Genome-Wide Association Studies of Image Traits Reveal Genetic Architecture of Drought Resistance in Rice

Understanding how plants respond to drought can benefit drought resistance （DR） breeding. Using a non-destructive phenotyping facility, 51 image-based traits （i-traits） for 507 rice accessions were extracted. These i-traits can be used to monitor drought responses and evaluate DR. High heritability and large variation of these traits was observed under drought stress in the natural population. A genome-wide as- sociation study （GWAS） of i-traits and traditional DR traits identified 470 association loci, some containing known DR-related genes. Of these 470 loci, 443 loci （94%） were identified using i-traits, 437 loci （93%） co- localized with previously reported DR-related quantitative trait loci, and 313 loci （66.6%） were reproducibly identified by GWAS in different years. Association networks, established based on GWAS results, revealed hub i-traits and hub loci. This demonstrates the feasibility and necessity of dissecting the complex DR trait into heritable and simple i-traits. As proof of principle, we illustrated the power of this integrated approach to identify previously unreported DR-related genes. OsPP15 was associated with a hub i-trait, and its role in DR was confirmed by genetic transformation experiments. Furthermore, i-traits can be used for DR linkage analyses, and 69 i-trait locus associations were identified by both GWAS and linkage analysis of a recom- binant inbred line population. Finally, we confirmed the relevance of i-traits to DR in the field. Our study pro- vides a promising novel approach for the genetic dissection and discovery of causal genes for DR.

Reversible Histone H2B Monoubiquitination Fine-Tunes Abscisic Acid Signaling and Drought Response in Rice

Histone H2B monoubiquitination (H2Bub1) plays important roles in several physiological and developmental processes, but its roles in the regulation of plant stress responses remain elusive. Here, we report that H2Bub1 is crucially involved in abscisic acid (ABA) signaling and drought response in rice. We found that rice HISTONE MONOUBIQUITINATION2 (OsHUB2), an E3 ligase for H2Bub1, in teracted with OsbZIP46, a key transcription factor regulating ABA signaling and drought response in rice. Genetic analyses suggest that OsHUB2, upregulated by drought and ABA, positively modulates ABA sensitivity and drought resistance. The H2Bub1 levels were in creased in the target genes of OsbZIP46 under the drought stress and ABA treat- merits, which were positively correlated with their increased expression levels. Interestingly, MODD, a reported suppressor of ABA signaling and drought resistance by mediating OsbZIP46 deactivation and degradation, could reduce the H2Bub1 levels in the target genes of OsbZIP46 by recruiting a putative deubiquitinase OsOTLD1 . Suppression of OsOTLD1in vivo resulted in increased H2Bub1 levels and expression of OsbZIP46 target genes. Collectively, these fin dings established an elaborate mecha nism of histone monoubiquitination in the fine-turning of ABA signaling and drought response by balancing H2Bub1 deposition and removal.

Genome-wide association study revealed genetic variations of ABA sensitivity controlled by multiple stress-related genes in rice

Abscisic acid(ABA)is a critical phytohormone that regulates multiple physiological processes including plant growth and stress tolerance.The core ABA signaling pathway has been well established,but genetic variations mediating ABA responses remain largely unknown.In this study,we performed genome-wide association study(GWAS)to identify loci and genes associated with ABA sensitivity(reflected by seed germination inhibition by ABA)in a panel of 425 rice accessions.The seed germination assay revealed that Aus and indica rice had stronger ABA sensitivity than japonica rice.A total of 48 non-redundant association loci were detected in the indica subpopulation and whole population,and 386 genes in these loci were responsive to ABA or abiotic stresses.Eight association loci were overlapped with previously reported loci for yield under drought stress or for droughtindicative image traits.Haplotype analyses of important candidate genes such as OsSAPK6,a key component in the ABA signaling core,were performed to identify key SNPs/InDels that may affect gene functions through promoter activity regulation,amino acid variation,or gene splicing.These results provide insights into the genetic basis of ABA sensitivity related to stress responses.

IQ67 DOMAIN protein 21 is critical for indentation formation in pavement cell morphogenesis

In plants, cortical microtubules anchor to the plasma membrane in arrays and play important roles in cell shape. However, the molecular mechanism of microtubule binding proteins, which connect the plasma membrane and cortical microtubules in cell morphology remains largely unknown. Here, we report that a plasma membrane and microtubule duallocalized IQ67 domain protein, IQD21, is critical for cotyledon pavement cell(PC) morphogenesis in Arabidopsis. iqd21 mutation caused increased indentation width, decreased lobe length, and similar lobe number of PCs, whereas IQD21 overexpression had a different effect on cotyledon PC shape. Weak overexpression led to increased lobe number, decreased indentation width, and similar lobe length, while moderate or great overexpression resulted in decreased lobe number, indentation width, and lobe length of PCs. Live-cell observations revealed that IQD21 accumulation at indentation regions correlates with lobe initiation and outgrowth during PC development. Cell biological and genetic approaches revealed that IQD21 promotes transfacial microtubules anchoring to the plasma membrane via its polybasic sites and bundling at the indentation regions in both periclinal and anticlinal walls. IQD21 controls cortical microtubule organization mainly through promoting Katanin 1-mediated microtubule severing during PC interdigitation. These findings provide the genetic evidence that transfacial microtubule arrays play a determinant role in lobe formation, and the insight into the molecular mechanism of IQD21 in transfacial microtubule organization at indentations and puzzle-shaped PC development.