Improving the phenotypic expression of rice genotypes:Rethinking “intensification” for production systems and selection practices for rice breeding

Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification available. More productive crop phenotypes, with traits such as more resistance to biotic and abiotic stresses and shorter crop cycles, are possible through modifications in the management of rice plants, soil, water, and nutrients, reducing rather than increasing material inputs. Greater factor productivity can be achieved through the application of new knowledge and more skill, and(initially) more labor, as seen from the System of Rice Intensification(SRI), whose practices are used in various combinations by as many as 10 million farmers on about 4 million hectares in over 50 countries. The highest yields achieved with these management methods have come from hybrids and improved rice varieties, confirming the importance of making genetic improvements. However,unimproved varieties are also responsive to these changes, which induce better growth and functioning of rice root systems and more abundance, diversity, and activity of beneficial soil organisms. Some of these organisms as symbiotic endophytes can affect and enhance the expression of rice plants' genetic potential as well as their phenotypic resilience to multiple stresses, including those of climate change. SRI experience and data suggest that decades of plant breeding have been selecting for the best crop genetic endowments under suboptimal growing conditions, with crowding of plants that impedes their photosynthesis and growth, flooding of rice paddies that causes roots to degenerate and forgoes benefits derived from aerobic soil organisms, and overuse of agrochemicals that adversely affect these organisms as well as soil and human health. This review paper reports evidence from research in India and Indonesia that changes in crop and water management can improve the expression of rice plants' genetic potential, thereby creating more productive and robustphenotypes from given rice genotypes. Data indicate that increased plant density does not necessarily enhance crop yield potential, as classical breeding methods suggest. Developing cultivars that can achieve their higher productivity under a wide range of plant densities—breeding for density-neutral cultivars using alternative selection strategies—will enable more effective exploitation of available crop growth resources. Density-neutral cultivars that achieve high productivity under ample environmental growth resources can also achieve optimal productivity under limited resources, where lower densities can avert crop failure due to overcrowding. This will become more important to the extent that climatic and other factors become more adverse to crop production. Focusing more on which management practices can evoke the most productive and robust phenotypes from given genotypes is important for rice breeding and improvement programs since it is phenotypes that feed our human populations.

Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm(Phoenix dactylifera) and related species

Date palm(Phoenix dactylifera),one of the most ancient crops,is grown commercially in>30 countries.Using whole plastome assemblies,phylogenetic analyses revealed that cultivated date palm accessions share the same clade with Phoenix sylvestris,Phoenix pusilla and Phoenix acaulis,which are native to the Indian subcontinent,and Phoenix caespitosa that is native to the Arabian Peninsula and the deserts of Somalia.Analysis of genetic diversity and genetic relationships among date palm accessions from 13 producing countries involved 195 date palm accessions that were genotyped at 19 microsatellite loci.Extensive genetic diversity was observed,with many accessions heterozygous for most markers in this clonally propagated crop.The average number of alleles per locus(42.1),expected heterozygosity(0.8),observed heterozygosity(0.47)and fixation indices(FST=0.42)demonstrated substantial genetic diversity and population structure.Iraqi accessions were found to have the richest allelic diversity,and the most private alleles.The model-based Bayesian method indicated that these accessions could be broadly divided into two structure groups,one group with predominantly African accessions and another predominantly Asian.Some germplasm,especially from Tunisia and Iraq,deviated from this generalization.Many accessions in the STRUCTURE-derived groups were found to be genetic admixtures,with gene flow between Asian and African groups.Indian and Pakistani date palms were found to be most closely related to North African germplasm.

Exploiting the diversity of tomato:the development of a phenotypically and genetically detailed germplasm collection

A collection of 163 accessions,including Solanum pimpinellifolium,Solanum lycopersicum var.cerasiforme and Solanum lycopersicum var.lycopersicum,was selected to represent the genetic and morphological variability of tomato at its centers of origin and domestication:Andean regions of Peru and Ecuador and Mesoamerica.The collection is enriched with S.lycopersicum var.cerasiforme from the Amazonian region that has not been analyzed previously nor used extensively.The collection has been morphologically characterized showing diversity for fruit,flower and vegetative traits.Their genomes were sequenced in the Varitome project and are publicly available(solgenomics.net/projects/varitome).The identified SNPs have been annotated with respect to their impact and a total number of 37,974 out of 19,364,146 SNPs have been described as high impact by the SnpEeff analysis.GWAS has shown associations for different traits,demonstrating the potential of this collection for this kind of analysis.We have not only identified known QTLs and genes,but also new regions associated with traits such as fruit color,number of flowers per inflorescence or inflorescence architecture.To speed up and facilitate the use of this information,F2 populations were constructed by crossing the whole collection with three different parents.This F2 collection is useful for testing SNPs identified by GWAs,selection sweeps or any other candidate gene.All data is available on Solanaceae Genomics Network and the accession and F2 seeds are freely available at COMAV and at TGRC genebanks.All these resources together make this collection a good candidate for genetic studies.

