scholarly journals Transcriptome and genome sequencing elucidates the molecular basis for the high yield and good quality of the hybrid rice variety Chuanyou6203

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Juansheng Ren ◽  
Fan Zhang ◽  
Fangyuan Gao ◽  
Lihua Zeng ◽  
Xianjun Lu ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Hybrid Rice ◽  
Rice Variety ◽  
Utilization Efficiency ◽  
High Yield ◽  
Mrna Editing ◽  
High Quality ◽  
Flag Leaves ◽  
Yield And Quality

AbstractThe yield heterosis of rice is sought by farmers and strong contributes to food safety, but the quality of hybrid rice may be reduced. Therefore, developing new varieties with both high yield and good quality is a heavily researched topic in hybrid rice breeding. However, the molecular mechanism governing yield heterosis and high rice quality has not been elucidated to date. In this study, a comparative transcriptomics and genomic analysis was performed on a hybrid rice variety, Chuanyou6203 (CY6203), and its parents to investigate the molecular mechanism and gene regulation network governing the formation of yield and quality stages. A total of 66,319 SNPs and InDels between CH3203 and C106B were detected in the 5′-UTR, exon, intronic, and 3′-UTR regions according to the reference genome annotation, which involved 7473 genes. A total of 436, 70, 551, 993, and 1216 common DEGs between CY6203 and both of its parents were identified at the same stage in panicles and flag leaves. Of the common DEGs, the numbers of upregulated DEGs between CY6203 and CH3203 were all greater than those of upregulated DEGs between CY6203 and C106B in panicles and flag leaves at the booting, flowering, and middle filling stages. Approximately 40.61% of mRNA editing ratios were between 0.4 and 0.6, and 1.68% of mRNA editing events (editing ratio ≥ 0.8) in CY6203 favored one of its parents at three stages or a particular stage, suggesting that the hypothetical heterosis mechanism of CY6203 might involve dominance or epistasis. Also 15,934 DEGs were classified into 19 distinct modules that were classified into three groups by the weighted gene coexpression network analysis. Through transcriptome analysis of panicles and flag leaves in the yield and quality stages, the DEGs in the green-yellow module primarily contributed to the increase in the source of CY6203 due to an in increase in photosynthetic efficiency and nitrogen utilization efficiency, and a small number of DEGs related to the grain number added spikelet number per panicle amplified its sink. The balanced expression of the major high-quality alleles of C106B and CH3203 in CY6203 contributed to the outstanding quality of CY6203. Our transcriptome and genome analyses offer a new data set that may help to elucidate the molecular mechanism governing the yield heterosis and high quality of a hybrid rice variety.

scholarly journals A universal method for high-quality RNA extraction from plant tissues rich in starch, proteins and fiber

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Amaranatha R. Vennapusa ◽  
Impa M. Somayanda ◽  
Colleen J. Doherty ◽  
S. V. Krishna Jagadish
Keyword(s):  
Rna Extraction ◽  
Poor Quality ◽  
High Yield ◽  
Plant Tissues ◽  
Universal Method ◽  
High Quality ◽  
Yield And Quality ◽  
Extraction Buffer ◽  
Co Precipitation

Abstract Using existing protocols, RNA extracted from seeds rich in starch often results in poor quality RNA, making it inappropriate for downstream applications. Though some methods are proposed for extracting RNA from plant tissue rich in starch and other polysaccharides, they invariably yield less and poor quality RNA. In order to obtain high yield and quality RNA from seeds and other plant tissues including roots a modified SDS-LiCl method was compared with existing methods, including TRIZOL kit (Invitrogen), Plant RNeasy mini kit (Qiagen), Furtado (2014) method, and CTAB-LiCl method. Modifications in the extraction buffer and solutions used for RNA precipitation resulted in a robust method for extracting RNA in seeds and roots, where extracting quality RNA is challenging. The modified SDS-LiCl method revealed intense RNA bands through gel electrophoresis and a nanodrop spectrophotometer detected ratios of ≥ 2 and 1.8 for A260/A230 and A260/A280, respectively. The absence of starch co-precipitation during RNA extraction resulted in enhanced yield and quality of RNA with RIN values of 7–9, quantified using a bioanalyzer. The high-quality RNA obtained was demonstrated to be suitable for downstream applications, such as cDNA synthesis, gene amplification, and RT-qPCR. The method was also effective in extracting RNA from seeds of other cereals including field-grown sorghum and corn. The modified SDS-LiCl method is a robust and highly reproducible RNA extraction method for plant tissues rich in starch and other secondary metabolites. The modified SDS-LiCl method successfully extracted high yield and quality RNA from mature, developing, and germinated seeds, leaves, and roots exposed to different abiotic stresses.

