The ABA synthesis enzyme allele OsNCED2^(T)promotes dryland adaptation in upland rice

Upland rice shows dryland adaptation in the form of a deeper and denser root system and greater drought resistance than its counterpart,irrigated rice.Our previous study revealed a difference in the frequency of the OsNCED2 gene between upland and irrigated populations.A nonsynonymous mutation(C to T,from irrigated to upland rice)may have led to functional variation fixed by artificial selection,but the exact biological function in dryland adaptation is unclear.In this study,transgenic and association analysis indicated that the domesticated fixed mutation caused functional variation in OsNCED2,increasing ABA levels,root development,and drought tolerance in upland rice under dryland conditions.OsNCED2-overexpressing rice showed increased reactive oxygen species-scavenging abilities and transcription levels of many genes functioning in stress response and development that may regulate root development and drought tolerance.OsNCED2^(T)-NILs showed a denser root system and drought resistance,promoting the yield of rice under dryland conditions.OsNCED2^(T)may confer dryland adaptation in upland rice and may find use in breeding dryland-adapted,water-saving rice.

Artificial selection of the Green Revolution gene Semidwarf 1 is implicated in upland rice breeding

Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a principal role in determining rice plant height. Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production. The plant height mediated by SD1 also favors grain yield under certain conditions. However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production. In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions. In response to dryland environments, rice requires a reduction in plant height to cope with water deficits. Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation. Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem. Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields. In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height. During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height. Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production. All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding.

Effect of various crop rotations on rice yield and nitrogen use efficiency in paddy–upland systems in southeastern China

To evaluate the effects of various rotation systems on rice grain yield and N use efficiency, a paddy–upland cropping experiment(2013–2016) was conducted in southeastern China. The experiment was designed using six different rice––winter crop rotations: rice–fallow(RF),rice–wheat(RW), rice–potato with rice straw mulch(RP), rice–green manure(Chinese milk vetch; RC–G), rice–oilseed rape(RO), and rice–green manure crop(oilseed rape with fresh straw incorporated into soil at flowering; RO–G) and three N rates, N0(0 kg N ha-1), N1(142.5 kg N ha-1), and N2(202.5 kg N ha-1). Average rice yields in the RF(5.93 t ha-1) rotation were significantly lower than those in the rotations with winter crops(7.20–7.48 t ha-1)under the N0 treatment, suggesting that incorporation of straw might be more effective for increasing soil N than winter fallow. The rice yield differences among the rotations varied by year with the N input. In general, the grain yields in the RP and RO–G rotations –were respectively 11.6–28.5% and 14.80–37.19% higher than those in the RF in plots with N applied. Increasing the N rate may have tended to minimize the average yield gap between the RF and the other rotations; the yield gaps were 18.55%, 4.14%, and 0.23% in N0, N1, and N2, respectively. However, the N recovery efficiency in the RF was significantly lower than that in other rotations, except for 2015 under both N1 and N2 rates, a finding that implies a large amount of chemical N loss. No significant differences in nitrogen agronomic efficiency(NAE) and physiological efficiency(NPE) were found between the rotations with legume(RC–G) and non–legume(RO and RW) winter crops, a result that may be due partly to straw incorporation. For this reason, we concluded that the return of straw could reduce differences in N use efficiency between rotations with and without legume crops. The degree of synchrony between the crop N demand and the N supply was evaluated by comparison of nitrogen balance degree(NBD) values. The NBD values in the RP and RW were significantly lower than those in the other rotations under both N1 and N2 rates. Thus,in view of the higher grain yield in the RP compared to the RW under the N1 rate, the RP rotation might be a promising practice with comparable grain yield and greater N use efficiency under reduced N input relative to the other rotations. The primary yield components of the RF and RP were identified as number of panicles m-2 and numbers of kernels panicle-1, respectively. The NAE and NPE were positively correlated with harvest index, possibly providing a useful indicator for evaluating N use efficiency.

