Assessing the importance of genotype × environment interaction for root traits in rice using a mapping population III: QTL analysis by mixed models

The phenotypic analysis of field experiments includes information about the experimental design, the randomization structure and a number of putative dependencies of environment and design factors on the trait investigated. In QTL studies, the genetic correlation across environments, which arises when the same set of lines is tested in multiple environments, plays an important role. This paper investigates the effect of model choice on the set and magnitude of detected root QTL in rice. Published studies on QTLs for root traits indicate that different results are obtained if varying genetic populations are used and also if different environmental conditions are included. An experiment was conducted with 168 RILs of the Bala × Azucena mapping population plus parents as checks under four environmental conditions (low light, low nitrogen, drought and a control environment). We propose a model that incorporates all relevant experimental information into a composite interval mapping approach based on a mixed model, which especially considers the correlation of genotypes in different environments. An extensive sequential model selection procedure was applied based on the phenotypic model, using the AIC to determine an appropriate random structure and Type 3 Wald F-tests for selection of fixed effects. In a first step we checked whether any of the fixed effects and random (nested) design effects could be dropped. Secondly, an appropriate covariance structure was chosen for genotype × environment interaction. In a third step Box-Cox transformations were applied based on residual analysis. We compared profiles of composite interval mapping scans with and without the inclusion of genotype × environment interaction and the experimental design information. Some distinct differences in profiles indicate that insufficient modeling of the non-QTL part can lead to an overly optimistic interpretation of QTL main effects in interval mapping. It is concluded that mixed model QTL mapping offers a reasonable way to separate environmental and genetic influences in the evaluation of quantitative genes and especially enables a more realistic assessment of QTL and QTL × environment effects than standard approaches by including all relevant effects.     

Mapping quantitative trait loci (QTL) for grain size in rice using a RIL population from Basmati × indica cross showing high segregation distortion

Grain size is one of the three productivity related traits in rice and hence a major target for genetic improvement. Since understanding genetic variation in grain size between Basmati and indica genotypes is important for rice improvement, a recombinant inbred population was developed from a traditional aromatic cultivar ‘Basmati 370’ and a non-aromatic indica genotype ‘IRBB60’. This population was phenotyped in two locations for grain length (GL), grain breadth (GB), GL/GB ratio (LBR) and grain weight (GW). Though the RIL population reported in the current study exhibited segregation distortion (SD) for 54 % of the markers, they were utilized in analysis using an appropriate statistical package, PROC QTL in the SAS environment. Interval mapping revealed a total of 15 QTLs for GL, seven for GB, 15 for LBR and two for GW. Among them 13 were not reported earlier and thus novel. For a known major QTL identified in the study, GW8 for GB, a PCR based functional marker was designed and validated. This is the first report wherein a very high proportion of markers (>50 %) exhibiting SD have been successfully used for QTL mapping.     

Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross

Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F₂ mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC₄F₂ lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains. We compared the ability of these materials to reveal QTLs for grain shape with that of an F₂ population. Only 8 QTLs for grain length or grain width were detected in the F₂ population, versus 47 in the CSSL population and 65 in the BC₄F₂ population. These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.     

Molecular mapping of quantitative trait loci for domestication traits and β-glucan content in a wheat recombinant inbred line population

Genetic maps are useful for analysis of quantitative trait loci (QTLs) and for marker-assisted selection (MAS) in breeding. A simple sequence repeat (SSR) marker linkage map of common wheat was constructed based on recombination inbred lines (RILs) derived from a cross between Chinese Spring and spelt wheat. The map included 264 loci on all wheat chromosomes covering 2,345.2 cM with 962, 794.6, and 588.6 cM for the A, B, and D genomes, respectively. Using the RILs and the map, we detected 42 putative QTLs on 15 chromosomes for ear length, spikelet number, spike compactness, kernel length, kernel width, kernel height and β-glucan content. Each QTL explained 4–45% of the phenotypic variation. Five QTL cluster regions were detected on chromosomes 1A, 5AL, 2B, 2D, and 4D. The first QTLs for β-glucan content in wheat were identified on chromosomes 3A, 1B, 5B, and 6D.     