scholarly journals Generation of a New Glutinous Photothermosensitive Genic-Male-Sterile (PTGMS) Line by CRISPR/Cas9-Directed Mutagenesis of Wx in Rice (Oryza sativa L.)

Agriculture ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1044
Author(s):  
Kaichong Teng ◽  
Xin Wang ◽  
Xinying Guo ◽  
Yaoguang Liu ◽  
Rongbai Li
Keyword(s):  
Mutation Rate ◽  
Hybrid Rice ◽  
Amylose Content ◽  
Rice Variety ◽  
High Yield ◽  
Male Sterile ◽  
High Quality ◽  
Glutinous Rice ◽  
Homozygous Mutant ◽  
Wx Gene

The Photothermosensitive Genic-Male-Sterile (PTGMS) line, Y58S, an indica rice variety, combines high-quality and high-light-efficiency use, disease and stress resistance, and excellent plant type and mating force. Y58S is widely used to assemble two-line hybrid rice varieties, especially super hybrids. The Wx gene is the main effector gene for controlling amylose synthesis, which determines the amylose content (AC) of rice grains. By editing this gene, a glutinous line with a low AC can be obtained. In this study, the CRISPR/Cas9 system was used to mediate the editing of the Wx gene, which caused ultra-low AC mutations that produced a PTGMS glutinous rice strain with excellent waxiness. The results showed that 18 positively transformed plants were obtained from the T0 generation, with a mutation rate of 64.29%, of which six were homozygous mutant plants, indicating that the gene-editing target had a higher targeting efficiency and a higher homozygosity mutation rate. Compared to the wild type, the AC of the mutants was significantly lower. Through molecular marker detection and screening of T1 and T2 generations, five homozygous T-DNA-free mutant strains were identified that were consistent with Y58S in fertility and other agronomic traits except for AC. Among these, the AC of the W-1-B-5 homozygous mutant, the glutinous PTGMS line wx-Y58S, was as low as 0.6%. Our research revealed that the Wx gene of excellent PTGMS rice can be edited to generate a new waxy PTGMS line using the CRISPR/Cas9 system. This study provided a simple and effective strategy for breeding high-yield, high-quality, and glutinous two-line hybrid rice, and provided excellent sterile lines for their large-scale application. Once put into use, waxy hybrid rice will greatly improve the yield of glutinous rice and increase social benefits.

High Microsatellite and SNP Genotyping Success Rates Established in a Large Number of Genomic DNA Samples Extracted From Mouth Swabs and Genotypes

2006 ◽  
Vol 9 (4) ◽  
pp. 501-506 ◽  
Author(s):  
Josine L. Min ◽  
Nico Lakenberg ◽  
Margreet Bakker-Verweij ◽  
Eka Suchiman ◽  
Dorret I. Boomsma ◽  
...  
Keyword(s):  
Success Rate ◽  
Genomic Dna ◽  
Snp Genotyping ◽  
High Yield ◽  
Success Rates ◽  
Nucleotide Polymorphism ◽  
High Quality ◽  
Single Nucleotide ◽  
Dna Yield ◽  
Yield And Quality