Effect of Plant Growth Stimulants on Alfalfa Response to Salt Stress

Salinity is a major impediment to crop production. This study was undertaken to compare the effect of seaweed extract, humic acid, and potassium sulfate nanoparticles in alleviating salt stress in Alfalfa (Medicago sativa L.). Seeds of ten alfalfa genotypes were germinated in a growth chamber at five salt concentrations (0%, 0.5%, 1.0%, 1.5%, and 2.00%). Salt concentrations above 1% reduced seed germination by more than 70% in most genotypes. One salt tolerant genotype (Mesa-Sirsa) and one salt sensitive (Bulldog 505) were selected and planted in greenhouse pots containing 2 kg of sand and subjected to two salt levels (10 and 15 dS· m-1). Four treatments consisting of 1) control (Hoagland solution, no-salt), 2) seaweed extract at 4 Kg·ha-1, 3) humic acid at 28 L· ha-1, and 4) potassium sulfate at 300 Kg· ha-1. Plant biomass was reduced under both salt concentrations in both genotypes, with a greater magnitude in the salt sensitive genotype. Application of seaweed extract resulted in higher relative water content and proline under both salt concentrations (10 and 15 dS·m-1) in the salt sensitive genotype, and lower electrolyte leakage in both salt tolerant and salt sensitive genotypes, under both salt concentrations. Seaweed extract also resulted in higher catalase and SOD activities in both genotypes under 10 dS·m-1. Catalase and SOD activities were associated with significantly (p < 0.01) reduced electrolyte leakage and increased shoot dry weight. Overall, seaweed extract seemed to have a positive effect in alleviating salt stress in alfalfa.

Allelopathic Effects of Cereal Rye on Weed Suppression and Forage Yield in Alfalfa

Cereal rye (Secale cereale L.) is widely used as cover crop because of its allelopathic effects and effectiveness in weed suppression. In the Southeastern US, rye is traditionally grown for winter grazing in dormant bermudagrass pastures, where alfalfa (Medicago sativa L.) is increasingly planted as a companion crop. The effect of cereal rye on alfalfa as a succeeding crop is not known. Therefore, the objective of this study was to evaluate the effect of cereal rye on alfalfa seedling emergence, growth, forage yield, and weed suppression in field conditions. Rye was planted in the fall (mid-October) and the biomass was harvested in spring (March) followed by disking and incorporation of the remaining stubble in the soil. Alfalfa seed was planted four weeks later. The experiment design was a split-plot design with the main plots being no-rye and after-rye and the sub-plots being alfalfa cultivars. Ten alfalfa cultivars were planted in three replications after-rye and three replications with no-rye as a previous crop. In the establishment year, weed density was significantly (p < 0.01) lower in the after-rye alfalfa plots by nearly 77%. Alfalfa seedling counts were also significantly lower (p 0.01) among the cultivars planted in the after-rye block compared to the no-rye, with a seedling count reduction between 35% and 64%. Reduction in total dry biomass yield varied from 15% to 43% among the cultivars planted in the after-rye block. The results of this study also suggest that the allelopathic effect of rye on alfalfa may not persist beyond the establishment season, but the enormous yield reduction in the first production season may constitute a costly economic penalty in terms of forage production. There was variation in the response of different alfalfa cultivars to the effect of rye residue as indicated by the variation in the magnitude of reduction in stand count and forage yield. This warrants more research in multi-location trials with and without rye in order to establish whether there is genetic variation in alfalfa germplasm in their tolerance to cereal rye allelopathy.

Response of Alfalfa under Salt Stress to the Application of Potassium Sulfate Nanoparticles

A greenhouse study was conducted to explore the effect of various rates of potassium sulfate (K2SO4) nanoparticles on alfalfa (Medicago sativa L.) growth and physiological response under salt stress. One salt-tolerant genotype (Mesa-Sirsa) and one salt-sensitive genotype (Bulldog 505) were selected based on germination under salt and were planted in pots containing 2 kg of sand. The two genotypes were subjected to 0 and 6 dS·m-1 salt levels using CaCl2·2H2O: NaCl (2:1) mixed with Hoagland solution. Three K2SO4 nanoparticle treatments consisting of, 1/4, 1/8, and 1/10 of the potassium (K) level in full strength Hoagland solution (235 mg·L-1) were applied. Adding K2SO4 nanoparticles at the 1/8 level resulted in the highest shoot dry weight, relative yield, root length and root dry weight in both genotypes. The different rates of K2SO4 nanoparticles affected significantly Na/K ratio and the concentrations of Calcium (Ca), Phosphorus (P), Copper (Cu), Manganese (Mn), and Zinc (Zn) in plant tissue. The application of K2SO4 nanoparticles at the 1/8 rate enhanced the plant’s physiological response to salt stress by reducing electrolyte leakage, increasing catalase and proline content, and increasing antioxidant enzymes, activity. These results suggest that the application of K nanoparticles may have better efficiency than conventional K fertilizers in providing adequate plant nutrition and overcoming the negative effects of salt stress in alfalfa.