QTL examination of a bi-parental mapping population segregating for “short-stature” in hop (<Emphasis Type="Italic">Humulus lupulus</Emphasis> L.)

Increased labor costs and reduced labor pools for hop production necessitate the development of strategies that improve efficiency and automation of hop production. One solution for reducing labor inputs is the use of “short-trellis” hop varieties. Unfortunately, little information exists on the genetic control of this trait in hop, and there are no known molecular markers available for selection. This preliminary study was enacted to identify QTLs associated with expression of short-stature growth phenotype using SNPs identified within genome-assembled scaffolds. A bi-parental mapping population of 87 offspring was obtained from the cross, “Pioneer × 25/95/15”. Genotyping-by-sequencing was performed on parents and offspring. SNPs were identified using TASSEL v3.0 with either ‘Teamaker’ reference genome or ‘Shinsuwase’ genome. The genetic map derived from ‘Teamaker’ SNPs was far superior and was used for all further analysis. QTL analysis identified eight QTLs linked to short stature with five showing strong statistical association based upon three different statistical analyses. All eight QTLs were found on linkage group one. Evaluation of scaffolds containing SNP markers located at or surrounding QTL regions (±1 cM) identified 67 putative genes—several of which are known structural genes. A genome-wide scan of SNP markers identified an additional marker found on a scaffold containing a putative gene (Aspartyl protease family protein) known to induce dwarf characteristics in other species. Further validation of significantly associated markers on different populations is necessary prior to implementation in marker-assisted selection.     

Mineral nitrogen dynamics in irrigated rice–wheat system under different irrigation and establishment methods and residue levels in arid drylands of Central Asia

Increasing water shortage and low water productivity in the irrigated drylands of Central Asia are compelling farmers to develop and adopt resource conservation technologies. Nitrogen (N) is the key nutrient for crop production in rice–wheat cropping systems in this region. Nitrogen dynamics of dry seeded rice-(aerobic, anaerobic) planted in rotation with wheat (well drained, aerobic) can differ greatly from those of conventional rice cultivation. Soil mineral N dynamics in flood irrigated rice has extensively been studied and understood, however, the impact of establishment method and residue levels on this dynamics remains unknown. Experiments on resource conservation technologies were conducted between 2008 and 2009 to assess the impact of two establishment methods (beds and flats) in combination with three (R0, R50 and R100) residue levels and two irrigation modes (alternate wet and dry (AWD) irrigation (all zero till), and a continuously flooded conventional tillage (dry tillage)) with water seeded rice (WSR) on the mineral N dynamics under dry seeded rice (DSR)-surface seeded wheat systems. N balance from the top 80 cm soil layers indicated that 32–70% (122–236 kg ha⁻¹) mineral N was unaccounted (lost) during rice cropping. The amount of unaccounted mineral N was affected by the irrigation method. Residue retention increased (p < 0.001) the unaccounted mineral N content by 38%. With AWD irrigation, the N loss was not different among dry seeded rice in flat (DSRF), dry seeded rice in bed (DSRB), and conventional tillage WSR. Under different irrigation, establishment methods and residue levels, unaccounted mineral N was mainly affected by plant N uptake and soil mineral N content. Major amounts (43–58%) of unaccounted mineral N from DSR field occurred between seeding and panicle initiation (PI). During the entire rice and wheat growing seasons, NH₄N consistently remained at very high levels, while, NO₃N remained at very low levels in all treatments. In rice, the irrigation method affected NH₄N content. Effect of residue retention and establishment methods were not significant on NH₄N and NO₃N dynamics in both crops and years. Further evidence of the continuously fluctuating water filled pore spaces (WFPS) of 64% and the microbial aerobic activity of 93% at the top 10 cm soil surface during rice growing season indicates soil in the DSR treatments was under frequent aerobic–anaerobic transformation, a conditions very conducive for higher amounts of N loss. In DSR treatments, the losses appeared to be caused by a combination of denitrification, leaching and N immobilization. When intending to use a DSR management strategies need to be developed for appropriate N management, irrigation scheduling, and residue use to increase mineral N availability and uptake before this practices can be recommended.     