The effects of water and nitrogen on the roots and yield of upland and paddy rice

It is of great significance to study the root characteristics of rice to improve water and nitrogen(N) use efficiency and reduce environmental pollution. This study investigated whether root traits and architecture of rice influence grain yield, as well as water and N utilization efficiency. An experiment was conducted using the upland rice cultivar Zhonghan 3(a japonica cultivar) and paddy rice cultivar Huaidao 5(also a japonica cultivar) using three N levels, namely, 2 g urea/pot(low amount, LN), 3 g urea/pot(normal amount, NN), and 4 g urea/pot(high amount, HN), and three soil water potentials(SWPs, namely, well-watered(0 kPa), mildly dried(–20 kPa) and severely dried(–40 kPa). The results showed that with decreasing SWP, the percentage of upland rice roots increased in the 0–5 cm tillage layer, and decreased in the 5–10 and 10–20 cm tillage layers, whereas paddy rice roots showed the opposite trend. With increasing amounts of N, the yield of upland and paddy rice increased, and the percentage of root volume ratios of the two rice cultivars in the 0–5 and 5–10 cm tillage layers increased, whereas that in the 10–20 cm tillage layer decreased. The roots of upland rice are mainly distributed in the 10–20 cm tillage layer, whereas most paddy rice roots are in the 0–5 cm tillage layer. These results indicate that the combination of-20 kPa SWP and NN in upland rice and 0 kPa SWP and LN in paddy rice promotes the growth of the root system during the middle and late stages, which in turn may decrease the requirements for water and N fertilizer and increase rice yield.

A new method for evaluating the drought tolerance of upland rice cultivars

Worldwide, approximately 27 million ha of rice are grown in upland rather than paddy fields, and is subject to drought stress. To counter this stress, it is desirable to breed new rice cultivars with improved drought tolerance. For breeding purposes, especially for breeding upland rice, it is desirable to develop a simple and accurate method to evaluate rice drought tolerance. We describe a new method that can be used to evaluate efficiently the drought tolerance degree(DTD) of upland rice cultivars, and call it the DTD method.DTD is defined as the mean of the ratios of green leaf length to total leaf length of the top three leaves in every rice seedling after drought treatment, and thus takes values from zero to one. To test whether the DTD method works effectively to evaluate drought tolerance of upland rice cultivars, we determined the DTD values of 13 upland rice cultivars showing varying degrees of drought tolerance in drought-tolerance trials. The idrl-1 mutant, which displayed the strongest drought tolerance of the 13 cultivars as identified by drought-tolerance trials under severe drought stress, had the highest DTD value and297-28, displaying the weakest drought tolerance, had the lowest DTD value. Further analyses of water potential, survival rate, panicles per plant, spikelets per panicle, seed setting rate, yield per plant, and contents of proline, chlorophyll, and malondialdehyde(MDA) indicated that DTD values are in general correlated with the values of these traits,making this new method useful for assessing the drought tolerance of upland rice cultivars.These results show that the DTD method is a simple, direct and relatively accurate evaluation method for drought-tolerance breeding of upland rice.

Arbuscular Mycorrhizal Fungi Colonization in Upland Rice as Influenced by Agrochemical Application

Mycorrhizal status of rice under upland conditions was studied using potted seedlings, Percentage of arbuscular mycorrhizal fungi （AMF） root colonization varied between 17.35% and 37.18% over an age series of 7 to 70 days old rice plants, AMF root colonization was increased up to 35-42 days, beyond which the root colonization steadily declined, The vesicles appeared after two weeks and reached their maximum intensity on the 35th day. The arbuscules were formed late on the 42^rd day （2.93%） and slightly varied up to the 70^th day （3.03%）. Higher dosage of urea application suppressed plant growth whereas the superphosphate treatment had no marked impact on plant growth. Generally, application of these agrochemicals registered less influence on the hyphal colonization of AMF in rice plants, whereas arbuscular colonization was adversely affected by higher dosages of fertilizers. There were pronounced decreases in both the plant growth and their AMF colonization due to the application of systemic fungicides, carbendazim and thiophanate methyl. The application of single sprays of fungicides was less deleterious over multiple sprays.