AbstractIn this article, we present the genomic DNA yield and the microsatellite and single nucleotide polymorphism (SNP) genotyping success rates of genomic DNA extracted from a large number of mouth swab samples. In total, the median yield and quality was determined in 714 individuals and the success rates in 378,480 genotypings of 915 individuals. The median yield of genomic DNA per mouth swab was 4.1 μg (range 0.1–42.2 μg) and was not reduced when mouth swabs were stored for at least 21 months prior to extraction. A maximum of 20 mouth swabs is collected per participant. Mouth swab samples showed in, respectively, 89% for 390 microsatellites and 99% for 24 SNPs a genotyping success rate higher than 75%. A very low success rate of genotyping (0%–10%) was obtained for 3.2% of the 915 mouth swab samples using microsatellite markers. Only 0.005% of the mouth swab samples showed a geno-typing success rate lower than 75% (range 58%–71%) using SNPs. Our results show that mouth swabs can be easily collected, stored by our conditions for months prior to DNA extraction and result in high yield and high-quality DNA appropriate for genotyping with high success rate including whole genome searches using microsatellites or SNPs.

scholarly journals Stomatal Conductance and Chlorophyll Characteristics and Their Relationship with Yield of Some Cocoa Clones Under Tectona grandis, Leucaena sp., and Cassia surattensis.

2015 ◽  
Vol 31 (2) ◽  
pp. 99-108
Author(s):  
Fakhrusy Zakariyya ◽  
Adi Prawoto
Keyword(s):  
Stomatal Conductance ◽  
Chlorophyll Content ◽  
Tectona Grandis ◽  
High Yield ◽  
Climate Type ◽  
Pod Yield ◽  
Yield And Quality ◽  
Diffusive Resistance ◽  
Cocoa Production

An optimum physiological condition will support high yield and quality of cocoa production. The research was aimed to study the effects of stomatal conductance and chlorophyll content related to cocoa production under three shade regimes.This research was conducted in Kaliwining Experimental Station, elevation of 45 m above sea level with D climate type based on Schmidt & Fergusson. Cocoa trees which were planted in 1994 at a spacing of 3 X 3 m were used in the study planted by using split plot design. The shade tree species were teak (Tectona grandis), krete (Cassiasurattensis), and lamtoro (Leucaena sp.) as the main plots, and cocoa clones of Sulawesi 01,Sulawesi 02, KKM 22 and KW 165 as sub plots. This study showed that there was interaction between cocoa clone and shade species for stomatal conductance where stomatal diffusive resistance of KKM 22 was the best under Leucaena sp.and Cassiasurattensis with the values of 1.38 and 1.34 s.cm -1, respectively. The highest chlorophyll content, stomatal index and transpiration values was under Leucaena sp. shade. There was positive correlation between chlorophyll content and transpiration with pod yield of cocoa. The highest yield and the lowest bean count wereobtainedon Sulawesi 01 clone under Leucaenasp. shade.Keywords: stomatal conductance, transpiration, diffusive resistance, shades trees, clones,pod yield

scholarly journals Scientific and practical fundamentals of growing cabbage (Brassica capitata lizg.) in Uzbekistan

2021 ◽  
Vol 939 (1) ◽  
pp. 012044
Author(s):  
A J Shokirov ◽  
S S Lapasov ◽  
K J Shokirov
Keyword(s):  
Large Scale ◽  
Scientific Research ◽  
Mineral Fertilizers ◽  
Biological Productivity ◽  
High Quality ◽  
Planting Time ◽  
Yield And Quality ◽  
White Cabbage ◽  
Urgent Task

Abstract At present, scientific research is underway to further develop vegetable growing in the secondary crop, in particular to further increase the yield and quality of white cabbage, to select a system of planting time-sowing scheme that maximizes the biological productivity of varieties, and to apply the most optimal standards of fertilization and irrigation. In this regard, the urgent task remains to determine the optimal varieties of cabbage that can be grown in repeated crops, their optimal planting scheme, timing, development and implementation of optimal standards for each variety of mineral fertilizers and irrigation, and its solution is large-scale throughout the country. Besides that a number of problematic issues are addressed, which could allow to get high and high-quality harvest of white cabbage in repeated sowing in grain-free areas.