Detection of downy and powdery mildew resistance QTL in a ‘Regent’ × ‘RedGlobe’ population

One hundred and eighty six F₁ plants from a ‘Regent’ × ‘RedGlobe’ cross were used to generate a partial linkage map with 139 microsatellite markers spanning all 19 chromosomes. Phenotypic scores for downy mildew, taken over two years, confirmed a major resistance QTL (Rpv3) against downy mildew in the interval VVIN16-cjvh to UDV108 on chromosome 18 of ‘Regent’. This locus explained up to 62 % of the phenotypic variance observed. Additionally a putative minor downy mildew resistance locus was observed on chromosome 1 in one season. A major resistance locus against powdery mildew (Ren3) was also identified on chromosome 15 of ‘Regent’ in the interval UDV116 to VChr15CenGen06. This study established the efficacy of and validated the ‘Regent’-derived downy and powdery mildew major resistance genes/QTL under South African conditions. Closely linked SSR markers for marker-assisted selection and gene pyramiding strategies were identified.     

Advances in QTL mapping for ethylene production in apple (Malus × domestica Borkh.)

Ethylene is a gaseous hormone that coordinates several important physiological processes resulting in the final fruit quality in apple. Due to its genetic heterozygousity, apple offers the possibility to exploit the natural allelic variation existing at the level of two genes involved in the ethylene biosynthetic pathway, Md-ACS1 and Md-ACO1. The allelism of these two genes can be exploited for the advanced selection of genotypes characterized by low ethylene production, with a consequent extended postharvest storability. The impact of these two elements in ethylene control was verified using two specific apple populations (‘GDxBr’ and ‘FjxMG’) presenting distinct allelotype configurations. In the first progeny, two QTLs were identified in genetic positions corresponding with these genes, and for the first time the association of a QTL for ethylene production with Md-ACO1 in apple was established. However, the analysis carried out on the second population, homozygous for the allele of Md-ACS1 associated with a low ethylene production, suggested the possible involvement of other genetic elements in the regulation of ethylene production. In the end we also present, in parallel to the GC assessment, a novel methodology based on proton transfer reaction-time of flight-mass spectrometry (PTR-ToF-MS) for a more reliable, fast and efficient monitoring of the ethylene production in apple.     

Identifying QTL–allele system of seed protein content in Chinese soybean landraces for population differentiation studies and optimal cross predictions

Soybean originated in ancient China has been quickly extended globally as a major protein and oil crop. The QTL–allele constitution of seed protein content (SPC) in the Chinese soybean landrace population (CSLRP) was studied using a representative sample composed of 365 accessions tested under multiple environments and analysed under the novel restricted two-stage multi-locus genome-wide association study (RTM-GWAS) procedure based on 29,121 SNPLDB (single nucleotide polymorphism linkage disequilibrium blocks) markers. The SPC varied from 37.51 to 50.46% among accessions, for which 89 QTLs, each with 2–9 alleles in a total of 255 alleles were identified, accounting for 83.16% of the phenotypic variation covering most of the genetic variation (h²?=?84.31%). The QTL–alleles of the 365 landraces were organized into a 255?×?365 QTL–allele matrix as the compact form of SPC genetic constitution in CSLRP. Of the 89 QTLs, 53 showed significantly differentiated allele frequency distribution patterns among geographic eco-regions (sub-populations). There were 32.09% alleles not common among sub-populations but found only in some sub-populations; new allele(s) emerged on some loci in some respective sub-populations, with Eco-region III showing less but Eco-region VI more emergence. The QTL–allele matrix was also used for prediction of optimal crosses for breeding purpose to reach a 99th percentile potential of up to 54.81%, more than the highest accession (50.46%). From the 89 QTLs, 59 SPC candidate genes involving biological processes, cellular components and molecular functions were annotated. Among them, Glyma18g13574 and Glyma20g21370 were inferred as two of the major SPC genes in the whole genome.     

