Rice-duck co-culture is an integrated farming technology that benefits rice production, grain quality, and ecological sustainability in paddy fields. However, little is known about the effects of rice-duck co-culture on enzyme activity involved in the biosynthesis of 2-acetyl-1-pyrroline (2-AP), the volatile that gives fragrant rice its' distinctive and sought-after aroma. The present study aimed to examine the influence of rice-duck co-culture on the photosynthesis, yield, grain quality, rice aroma, and the enzymes involved in 2-acetyl-1-pyrroline biosynthesis in the cultivar Meixiangzhan 2 during the early and late rice growing seasons of 2016 in Guangzhou, China. We compared the rice grown in paddy fields with and without ducks. We found that rice-duck co-culture not only improved the yield and quality of fragrant rice grain, but also promoted the precursors of 2-AP biosynthesis formation and 2-AP accumulation in the grain. Grain 2-AP content in rice-duck co-culture was noticeably increased with 9.60% and 20.81% in early and late seasons, respectively. Proline and pyrroline-5-carboxylic acid (P5C) (precursors of 2-AP biosynthesis) and the activity of enzymes such as proline dehydrogenase (ProDH), ornithine aminotransferase (OAT) and Δ1 pyrroline-5-carboxylic acid synthetase (P5CS) were all improved by 10.15%-12.99%, 32.91%-47.75%, 17.81%-26.71%, 6.25%-21.78%, and 10.58%-38.87% under rice-duck co-culture in both seasons, respectively. Overall, our results suggest that rice-duck co-culture is an environmentally-friendly and sustainable approach to improving rice aroma and grain quality of fragrant rice.
Leaf rolling and discoloration are two chilling-injury symptoms that are widely used as indicators for the evaluation of cold tolerance at the seedling stage in rice. However, the difference in cold-response mechanisms underlying these two traits remains unknown. In the present study, a cold-tolerant rice cultivar, Lijiangxintuanheigu, and a cold-sensitive cultivar, Sanhuangzhan-2, were subjected to low-temperature treatments and physiological and genome-wide gene expression analyses were conducted. Leaf rolling occurred at temperatures lower than 11?°C, whereas discoloration appeared at moderately low temperatures such as 13?°C. Chlorophyll contents in both cultivars were significantly decreased at 13?°C, but not altered at 11?°C. In contrast, the relative water content and relative electrolyte leakage of both cultivars decreased significantly at 11?°C, but did not change at 13?°C. Expression of genes associated with calcium signaling and abscisic acid (ABA) degradation was significantly altered at 11?°C in comparison with 25?°C and 13?°C. Numerous genes in the DREB, MYB, bZIP, NAC, Zinc finger, bHLH, and WRKY gene families were differentially expressed. Many aquaporin genes and the key genes in trehalose and starch synthesis were down regulated at 11?°C in comparison with 25?°C and 13?°C. These results suggest that the two chilling injury symptoms are temperature-specific and are controlled by different mechanisms. Cold-induced leaf rolling is associated with calcium and ABA signaling pathways and is regulated by multiple transcriptional regulators. The suppression of aquaporin genes and reduced accumulation of soluble sugars under cold stress results in a reduction in cellular water potential and consequently leaf rolling.
In previous studies, integrative crop management (ICM) improved shoot growth and grain yield of rice (Oryza sativa L.). However, little is known about the effect of ICM on root growth and methane (CH4) emission of paddy rice. In this study, two rice varieties, Wuyunjing 24 and Yongyou 2640, were grown. A field experiment was conducted with three crop management treatments including zero nitrogen fertilization (0N), local farmer practice (LFP), and ICM. Root morphophysiological traits and CH4 emission from the paddy field were investigated. ICM significantly increased mean grain yield by 29.9%, with the effect attributed mainly to an increase in mean total number of spikelets by 26.4% compared to LFP. ICM increased root and shoot biomass, root length, number of roots, root oxidation activity (ROA), root bleeding rate, and root total and active absorbing surface area by respectively 24.4%, 25.7%, 17.1%, 9.3%, 18.7%, 29.5%, 12.1%, and 24.7%. The concentrations of malic, succinic, and acetic acids in root exudates were respectively 5.8%, 6.0%, and 10.5% higher in ICM than in LFP. Compared to LFP, ICM significantly decreased the rate of CH4 emission during emission peak stages and reduced total CH4 emission by 17.1%. The root morphophysiological traits were positively and significantly correlated with grain yield, whereas root length, specific root length, ROA, and root total and active absorbing surface area were negatively and significantly correlated with total CH4 emission. These results suggest that ICM could achieve the dual goals of increasing grain yield and reducing the greenhouse gas effect by improving the root morphology and physiological traits of paddy rice.
