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Assessing genetic variability is essential to crop breeding and represents the basis for a successful crop selection, including rice (Oryza sativa L.). Root system shows a large range of roles that could be improved genetically. However, it has been virtually neglected by most breeders. The objective was to characterize a selected sample of the Brazilian rice germplasm, regarding on root growth and development, and to combine this data to shoot traits, aiming to depict the genetic variability within this germplasm. Sixteen Brazilian accessions of rice were analyzed with basis on root and shoot traits in two distinct experiments, mainly cultivars launched in the past four decades and presenting unique characteristics. The first experiment was carried out at hydroponic conditions to evaluate the performance of rice accessions during the seedling stage. The second was carried out in long PVC tubes to assay the rice accessions at the reproductive period. Traits were treated individually as well as analyzed jointly by different multivariate methods of genetic variability assessment. Most of the rice accessions showed similar results for a part of the studied traits, however differences were observed for some traits. The clustering methods agreed to group a large number of rice accessions into a single group, distinguishing only the best performing genotypes. [ABSTRACT FROM AUTHOR]

Abstract: Key messageDevelopment of MAALs and disomic introgression lines derived from the cross betweenO. sativaandO. rhizomatisto exploit and utilize the valuable traits for rice improvement.Abstract: The CC genome wild species, Oryza rhizomatis, possesses valuable traits for rice improvement. Unlike other CC genome wild rice, O. rhizomatis is less studied and none of the research has focused on the utilization of this resource in rice breeding. The transfer of novel genes governing the valuable traits from O. rhizomatis is difficult due to high genome incompatibility with O. sativa. Here we report the development of backcross progenies and complete sets of monosomic alien addition lines (MAALs) for the first time from O. rhizomatis in O. sativa line IR31917-45-3-2. Autotetraploid IR31917-45-3-2 (4x = AAAA) was used to generate allotriploid F1, and the F1 plant was backcrossed to IR31917-45-3-2 (2x). Forty-seven BC1F1 and 73 BC2F1 plants were produced with chromosome numbers ranging from 24 to 33 (2x + 9) and 24 to 27 (2x + 3), respectively. A complete set of MAALs were identified by morphological, cytological and marker-based analysis. A total of 116 CC genome-specific InDel markers across the 12 chromosome of rice were used to detect O. rhizomatis chromosome segments in F1, BC1F1, BC2F2, MAALs and disomic introgression lines (DILs). Expressions of major phenotypic traits inherited from O. rhizomatis were observed in MAAL-derived DILs. Small chromosomal segments of O. rhizomatis for chromosomes 1, 2, 4, 5, 6, 7, 10 and 12 were detected in DILs, and some of the introgression lines showed insect resistance against brown planthopper and green leafhopper. These newly developed MAALs and DILs will be useful for gene mining and more precise faster transfer of favorable genes to improve rice cultivars. [ABSTRACT FROM AUTHOR]

The effects of different nitrogen application rate on the physical characteristics and anatomic structure of rice stems were investigated with rice cultivars Guangliangyou 1128 (with high resistance) and Zhunliangyou 527 (with low resistance) as materials. The results showed that, firstly, plant height, gravity center height and basal internode length of the 2 rice cultivars increased with the increase of nitrogen application rate, while wall thicknees and internode fiiling degree decreased. The breaking-resistance strength per stem and thrust-resistance strength of plants declined with the increase of nitrogen application rate. Secondly, as nitrogen input increased, the number of vascular bundles and the area of vascular bundles increased between the 2 rice cultivas. Thirdly, with the increase of nitrogen application rate, the stem section area of Guangliangyou 1128, which had strong lodging resistance, graduHy increased, while that of Zhunliangyou 527 increased firstly and then decreased. The maximum application amount of nitrogen was 240 kg/hm2. Nitrogen fertilizer mainly affected the relative gravity center height, stem WXI thicknees and internode fiiling degree of the 2 cultivars, thereby reducing the basal stem breaking resistance and plant thrust-resistance strength. [ABSTRACT FROM AUTHOR]

The eefects of soil moisture content, pot seedling buried depth, and pot seedling height on the survival rate and growth of dry planted seedlings were researched by field experiment. The results showed that the seedling survival rate and growth were enhanced with the increase of soil moisture content after pot seedling transplanting, but there was no significant difference in the survival rate and growth of seedlings with 85 V and 100 V of soil moisture content. Pot seedling buried depth was one of the important factors affecting the survival rate, and when the pot seedlings were buried 2 cm deep, the seedlings showed high survival rate and excellent growth. Under the same condition of soil moisture content and buried depth, seedlings with pot seedling height of 15 cm had the best survival rate and growth. Therefore, the optimized conditions for dry-cultivated rice seedling planting were soil moisture content of 85V, pot seedling buried depth of 2 cm, and pot seedling height of 15 cm. [ABSTRACT FROM AUTHOR]

Grain length is one of the determinants of yield in rice and auxin plays an important role in regulating it by mediating cell growth. Although several genes in the auxin pathway are involved in regulating grain length, the underlying molecular mechanisms remain unclear. In this study we identify a R ING-finger a nd w d40- a ssociated u biquitin- l ike (RAWUL) domain-containing protein, Gnp4/LAX2, with a hitherto unknown role in regulation of grain length by its influence on cell expansion. Gnp4/LAX2 is broadly expressed in the plant and subcellular localization analysis shows that it encodes a nuclear protein. Overexpression of Gnp4/LAX2 can significantly increase grain length and thousand-kernel weight. Moreover, Gnp4/LAX2 physically interacts with OsIAA3 and consequently interferes with the OsIAA3–OsARF25 interaction in vitro and in vivo. OsIAA3 RNAi plants consistently exhibit longer grains, while the mutant osarf25 has small grains. In addition, OsARF25 binds to the promoter of OsERF142/SMOS1, a regulator of organ size, and positively regulates its expression. Taken together, the results reveal that Gnp4/LAX2 functions as a regulator of grain length through participation in the OsIAA3–OsARF25–OsERF142 pathway and that it has potential value for molecular breeding in rice. [ABSTRACT FROM AUTHOR]

The H2A.Z histone variant plays a role in the modulation of environmental responses, but the nature of the associated mechanisms remains enigmatic. We investigated global H2A.Z deposition and transcriptomic changes in rice (Oryza sativa) upon exposure to phosphate (Pi) deficiency and in response to RNAi knockdown of OsARP6, which encodes a key component of the H2A.Z exchange complex. Both Pi deficiency and OsARP6 -knockdown resulted in similar, profound effects on global H2A.Z distribution. H2A.Z in the gene body of stress-responsive genes was negatively correlated with gene expression, and this was more apparent in response to Pi deficiency. In contrast, the role of H2A.Z at the transcription start site (TSS) was more context dependent, acting as a repressor of some stress-responsive genes, but an activator of some genes with housekeeping functions. This was especially evident upon OsARP6 -knockdown, which resulted in down-regulation of a number of genes linked to chloroplast function that contained decreases in H2A.Z at the TSS. Consistently, OsARP6 -RNAi plants exhibited lower chlorophyll content relative to the wild-type. Our results demonstrate that gene body-localized H2A.Z plays a prominent role in repressing stress-responsive genes under non-inductive conditions, whereas H2A.Z at the TSS functions as a positive or negative regulator of transcription. [ABSTRACT FROM AUTHOR]