Identification of a novel gene (Apq1) from the indica rice cultivar ‘Habataki’ that improves the quality of grains produced under high temperature stress

The appearance of brown rice grown under high temperature conditions is an important characteristic for improvement in Japanese rice breeding programs. We performed a QTL analysis of the appearance quality of brown rice using chromosome segment substitution lines of the indica cultivar ‘Habataki’ in the ‘Koshihikari’ genetic background. A line carrying a ‘Habataki’ segment on chromosome 7 showed a high percentage of perfect grains produced under high temperature conditions during the ripening period. To verify the role of this segment, and to narrow down the region containing the useful allele, substitution mapping was performed using multiple paired lines. As a result, the chromosomal location of a gene that we named Appearance quality of brown rice 1 (Apq1) was delimited to a 48-kb region. In addition, we developed an Apq1-near isogenic line (NIL) to evaluate the effect of Apq1 on various agronomic traits. Under high temperature conditions during the ripening period, the Apq1-NIL produced significantly higher percentages of perfect grains than ‘Koshihikari’. Other agronomic traits, including yield and palatability, were similar between the Apq1-NIL and ‘Koshihikari’. Therefore, the ‘Habataki’ allele of Apq1 will be useful in breeding programs aimed at improving the quality of grains ripened under high temperature conditions.     

Inheritance and QTL mapping of leaf rust resistance in the European winter wheat cultivar ‘Beaver’

Genetic studies were conducted on an European winter wheat cultivar, Beaver, to determine the mode of inheritance of leaf rust resistance at seedling and adult plant growth stages using a recombinant doubled haploid population, Beaver/Soissons. Greenhouse studies indicated the involvement of genes Lr13 and Lr26 in governing leaf rust resistance at seedling growth stages, whereas, adult plant resistance (APR) in the field with pathotypes carrying virulence individually for Lr13 and Lr26 showed trigenic inheritance for the population. Marker regression analysis of adult plant field data indicated the involvement of six significant QTLs (chromosomes 1B, 3B, 3D, 4B, 4D and 5A) in year 2005, four QTLs (1B, 3B, 4B and 5A) in 2006, and six QTLs (1A, 1B, 3B, 4A, 4B and 5A) in 2007 for reducing leaf rust severity. QTLs on chromosomes 1B, 4B and 5A were considered the most important because of their detection across years, whereas QTLs on chromosomes 1A, 3B, 3D and 4A were either inconsistent or non-significant and unexplained. Based on an association of closely linked markers with phenotypic data, putative single gene stocks were identified for each consistent QTL and crossing was initiated to develop populations segregating for each to permit fine mapping of the identified regions.     

Comparison and analysis of main effects,epistatic effects,and QTL × environment interactions of QTLs for agronomic traits using DH and RILs populations in rice

Two genetic linkage maps based on doubled haploid (DH) and recombinant inbred lines (RILs) populations, derived from the same indica-japonica cross ‘Samgang × Nagdong’, were constructed to analyze the quantitative trait loci (QTLs) affecting agronomic traits in rice. The segregations of agronomic traits in RILs population showed larger variations than those in DH population. A total of 10 and 12 QTLs were identified on six chromosomes using DH population and seven chromosomes using RILs population, respectively. Three stable QTLs including pl9.1, ph1.1, and gwp11.1 were detected through different years. The percentages of phenotypic variation explained by individual QTLs ranged from 8 to 18% in the DH population and 9 to 33% in the RILs population. Twenty-three epistatic QTLs were identified in the DH population, while 21 epistatic QTLs were detected in the RILs population. Epistatic interactions played an important role in controlling the agronomic traits genetically. Four significant main-effect QTLs were involved in the digenic interactions. Significant interactions between QTLs and environments (QE) were identified in two populations. The QTLs affecting grain weight per panicle (GWP) were more sensitive to the environmental changes. The comparison and QTLs analysis between two populations across different years should help rice breeders to comprehend the genetic mechanisms of quantitative traits and improve breeding programs in marker-assisted selection (MAS).     