Variation in Grain Quality of Upland Rice from Luang Prabang Province, Lao PDR

Luang Prabang Province is located within the area recognized as the center of rice(Oryza sativa L.) diversity in Lao PDR. This study reported on grain quality characteristics of 60 upland rice seed samples sharing 49 variety names collected from 6 villages in Luang Prabang in 2015. Most of the samples has non-pigmented pericarp, while red pericarp was found in four samples and purple in five samples. Almost all of the samples were of large grain type, with glutinous endosperm in 70% and non-glutinous endosperm in 30%. The brown(unpolished) rice was found with a wide range of grain nutritional quality, including protein(9.2% ± 0.9%), Fe(15.9 ± 6.9 mg/kg), Zn(19.6 ± 2.1 mg/kg), anthocyanin(0.774 ± 0.880 mg/g), and anti-oxidative capacity(2.071 ± 1.373 mg/g). The varieties sharing similar names had similar morphological characteristics but varied in nutritional concentration, with required confirmation in genetic variation analysis. This study found that some rice varieties with high grain quality may benefit the farmers directly or could be used in varietal improvement programs.

Revealing Genetic Relationship and Prospecting of Novel Donors Among Upland Rice Genotypes Using qDTY-Linked SSR Markers

A total of 17 simple sequence repeat(SSR) markers linked to QTLs(qDTYs) governing grain yield under reproductive stage(RS) drought stress were used to assess the genetic relationship and prospecting new donors for q DTYs among 32 popular upland rice genotypes. These SSR markers generated a total of 36 alleles with an average allele count of 2.1 per locus. Polymorphic information content value of the markers ranged from 0.376 to 0.662 with an average value of 0.484. The expected heterozyogosity ranged from 0.381 to 0.632. STRUCTURE analysis divided the 32 genotypes into three sub-populations. Subsequent phenotyping revealed that all the tolerant genotypes were grouped into one sub-population, whereas the moderately tolerant and susceptible genotypes were grouped into separate sub-populations. Phylogenetic tree constructed by the unweighted neighbour-joining method also divided the genotypes into three clusters. The grouping pattern of genotypes into the clusters was similar to that into the STRUCTURE analysis, on the basis of drought tolerance level. The average value of genetic dissimilarity coefficient among the genotypes was observed to be 0.486. Furthermore, by combining genotyping data with phenotyping data, 16 new donors for 6 qDTYs were identified.

Genetic Diversity of Rice Landraces from Lowland and Upland Accessions of China

Genetic diversity of rice landraces from lowland and upland accessions of China was investigated using 66 polymorphic simple sequence repeat （SSR） markers. The total number of alleles detected from all 324 tested accessions was 555 with an average allele number （Na） of 8.409 per locus, the average effective number of alleles （Ne） of 3.574 and the average Shannon＇s information index （I） of 1.378. The genetic diversity was higher for the indica landraces compared to the japonica landraces, and the upland landraces were more genetically diverse than the lowland landraces. The SSR markers, RM72, RM232, RM219, RM241, RM224 and RM3 showed the highest rates of polymorphism and these SSR markers were suitable to assess the genetic diversity of rice germplasm resources. A dendrogram of 324 accessions of lowland and upland landraces showed that all rice accessions were mainly subdivided into two groups, japonica and indica, with some being intermediate. The distribution of lowland and upland landraces among the japonica and indica rice groups was distinct, with obvious differentiation between the lowland and upland landraces in japonica rice, but no such clear distinction in indica rice.

Molecular Variation and Application from Aerospace Mutagenesis in Upland Rice Huhan 3 and Huhan 7

To further improve upland rice varieties Huhan 3 and Huhan 7, seed samples were sent to outer space with two recoverable spaceships for approximately 1 and 5 d and were propagated for 7 and 5 generations, respectively. Phenotypic analysis revealed that the morphological traits and the protein and amylose contents of grains changed. Characterization of genomic mutations by the gene-associated simple sequence repeat （SSR） and insertion-delete （InDel） markers indicated that the mutation pattern was very complex. Most of the mutations occurred at the 3＇- or 5＇-end of the fragments in the simple sequence repeat fragment. Reverse transcription-polymerase chain reaction （RT-PCR） assay showed that mutations in those parts of the SSR affected their gene expression, indicating that gene associated markers would be helpful to isolate functional genes. Field survey for breeding also revealed that more lines with high yield, high quality and drought-tolerance could be selected through aerospace breeding. The results indicate that aerospace mutagenesis resulted in molecular variation, as well as physiological and morphological changes for rice breeding.