Anther culture can be used to accelerate plant breeding program in producing superior variety of rice. The aims of this research were to determine agronomic performance and yield of doubled haploid (DH) lines of lowland rice and select the best genotypes for multilocation yield trials. The research was conducted in Indonesia at three locations, i.e. Subang (West Java), Cianjur (West Java) and Malang (East Java) using a randomized complete block design. It consisted of 35 genotypes and three check varieties (Ciherang, Inpari 13 and Inpara 5) as treatments. The treatments were repeated 3 times. The results showed that interaction of genotype and environment was significant on all traits. Genotypic variance and heritability estimates of all traits were in the high category and ranged between 1.57 - 458.51 and 0.58 - 0.96, except for tiller number and the productivity which were moderate. Fourteen DH lines were selected based on yield and selection index, which takes, into account a combination of traits, i.e. tiller number, filled grain per panicle, percentage of filled grain per panicle, 1000-grain weight, days to harvest and productivity, according to their relative weightage. The yield of the lines ranged between 4.82 - 6.60 ton/ha. Yield of Ciherang, Inpari 13 and Inpara 5 were 5.76, 4.85, and 4.82 ton/ha respectively. The selected DH lines will be used further in multilocation yield trial. [ABSTRACT FROM AUTHOR]

Rice breeders in Asia and elsewhere in the world have long overlooked trying to shorten the time it takes to develop new varieties. Plant breeders have proposed a technique called Rapid Generation Advance (RGA) as a way to accelerate the results of public rice breeding programs. However, little is known about RGA’s potential impact. Here, we present the first results of a global impact study of RGA. More specifically, we calculated the multiplicator effects of RGA on the research benefits generated by conventional rice breeding programs and applied them to a meta-analysis of selected impact studies in the literature. These insights are a first crucial step in developing a targeted approach for disseminating RGA technology among rice breeders to accelerate the impact of their public rice breeding programs around the world. We show that the additional benefits due to time savings are considerable and offer some insights into the economics of breeding. Our results confirm that the adoption of accelerated breeding would lead to substantial advantages to rice breeding programs and the earlier variety release leads to significant economic benefits to society. This can be important to policy makers when reshaping their public breeding methods and optimising their return on research investments in breeding. [ABSTRACT FROM AUTHOR]

While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI) genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR) markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC) indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35). While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V), a similar SSR analysis yielded only three major groups (I, II, and III), and a model-based population structure analysis yielded four (A, B, C and D). Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA), as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207) among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular breeding programs. [ABSTRACT FROM AUTHOR]

Experiments were carried out to measure the specific enzyme activity of carboxyl esterase (CE), glutathione-S-transferase (GST) and mixed function oxidase (MFO) in the leaffolder population collected from different rice growing regions of Tamil Nadu. The specific enzyme activity of GST and CE levels were higher as compared to specific activity of MFO. The enzyme activity in the different field populations of rice leaffolder was assessed in order to compare with the susceptible population and the specific activities of all the three enzymes were high in the most resistant population, Bhavanisagar. In the study, carboxyl esterase (CE) was high in all the four locations compared to glutathione-S-transferase (GST) and mixed function oxidase (MFO). Unlike the other enzymes, the specific activity of carboxyl esterases showed a wide variation from 107.82 to 307.17 µmol min-1 mg of protein1. The specific activity of GST varied from 32.29 to 196.95 µmol min-1 mg of protein-1 among five (glass house reared susceptible population, field population of Trichy, Coimbatore, Aduthurai and Bhavanisagar) different leaffolder populations. MFO exhibited low specific activity which was evidenced from the enzyme activity observed in field populations of Bhavanisagar, Aduthurai, Coimbatore and Trichy which recorded a specific activity of 51.01, 38.17, 34.30 and 29.79 µmoles min-1 mg protein-1, respectively. [ABSTRACT FROM AUTHOR]

Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS) of salt tolerance-related phenotypes in rice at the seedling stage and obtained 93 candidate genes with high association peaks across six phenotypes. We constructed a protein interaction network using the candidate genes identified here, and 33 genes were associated. Based on the expression patterns, we found that most of these genes showed a different expression level under control and salt stress conditions. In addition, haplotype network and sequence analysis of one 'key' gene, a transcription factor (Os12g0176700) encoding a SWIRM domain-containing protein, in the interaction network was investigated to explore its possible role in the network. Our study revealed candidate salt tolerance-related genes in rice at the seedling stage, and demonstrated the feasibility of using GWAS to identify genetic architecture underlying salt tolerance. The data generated here may provide resources for molecular breeding and functional analysis of salt tolerance in rice seedlings. [ABSTRACT FROM AUTHOR]

Growing concerns about food security and human health make the identification of beneficial nutritional traits in crops a priority. The aim of the present study was to compare the elemental and nutritional characteristics of landraces and hybrid rice varieties. Landraces, valuable for their biodiversity, are a source of genes that can improve elite varieties and ensure food security. We were able to demonstrate significant variations in elemental composition, especially for calcium, rubidium and selenium, between the two rice types. Pigmented rice varieties were found to be more functional, as they had higher levels of antioxidants such as phenolic compounds, flavonoids and anthocyanins. Statistical analysis using principal component analysis and agglomerative hierarchical clustering grouped the rice varieties into clusters. The results showed that 99.87% of the variance was within the class, and 0.13% was between classes. Many of the landraces studied had high levels of amylose, selenium and antioxidants. Landraces are thus an important source of nutraceutical factors and of high importance for rice improvement and breeding. The results of this study will certainly inform works into improving the dietary system and enable us to direct conventional plant breeding exercises or apply molecular techniques to develop new varieties to ensure on-going food security. [ABSTRACT FROM AUTHOR]

Background: Short-culm mutants have been widely used in breeding programs to increase lodging resistance. In barley ( Hordeum vulgare L.), several hundreds of short-culm mutants have been isolated over the years. The objective of the present study was to identify the Brachytic1 ( Brh1) semi-dwarfing gene and to test its effect on yield and malting quality. Results: Double-haploid lines generated through a cross between a brh1.a mutant and the European elite malting cultivar Quench, showed good malting quality but a decrease in yield. Especially the activities of the starch degrading enzymes β-amylase and free limit dextrinase were high. A syntenic approach comparing markers in barley to those in rice ( Oryza sativa L.), sorghum ( Sorghum bicolor Moench) and brachypodium ( Brachypodium distachyon P. Beauv) helped us to identify Brh1 as an orthologue of rice D1 encoding the Gα subunit of a heterotrimeric G protein. We demonstrated that Brh1 is allelic to Ari-m. Sixteen different mutant alleles were described at the DNA level. Conclusions: Mutants in the Brh1 locus are deficient in the Gα subunit of a heterotrimeric G protein, which shows that heterotrimeric G proteins are important regulators of culm length in barley. Mutant alleles do not have any major negative effects on malting quality. [ABSTRACT FROM AUTHOR]