Retrotransposons account for a large proportion of the genome and genomic variation, and play key roles in creating novel genes and diversifying the genome in many eukaryotic species. Although retrotransposons are abundant in plants, their roles had been underestimated because of a lack of research. Here, we characterized a gibberellin Acid (GA)-insensitive dwarf mutant, 84133, in foxtail millet. Map-based cloning revealed a 5.5-kb Copia-like retrotransposon insertion in DWARF1 (D1), which encodes a DELLA protein. Transcriptional analysis showed that the Copia retrotransposon mediated the transcriptional reprogramming of D1 leading to a novel N-terminal-deleted truncated DELLA transcript that was putatively driven by Copia's LTR, namely D1-TT, and another chimeric transcript. The presence of D1-TT was confirmed by protein immunodetection analysis. Furthermore, D1-TT protein was resistant to GA3 treatment compared with the intact DELLA protein due to its inability to interact with the GA receptor, SiGID1. Overexpression of D1-TT in foxtail millet resulted in dwarf plants, confirming that it determines the dwarfism of 84133. Thus, our study documents a rare instance of long terminal repeat (LTR) retrotransposon-mediated transcriptional reprograming in the plant kingdom. These results shed light on the function of LTR retrotransposons in generating new gene functions and genetic diversity.
Deficiency of vitamin-E or tocopherol causes neurological and cardiovascular disorders in humans. Though maize kernel is rich in total tocopherol, the level of α-tocopherol possessing the highest vitamin-E activity is low. Mutant allele of ZmVTE4 with deletion of 7?bp and 118?bp (0/0: most favorable haplotype) in 5′UTR and promoter region, respectively significantly enhances α-tocopherol in maize kernel than wild type haplotype (7/118). α-tocopherol estimation in 15 diverse inbreds revealed that mean α-/γ-tocopherol and α-/total-tocopherol was much higher in genotypes with favorable haplotype (1.51 and 0.41) than unfavorable class (0.19 and 0.13), respectively. However even within favorable class, α-tocopherol ranged from 4.76 to 30.07?μg?g−1. Sequence analysis of part of 5′UTR and promoter of ZmVTE4 among the genotypes with favorable haplotype revealed 14 SNPs (SNP1 to SNP14) and eight InDels (InDel1 to InDel8). SNP7 at 606?bp (G to A), and InDels viz., InDel1 (27?bp), InDel4 (27?bp) and InDel8 (14?bp) differentiated low and high α-tocopherol accumulating inbreds with favorable haplotype. Hence the newly identified SNP and InDels in addition to the already reported InDels can be useful in selection of favorable genotypes with higher α-tocopherol in maize.
Wheat is a staple crop worldwide, but yields may diminish as climate change causes increasingly unpredictable patterns of precipitation and soil nutrient availability. Farmers are thus challenged to maximize planting efficiency to increase yield, while also improving their resource use efficiency. In this study the effectiveness of tridimensional uniform sowing was tested across a range of planting densities for winter wheat crops on the North China Plain. Tridimensional uniform sowing was tested against conventional drilling at three planting densities (180?×?104, 270?×?104, and 360?×?104?plants?ha−1) and assessed for water consumption, biomass, nitrogen uptake and allocation, and aspects of yield. The tridimensional uniform sowing treatment outperformed the conventional drilling treatment in most metrics and at most planting densities, while performing markedly better at higher planting densities. Water consumption decreased and nitrogen efficiency increased. Tiller number and percentage of productive tillers, leaf area index, dry weight, and yield increased without a significant decline in grain protein. Nitrogen allocation was more efficient under tridimensional uniform sowing than with conventional drilling, and also varied according to annual precipitation and planting density. Both yield and grain protein contents were significantly correlated with the amount of pre-anthesis accumulated nitrogen translocated from vegetative organs to kernels after anthesis. Overall, a density of 270?×?104?plants?ha−1 provided the highest water use efficiency and grain yield. Tridimensional uniform sowing will benefit farmers by forming stronger overall crops, promoting the coordinated improvement of yield, nitrogen uptake and efficiency, and increasing grain protein content at higher planting densities.