QTL analysis for eating quality-related traits in an F2:3 population derived from waxy corn × sweet corn cross

In order to identify quantitative trait loci (QTL) for the eating quality of waxy corn and sweet corn (Zea mays L.), QTL analysis was conducted on an F₂ population derived from a cross between a waxy corn inbred line and a sweet corn inbred line. Ten QTLs for pericarp thickness (PER), amylose content (AMY), dextrose content (DEX) and sucrose content (SUC) were found in the 158 F₂ families. Among them, four QTLs, qAMY4 (10.43%), qAMY9 (19.33%), qDEX4 (21.31%) and qSUC4 (30.71%), may be considered as major QTLs. Three of these, qAMY4, qDEX4 and qSUC4, were found to be located within a region flanked by two adjacent SSR markers on chromosome 4 (umc1088 and bnlg1265), making this SSR marker pair a useful selection tool for screening the eating quality traits of AMY, DEX and SUC. The QTL for amylose content was found to be located between markers phi027 and umc1634, raising the possibility of its identity being the Wx1 gene, which encodes a granule-bound amylose synthase. The new QTLs identified by the present study could serve as useful molecular markers for selecting important eating quality traits in subsequent waxy corn breeding studies.     

Genetics of parthenocarpy in tomato under a low temperature regime: II Cultivar ‘Severianin’

Summary Genetics of parthenocarpy in cv Severianin was tested under natural low-temperature conditions under which only seedless fruits were produced. Results were consistent with the hypothesis that two recessive genes are involved in the expression of parthenocarpy under low-temperature conditions. One gene, pat-2, has major effects on the expression of parthenocarpy. A second gene, mp, in the homozygous form, influences expression of pat-2 in both the homozygous and heterozygous conformation and may be present in non parthenocarpic phenotypes. Linkage tests, using 26 morphological marker genes, located pat-2 between solanifolia, sf (chromosome 3 site 111) and baby-lea syndrome, bls (chromosome 3 L site 74) close to sf. The location of the minor gene for parthenocarpy, mp, was not detected.     

Global warming over 1960–2009 did increase heat stress and reduce cold stress in the major rice-planting areas across China

Increasing extreme temperature events have raised concerns regarding the risk of rice production to extreme temperature stress (ETS). However, across China what places were exposed to higher ETS during rice-growing period and how ETS has changed over the past five decades, remain unclear. Here, we first compared two indexes for characterizing ETS on rice crop, including Duration-based ETS index (DETS) and Growing Degree Days (GDD). Then, based on the better-performing index and an improved dataset of rice phenological records, we comprehensively assessed the spatio-temporal patterns of ETS at county scale in the major rice-planting areas across China during 1960–2009. The results showed that GDD had an advantage over DETS in characterizing ETS, due to fully consideration of both the specific intensity and duration of extreme temperature events. Based on GDD, we found that ETS on rice crops had significantly changed in both space and time over the last five decades. Spatially, single rice in Northeast China (Region I) and late rice in southern China (Region IV) saw high exposure to cold stress, especially during the heading-flowering stage. The hot spots of heat stress were found for single rice in the Yangtze River basin (Region III) (2.25 °C) during the booting stage, and for early rice in Region IV (4.42 °C) during the heading-flowering stage. During 1960–2009, global warming did increase heat stress (0.04 and 0.12 °C year⁻¹ for the stages of booting and heading-flowering, respectively) and reduce cold stress (−0.03 and −0.21 °C year⁻¹ for the stages of booting and heading-flowering, respectively) in the major rice-planting areas across China. Some particular areas, such as Yunan Province (P4) with increasing cold stress and Zhejiang Province (P13) with increasing heat stress, should be priorities for adaptations to cope with the rising risk of ETS under climate warming.     