The lowland rice breeding program, developed in the state of Minas Gerais, has as basic objective to release new commercial cultivars. In this way, this program is making available a new cultivar named BRSMG Rubelita, which has as main characteristics: medium cycle, high tillering, lodging tolerance, diseases tolerance, high grain quality, and high grain yield. [ABSTRACT FROM AUTHOR]

Plant architecture is an important agronomic trait, and improving plant architecture has attracted the attention of scientists for decades, particularly studies to create desirable plant architecture for high grain yields through breeding and culture practices. However, many important structural phenotypic traits still lack quantitative description and modeling on structural-functional relativity. This study defined new architecture indices (AIs) derived from the digitalized plant architecture using the virtual blade method. The influences of varieties and crop management on these indices and the influences of these indices on biomass accumulation were analyzed using field experiment data at two crop growth stages: early and late panicle initiation. The results indicated that the vertical architecture indices (LAI, PH, 90%-DRI, MDI, 90%-LI) were significantly influenced by variety, water, nitrogen management and the interaction of water and nitrogen, and compact architecture indices (H-CI, Q-CI, 90%-LI, 50%-LI) were significantly influenced by nitrogen management and the interaction of variety and water. Furthermore, there were certain trends in the influence of variety, water, and nitrogen management on AIs. Biomass accumulation has a positive linear correlation with vertical architecture indices and has a quadratic correlation with compact architecture indices, respectively. Furthermore, the combination of vertical and compact architecture indices is the indicator for evaluating the effects of plant architecture on biomass accumulation. [ABSTRACT FROM AUTHOR]

Genetic improvement mainly depends on the extent of genetic variability present in the population. The molecular marker is a useful tool for assessing genetic variations and resolving cultivar identities. The objective of this study was to evaluate the genetic divergence of 40 germplasm lines of ricebean. Forty-four SSR markers were used in the present study, out of which only seven were found to be polymorphic. The dendrogram based on SSR marker analysis grouped the 40 ricebean genotypes into 2 clusters, where cluster I was the largest with 37 genotypes. STRUCTURE analysis for the estimation of population structure divided 40 genotypes into 4 groups in which P1 group consisted of 5 genotypes, P2 with 23 genotypes, P3 with maximum number of 7 genotypes, whereas, P4 consisted of 5 genotypes. The genetic variation revealed by SSR analysis will be used in the future breeding programme of ricebean for the selection of diverse parents for hybridization. [ABSTRACT FROM AUTHOR]

BRS Pampeira is a rice cultivar developed by Embrapa, recommended for irrigated cultivation in Brazil. It shows modern architecture, with high tillering and tolerance to lodging. It stands out for its high yield potential, medium cycle and good grain quality. [ABSTRACT FROM AUTHOR]

A total of 787 non-waxy rice lines– 116 hybrids and 671 inbreds–were used to study the apparent amylose content (AAC), gelatinization temperature (GT), and rapid visco analyzer (RVA) pasting viscosity properties of rice starch to understand their importance in breeding better rice varieties. The investigated traits showed a wide range of diversity for both hybrid (HG) and inbred (IG) groups. The combinations of the different categories of AAC and GT were random in HG but were non-random in IG. For inbred lines, the high level of AAC tended to combine with the low level of GT, the intermediate level of AAC tended to have high or intermediate GT, and the low level of AAC tended to have high or low GT. Some stable correlations of the AAC, GT, and RVA properties may be the results derived from the physicochemical relationships among these traits, which rice breeders could utilize for selection in advanced breeding generations. Through cluster analysis, IG and HG were divided into 52 and 31 sub-clusters, respectively. Identifying the cultivars having AAC, GT, and RVA properties similar to that of popular high-quality rice varieties seems to be an interesting strategy and could be directly used for adaptation trials to breed high-quality rice varieties in targeted areas in a more customized manner. [ABSTRACT FROM AUTHOR]

Rice blast (Magnaporthe oryzae) is a key concern in combating global food insecurity given the disease is responsible for approximately 30% of rice production losses globally—the equivalent of feeding 60 million people. These losses increase the global rice price and reduce consumer welfare and food security. Rice is the staple crop for more than half the world’s population so any reduction in rice blast would have substantial beneficial effects on consumer livelihoods. In 2012, researchers in the US began analyzing the feasibility of creating blast-resistant rice through cisgenic breeding. Correspondingly, our study evaluates the changes in producer, consumer, and environmental welfare, if all the rice produced in the Mid-South of the US were blast resistant through a process like cisgenics, using both international trade and environmental assessment modeling. Our results show that US rice producers would gain 69.34 million dollars annually and increase the rice supply to feed an additional one million consumers globally by eliminating blast from production in the Mid-South. These results suggest that blast alleviation could be even more significant in increasing global food security given that the US is a small rice producer by global standards and likely experiences lower losses from blast than other rice-producing countries because of its ongoing investment in production technology and management. Furthermore, results from our detailed life cycle assessment (LCA) show that producing blast-resistant rice has lower environmental (fossil fuel depletion, ecotoxicity, carcinogenics, eutrophication, acidification, global warming potential, and ozone depletion) impacts per unit of rice than non-blast resistant rice production. Our findings suggest that any reduction in blast via breeding will have significantly positive impacts on reducing global food insecurity through increased supply, as well as decreased price and environmental impacts in production. [ABSTRACT FROM AUTHOR]

Genome-wide association study (GWAS) is an effective approach for the identification of marker-trait associations (MTA) using more diverse germplasm not constrained by specific crossing. This study used a collection of 327 advanced indica breeding lines and varieties genotyped using a genotyping-by-sequencing method and phenotyped in eight environments to identify MTA for grain yield (GY) and 10 related traits. The current panel of indica breeding lines were divided into two subpopulations by three analytical methods including STRUCTURE, principal component analysis (PCA) and neighbour joining (NJ) tree. STRUCTURE and PCA gave the same classification of genotypes while the NJ tree results are slight difference in assigning genotypes to subpopulation from STRCUTURE and PCA. Wide variation was observed for all the 11 traits in the whole panel and the two subpopulations inferred by STRUCTURE analysis. Linkage disequilibrium (LD) analysis showed that LD decay varied across the chromosomes and average pairwise squared correlation coefficient (r 2 ) dropped to half of its maximum value (r 2 = 0.25) within a physical distance of 200 kb in the whole population. A MLM model controlling both population structure and cryptic relatedness was chosen to identify MTA for all the 11 tested traits. A total of 452 MTA that were delineated into 43 QTL were identified for all traits but PB, SB, and SR with 39 QTL being not reported before. Three QTL on chromosome 6, 9 and 12 were identified for GY but only in DS2. The numbers of QTL identified for the remaining traits varied from two to 26. Most of the detected QTL were found in only one environment. Four QTL were located in the regions containing genes/QTL previously identified for other related traits. The effects of identified QTL were relatively small with the highest percentage of phenotypic variance explained by a single QTL being 9.6%. The identified QTL are directly relevant to and can be more effectively used in breeding programs. [ABSTRACT FROM AUTHOR]