A chromosome segment substitution line (CSSL) is a powerful tool for combining quantitative trait locus (QTL) mapping with the pyramiding of desirable alleles. The rice CSSL Z1364 with increased kernel number was identified in a BC3F8 population derived from a cross of Nipponbare as the recipient with Xihui 18 as the donor parent. Z1364 carried three substitution segments distributed on chromosomes 1, 6, and 8. The mean substitution length was 1.19?Mb. Of 17 QTL identified on the substitution segments, qSP1 for spikelets per panicle, qSSD1 for seed-set density, and qNSB1 for number of secondary branches explained respectively 57.34%, 87.7%, and 49.44% of the corresponding phenotypic variance and were all linked to RM6777. Chi-square analysis showed that the increased kernel number in Z1364 was inherited recessively by a single gene. By fine mapping, qSP1 was delimited to a 50-kb region on the short arm of chromosome 1. Based on DNA sequence, a previously uncharacterized rice homolog of Arabidopsis thaliana AT4G32551 was identified as a candidate gene for qSP1 in which mutation increases the number of spikelets and kernels in Z1364. qSP1 was expressed in all tissues, but particularly in 1-cm panicles. The expression levels of OsMADS22, GN1A, and DST were upregulated and those of LAX2, GNP1, and GHD7 were downregulated in Nipponbare. These results provide a foundation for functional research on qSP1.
The β subunit of soybean [Glycine max (L.) Merr.] seed storage protein is of great significance in sulfur-containing amino acid balance and soybean processing properties. The objective of this study was to elucidate the relationship between the β subunit and sulfur-containing amino acid composition, and the potential regulatory mechanism. The β subunit was independently accumulated in comparison with other major subunits (α/α′, acidic, basic, and A3) during seed filling, and a low level of β subunit content (BSC) was formed during the accumulation process. In low-BSC mature seeds, crude protein, oil content, and fatty acid composition were not changed, but sulfur-containing amino acids (Cys?+?Met) in the low-BSC seeds increased significantly (by 31.5%), suggesting that an internal regulatory mechanism within seed might be responsible for the rebalance of seed protein composition and that sulfur assimilation might be deeply involved in β subunit accumulation. Transcriptomic analysis revealed that genes involved in anabolism of cysteine, methionine, and glutathione were up-regulated but those involved in the catabolism of these compounds were down-regulated, suggesting a relationship between the elevation of methionine and glutathione and low BSC. Our study sheds light on seed composition in low BSC lines and on the potential molecular regulatory mechanism of β subunit accumulation, broadening our understanding of soybean seed protein synthesis and its regulation.
Leymus mollis (Trin.) Pilger (2n?=?4x?=?28, NsNsXmXm,), a wild relative of common wheat, possesses many potentially valuable traits for genetic improvement of wheat, including strong, short stems, long spikes with numerous spikelets, tolerance to drought and cold stresses, and resistance to many fungal and bacterial diseases. In the present study, a wheat-L. mollis double substitution line DM96 was selected from a F6 progeny of a cross between M842-16 (an octoploid Tritileymus line) and D4286 (a Triticum durum line) using genomic in situ hybridization (GISH), simple sequence repeat (SSR) markers, and expressed sequence tagged sequence site (EST-STS) markers. Chromosome analysis at mitosis and meiosis showed that DM96 had a chromosome constitution of 2n?=?42?=?21II. GISH analysis indicated that DM96 carried 38 chromosomes from wheat and two homologous pairs of Ns chromosomes from L. mollis. Fluorescent in situ hybridization (FISH) showed that chromosomes 2Ns and 3Ns from L. mollis had replaced wheat chromosomes 2D and 3D in DM96, which was confirmed by SSR and STS markers. The newly developed substitution line DM96 has shorter height, longer spikes and more kernels than its parents and showed high resistance to stripe rust and Fusarium head blight (FHB). Thus, this line is a new bridge material for the production of useful translocation lines for wheat genetic research and genetic improvement of wheat yield and disease resistance in breeding programs.
Crop yield potential can be increased through the use of appropriate agronomic practices. Integrated agronomic practice (IAP) is an effective way to increase maize (Zea mays L.) grain yield and nitrogen use efficiency (NUE); however, the physiological processes associated with gains in yield potential obtained from IAP, particularly the different under various soil fertility conditions, remain poorly understood. An IAP strategy including optimal planting density, split fertilizer application, and subsoiling tillage was evaluated over two growing seasons to determine whether the effects of IAP on maize yield and NUE differ under different levels of soil fertility. Compared to farmers' practices (FP), IAP increased maize grain yield in 2013 and 2014 by 25% and 28%, respectively, in low soil fertility (LSF) fields and by 36% and 37%, respectively, in high soil fertility (HSF) fields. The large yield gap was attributed mainly to greater dry matter (DM) and N accumulation with IAP than with FP owing to increased leaf area index (LAI) and DM accumulation rate, which were promoted by greater soil mineral N content (Nmin) and root length. Post-silking DM and N accumulation were also greater with IAP than with FP under HSF conditions, accounting for 60% and 43%, respectively, of total biomass and N accumulation; however, no significant differences were found for post-silking DM and N accumulation between IAP and FP under LSF conditions. Thus, the increase in grain yield with IAP was greater under HSF than under LSF. Because of greater grain yield and N uptake, IAP significantly increased N partial factor productivity, agronomic N efficiency, N recovery efficiency, and physiological efficiency of applied N compared to FP, particularly in the HSF fields. These results indicate that considerable further increases in yield and NUE can be obtained by increasing effective soil N content and maize root length to promote post-silking N and DM accumulation in maize planted at high plant density, especially in fields with low soil fertility.