Genetic control of pre-heading phases in the Steptoe × Morex barley population under different conditions of photoperiod and temperature

Although there are numerous studies on the genetic control of flowering time in barley, little is known on the genetic control of duration of different particular pre-heading phases. Extending the stem elongation phase (SE), without modifying total time to heading, has been proposed as a trait to raise yield potential. Moreover, studying the genetic control of pre-heading phases would be of interest for a better understanding of crop phenology which is crucial for adaptation. We studied the genetic control of the leaf and spikelet intitiation phase (LS), the stem elongation phase, and within this, from the onset of jointing to flag leaf (J-FL), and from then to heading (FL-HD), in the Steptoe × Morex population, which is known to segregate for some major developmental genes, under different environmental conditions. After a preliminary greenhouse study in which the appropriateness of the population was tested, 130 double haploid lines and the two parents were grown under four field environments that differed in photoperiod and temperature conditions. Amongst all QTLs detected (13), only three were significant for HD and for both LS and SE and with the same allele direction (although with greater effects in one phase than the other in some cases). Genotype by environment interactions for LS and HD were due to both photoperiod and other factors as temperature or its interaction with photoperiod, while for SE responses to only photoperiod were negligible. QTL × E interactions were important for some QTLs, and either cross-over (e.g. Ppd-H1) or quantitative (e.g. Ppd-H2). However, heritability across field environments for the ratio SE/LS was high (0.8) and several of the QTL effects that were significant for only LS or SE, were conserved across different environments, that is, they were significant with the increasing allele derived from the same parent in all or most environments.     

Quantitative trait locus mapping for Verticillium wilt resistance in a backcross inbred line population of cotton (Gossypium hirsutum × Gossypium barbadense) based on RGA-AFLP analysis

Verticillium wilt (VW), caused by Verticillium dahliae Kleb., is one of the most important diseases in cotton. The objective of this study was to map quantitative trait loci (QTLs) conferring VW resistance using resistance gene analog (RGA)-targeted amplified fragment length polymorphism (RGA-AFLP) markers in an interspecific backcross inbred line mapping population, consisting of 146 lines from a susceptible Sure-Grow 747 (Gossypium hirsutum L.) × resistant Pima S-7 (G. barbadense L.) cross. VW resistance was evaluated in replicated tests based on disease incidence in the field, and disease incidence and severity in the greenhouse. Of 160 polymorphic RGA-AFLP markers, 42 were significantly correlated with one or more VW traits and 41 were placed on a linkage map which covered 1,226 cM of the cotton genome and contained 251 other molecular markers. Three QTLs for VW resistance were detected, each of which explained 12.0–18.6 % of the phenotypic variation. Two of these QTLs for disease incidence and severity detected in the greenhouse inoculation tests using root wounding are located on chromosome c4. Both are closely linked to four RGA-AFLP markers and therefore considered as the same QTL for VW resistance. The other QTL detected in the field test was located on c19 and flanked by several RGA-AFLP markers. The desirable QTL allele on c4 for VW resistance detected in the greenhouse was from the VW susceptible Upland parent and absent from the resistant Pima parent which was more VW susceptible due to the disarmament of the first line of defense mechanism due to root wounding during inoculation. The other desirable VW resistance QTL allele, on c19, was from the resistant parent Pima S-7, consistent with the fact that Pima cotton was more resistant to VW when naturally infected in the field. The results should facilitate the development of more sequence specific markers and the transfer of VW resistance from Pima to Upland cotton through marker-assisted selection.     

