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At the reproductive development stage of rice (Oryza sativa L.), temperature stress can decrease spikelet fertility, ultimately resulting in a yield loss. In this study, a total of 98 rice varieties were used in genome-wide association study (GWAS) to understand spikelet fertility under a high temperature (SFHT). GWAS results revealed that two lead SNPs were significantly associated with SFHT. Candidate genes located within ± 250 kb of the corresponding SNP position were discovered, resulting in a total of 21 candidate genes on chromosome 10 and 18 candidate genes on chromosome 11. Based on previously reported function and haplotype analysis, Os10g0177200 (EF-HAND 2domain containing protein) as one candidate gene showed significant differences among groups of haplotypes. This candidate gene will be further evaluated for its function to determine whether it is useful for improving molecular breeding studies and developing new high temperature tolerant rice varieties.

Rice (Oryza sativa L.) pollen grains are highly sensitive to extreme temperatures. Studies on the proteomic analysis of pollen at different developmental stages are limited. In this study, to identify proteins expressed during pollen development, we performed shotgun proteomic analysis of rice anthers harvested at 8, 3, and 0 days before heading (DBH). A total of 4509 non-redundant proteins were identified in rice anthers at each of the three time points with three replications per time point. Among these, 2968 proteins were reproducible, of which 1919 were specifically expressed at a given stage of anther development. Clustering and gene ontology (GO) enrichment analyses categorized the specifically expressed proteins into four groups. Group I comprised proteins involved in cell differentiation, reproduction, and stress response; Group II contained proteins related to cell growth and carbohydrate metabolic process; Group III included proteins related to starch accumulation and lipid metabolic process; Group IV comprised proteins related to structure morphogenesis and cellular components. Proteins in Group I steadily increased during anther development, whereas those in Group I steadily decreased. Group III proteins showed the highest expression at 3 DBH, whereas Group IV proteins exhibited the lowest expression at 3 DBH.

The complete chloroplast genome sequence of Korean Cymbidium goeringii acc. smg222 was analyzed. Based on a comparison with Chinese C. goeringii, losses of nine ndh subunits (ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhH, ndhJ, and ndhK), three protein-coding genes (ycf 1-like, ycf 15, and ycf 68), six transfer RNAs, and one conserved open reading frame (orf 42). In addition, 219 InDels (insertion or deletion) and 171 simple sequence repeats were observed. Twenty-Five of which InDel markers have been evaluated, that useful for distinguishing Korean and Chinese Cymbidium associations based on the polymorphisms of chloroplast genomes between Korean Cymbidium goeringii acc. smg222 and Chinese C. goeringii and evaluation of genetic diversity. Finally, the phylogenetic relationships of the 39 Korean and 22 Chinese species was constructed based on the five InDel markers of them and obtained high support, indicating that our data may be useful in resolving relationships in this genus. The information about chloroplast DNA structure and gene variants of C. goeringii acc. smg222 chloroplast genome will provide sufficient phylogenetic information for resolving evolutionary relationships. The molecular markers developed in here will contribute to further research of Cymbidium species and conservation of endemic Cymbidium species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-019-2020-1) contains supplementary material, which is available to authorized users.

Rice crops are vulnerable to low temperatures. During development, the reproductive stage is particularly sensitive to cold exposure, which causes abnormal pollen development and a high degree of male sterility. In this study, shotgun proteomic analysis was used to analyze rice anthers containing pollen grains from a cold-tolerant variety, Dianxi 4. Protein expression was compared between normal anthers and anthers exposed to cold temperatures at the young microspore stage. In total, 3835 non-redundant proteins were identified in the rice anther. Of these, 441 proteins were differentially expressed between normal and cold-treated anthers. Pollen allergens, ATP synthase, actin, profilin, and β-expansin proteins were highly abundant, reflecting anther development, pollen germination, and pollen tube elongation. Starch and sucrose metabolic proteins such as α-amylase precursor and 4-α-glucanotransferase exhibited reduced expression after cold exposure. Among the proteins that exhibited increased expression after cold exposure, C2 domain proteins, and GRPs were identified as candidate signaling factors for mediation of the cold tolerance response. Through high-throughput proteomic analysis we were able to reveal proteomic changes against cold stress and suggest two signaling factors as the candidate genes.

In this study, relative germination percentage (RGP) and delayed mean germination time (DMGT) were measured in various rice accessions at the germination stage and carried out association analysis to identify candidate genes related to low temperature germination (LTG) using a natural population comprising 137 rice cultivars and inbred lines selected from the Korean rice core set. Genome-wide association study using ~ 1.44 million high-quality SNPs, which were identified by re-sequencing all rice collections, revealed 48 candidate genes on chromosome 10 and 55 candidate genes on chromosome 11 in the high peak SNP sites of associated loci for RGP and DMGT, respectively. By detecting highly associated variations located inside genic regions and performing functional annotation of the genes, we detected 23 candidate genes for RGP and 18 genes for DMGT for LTG. In addition, the haplotype and sequence analysis of the candidate gene (Os10g0371100) with RGP trait and the candidate gene (Os11t0104240-00) with DMGT revealed correlation between sequences of functional variations and phenotypes. Several novel LTG-related candidate genes previously were known for the function during rice germination and uncovered their substantial natural variations. These candidate genes represent valuable resources for molecular breeding and genetic improvement of cold tolerance during rice germination. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-018-1252-9) contains supplementary material, which is available to authorized users.