Genetic linkage maps are essential for studies of genetics, genomic structure, and genomic evolution, and for mapping quantitative trait loci (QTL). Identification of molecular markers and construction of genetic linkage maps in tobacco (Nicotiana tabacum L.), a classical model plant and important economic crop, have remained limited. In the present study we identified a large number of single nucleotide polymorphism (SNP) markers and constructed a high-density SNP genetic map for tobacco using restriction site-associated DNA sequencing. In 1216.30 Gb of clean sequence obtained using the Illumina HiSeq 2000 sequencing platform, 99,647,735 SNPs were identified that differed between 203 sequenced plant genomes and the tobacco reference genome. Finally, 13,273 SNP markers were mapped on 24 high-density tobacco genetic linkage groups. The entire linkage map spanned 3421.80?cM, with a mean distance of 0.26?cM between adjacent markers. Compared with genetic linkage maps published previously, this version represents a considerable improvement in the number and density of markers. Seven QTL for resistance to cucumber mosaic virus (CMV) in tobacco were mapped to groups 5 and 8. This high-density genetic map is a promising tool for elucidation of the genetic bases of QTL and for molecular breeding in tobacco.
Seed size is one of the vital traits determining seed appearance, quality, and yield. Untangling the genetic mechanisms regulating soybean 100-seed weight (100-SW), seed length and seed width across environments may provide a theoretical basis for improving seed yield. However, there are few reports related to QTL mapping of 100-SW across multiple ecological regions. In this study, 21 loci associated with seed size traits were identified using a genome-wide association of 5361 single nucleotide polymorphisms (SNPs) across three ecoregions in China, which could explain 8.12%-14.25% of the phenotypic variance respectively. A new locus, named as SW9-1 on chromosome 9 that explained 10.05%-10.93% of the seed weight variance was found significantly related to seed size traits, and was not previously reported. The selection effect analysis showed that SW9-1 locus has a relatively high phenotypic effect (13.67) on 100-SW, with a greater contribution by the accessions with bigger seeds (3.69) than the accessions with small seeds (1.66). Increases in seed weight were accompanied by increases in the frequency of SW9-1T allele, with >90% of the bred varieties with a 100-SW >30?g carrying SW9-1T. Analysis of SW9-1 allelic variation in additional soybean accessions showed that SW9-1T allele accounting for 13.83% of the wild accessions, while in 46.55% and 51.57% of the landraces and bred accessions, respectively, this results indicating that the SW9-1 locus has been subjected to artificial selection during the early stages of soybean breeding, especially the utilization of SW9-1T in edamame for big seed. These results suggest that SW9-1 is a novel and reliable locus associated with seed size traits, and might have an important implication for increasing soybean seed weight in molecular design breeding. Cloning this locus in future may provide new insights into the genetic mechanisms underlying soybean seed size traits.
Malnutrition is one of the prevailing health problems worldwide, affecting a large proportion of the populations in rice-consuming countries. Breeding rice varieties with increased concentrations of elements in the grain is considered the most cost-effective approach to alleviate malnutrition. Development of molecular markers for high grain concentrations of essential elements, particularly Zn, for use in marker-assisted selection (MAS) can hasten breeding efforts to develop rice varieties with nutrient-dense grain. We performed QTL mapping for four agronomic traits: days to 50% flowering, plant height, number of tillers, grain yield, and 13 grain elements: As, B, Ca, Co, Cu, Fe, K, Mg, Mn, Mo, Na, P, and Zn, in two doubled-haploid populations derived from the crosses IR64?×?IR69428 and BR29?×?IR75862. These populations were phenotyped during 2015DS and 2015WS at IRRI, Los Baños, The Philippines, and genotyped them with a 6?K SNP chip. Inclusive composite interval mapping revealed 15 QTL for agronomic traits and 50 QTL for grain element concentration. Of these, eight QTL showed phenotypic variance of >25% and 11 QTL were consistent across seasons. There were seven QTL co-localization regions containing QTL for more than two traits. Twenty five epistatic interactions were detected for two agronomic traits and seven mineral elements. Several DH lines with high Fe and Zn in polished rice were identified. These lines can be used as donors for breeding high-Zn rice varieties. Some of the major QTL can be further validated and used in MAS to improve the concentrations of nutritive elements in rice grain.
