Additional file 1 of OsVPE2, a Member of Vacuolar Processing Enzyme Family, Decreases Chilling Tolerance of Rice

Supplementary Material 1. Table S1: Primers used in this study. Table S2: The low-temperature seedling survivability (LTSS) of rice varieties with the two main haplotypes of OsVPE

Image_1_Integrative transcriptomic analysis deciphering the role of rice bHLH transcription factor Os04g0301500 in mediating responses to biotic and abiotic stresses.pdf

Understanding the signaling pathways activated in response to these combined stresses and their crosstalk is crucial to breeding crop varieties with dual or multiple tolerances. However, most studies to date have predominantly focused on individual stress factors, leaving a significant gap in understanding plant responses to combined biotic and abiotic stresses. The bHLH family plays a multifaceted regulatory role in plant response to both abiotic and biotic stresses. In order to comprehensively identify and analyze the bHLH gene family in rice, we identified putative OsbHLHs by multi-step homolog search, and phylogenic analysis, molecular weights, isoelectric points, conserved domain screening were processed using MEGAX version 10.2.6. Following, integrative transcriptome analysis using 6 RNA-seq data including Xoo infection, heat, and cold stress was processed. The results showed that 106 OsbHLHs were identified and clustered into 17 clades. Os04g0301500 and Os04g0489600 are potential negative regulators of Xoo resistance in rice. In addition, Os04g0301500 was involved in non-freezing temperatures (around 4°C) but not to 10°C cold stresses, suggesting a complex interplay with temperature signaling pathways. The study concludes that Os04g0301500 may play a crucial role in integrating biotic and abiotic stress responses in rice, potentially serving as a key regulator of plant resilience under changing environmental conditions, which could be important for further multiple stresses enhancement and molecular breeding through genetic engineering in rice.</p

Coefficients of genetic parameters for the RIL based aTTC Z_1i, Z_2i and Z_4i data under the F_∞metric model.

<p>Coefficients of genetic parameters for the RIL based aTTC Z_1i, Z_2i and Z_4i data under the F_∞metric model.</p

Genetic dissection of main and epistatic effects of QTL based on augmented triple test cross design

<div><p>The use of heterosis has considerably increased the productivity of many crops; however, the biological mechanism underpinning the technique remains elusive. The North Carolina design III (NCIII) and the triple test cross (TTC) are powerful and popular genetic mating design that can be used to decipher the genetic basis of heterosis. However, when using the NCIII design with the present quantitative trait locus (QTL) mapping method, if epistasis exists, the estimated additive or dominant effects are confounded with epistatic effects. Here, we propose a two-step approach to dissect all genetic effects of QTL and digenic interactions on a whole genome without sacrificing statistical power based on an augmented TTC (aTTC) design. Because the aTTC design has more transformation combinations than do the NCIII and TTC designs, it greatly enriches the QTL mapping for studying heterosis. When the basic population comprises recombinant inbred lines (RIL), we can use the same materials in the NCIII design for aTTC-design QTL mapping with transformation combination Z₁, Z₂, and Z₄ to obtain genetic effect of QTL and digenic interactions. Compared with RIL-based TTC design, RIL-based aTTC design saves time, money, and labor for basic population crossed with F₁. Several Monte Carlo simulation studies were carried out to confirm the proposed approach; the present genetic parameters could be identified with high statistical power, precision, and calculation speed, even at small sample size or low heritability. Additionally, two elite rice hybrid datasets for nine agronomic traits were estimated for real data analysis. We dissected the genetic effects and calculated the dominance degree of each QTL and digenic interaction. Real mapping results suggested that the dominance degree in Z₂ that mainly characterize heterosis showed overdominance and dominance for QTL and digenic interactions. Dominance and overdominance were the major genetic foundations of heterosis in rice.</p></div

Dissected main and epistatic effects in <i>II</i> hybrid.

<p>Dissected main and epistatic effects in <i>II</i> hybrid.</p

QTL mapping results for Z₄ in RIL-based aTTC design under the F_∞ metric model in simulation study.

<p>QTL mapping results for Z₄ in RIL-based aTTC design under the F_∞ metric model in simulation study.</p

Comparison of the QTL mapping results by the proposed approach with previous results in Li <i>et al</i> in <i>IJ</i> hybrid.

<p>Comparison of the QTL mapping results by the proposed approach with previous results in Li <i>et al</i> in <i>IJ</i> hybrid.</p

The mean statistic power of augmented epistatic effect interactions in Z₄.

<p>Epis-1 refer the augmented epistatic effect (<i>i</i>_<i>aa</i><i>—i</i>_<i>dd</i>) interaction, epis-2 refer the augmented epistatic effect (<i>i</i>_<i>ad</i><i>—i</i>_<i>da</i>) interaction.</p

Model parameter components for Z_1i, Z_2i, Z_3i, Z_4i, Z_5i and Z_6i in the RIL-based aTTC design under both the F_∞ model.

<p>Model parameter components for Z_1i, Z_2i, Z_3i, Z_4i, Z_5i and Z_6i in the RIL-based aTTC design under both the F_∞ model.</p

Dissected main and epistatic effects in <i>IJ</i> hybrid.

<p>Dissected main and epistatic effects in <i>IJ</i> hybrid.</p