Effects of Phosphorus on Grain Quality of Upland and Paddy Rice under Different Cultivation

We investigated how upland and paddy japonica rice responded to phosphorous （P） fertilizer under two cultivation methods. The upland rice Zhonghan 3 and the paddy rice Yangfujing 8 were both grown under moist cultivation （MC, control） and bare dry cultivation （DC） with three P levels, low （LP, 45 kg/hm2）, normal （NP, 90 kg/hm2） and high （HI：）, 135 kg/hm2）. As P level increased, grain yields of both upland and paddy rice increased under DC. There were no significant differences in grain yields between HP and NP for either rice, although upland rice slightly increased and paddy rice slightly decreased in grain yield. Under DC at LP, Zhonghan 3 showed a higher head milled rice rate and better appearance, cooking and eating qualities than at HP or NP. Yangfujing 8 was similar to Zhonghan 3 except that Yangfujing 8 had better appearance quality at NP. Under MC, Zhonghan 3 had a higher head milled rice rate at LP and better cooking and eating qualities at NP. Yangfujing 8 was similar to Zhonghan 3 except in appearance quality. DC improved head milled rice rate and appearance quality of both upland and paddy rice, and cooking and nutrient qualities of paddy rice. Compared with paddy rice, upland rice had better processing, nutrient and eating qualities. The results suggest that upland and paddy rice respond differently to cultivation method and phosphorus level.

Ammonium Effects on Nitrate Uptake by Roots of Upland and Paddy Rice Seedlings Related to Membrane Potential Differences

Nitrate uptake characteristics and ammonium effects on nitrate uptake were compared between upland rice （Brazilian upland rice） and paddy rice （Wuyujing 3 and Yangdao 6） through the glass microelectrode technique and the concentration gradient method of uptake kinetics.Results indicated that nitrate uptake by rice seedlings and ammonium effects were depending on membrane potential of root cells.And upland rice and paddy rice presented obviously different responses.For all cultivars,the nitrate treatments induced rapid depolarization and then slow repolarization of membrane potential in root epidermal cells,and even hyperpolarization was observed when nitrate concentration was low.The membrane potential of epidermal cells in Brazilian upland rice roots was larger and its response to NO3- was bigger than those of two paddy rice cultivars.Depolarization of membrane potential was amplified when ammonium was simultaneously added with nitrate into the measure medium,but repolarization was reduced,even disappeared.Brazilian upland rice seedlings had high Vmax of nitrate uptake and low Km,furthermore,Vmax and Km were little affected by ammonium,but Vmax of Wuyujing 3 was reduced significantly.Therefore,inhibition of NH4＋ differed obviously between upland rice and paddy rice.

Evaluation of stability and yield potential of upland rice genotypes in North and Northeast Thailand

The planting of upland rice is one cropping option in area with limited water availability and low soil fertility in North and Northeast Thailand. The varietal selection was determined by grain yield potential, wide adaptation, and good stability. This study was aimed at evaluation of indigenous upland rice germplasm for yield and yield stability in multi-locations. Thirty-six upland rice genotypes collected from six provinces of the North and Northeast Thailand and one check variety （Sewmaejan） were assessed under five locations in the rainy seasons of 2009 and 2010. The experiment was laid out in a randomized complete block design with three replications. The genotype grain yield was highly affected by location （59.90%）, followed by genotypes （G）xlocation （L） interaction （12.80%） and genotype （6.79%）. The most suitable location for the genotype eval- uation was L3 （Khon Kaen-KKU 10） which associated with stability of grain yield for all genotypes. Furthermore, biplot and regression analysis indicated that genotype numbers 6 （Jaowmong 1）, 10 （Neawmong 1）, 18 （Neawdum 1）, 19 （Leamna）, 20 （Prayaleamkang）, 32 （Kunwang 2）, and 33 （Kunwang 3） showed great yield stability over five locations. The genotypes will be applicant for upland rice production area and parental base in breeding program.