scholarly journals EFFECT OF BIOFERTILIZER AND COMPOST ON NITRATE STATUS, YIELD AND QUALITY OF POTATO TUBER UNDER NEWLY RECLAIMED SANDY SOIL

AGROFOR ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
S.F. EL-SAYED ◽  
A.A. GAHRIB ◽  
Rasha R. EID
Keyword(s):  
Sandy Soil ◽  
Control Treatment ◽  
High Yield ◽  
Potato Tubers ◽  
Treatment Control ◽  
Mineral Fertilization ◽  
Marketable Yield ◽  
Yield And Quality ◽  
Compost Treatment

This investigation was carried out during the two summer seasons of 2015 and2016 in sandy soil on potato culitvar "Sante" to study the effect of using 100%compost (15 t/fed.) and 50% compost + nitrogen fixing bacteria (Azotobacter, andPseudomonas alone or together) on potato yield and quality as compared to theconventional mineral fertilization (120-75-150 kg/fed. NPK + 5 toncompost/fed.(control)). No significant differences in tubers yield/fed. were detectedbetween mineral fertilization (control) and using 100% compost (15t/fed).However, control treatment significantly produced a high yield per feddan,more than using 50% compost + any biofertilizer treatment.Using composttreatment at 15 t/fed.execeed all biofertilizer treatments in marketable yield in bothseasons, but without significant differences as compared with mineral fertilization(control).No significant differences in tuber dray matter and content of starch intuber were found between using compost treatment at 15 ton/fed. and mineralfertilization treatment (control)in both seasons. Nevertheless, application of 50%compost+ 4 applications of Azotobacter and Pseudomonas had the highest tuberconcentrations of starch and nitrogen with significant differences as compared withthe mineral fertilization.Using50% compost + 4 applications of Azotobacter orPseudomonas or both (Azotobacter + Pseudomonas )and application of 100%compost caused producing potato tubers with the lowest concentration of nitratewith significant differences as compared with the mineral fertilization. Nosignificant differences were detected between mineral and organic fertilizersconcerning P and K concentrations in tubers.

scholarly journals Determination of the Effect of Humic Acid on Growth and Development Parameters of Parsley (Petroselinum sativum Hoffm.) Grown in Boron Soil

2018 ◽  
Vol 47 (1) ◽  
pp. 183-193 ◽  
Author(s):  
Tuncay TURSUN ◽  
Sener AKINCI ◽  
Esin BOZKURT
Keyword(s):  
Humic Acid ◽  
Growth Parameters ◽  
Dry Weight ◽  
High Yield ◽  
Yield And Quality ◽  
Icp Ms ◽  
Growth Analyses ◽  
Nutrient Solutions

Boron is an important micronutrient, required for all plant growth, and critical for high yield and quality of crops. The aim of the present research was to determine the effects of boron on pot-grown parsley (Petroselinum sativum Hoffm.). The experimental design consisted of four treatments using Hoagland-Arnon (1950) nutrient solutions with two different boron concentrations (B1 - 15 ppm and B2 - 150 ppm), each with and without 10 ml humic acid addition (HB1 and HB2), and controls with full strength Hoagland-Arnon solutions. Growth analyses of the parsley revealed that 15 ppm boron application caused an increase in root length leaf fresh and dry weight root fresh and dry weight and leaf area compared to control values. 150 ppm B (B2) concentration decreased all growth parameters compared to controls. The two humic acid treatments (HB1 and HB2) did not increase any of those growth parameters either in controls (C) or in the two boron (B1 and B2) concentrations. Analysis by (ICP-MS) revealed that B content in the leaves increased gradually in B1 and B2, as well as in both humic treatments where in HB2 it increased to 99.38% compared to B1. In the leaves, Mn, Zn and Fe contents behaved the same as B, increasing in all treatments, with the amounts in HB2 being significantly greater than in C, B1 and B2 leaves.

