Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions

Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies(GWAS). Several rice populations have been re-sequenced in the past decade;however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China. The population was divided into three indica/Xian and three japonica/Geng phylogenetic subgroups that correlate strongly with their geographic or breeding origins. We acquired a total of 146 phenotypic datasets for 29 agronomic traits under multi-environments for different subpopulations. With GWAS, we identified a total of 143 significant association loci, including three newly identified candidate genes or alleles that control heading date or amylose content. Our genotypic analysis of agronomically important genes in the population revealed that many favorable alleles are underused in elite accessions, suggesting they may be used to provide improvements in future breeding efforts. Our study provides useful resources for rice genetics research and breeding.

The Interactions among DWARF10,Auxin and Cytokinin Underlie Lateral Bud Outgrowth in Rice

Previous studies have shown that DWARFIO （D10） is a rice ortholog of MAX41RMS1/DAD1, encoding a carotenoid cleavage dioxygenase and functioning in strigolactones/strigolactone-derivatives （SL） biosynthesis. Here we use DIO. RNA interference （RNAi） transgenic plants similar to dlO mutant in phenotypes to investigate the interactions among DIO, auxin and cytokinin in regulating rice shoot branching. Auxin levels in node 1 of both decapitated DIO.RNAi and wild type plants decreased significantly, showing that decapitation does reduce endogenous auxin concentration, but decapitation has no clear effects on auxin levels in node 2 of the same plants. This implies that node 1 may be the location where a possible interaction between auxin and DIO gene would be detected. DIO expression in node 1 is inhibited by decapitation, and this inhibition can be restored by exogenous auxin application, indicating that DIO may play an important role in auxin regulation of SL. The decreased expression of most OsPINs in shoot nodes of DIO-RNAi plants may cause a reduced auxin transport capacity. Furthermore, effects of auxin treatment of decapitated plants on the expression of cytokinin biosynthetic genes suggest that DIO promotes cytokinin biosynthesis by reducing auxin levels. Besides, in DIO-RNAi plants, decreased storage cytokinin levels in the shoot node may partly account for the increased active cytokinin contents, resulting in more tillering phenotypes.

Transcriptional Characteristics of Xa21-mediated Defense Responses in Rice

Bacterial blight,caused by Xanthomonas oryzae pv.oryzae（Xoo）,is the most destructive bacterial disease of rice.The cloned rice gene Xa21 confers resistance to a broad spectrum of Xoo races.To identify genes involved in Xa21-mediated immunity,a whole-genome oligonucleotide microarray of rice was used to profile the expression of rice genes between incompatible interactions and mock treatments at 0,4,8,24,72 and 120 h post inoculation（hpi） or between incompatible and compatible interactions at 4 hpi,respectively.A total of 441 differentially expressed genes,designated as XDGs（Xa21 mediated differentially expressed genes）,were identified.Based on their functional annotations,the XDGs were assigned to 14 categories,including defense-related,signaling,transcriptional regulators.Most of the defense-related genes belonged to the pathogenesis-related gene family,which was induced dramatically at 72 and 120 hpi.Interestingly,most signaling and transcriptional regulator genes were downregulated at 4 and 8 hpi,suggesting that negative regulation of cellular signaling may play a role in the Xa21-mediated defense response.Comparison of expression profiles between Xa21- and other R gene-mediated defense systems revealed interesting common responses.Representative XDGs with supporting evidences were also discussed.

Positivity of Fock Toeplitz Operators via the Berezin Transform

This paper deals with the relationship between the positivity of the Fock Toeplitz operators and their Berezin transforms. The author considers the special case of the bounded radial function φ(z) = a + be^(-α|z|^2)+ ce^(-β|z|^2), where a, b, c are real numbers and α, β are positive numbers. For this type of φ, one can choose these parameters such that the Berezin transform of φ is a nonnegative function on the complex plane, but the corresponding Toeplitz operator Tφ is not positive on the Fock space.

Invertibility of Bergman Toeplitz operators with harmonic polynomial symbols

Let p be an analytic polynomial on the unit disk.We obtain a necessary and sufficient condition for Toeplitz operators with the symbol z+p to be invertible on the Bergman space when all coefficients of p are real numbers.Furthermore,we establish several necessary and sufficient,easy-to-check conditions for Toeplitz operators with the symbol z+p to be invertible on the Bergman space when some coefficients of p are complex numbers.