Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.).

BACKGROUND: Breeding of conventional and hybrid rice (Oryza sativa L.) have solved hunger problems and increased farmers' income in the world. Molecular markers have been widely used in marker-assisted breeding and identification of larger numbers of different bred varieties in the past decades. The recently developed SNP markers are applied for more stable and detectable compared with other markers. But the cost of genotyping lots SNPs is high. So, it is essential to select less representative SNPs and inexpensive detecting methods to lower the cost and accelerate variety identification and breeding process. KASP (Kompetitive Allele-Specific PCR) is a flexible method to detect the SNPs, and large number of KASP markers have been widely used in variety identification and breeding. However, the ability of less KASP markers on massive variety identification and breeding remains unknown. RESULTS: Here, 48 KASP markers were selected from 378 markers to classify and analyze 518 varieties including conventional and hybrid rice. Through analyzing the population structure, the 48 markers could almost represent the 378 markers. In terms of variety identification, the 48 KASP markers had a 100% discrimination rate in 53 conventional indica varieties and 193 hybrid varieties, while they could distinguish 89.1% conventional japonica rice from different breeding institutes. Two more markers added would increase the ratio from 68.38 to 77.94%. Additionally, the 48 markers could be used for classification of subpopulations in the bred variety. Also, 8 markers had almost completely different genotypes between japonica and indica, and 3 markers were found to be very important for japonica hybrid rice. In hybrid varieties, the heterozygosity of chromosomes 3, 6 and 11 was relatively higher than others. CONCLUSIONS: Our results showed that 48 KASP markers could be used to identify rice varieties, and the panel we tested could provide a database for breeders to identify new breeding lines. Also, the specific markers we found were useful for marker-assisted breeding in rice, including conventional and hybrid.

Effects of mid-stage nitrogen application timing on the morphological structure and physicochemical properties of japonica rice starch.

BACKGROUND: Nitrogen management of crops, especially when mid-stage nitrogen is applied, is a key factor affecting the yield and grain quality of rice (Oryza sativa). Here, the timing of mid-stage nitrogen application was evaluated for its effect on rice grain quality by assessing the morphological structure and physicochemical properties of starch from two japonica rice cultivars growing in fields (Nangeng 9108 and Nangeng 5055). RESULTS: The experiment was arranged in a split-plot design, with the two rice cultivars as the main plot factor and three timings of mid-stage nitrogen application as the within-plot factor. Briefly, three applications were made: at the emergence of the top-sixth-leaf (ahead), the top-fourth-leaf (normal), and the top-second-leaf (delayed) of the main stem. Delaying mid-stage nitrogen application caused the starch granule surface to become uneven and significantly reduced its particle size, whereas it increased the polished rice rate, chalkiness degree, and protein content. Furthermore, the apparent amylose content decreased with a delay in mid-stage nitrogen application, thereby resulting in higher relative crystallinity, swelling power, water solubility, gelatinization enthalpy, and low retrogradation. Finally, we also found that delaying this nitrogen application lowered the characteristic values of rice flour viscosities, leading to cooking quality deterioration. CONCLUSION: These results therefore suggest that delaying mid-stage nitrogen application enhances the processing and nutritional qualities of japonica rice but evidently has an adverse effect upon its appearance and cooking qualities. © 2020 Society of Chemical Industry.

miR-1231 Is Downregulated in Prostate Cancer with Prognostic and Functional Implications.

BACKGROUND: Our study investigated the expression levels of miR-1231 in prostate cancer tissues and cell lines and explored its potential prognostic significance as well as its functional effects on prostate cancer cells. METHODS: miR-1231 expression levels were detected in prostate cancer tissues and prostate cancer cell lines using qRT-PCR. The prognostic significance of miR-1231 in prostate cancer was assessed using the Kaplan-Meier curve and Cox regression analyses. Evaluation of the impact of ectopic expression or inhibition of miR-1231 on aggressive tumor behavior (cellular proliferation, migration, and invasion) of prostate cancer cell lines involved the CCK-8 and Transwell assays. RESULTS: miR-1231 expression was downregulated in both prostate cancer tissues and cell lines. Downregulation of miR-1231 was significantly associated with lymph node metastasis, higher TNM stage, higher clinical stage, and shorter overall survival. The expression of miR-1231 was predicted as a prognostic factor for prostate cancer patients. Additionally, we found overexpression of miR-1231 suppressed proliferation, migration, and invasion of prostate cancer cell linesin vitro. EGFR was a direct target of miR-1231. CONCLUSION: Taken together, our results indicate that miR-1231 expression plays a tumor-suppressive role in prostate cancer. It is downregulated in prostate cancer and may suppress prostate cancer cell proliferation, migration, and invasion by targeting EGFR, and it may be a prognostic biomarker and potential therapeutic strategy for prostate cancer treatment in the future.

