(\mathbb R^2)$ a real-valued weak solution to $-\Delta u - \nabla \cdot ( W_1 u ) +W_2 \cdot \nabla u + V u = 0$ in $\mathbb R^2$, satisfying for $\delta>0$, $|u(x)| \leq \exp(- |x|^{1+\delta})$, $x \in \mathbb R^2$, then $u \equiv 0$. Our methodology of proof is inspired by the one recently developed by Logunov, Malinnikova, Nadirashvili, and Nazarov that have treated the equation $-\Delta u + V u = 0$ in $\mathbb R^2$. Nevertheless, several differences and additional difficulties appear. New weak quantitative maximum principles are established for the construction of a positive multiplier in a suitable perforated domain, depending on the nodal set of $u$. The resulted divergence elliptic equation is then transformed into a non-homogeneous $\partial_{\overline{z}}$ equation thanks to a generalization of Stoilow factorization theorem obtained by the theory of quasiconformal mappings, an approximate type Poincar\'e lemma and the use of the Cauchy transform. Finally, a suitable Carleman estimate applied to the operator $\partial_{\overline{z}}$ is the last ingredient of our proof.Comment: Comments welcom

Chandrasekhar's Dynamical Friction and non-extensive statistics

The motion of a point like object of mass $M$ passing through the background potential of massive collisionless particles ($m << M$) suffers a steady deceleration named dynamical friction. In his classical work, Chandrasekhar assumed a Maxwellian velocity distribution in the halo and neglected the self gravity of the wake induced by the gravitational focusing of the mass $M$. In this paper, by relaxing the validity of the Maxwellian distribution due to the presence of long range forces, we derive an analytical formula for the dynamical friction in the context of the $q$-nonextensive kinetic theory. In the extensive limiting case ($q = 1$), the classical Gaussian Chandrasekhar result is recovered. As an application, the dynamical friction timescale for Globular Clusters spiraling to the galactic center is explicitly obtained. Our results suggest that the problem concerning the large timescale as derived by numerical $N$-body simulations or semi-analytical models can be understood as a departure from the standard extensive Maxwellian regime as measured by the Tsallis nonextensive $q$-parameter.Comment: 16pp 5 figs, revised and extended version of arXiv:1202.1873 . Accepted for publication by JCA

Midday measurements of leaf water potential and stomatal conductance are highly correlated with daily water use of Thompson Seedless grapevines

A study was conducted to determine the relationship between midday measurements of vine water status and daily water use of grapevines measured with a weighing lysimeter. Water applications to the vines were terminated on August 24th for 9 days and again on September 14th for 22 days. Daily water use of the vines in the lysimeter (ETLYS) was approximately 40 L vine−1 (5.3 mm) prior to turning the pump off, and it decreased to 22.3 L vine−1 by September 2nd. Pre-dawn leaf water potential (ΨPD) and midday Ψl on August 24th were −0.075 and −0.76 MPa, respectively, with midday Ψl decreasing to −1.28 MPa on September 2nd. Leaf g s decreased from ~500 to ~200 mmol m−2 s−1 during the two dry-down periods. Midday measurements of g s and Ψl were significantly correlated with one another (r = 0.96) and both with ETLYS/ETo (r = ~0.9). The decreases in Ψl, g s, and ETLYS/ETo in this study were also a linear function of the decrease in volumetric soil water content. The results indicate that even modest water stress can greatly reduce grapevine water use and that short-term measures of vine water status taken at midday are a reflection of daily grapevine water us