Insights into Seasonal Dormancy of Perennial Herbaceous Forages

Seasonal dormancy is an adaptive mechanism where plants suspend growth and become physiologically inactive to avoid extreme environmental conditions. Environmental factors like temperature, photoperiod, nutrients, and soil moisture control plant growth and development through various complex molecular mechanisms. Crown and seed dormancy of plants are mostly influenced by day length and temperature. Genes and physiological pathways triggered by these two factors along with genotype variability are some targets to manipulate seasonal dormancy. There is genetic variation in the depth and duration of seasonal dormancy. Therefore, their genetic manipulation is possible. Manipulations of summer and fall dormancy are relatively easier compared to winter dormancy because plants require protection of their apical meristem from freezing temperatures and limited water supply. Genetic factors that regulate seed dormancy may also have regulatory role for seasonal dormancy of the maternal plants. Limited genetic and genomic information are available for seasonal dormancy in herbaceous perennial species. Knowledge of genes controlling seasonal dormancy of eudicots, forest trees, and horticultural crops could be interpolated to explore possible dormancy mechanisms in perennial forages. This study reviews current knowledge of seasonal dormancy of herbaceous forages emphasizing the genetic and physiological context that would be valuable to breeders and plant biologists to expand the production season of perennial species by developing non-dormant and semi-dormant cultivars.

Intra-and interspecific diversity analyses in the genus Eremurus in Iran using genotyping-bysequencing reveal geographic population structure

Eremurus species,better known as‘Foxtail Lily’or‘Desert Candle’,are important worldwide in landscaping and the cutflower industry.One of the centers of highest diversity of the genus Eremurus is Iran,which has seven species.However,little is known about the genetic diversity within the genus Eremurus.With the advent of genotyping-bysequencing(GBS),it is possible to develop and employ single nucleotide polymorphism(SNP)markers in a costefficient manner in any species,regardless of its ploidy level,genome size or availability of a reference genome.Population structure and phylogeographic analyses of the genus Eremurus in Iran using a minimum of 3002 SNP markers identified either at the genus level or at the species level from GBS data showed longitudinal geographic structuring at the country scale for the genus and for the species E.spectabilis and E.luteus,and at the regional scale for E.olgae.Our analyses furthermore showed a close genetic relatedness between E.olgae and E.stenophyllus to the extent that they should be considered subspecies within an E.olgae/stenophyllus species complex.Their close genetic relatedness may explain why crosses between these two(sub)species have been found in the wild and are exploited extensively as ornamentals.Last,current species identification,while robust,relies on flower morphology.A subset of seven SNPs with species-specific(private)alleles were selected that differentiate the seven Eremurus species.The markers will be especially useful for cultivar protection and in hybrid production,where true hybrids could be identified at the seedling stage.

Determining the earliest growth stage to detect the presence of endophytes in tall fescue and perennial ryegrass seedlings using molecular markers

Background:Tall fescue(Festuca arundinacea[Schreb.],Lolium arundinaceum[Schreb.]Darbysh)and perennial ryegrass(Lolium perenne)are important cool-season forage and amenity grasses that have a mutualistic association with an endophytic fungus.Endophytes confer insect and drought resistance to plants but can produce mammalian toxins.Novel endophytes that do not produce mammalian toxins have been introduced to elite cultivars for commercial production.Seed companies need to maintain adequate levels of novel endophytes within the elite forage cultivars.Endophyte detection is performed using immunochemical and molecular techniques because of their speed and reliability.Early detection in seedlings is essential to evaluate the viability of the endophyte within seed lots.Methods:This research aimed to identify the earliest growth stage in which immunochemical and molecular methods can detect viable endophyte in seedlings of tall fescue cultivars BarOptima(e34),Texoma MaxQII(584),and Jesup MaxQ(542),as well as the perennial ryegrass cultivar Remington(NEA2).Results:Immunochemical testing detected endophytes in seedlings 14 days after germination(DAG),but the detection rate increased until 42 DAG in some cultivars tested.The molecular marker Tef1exon detected endophytes at a lower rate than the immunochemical method at 28–42 DAG.However,there was insufficient DNA to detect endophytes in 14 DAG seedlings using markers.Conclusions:We conclude that the most accurate detection of viable endophytes in seedlings was 42 DAG,at which sufficient and consistent endophyte colonization occurred.

Blossom-end rot:a century-old problem in tomato(Solanum lycopersicum L.)and other vegetables

Blossom-end rot(BER)is a devastating physiological disorder affecting vegetable production worldwide.Extensive research into the physiological aspects of the disorder has demonstrated that the underlying causes of BER are associated with perturbed calcium(Ca^(2+))homeostasis and irregular watering conditions in predominantly cultivated accessions.Further,Reactive Oxygen Species(ROS)are critical players in BER development which,combined with unbalanced Ca^(2+)concentrations,greatly affect the severity of the disorder.The availability of a high-quality reference tomato genome as well as the whole genome resequencing of many accessions has recently permitted the genetic dissection of BER in segregating populations derived from crosses between cultivated tomato accessions.This has led to the identification of five loci contributing to BER from several studies.The eventual cloning of the genes contributing to BER would result in a deeper understanding of the molecular bases of the disorder.This will undoubtedly create crop improvement strategies for tomato as well as many other vegetables that suffer from BER.