The effects of field pre-harvest sprouting on the morphological structure and physicochemical properties of rice (Oryza sativa L.) starch.

This study investigates the effects of field pre-harvest sprouting (PHS) on the morphological structure and physicochemical properties of starches from four rice varieties during the rice harvesting period. The results of the study showed that PHS significantly affected the grain characteristics, starch structure, and physicochemical properties of the four rice varieties. Moreover, PHS led to a significant decrease in the grain processing quality and protein content of the four varieties, pitting and unevenness on the surface of the starch granules, and smaller starch granules. In addition, PHS led to starches with lower amylose content, which resulted in a higher swelling power, solubility, and relative crystallinity. Higher gelatinization enthalpy and lower gelatinization temperature were also observed under PHS conditions. The results indicated that PHS can lead to degradation in grain processing and appearance quality, but it can also lead to some improvements in the gelatinization properties of starch.

The effects of chilling stress after anthesis on the physicochemical properties of rice (Oryza sativa L) starch.

This study investigates the effect of chilling stress, over a period of three days after anthesis, on the physicochemical properties of starches derived from six rice cultivars. Chilling stress significantly affected the grain characteristics and physicochemical properties of rice starches, except for those of two varieties, NJ 9108 and ZD 18. In the other four rice cultivars subjected to chilling stress, the content of medium, and large sized granules showed a decrease, and an increase, respectively. Amylose content increased as a result of chilling stress, thereby resulting in starch with a lower swelling power, water solubility, and higher retrogradation enthalpy and gelatinization temperature. Chilling stress led to deterioration of cooked rice quality as determined by the pasting properties of starch. This study indicated that among the cultivars studied, the two rice varieties most resistant to chilling stress after rice anthesis were NJ 9108 and ZD 18.

Chromosomal location of the fosA3 and blaCTX-M genes in Proteus mirabilis and clonal spread of Escherichia coli ST117 carrying fosA3-positive IncHI2/ST3 or F2:A-:B- plasmids in a chicken farm.

The aim of this study was to investigate the spread and location of the fosA3 gene among Enterobacteriaceae from diseased broiler chickens. Twenty-nine Escherichia coli and seven Proteus mirabilis isolates recovered from one chicken farm were screened for the presence of plasmid-mediated fosfomycin resistance genes by PCR. The clonal relatedness of fosA3-positive isolates, the transferability and location of fosA3, and the genetic context of the fosA3 gene were determined. Seven P. mirabilis isolates with three different pulsed-field gel electrophoresis (PFGE) patterns and five E. coli isolates belonging to sequence type 117 (ST117) and phylogenetic group D were positive for fosA3 and all carried the blaCTX-M gene. In E. coli, the genetic structures IS26-ISEcp1-blaCTX-M-65-IS26-fosA3-1758 bp-IS26 and IS26-ISEcp1-blaCTX-M-3-blaTEM-1-IS26-fosA3-1758 bp-IS26 were present on transferable IncHI2/ST3 and F2:A-:B- plasmids, respectively. However, fosA3 was located on the chromosome of the seven P. mirabilis isolates. IS26-ISEcp1-blaCTX-M-65-IS26-fosA3-1758 bp-IS26 and IS26-blaCTX-M-14-611 bp-fosA3-1222 bp-IS26 were detected in three and four P. mirabilis isolates, respectively. Minicircles that contained both fosA3 and blaCTX-M-65 were shared between E. coli and P. mirabilis. This is the first report of the fosA3 gene integrated into the chromosome of P. mirabilis isolates with the blaCTX-M gene. The emergence and clonal spread of avian pathogenic E. coli ST117 with the feature of multidrug resistance and high virulence are a serious problem.

Effect of Nitrogen Management on the Structure and Physicochemical Properties of Rice Starch.

Nitrogen management (nitrogen application ratio at transplanting, tillering, and panicle initiation growth stages) is an important parameter in crop cultivation and is closely associated with rice yield and grain quality. The physicochemical and structural properties of starches separated from two rice varieties grown under three different nitrogen management ratios (9:1; 7:3; 6:4) were investigated. As the percentage of nitrogen used in the panicle initiation stage increased, the content of small starch granules improved, whereas the content of large granules decreased. Amylose content decreased with increasing nitrogen ratio at the panicle initiation stage, thereby resulting in high swelling power, water solubility, gelatinization enthalpy, and low retrogradation. The X-ray diffraction patterns of the starches were found to be A type. The present study indicated that the best nitrogen management ratio for the cultivation of rice with the highest yield, desirable starch physicochemical properties for high quality cooked rice, and a moderate protein level is 7:3.