Variability in Grain Quality Characters of Upland Rice of Assam,India

The grain quality of 100 uplandlahu rice genotypes from Assam, India was assessed. The characteristics measured were grain length, grain width, cooked grain length, cooked grain width, grain elongation ratio after cooking, grain widening ratio after cooking, alkali spreading value, gel consistency, as well as starch, amylose, amylopectin and total soluble sugar contents. Considerable genetic variability among the 100 rice genotypes was observed for the characteristics under study. Analysis of vadance revealed highly significant differences among the genotypes for all the characteristics. The difference between genotypic coefficient of variation （GCV） and phenotypic coefficient of variation （PCV） was very small for all the characteristics analyzed. High GCV and PCV were found in the characteristic of total soluble sugar content followed by alkali spreading value. The high values for these traits signify the scope for selection to develop superior genotypes. High heritability was recorded in all the characteristics analyzed along with diverse genetic advance which varied from 9.71% to 52.83%. The characteristic of total soluble sugar content showed high heritability with high genetic advance, whereas alkali spreading value and grain widening ratio presented high hedtability with moderate genetic advance. This implies that these characteristics are mainly under additive gene effects and could be relied upon further selection based on phenotypic performance. The genotypic correlation coefficient was higher than the phenotypic correlation coefficient, indicating strong inherent associations among the characteristics studied.

Improvement of Upland Rice Variety by Pyramiding Drought Tolerance QTL with Two Major Blast Resistance Genes for Sustainable Rice Production

Varalu is an early maturing rice variety widely grown in the rainfed ecosystem preferred for its grain type and cooking quality.However,the yield of Varalu is substantially low since it is being affected by reproductive drought stress along with the blast disease.The genetic improvement of Varalu was done by introgressing a major yield QTL,qDTY_(12.1),along with two major blast resistance genes i.e.Pi54 and Pi1 through marker-assisted backcross breeding.Both traits were transferred till BC_(2) generation and intercrossing was followed to pyramid the two traits.Stringent foreground selection was carried out using linked markers as well as peak markers(RM28099,RM28130,RM511 and RM28163)for the targeted QTL(qDTY_(12.1)),RM206 for Pi54 and RM224 for Pi1.Extensive background selection was done using genome-wide SSR markers.Six best lines(MSM-36,MSM-49,MSM-53,MSM-57,MSM-60 and MSM-63)having qDTY_(12.1) and two blast resistance genes in homozygous condition with recurrent parent genome of 95.0%-96.5% having minimal linkage drag of about 0.1 to 0.7 Mb were identified.These lines showed yield advantage under drought stress as well as irrigated conditions.MSM-36 showed better performance in the national coordinated trials conducted across India,which indicated that improved lines of Varalu expected to replace Varalu and may have an important role in sustaining rice production.The present study demonstrated the successful marker-assisted pyramiding strategy for introgression of genes/QTLs conferring biotic stress resistance and yield under abiotic stress in rice.

The differenee in protein content,MDH,POD and COD isozymes during root different developmental stages in lowland rice and upland rice

The difference in protein content, MDH,POD and COD isozymes have been seenbetween lowland rice roots and upland rice roots during root growth and development. High pro-tein content has been examined in upland rice roots,but isozyme bands in lowland rice roots aremore than that in upland rice roots.Total area of POD isozyme bands at seedling and tilleringstages of upland rice is larger than that of lowland rice.The POD isozymes zymogram in the rootof upland rice is more stable compared with that of lowland rice.More COD isozyme numbershave been showed in roots of upland rice,but the relative activity of COD isozyme in roots of up-land rice at the seedling and tillering stages is lower than that of lowland rice.COD7 band can beshown in upland rice root at flowering stage,but it is absent in lowland rice.Therefore,COD7,band can be taken as an index for resistance of the upland rice to drought environment.