Quantitative trait loci conferring high grain yield under drought in rice are important genomic resources for climate resilient breeding. Major and consistent drought grain yield QTLs usually co-locate with flowering and/or plant height QTLs, which could be due to either linkage or pleiotropy. Five mapping populations used for the identification of major and consistent drought grain yield QTLs underwent multiple-trait, multiple-interval mapping test (MT-MIM) to estimate the significance of pleiotropy effects. Results indicated towards possible linkages between the drought grain yield QTLs with co-locating flowering and/or plant height QTLs. Linkages of days to flowering and plant height were eliminated through a marker-assisted breeding approach. Drought grain yield QTLs also showed interaction effects with flowering QTLs. Drought responsiveness of the flowering locus on chromosome 3 (qDTY3 . 2) has been revealed through allelic analysis. Considering linkage and interaction effects associated with drought QTLs, a comprehensive marker-assisted breeding strategy was followed to develop rice genotypes with improved grain yield under drought stress. [ABSTRACT FROM AUTHOR]

Understanding the inheritance pattern of traits underlying horizontal resistance (HR) against rice blast is essential for developing breeding strategies aimed at genetically controlling the disease. Eight rice ( Oryza sativa L.) genotypes, along with their F2 segregants derived from a complete diallel mating design, were exposed to the rice blast pathogen to determine combining ability and gene actions for the number and size of sporulating lesions developed on the plants, and area under the disease progress curve (AUDPC), following the fixed effects model of Griffing's Method 1. Results showed that both additive and non-additive gene actions were involved in the inheritance of lesion number (LN), lesion size (LS), and AUDPC. However, additive effects were more important, as indicated by the high ratio of general combining ability to specific combining ability found for the traits. Graphical analysis of the covariance and variances of the traits ruled out epitasis as a contributor to the limited non-additive gene action revealed for LN, LS and AUDPC. The graphical analysis further showed that dominance gene action detected in the parents was rather partial. The overall results suggest that selection for LN, LS and AUDPC could be useful for breeding rice with higher levels of HR against rice blast, using all of the parents but P1, which appeared to be the worst combiner. High estimates of heritability and phenotypic correlation were found for all three traits, which suggested that selection for the traits under controlled environment conditions would be effective in a recurrent selection programme. [ABSTRACT FROM AUTHOR]

• Co-elevated CO 2 and temperature increased plant N uptake and yield of the rice cultivars. • The increase of rice N under climate change was mainly derived from soil-N rather than urea fertilizer. • Urea fertilizer supply further enhanced the uptake of soil-derived N under climate change. • Climate change may accelerate the N mineralization in paddy soils and fertilizer N loss. Plant nitrogen (N) acquisition is essential to both crop growth and yield. A rational N management strategy for agricultural systems under climate change is required but a knowledge gap still exists regarding plant N uptake and N origin (soil-derived N or fertilizer-derived N) in response to elevated atmospheric CO 2 and warming. Our study investigated the responses of soil- or fertilizer-derived N uptake and yield of different cultivars of rice (Oryza sativa L.) to climate change. Five cultivars in the pedigree of a widely-grown rice cultivar Wuyoudao1 were supplied with and without urea, a commonly used N fertilizer in paddy soils and grown in open-top chambers under elevated CO 2 (700 ppm) and warming (2°C higher than the air temperature). Plant N origins were traced using 15N-labeling technique (urea of 5% 15N atom). Compared to the control, elevated CO 2 and warming increased N uptake by 17%, irrespective of N supply. Soil-N rather than fertilizer-N was the source of the increased N uptake. The increased soil-N uptake resulted in the enhancement of rice yield under climate change. Urea application did not alter the yield response to elevated CO 2 and warming compared to the non-N supply, but did stimulate plant uptake of the soil-derived N. Although genetic improvement of rice germplasm resulted in an increase in plant N acquisition and yield, the history of crop breeding since 1935 did not alter the climate-change-induced response in terms of plant N acquisition. Our results suggest that climate change may lead to the depletion of the recalcitrant soil N pool in paddy soils, and that fertilizer-N-use efficiency may need to be factored into future breeding for rice genotypes adapting well to climate change. [Display omitted] [ABSTRACT FROM AUTHOR]

The area under rice crop is decreasing year by year due to various factors such as increased cost of inputs, labour shortage and less profitability. Transplanting of rice seedlings in the traditional way is a labourious, time consuming and causes drudgery. Non-availability of labourers for transplanting at appropriate time leads to late planting, which results in poor yields. In rice, planting methods have an impact on the growth, yield attributes and yield besides cost of cultivation and labour requirement. Rice transplanting is done manually and requires about 306 man-h ha"1, which is roughly 42 per cent of the total labor requirement of rice production. At transplanting time, acute labor shortage results in increased labor wages and delay in the transplanting operation. Manual transplanting also results in a non-uniform and inadequate seedling populations. These problems necessitated the introduction of mechanized rice transplanting to achieve timely planting and better crop stands. [ABSTRACT FROM AUTHOR]

Background: Grain length, as a critical trait for rice grain size and shape, has a great effect on grain yield and appearance quality. Although several grain size/shape genes have been cloned, the genetic interaction among these genes and the molecular mechanisms of grain size/shape architecture have not yet to be explored. Results: To investigate the genetic interaction between two major grain length loci of rice, GS3 and qGL3, we developed two near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3) and NIL-qgl3 (gs3/qgl3), in the genetic background of 93-11 (gs3/qGL3) by conventional backcrossing and marker-assisted selection (MAS). Another NIL-GS3/qgl3 (GS3/qgl3) was developed by crossing NIL-GS3 with NIL-qgl3 and using MAS. By comparing the grain lengths of 93-11, NIL-GS3, NIL-qgl3 and NIL-GS3/ qgl3, we investigated the effects of GS3, qGL3 and GS3 x qGL3 interaction on grain length based on two-way ANOVA. We found that GS3 and qGL3 had additive effects on rice grain length regulation. Comparative analysis of primary panicle transcriptomes in the four NILs revealed that the genes affected by GS3 and qGL3 partially overlapped, and both loci might be involved in brassinosteroid signaling. Conclusion: Our data provide new information to better understand the rice grain length regulation mechanism and help rice breeders improve rice yield and appearance quality by molecular design breeding. [ABSTRACT FROM AUTHOR]