White lupine as a beneficial crop in Southern Europe. II. Nitrogen recovery in a legume–oat rotation and a continuous oat–oat

One experiment lasting for two years was carried out at Pegões (central Portugal) to estimate the impact of mature white lupine residue (Lupinus albus L.) on yield of fodder oat (Avena sativa L. cv. Sta. Eulalia) as the next crop in rotation, comparing with the continuous cultivation of cereal, under two tillage practices (conventional tillage and no-till) and fertilized with five mineral nitrogen (N) rates, with three replicates. Oat as a first crop in the rotation provided more N to the agro-ecosystem (63 kg N ha⁻¹) than did lupine (30–59 kg N ha⁻¹). This was at a cost of 100 kg of mineral N ha⁻¹, whereas lupine was grown without addition of N. A positive response of oat as a second crop was obtained per kg of lupine-N added to the system when compared with the continuous oat–oat. The cereal also responded positively to mineral N in the legume amended soil in contrast with the oat–oat sequence where no response was observed, partly due to the fast mineralization rate of lupine residue and a greater soil N immobilization in the continuous oat system. Each kg N ha⁻¹ added to the soil through the application of 73 kg DM ha⁻¹ mature lupine residue (above- and belowground material) increased by 72 kg DM ha⁻¹ the oat biomass produced as the second crop in rotation when 150 kg mineral N ha⁻¹ were split in the season, independent of tillage practice. Mature legume residue conserved in the no-tilled soil depressed the yield of succeeding cereal but less than the continuous oat–oat for both tillage practices, where the application of mineral N did not improve the crop response.     

Rice–weed competition in response to nitrogen form under high and low transpirational demand

Implementation of water-saving irrigation practices in lowland rice results in increased availability of nitrate (NO₃⁻) in the soil and favours germination of upland weeds. Since plant species show a specific preference for either ammonium (NH₄⁺) or NO₃⁻ as nitrogen (N) source, changes in both soil NO₃⁻ concentration and weed flora may affect the competition between rice and weeds. Further, the transpirational demand of the atmosphere might affect growth and competitiveness of lowland (wetland) and upland (dryland) weeds differently due to their adaptation to different ecological environments. Therefore, the study aimed to evaluate the effects of N source on growth, N uptake and competition between rice and common upland and lowland weeds under high and low vapour pressure deficit (VPD). Two rice (Oryza sativa) varieties (NU838 and KD18) differing in growth characteristics and two weed species (Echinochloa crus-galli and Solanum nigrum) differing in their natural habitat were selected and grown hydroponically as monoculture or mixed culture at low or high VPD. N was supplied as 75%/25% or 25%/75% NH₄⁺/NO₃⁻. N uptake rates were measured in the first week, whereas dry matter (DM), N concentration in the plant, total N uptake and the activities of nitrate reductase and glutamine synthetase in the fresh leaves were determined two weeks after the onset of treatments. Independent of N source, both rice varieties and E. crus-galli took up a larger share of NH₄⁺, whereas S. nigrum took up a larger share of NO₃⁻. N uptake of rice and E. crus-galli was hardly affected by N source, whereas high NO₃⁻ led to significantly higher N uptake rates and total N uptake of S. nigrum. NU838 showed a higher competitiveness against weeds than KD18. In competition, high NO₃⁻ decreased the competitiveness of E. crus-galli against NU838 but increased the competitiveness of S. nigrum against NU838. High VPD did not affect DM but increased N uptake of S. nigrum, leading to increased competitiveness of the weed at high transpirational demand. Competitiveness for N uptake appears to be an important trait as the relative N concentration in mixed plant communities was correlated with the activity of N-assimilating enzymes and leaf growth, with a stronger response in rice than in weeds. Our results support the hypothesis that increased availability of NO₃⁻ in aerobic rice soils may be advantageous for the competitiveness of upland weeds, especially at high VPD, whereas it may be disadvantageous for common lowland weeds.