Tracking Selection Signatures Based on Variation in <i>OsLEA</i>27 within Myanmar Landraces of Upland and Dryland Rice

To track the selection evident along the genome segment of OsLEA27?gene, a member of dehydrin gene family, 2.9-kbp nucleotide sequence containing the promoter 5’ upstream and transcribed region of OsLEA27?was determined for 35 upland and dryland Myanmar landraces from drought-prone areas. Nucleotide diversity, neutrality tests, haplotype network analysis, and linkage disequilibrium (LD) analysis were performed to infer the impact of selection and to investigate nonrandom associations of SNPs within all or part of the entire OsLEA27?region. The evidence for LD, the presence of two distinct haplotype groups across four different geographical regions, and the significant values obtained in a sliding-window analysis of mutation-drift tests all suggest the effects of selection on OsLEA27?in a set of 30 landraces. The neutrality test values for 5’ upstream region of OsLEA27?were significantly negative (p OsLEA27 region was significantly negative in accessions of the northern group, indicating a recent increase in population size or selection pressure. This evidence for selection signatures at OsLEA27 in this study sample provides insight into the roles of selection, crop adaptation, and genetic diversity in establishing present-day variation at the OsLEA27 locus.

Screening for Drought-Tolerant and Low-Input Responsive Upland Rice Landraces

Productivity potentials of upland rice landraces (URLs) are continuously compromised by scanty water supply due to competing priorities for irrigations and fluctuations in agro-ecological conditions peculiar to low-input farming systems. A growing demand for rice amidst decline in productive agricultural areas plunges into an urgent contribution of marginal areas critical in attaining food sufficiency among Filipino households. Agronomic performances of URLs locally found in Catanduanes province, Philippines were evaluated in a replicated trial utilizing three URLs: Kamanang [1], Kadari [2] and Bulaw [3]. The experimental set-up was closely monitored for consistent dry moisture content and zero fertilizer application. Results were significant for traditional upland landraces: Kamanang and Kadari, scored in terms of higher germination rate, increment plant height and the number of tillers during the vegetative stage. Leaf color gradations, although statistically not significant across cultivars, were suggestive of varying adaptive performance between traditional cultivars subjected to low-input system. Putative low-input responsive lines indicated by the higher survival percentage and overall agronomic responses were selected from the study site. Screened lines took part of the advance population which would be potentially able to tolerate poor soil conditions (i.e. poor storehouse of water and nutrients) especially in areas with edaphological constraints and changing rainfall distribution pattern. The development of putative drought tolerant lines among URLs forms the most economical solution implicated to areas with limited access to agricultural interventions.

Weed Management in Rainfed Upland Rice Fields under Varied Agro-Ecologies in Nigeria

The demand for rice to meet the dietary need in low-income countries is expected to witness an exponential rise as the population increases.Meeting the rice demand domestically has remained challenging due to significant yield loss caused by several biotic and abiotic factors.Among these factors,one of the most important is the high weed pressure that ravages the upland rice ecology.In Nigeria,several independent weed control techniques,such as physical,chemical and cultural methods,have been recommended and adopted for weed control across varying rice upland ecologies.However,outcomes of these approaches when used independently have not consistently led to an increase in yield.There remains an outstanding deficit between the actual yield and the potential rice yield.This review aimed to identify potential research gaps,and quest effective and sustainable weed management strategies in smallholder upland rice farming systems in Nigeria.A critical analysis of studies suggests the potential of sustainable weed management practices if adopted and adapted smartly in different upland ecologies in Nigeria.Competitiveness of upland rice against weeds can be enhanced through strategic integration of weed competitive cultivars,optimum nitrogen application timings(within weed-free periods),uniform plant spacing,and high seeding rates,with conventional herbicide/manual weed control practices.However,such management practices can only be engaged where inputs are supplied on time and the technical know-how is extended to farmers.The review equally highlights potential research gaps for further studies.