The success of a rice breeding program in developing salt tolerant varieties depends on genetic variation and the salt stress response of adapted and donor rice germplasm. In this study, we used a combination of morphological and physiological traits in multivariate analyses to elucidate the phenotypic and genetic variation in salinity tolerance of 30 Southern USA rice genotypes, along with 19 donor genotypes with varying degree of tolerance. Significant genotypic variation and correlations were found among the salt injury score (SIS), ion leakage, chlorophyll reduction, shoot length reduction, shoot K+ concentration, and shoot Na+/K+ ratio. Using these parameters, the combined methods of cluster analysis and discriminant analysis validated the salinity response of known genotypes and classified most of the USA varieties into sensitive groups, except for three and seven varieties placed in the tolerant and moderately tolerant groups, respectively. Discriminant function and MANOVA delineated the differences in tolerance and suggested no differences between sensitive and highly sensitive (HS) groups. DNA profiling using simple sequence repeat markers showed narrow genetic diversity among USA genotypes. However, the overall genetic clustering was mostly due to subspecies and grain type differentiation and not by varietal grouping based on salinity tolerance. Among the donor genotypes, Nona Bokra, Pokkali, and its derived breeding lines remained the donors of choice for improving salinity tolerance during the seedling stage. However, due to undesirable agronomic attributes and photosensitivity of these donors, alternative genotypes such as TCCP266, Geumgangbyeo, and R609 are recommended as useful and novel sources of salinity tolerance for USA rice breeding programs. [ABSTRACT FROM AUTHOR]

Genetic variability with mutagenic agents has been employed in plant breeding due to its significant contribution to the improvement of the existing rice genotypes by using genetically diverse parents. This study evaluated the genetic variability and diversity of mutant rice using quantitative traits and inter-simple sequence repeats (ISSR) molecular markers. A field experiment was carried out on M5 generation of 31 developed mutant lines and their parent (control). Morphological traits and 25 ISSR molecular markers were used as tools for determining cultivar identities and genetic diversity. The selected primers generated 443 clear polymorphic bands with an average number of 18 per primer. The bands were 85.10 % polymorphic. Un-weighted Pair Group of Arithmetic Means (UPGMA) with similarity coefficients were used for cluster analysis. Through this, all the genotypes were grouped into six clusters. It was shown that crosses between MR219-ML8 and MR219-ML22 could be done for development of high yielding varieties. Also, these mutants could be used as donor parents in rice breeding programs and some can be recommended as new rice varieties suitable for rice cultivation in Malaysia. [ABSTRACT FROM AUTHOR]

A strong case has been made in many publications for the adoption of highly client-oriented breeding (COB) since a greater role for farmers and clients can help produce and popularise varieties that better meet demands. Participatory varietal selection (PVS) – the testing of a diverse range of new varieties on farm by farmers – is an essential component of COB and has been broadly accepted. However, on the basis of published evidence, other aspects of COB have not been mainstreamed in national and international breeding programmes. This may be because there has been insufficient time for their benefits to become apparent. We review the outcomes from COB in maize ( Zea mays L.) and rice ( Oryza sativa L.) in India that resulted in the official release of a maize variety and two rice varieties. We review the substantial evidence on how all three were better accepted and much more widely adopted in several northern states of India than any of the conventionally bred alternatives that were currently available. This provides the most convincing evidence, so far, that client-oriented methods can be more effective. Prior to this, there was little documentation of the impact of COB programmes with few reports of them producing released varieties, so it may be unsurprising that there has been little institutionalisation of COB. The evidence presented here on its effectiveness ought to provide a stimulus for more breeders to adopt these approaches. However, the question of exactly how much evidence is needed remains rhetorical as evidence-based change is constrained by breeders who, for many reasons, are motivated to preserve the status quo. A greater weight of evidence may have to be accumulated before this inertia is overcome. [ABSTRACT FROM AUTHOR]

The application of heterosis (hybrid vigor) has brought great success to plant breeding, particularly of hybrid rice, achieving significant yield increases. Attempts to explore the heterosis of inter-subspecific hybrids between indica and japonica rice, which result in even greater yield increases, have greatly increased in the past decades. However, because of the reduced seed setting rate in F1 hybrids as a result of increased reproductive isolation, the application of inter-subspecific hybrids in rice has slowed. Understanding the balance between heterosis and the reproductive isolation of inter-subspecific hybrids will facilitate the strategic design of inter-subspecific hybrid breeding. In this study, five indica and seven japonica rice varieties were chosen as the parental lines of a complete diallel mating design. Data from six group traits from all of the hybrids and inbred lines were collected. We found that the grain weight per plant, grain number per panicle, tiller per plant, thousand grain weight and plant height, which reflected increased heterosis, were associated with the genetic divergence index (GDI) of the parents. Meanwhile, owing to the reduced seed setting rate, which was also associated with the parents' GDI, the grain production of the hybrids was negatively affected. After analyzing the relationships between the GDI of indica-japonica parents and the grain weight per plant of the F1 hybrids, an ideal GDI value (0.37) for the two indica-japonica parents that could provide an optimal balance between the inter-subspecific heterosis and reproductive isolation was proposed. Our findings will help in the strategic design of an inter-subspecific hybrid rice breeding program by identifying the ideal indica and japonica parents for a hybrid combination to achieve hybrid rice with an optimal yield. This strategic design of an inter-subspecific hybrid rice breeding program will be time saving and cost effective. [ABSTRACT FROM AUTHOR]

Key message: Two heterotic groups and four heterotic patterns were identified for IRRI hybrid rice germplasm to develop hybrid rice in the tropics based on SSR molecular data and field trials. Abstract: Information on heterotic groups and patterns is a fundamental prerequisite for hybrid crop breeding; however, no such clear information is available for tropical hybrid rice breeding after more than 30 years of hybrid rice commercialization. Based on a study of genetic diversity using molecular markers, 18 parents representing hybrid rice populations historically developed at the International Rice Research Institute (IRRI) were selected to form diallel crosses of hybrids and were evaluated in tropical environments. Yield, yield heterosis and combining ability were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis among marker-based parental groups, (2) examining the consistency between marker-based group and heterotic performance of hybrids, and (3) identifying foundational hybrid parents in discrete germplasm pools to provide a reference for tropical indica hybrid rice breeding. Significant differences in yield, yield heterosis and combining ability were detected among parents and among hybrids. On average, the hybrids yielded 14.8 % higher than the parents. Results revealed that inter-group hybrids yielded higher, with higher yield heterosis than intra-group hybrids. Four heterotic patterns within two heterotic groups based on current IRRI B- and R-line germplasm were identified. Parents in two marker-based groups were identified with limited breeding value among current IRRI hybrid rice germplasm because of their lowest contribution to heterotic hybrids. Heterotic hybrids are significantly correlated with high-yielding parents. The efficiency of breeding heterotic hybrids could be enhanced using selected parents within identified marker-based heterotic groups. This information is useful for exploiting those widely distributed IRRI hybrid rice parents. [ABSTRACT FROM AUTHOR]