Phytoestrogen-containing diets offer benefits for mouse embryology but lead to fewer offspring being produced

2020 ◽  
Vol 54 (6) ◽  
pp. 536-545
Author(s):  
Jussi Helppi ◽  
Ronald Naumann ◽  
Oliver Zierau
Keyword(s):  
Transgenic Mice ◽  
Diet Group ◽  
High Yield ◽  
Standard Diet ◽  
Potential Health ◽  
Protein Sources ◽  
Yield And Quality ◽  
Experimental Mouse ◽  
Standard Diet Group

One of the most commonly used protein sources in rodent diets is soy, which is naturally rich in phytoestrogens. Although phytoestrogens have shown potential health benefits in humans, they may also have the ability to disrupt reproduction. Consequently, there has been a tendency to try to exclude them from rodent diets. In the current study, we investigated whether phytoestrogen content in the mouse diet could affect reproduction in mice used as embryo donors. Donor mice (C57BL/6JOlaHsd) were maintained with three different diets: high phytoestrogen (ca. 400 mg/kg genistein), low phytoestrogen (ca. 10 mg/kg genistein) and standard breeding diet (ca. 120 mg/kg genistein). Mice fed a high phytoestrogen diet had a high yield of plugs, embryos, and injectable embryos, as well as producing good quality embryos. Results from donor mice fed a low phytoestrogen diet were consistently but only slightly inferior, whereas mice fed a standard diet performed the poorest. Interestingly, the largest number of born and weaned offspring were observed when recipient females received embryos from the standard diet group. Sperm yield and quality of stud males did not differ between the groups. We surmize that for experimental endpoints requiring fertilized embryos it may be more beneficial to feed mice a diet containing phytoestrogen, but if the goal is to produce transgenic mice, a diet high in phytoestrogen may be inadvisable. In conclusion, care should be taken when selecting a diet for experimental mouse colonies as phytoestrogen could influence the study outcome.

scholarly journals Heterosis-associated genes confer high yield in super hybrid rice

2020 ◽  
Vol 133 (12) ◽  
pp. 3287-3297
Author(s):  
Tianzi Lin ◽  
Cong Zhou ◽  
Gaoming Chen ◽  
Jun Yu ◽  
Wei Wu ◽  
...  
Keyword(s):  
Large Scale ◽  
Field Experiments ◽  
Hybrid Rice ◽  
Rice Variety ◽  
Female Parent ◽  
High Yield ◽  
Recurrent Parent ◽  
Sequencing Analysis ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines

Abstract Key message Heterosis QTLs, including qSS7 and qHD8, with dominance effects were identified through GBS and large-scale phenotyping of CSSLs and hybrid F1 populations in a paddy field. Abstract Heterosis has contributed immensely to agricultural production, but its genetic basis is unclear. We evaluated dominance effects by creating two hybrid populations: a B-homo set with a homozygous background and heterozygous chromosomal segments and a B-heter set with a heterozygous background and homozygous segments. This was achieved by crossing a set of 156 backcrossed-derived chromosome segment substitution lines (CSSLs) with their recurrent parent (9311), the male parent of the first super-high-yield hybrid Liangyoupei9 (LYP9), and with the female parent (PA64s) of the hybrid. The CSSLs were subjected to a genotyping-by-sequencing analysis to develop a genetic map of segments introduced from the PA64s. We evaluated the heterotic effects on eight yield-related traits in the hybrid variety and F1 populations in large-scale field experiments over 2 years. Using a linkage map consisting of high-density SNPs, we identified heterosis-associated genes in LYP9. Five candidate genes contributed to the high yield of LYP9, with qSS7 and qHD8 repeatedly detected in both B-hybrid populations. The heterozygous segments harboring qSS7 and qHD8 showed dominance effects that contributed to the heterosis of yield components in the hybrid rice variety Liangyoupei9.

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