Panicle architecture in rice can have a strong influence on yield. Using N-methyl-N-nitrosourea mutagenesis, we isolated an erect panicle mutant, Hep, from Hwasunchalbyeo, a glutinous japonica rice cultivar. Genetic analysis revealed that the erect panicle phenotype was controlled by a single recessive mutation designated erect panicle 3 (ep3). Genetic mapping revealed that the ep3 mutation was located on the short arm of chromosome 2 in a 0.1 cM region delimited by the STS markers STS5803-5 and STS5803-7. The ep3 locus corresponded to 46.8 kb region and contained six candidate genes. Comparison of the DNA sequences of the candidate genes from wild-type and erect panicle plants revealed a single base-pair change in the second exon of LOC_Os02g15950, which is predicted to result in a nonsense mutation. LOC_Os02g15950 encodes a putative F-box protein containing 515 amino acids and is expressed throughout the plant during all growth stages. A line carrying a T-DNA insertion in LOC_ Os02g15950 was obtained and shown to have the same phenotype as the ep3 mutant, thus confirming the identification of LOC_Os02g15950 as the ERECT PANICLE 3 (EP3) gene. The ep3 mutation causes a significant increase in the number of small vascular bundles as well as the thickness of parenchyma in the peduncle, which results in the erect panicle phenotype.

Brown planthopper (BPH) is one of the most destructive insect pests of rice. Wild species of rice are a valuable source of resistance genes for developing resistant cultivars. A molecular marker-based genetic analysis of BPH resistance was conducted using an F(2) population derived from a cross between an introgression line, 'IR71033-121-15', from Oryza minuta (Accession number 101141) and a susceptible Korean japonica variety, 'Junambyeo'. Resistance to BPH (biotype 1) was evaluated using 190 F(3) families. Two major quantitative trait loci (QTLs) and two significant digenic epistatic interactions between marker intervals were identified for BPH resistance. One QTL was mapped to 193.4-kb region located on the short arm of chromosome 4, and the other QTL was mapped to a 194.0-kb region on the long arm of chromosome 12. The two QTLs additively increased the resistance to BPH. Markers co-segregating with the two resistance QTLs were developed at each locus. Comparing the physical map positions of the two QTLs with previously reported BPH resistance genes, we conclude that these major QTLs are new BPH resistance loci and have designated them as Bph20(t) on chromosome 4 and Bph21(t) on chromosome 12. This is the first report of BPH resistance genes from the wild species O. minuta. These two new genes and markers reported here will be useful to rice breeding programs interested in new sources of BPH resistance.

Evaluation of eating quality in early breeding generations of rice is critical to developing varieties with better palatability. This paper reports DNA markers associated with eating quality of temperate japonica rice and an evaluation method aided by multiple regression analysis. A total of 30 markers comprising STSs, SNPs, and SSRs were tested for their association with palatability using 22 temperate japonica varieties with different palatability values. Eating quality-related traits of the 22 varieties were also measured. Of the 30 markers, 18 were found to be significantly associated with palatability and, consequently, a model regression equation with an R(2) value of 0.99 was formulated to estimate the palatability by the marker data set. Validation of the model equation using selected breeding lines indicated that the marker set and the equation are highly applicable to evaluation of the palatability of cooked rice in temperate japonica varieties.

Rice sucrose synthase 3 (RSUS3) is expressed predominantly in rice seed endosperm and is thought to play an important role in starch filling during the milky stage of rice seed ripening. Because the genetic diversity of this locus is not known yet, the full sequence of RSUS3 from 43 rice varieties was amplified to examine the distribution of DNA polymorphisms. A total of 254 sequence variants, including SNPs and insertion/deletions, were successfully identified in the 7733 bp sequence that comprises the promoter, exons and introns, and 3# downstream nontranscribed region (NTR). Eleven haplotypes were distinguished among the 43 rice varieties based on nucleotide variation in the 3 defined regions (5# NTR, transcript, and 3# NTR). The promoter region showed evidence of a base change on a cis-element that might influence the functional role of the motif in seed-specific expression. The genetic diversity of the RSUS3 gene sequences in the rice germplasm used in this study appears to be the result of nonrandom processes. Analysis of polymorphism sites indicated that at least 11 recombinations have occurred, primarily in the transcribed region. This finding provides insight into the development of a cladistic approach for establishing future genetic association studies of the RSUS3 locus.