Choosing new genotypes of rice based on the probability of overcoming the test-check. The objective of this work was to validate a statistical methodology for estimating the reliability or normalized response (RNi) and stability of four elite rice genotypes, compared with the control IDIAP 145-05. We used the database from the rice breeding program IDIAP, from experiments conducted from 2009 to 2011, in 31 environments under dryland conditions. The results of the study allowed us to verify that new genotypes significantly exceeded (P<0.05) in grain yield the control used. The four genotypes IDIAP FL 106-11, 137-11 FL IDIAP, IDIAP FL 155 and FL 156 IDIAP had a reliability average of 0.79, 0.75, 0.75 and 0.74, respectively. The normalized probability IDIAP FL 106-11 represents a differential response greater than zero with respect to IDIAP 145-05, in 8 of 10 cases. It also confirmed the reliability is related to the stability parameters based on regression models (bi and S²di). The AMMI multivariate model, considering the PCA1, identified the genotype IDIAP FL 156, as the most stable. GGE Biplot model, based on the PCA2, found that the genotype IDIAP FL 155, had greater stability. The study illustrates that the reliability or standardized response may be useful for more precise recommendations for the use of new genotypes commercially. [ABSTRACT FROM AUTHOR]

The current development of researchers in the field of genetic improvement in Cuba and the necessity of economizing experimental area and resources outlines the necessity to value experimental designs that facilitate an appropriate efficiency with a maximum of economy. This work intends to combine the kindness of DAM, with the adjustment method for line-column to control the soil heterogeneity, and the statistical multivariate techniques, offering the investigator a mathematical tool in the selection of test lines in rice breeding programs. DAM was structured by means of a Latin Square (4x4), with four controls lines (INCA LP-5, INCA LP-2, J-104 and Reforma) and 120 test lines distributed at random in the corresponding subplot. The use of DAM that allows to compare a considerable number of test lines, overcoming the limitations of a not replied experiment, what presupposes an economic benefit for the area reduction, the economy of experimental material and control of the environmental heterogeneity, in combination with statistical multivariate techniques provides a methodology more efficient in the selection of promissory lines in rice breeding program. [ABSTRACT FROM AUTHOR]

Cytoplasm has substantial genetic effects on progeny and is important for yield improvement in rice breeding. Studies on the cytoplasmic effects of cytoplasmic male sterility (CMS) show that most types of CMS have negative effects on yield-related traits and that these negative effects vary among CMS. Some types of genic male sterility (GMS), including photo-thermo sensitive male sterility (PTMS), have been widely used in rice breeding, but the cytoplasmic effects of GMS remain unknown. Here, we identified a GMS mutant line, h2s, which exhibited small, white anthers and failed to produce mature pollen. Unlike CMS, the h2s had significant positive cytoplasmic effects on the seed set rate, weight per panicle, yield, and general combining ability (GCA) for plant height, seed set rate, weight per panicle, and yield. These effects indicated that h2s cytoplasm may show promise for the improvement of rice yield. Genetic analysis suggested that the phenotype of h2s was controlled by a single recessive locus. We mapped h2s to a 152 kb region on chromosome 6, where 22 candidate genes were predicted. None of the 22 genes had previously been reported to be responsible for the phenotypes of h2s. Sequencing analysis showed a 12 bp deletion in the sixth exon of Loc_Os06g40550 in h2s in comparison to wild type, suggesting that Loc_Os06g40550 is the best candidate gene. These results lay a strong foundation for cloning of the H2S gene to elucidate the molecular mechanism of male reproduction. [ABSTRACT FROM AUTHOR]

A very high consumption growth rate has made rice one of the most important crops in Africa, but Africa's rice production growth rate is too low to match the consumption trend. A strong thrust is needed to boost rice production and productivity in Africa, especially in eastern and southern Africa (ESA), where large suitable land areas and resources with a congenial environment are available. Rice breeding activities in ESA, specifically for rainfed lowlands and irrigated ecosystems that have maximum area, did not receive enough attention in the past and hence lag behind in the development of appropriate high-yielding varieties. A poor rice variety development program for rainfed lowlands and irrigated areas was also marred by poor capacity, poor infrastructure, and a lack of proper policy support. This paper discusses the current issues related to the rice breeding scenario and the initiation of breeding support by CGIAR institutes such as IRRI in ESA. [ABSTRACT FROM AUTHOR]

Thirty six (36) cross combinations developed by crossing 2 Cytoplamic male sterility (CMS) lines with 18 testers in line x tester mating design were evaluated to find out best heterotic combinations in terms of yield and yield components of rice (Oryza sativa L.). Analysis of variance revealed significant differences among genotypes, crosses, lines, testers and line x tester interactions for all the traits studied. The specific combining ability (SCA) effects along with per se performance revealed that some of the crosses have shown desirable SCA effects, having superior per se performance for most of the traits thus indicating the selection of these crosses. Based on standard check varieties (SR-1 and Jhelum) assessment of heterosis for effective restored cross combinations showed a significant heterosis for all the traits except number of filled grains per panicle. The results revealed that the degree of heterosis varied from trait to trait. All combinations that showed superiority over standard checks for grain yield per plant also showed significant heterosis for majority of other traits. The average proportion of restorers, partial restorers, partial maintainers and maintainers were 16:22:33:27, respectively. The best cross combination for grain yield was SKAU 7A x K-08-61-2 and for early maturity SKAU 11A x SR-2 over check variety SR-1 only. Cross combinations SKAU 7Ax K-08-61-2, SKAU 7Ax SR-2, SKAU 11Ax K-08-60-2, SKAU 11Ax K-08-59-3 and SKAU 11A x SKAU-389 were the good specific combinations for grain yield per plant and other desirable traits and needs to be tested on large scale for their commercialization under temperate conditions. [ABSTRACT FROM AUTHOR]

Lowland rice is an important cereal crop that plays a key role in the food security and the economy of Thailand. Terminal water stress (TWS) in rainfed lowland areas poses threats to rice productivity due to stress occurrence at terminal crop stages and extreme sensitivity of rice to TWS. A two-year study was conducted to characterize the performance of yield and yield attributes of twelve Thai lowland rice genotypes under TWS, to identify stress-tolerant genotypes using stress response indices and to identify promising stress indices which are correlated with grain yield (GY) under well-watered (WW) and TWS conditions for their use as rapid identifiers in a rice crop breeding program for enhancing drought stress tolerance. Measurements were recorded under WW and TWS conditions. Highly significant variations were observed amongst assessed genotypes for their yield productivity responses. According to stress response indices, genotypes were categorized into stress-tolerant and stress susceptible genotypes. Genotypes Hom Pathum, Sang Yod, Dum Ja and Pathum Thani-1 were found highly stress tolerant and relatively high yielding; genotypes Look Pla and Lep Nok were stress tolerant, whereas genotypes Chor Lung, Hom Nang Kaew and Hom Chan were moderately tolerant genotypes. Hence, stress-tolerant genotypes could be potentially used for cultivation under rainfed and water-limited conditions, where TWS is predicted particularly in southern Thailand to stabilize rice productivity. Stress tolerance indices, including stress tolerance index (STI), geometric mean productivity (GMP), mean productivity index (MPRO) and harmonic mean index (MHAR), indicated strong and positive associations with GY under WW and TWS; thus, these indices could be used to indicate stress tolerance in rice crop breeding program aimed at a rapid screening of lowland rice genotypes for stress tolerance. [ABSTRACT FROM AUTHOR]

Rice is an important staple food and cash crop. Although many varieties of rice have been developed to date, few are adopted possibly because researchers did not take into account farmers’ preferences and perceptions on varieties during the development process. Because farmers increasingly rely on low-yielding landraces, production fails to meet demand. To provide an understanding of farmers’ preferences for rice cultivars and perceptions on drought stress and management practices as inputs to rice breeding research, this study was conducted in the Sikasso region of Mali in September 2005 using participatory rural appraisal approach. A total number of 125 farmers were randomly selected from 10 villages in three ecologies and interviewed individually and in groups. Results showed that farmers’ preferences, crop management practices and ranking of production constraints differed significantly across ecologies. Whereas farmers in the irrigated ecologies preferred high-yielding, long duration rice varieties, those in the upland and lowland ecologies preferred tall plants of short duration. While upland and lowland farmers preferred red and white long grains, respectively, irrigated ecologies were indifferent about grain colour. Farmers appeared willing to trade-off yield for grain quality and plant height, inconsistent with traditional breeders’ selection criteria. The high preference for tall varieties among farmers in the upland and lowland ecologies also contrasted sharply with the model of dwarf rice varieties responsible for the green revolution in Asia. The implication of these findings for rice breeders is that different plant idiotypes complemented by effective drought management practices should target different ecologies to increase impact. [ABSTRACT FROM AUTHOR]

We describe a participatory plant breeding (PPB) programme in rice for the rainfed uplands of eastern India. Collaborative participation (farmers grew and selected in segregating materials in their fields) and consultative participation (farmers selected among progenies in researchers' plots) were used. The PPB was started with only two crosses and, of these, Kalinga III/IR64 was the most successful and produced two released varieties: Ashoka 200F from collaborative breeding and Ashoka 228 from consultative breeding. Both yielded significantly more than control varieties, including Kalinga III, in research trials and in participatory trials in farmers' fields. Qualitative data from participatory trials was highly informative, statistically analysable, and cheaper to obtain than quantitative data. In low-yielding research-station and on-farm trials the two new upland varieties showed no significant genotype × environment interaction with the check varieties. However, in higher-yielding All India Coordinated Rice Improvement Project trials, both varieties were more adapted to low yielding environments than the national check variety. Farmers liked the varieties for their early maturity, improved lodging resistance, higher fodder and grain yield, long-slender grains and excellent cooking quality. Before certified seed production, farmer groups have produced large quantities of seed that have spread widely through informal channels. The returns from PPB, compared to conventional breeding, were higher because it cost less, the genetic gains per year were higher, and the benefits to farmers were realised earlier. [ABSTRACT FROM AUTHOR]

Agroecology is based on the optimization of ecological processes occurring in agrosystems, especially by improving beneficial interactions among organisms. Recent studies have provided evidence that the ability of plants to interact with free-living soil organisms can be influenced by plant breeding. The upland rice breeding programme in the Highlands of Madagascar aims to develop cultivars that are adapted to local climatic, soil fertility and pest constraints. However, it is still unknown whether this genetic improvement alters rice cultivar abilities to interact with free-living soil plant-mutualistic organisms such as earthworms. We assessed in mesocosms the response of six upland rice cultivars commonly used by farmers in the Highlands of Madagascar to the presence of the endogeic earthworm Pontoscolex corethrurus. Plant nutrition and growth-related traits were measured after eight weeks of growth. These traits were significantly improved in the presence of P. corethrurus for all cultivars compared to the control treatment. However, the magnitudes of earthworm effects on plant traits were strongly variable and were dependent on specific rice cultivars. Agronomic and phylogenetic distance matrices were computed using agronomic data and available phylogenetic data of the rice cultivars. We did not detect significant correlations between cultivar responses to earthworm inoculation and agronomic or phylogenetic distances. Our results suggest that (i) the ability of rice to exploit beneficial interactions involving free-living soil organisms is influenced by its genetic background, but (ii) the loss of earthworm-interactive abilities of rice crops is independent of the genetic distance among cultivars and breeders' agronomic criteria. Our findings are significant for attempts to use rice cultivars that optimize plant-soil interactions within agroecological practices and highlight the need to integrate free-living soil partners as life-long plant partners in future strategies for plant breeding. • P. corethrurus strongly enhanced rice nutrition and growth irrespective of cultivars. • The size of earthworm effects on rice traits was variable according to cultivars. • Loss in interactive rice abilities is independent of breeder's agronomic interactions. [ABSTRACT FROM AUTHOR]

With global warming and climate change, breeding crop plants tolerant to high-temperature stress is of immense significance. tRNA 2-thiolation is a highly conserved form of tRNA modification among living organisms. Here, we report the identification of SLG1 (Slender Guy 1), which encodes the cytosolic tRNA 2-thiolation protein 2 (RCTU2) in rice. SLG1 plays a key role in the response of rice plants to high-temperature stress at both seedling and reproductive stages. Dysfunction of SLG1 results in plants with thermosensitive phenotype, while overexpression of SLG1 enhances the tolerance of plants to high temperature. SLG1 is differentiated between the two Asian cultivated rice subspecies, indica and japonica, and the variations at both promoter and coding regions lead to an increased level of thiolated tRNA and enhanced thermotolerance of indica rice varieties. Our results demonstrate that the allelic differentiation of SLG1 confers indica rice to high-temperature tolerance, and tRNA thiolation pathway might be a potential target in the next generation rice breeding for the warming globe. Understanding the mechanism of high-temperature tolerance will help to breed crops adaptive to warming climate. Here, the authors show SLG1, a cytosolic tRNA 2-thiolation protein 2 encoding gene, is differentiated between the two Asian cultivated rice subspecies and confers high temperature tolerance of indica rice. [ABSTRACT FROM AUTHOR]

• We measured key crop traits on 40 rice varieties in a two-year experiment. • The panel of Italian varieties showed large variability in phenotypic expression. • Measured yield was highly variable, many pre-mechanization cultivars top ranked. • Sink-source organs balance and adequate crop duration were associated to high yields. • Three main yield strategies were identified across the panel. Plant breeding is one of the key strategies for further enhancement of crop yields; however, effective breeding strategies require phenotypic characterisation of the available germplasm. This study sought to characterise the phenotypic expression of fourteen crop traits related to phenology, plant architecture, and yield in a panel of 40 cultivars selected to represent the phenotypic variability present in Italian rice germplasm during a two-season field experiment. The observed range of phenotypic variation was high for many traits (coefficients of variation ranging from 5.9% to 45.4%) including yield (mean: 6.47 t ha−1; CV: 15.4 %; min: 2.19 t ha−1; max: 8.95 t ha−1), and multiple strong associations emerged in all the analysed traits. Cluster analysis extracted three groups of genotypes characterised by alternative yield strategies, i.e. "high-tillering", "early maturing", and "increased source-sink". Our findings highlight that rice yield decrease when one strategy is overemphasised. In contrast, the highest-yielding genotypes have a balanced ratio between sink and source organs, along with a proportional duration of vegetative and reproductive phases. This study depicts the phenotypic variability in Italian rice cultivars and proposes a novel classification based on yield-related traits which could be of use in multiple rice breeding applications. [ABSTRACT FROM AUTHOR]

The development of rice cultivars with desirable traits is essential. The decision-making is a crucial step in rice breeding programs. Breeders can make efficient and pragmatic decisions if an organized pedigree visualization platform is available for the accessions and cultivars in rice breeding germplasm. In the present study, the available data of all the rice varieties released by Rice Research and Development Institute, Sri Lanka, and the related landraces and genotypes were arranged in Pedimap, a pedigree visualization tool. Pedimap can showcase pedigree relationships, phenotypic, and molecular data. The identity by descent probabilities were calculated using FlexQTL software and included in the Pedimap database. The parentage selection based on the variations of phenotypic traits, selection of marker alleles for molecular breeding, and detection of the founders of genetic effects can be swiftly conducted using Pedimap. However, the power of harnessing the value of Pedimap for making breeding decisions relies on the availability of data for the traits, markers, and genomic sequences. Thus, it is imperative to characterize the breeding germplasms using standard phenomic and genomic characterization procedures such as the assessment of before organized into Pedimap. Thereby, the worldwide breeding programs can benefit from each other to produce improved varieties to meet global challenges. [ABSTRACT FROM AUTHOR]

Clary sage (Salvia sclarea L.), known for its aromatic and medicinal properties, belongs to the Lamiaceae family. Although the species grows wild throughout Sicily, knowledge of its production and qualitative properties is limited. The aim of this study was to evaluate the agronomic behavior of the species over two years of testing and to characterize the chemical properties of its wild counterparts in order to identify the most promising accessions for cropping or for use in breeding programs. Tests were carried out during 2008, 2009, and 2010. During the first year, the plot was established. Subsequently, the main parameters for bio-agronomic evaluation were taken in 2009 and 2010. Regarding qualitative characterization, essential oils (EO) were extracted from flowering samples of clary sage. The accessions in the study showed satisfactory adaptation capacity to cropping. The accessions examined belong to the "linalyl acetate" (range 36–43%) chemotype. Test results show good potential for Mediterranean cropping systems, helping to increase the range of medicinal and aromatic species in cultivation. [ABSTRACT FROM AUTHOR]

Basal or partial resistance has been considered race-non-specific and broad-spectrum. Therefore, the identification of genes or quantitative trait loci (QTLs) conferring basal resistance and germplasm containing them is of significance in breeding crops with durable resistance. In this study, we performed a bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) to identify QTLs controlling basal resistance to blast disease in an F2 population derived from two rice varieties, 02428 and LiXinGeng (LXG), which differ significantly in basal resistance to rice blast. Four candidate QTLs, qBBR-4, qBBR-7, qBBR-8, and qBBR-11, were mapped on chromosomes 4, 7, 8, and 11, respectively. Allelic and genotypic association analyses identified a novel haplotype of the durable blast resistance gene pi21 carrying double deletions of 30 bp and 33 bp in 02428 (pi21-2428) as a candidate gene of qBBR-4. We further assessed haplotypes of Pi21 in 325 rice accessions, and identified 11 haplotypes among the accessions, of which eight were novel types. While the resistant pi21 gene was found only in japonica before, three Chinese indica varieties, ShuHui881, Yong4, and ZhengDa4Hao, were detected carrying the resistant pi21-2428 allele. The pi21-2428 allele and pi21-2428-containing rice germplasm, thus, provide valuable resources for breeding rice varieties, especially indica rice varieties, with durable resistance to blast disease. Our results also lay the foundation for further identification and functional characterization of the other three QTLs to better understand the molecular mechanisms underlying rice basal resistance to blast disease. [ABSTRACT FROM AUTHOR]

• Dramatic differences in plant morphological, physiological and agronomic traits result in similar high yield of HHZ and 9311. • Completely different features are identified for high canopy photosynthetic efficiency at different growth stages. • A combination of computational models and systematic measurements can provide a new option to support high-yield crop breeding. Understanding mechanisms underlying high yield in elite cultivars and identifying new options to further increase rice yield are major focuses of current rice research. In this work, we develop a general method to tackle the above two challenges using two outstanding indica cultivars, i.e., Huang-Hua-Zhan (HHZ) and Yang-dao 6 (9311), which differ in their strategies to gain high yields. Briefly, HHZ grew slower during seedling stage, whereas accumulated more biomass from tillering to heading stage, and had a shorter leaf photosynthetic functional duration after heading; in contrast, 9311 had stronger seedling vigor, but less biomass accumulation from tillering to heading stage, and longer leaf photosynthetic functional duration after heading. To identify the mechanisms underlying these two different strategies, we dissected factors controlling daily canopy photosynthesis at four different growth stages throughout the growing season using a computational approach. Results showed that higher leaf area index (LAI) due to larger leaf width, regardless of a relatively lower leaf light-saturated photosynthetic rate, contributed to higher canopy photosynthesis and hence stronger seedling vigor of 9311 when LAI was low, whereas these same features decreased canopy photosynthetic rate at young panicle differentiation stage when LAI was high; while instead of increasing canopy photosynthesis to support seedling growth, lower LAI due to smaller leaf width, together with higher leaf light-saturated photosynthetic rate, favored biomass accumulation of HHZ between the late tillering stage and the heading stage. Concurrently, computational simulations revealed that earlier drooping of the panicle of HHZ could increase upper leaves' light intercept and thus canopy photosynthesis at heading stage by reducing shading from panicles, whereas higher leaf nitrogen content was the most important factor for higher canopy photosynthesis of 9311 during grain filling. Overall, the method presented here can be used to quantitatively identify key factors that limit canopy photosynthetic efficiency of current elite cultivars, which is the basis for crop yield potential, and can be used as targets for rice yield improvement by traditional breeding approaches or by genomic editing technologies. [ABSTRACT FROM AUTHOR]