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Salinity stress is a major constraint to rice production in many coastal regions due to saline groundwater and river sources, especially during the dry season in coastal areas when seawater intrudes further inland due to reduced river flows. Since salinity tolerance is a complex trait, breeding efforts can be assisted by mapping quantitative trait loci (QTLs) for complementary salt tolerance mechanisms, which can then be combined to provide higher levels of tolerance. While an abundance of seedling stage salinity tolerance QTLs have been mapped, few studies have investigated reproductive stage tolerance in rice due to the difficulty of achieving reliable stage-specific phenotyping techniques. In the current study, a BC1F2 mapping population consisting of 435 individuals derived from a cross between a salt-tolerant Saudi Arabian variety, Hasawi, and a salt-sensitive Bangladeshi variety, BRRI dhan28, was evaluated for yield components after exposure to EC 10 dS/m salinity stress during the reproductive stage. After selecting tolerant and sensitive progeny, 190 individuals were genotyped by skim sequencing, resulting in 6209 high quality single nucleotide polymorphic (SNP) markers. Subsequently, a total of 40 QTLs were identified, of which 24 were for key traits, including productive tillers, number and percent filled spikelets, and grain yield under stress. Importantly, three yield-related QTLs, one each for productive tillers (qPT3.1), number of filled spikelets (qNFS3.1) and grain yield (qGY3.1) under salinity stress, were mapped at the same position (6.7 Mb or 26.1 cM) on chromosome 3, which had not previously been associated with grain yield under salinity stress. These QTLs can be investigated further to dissect the molecular mechanisms underlying reproductive stage salinity tolerance in rice. [ABSTRACT FROM AUTHOR]

CRISPR-Cas gene editing technologies offer the potential to modify crops precisely; however, in vitro plant transformation and regeneration techniques present a bottleneck due to the lengthy and genotype-specific tissue culture process. Ideally, in planta transformation can bypass tissue culture and directly lead to transformed plants, but efficient in planta delivery and transformation remains a challenge. This study investigates transformation methods that have the potential to directly alter germline cells, eliminating the challenge of in vitro plant regeneration. Recent studies have demonstrated that carbon nanotubes (CNTs) loaded with plasmid DNA can diffuse through plant cell walls, facilitating transient expression of foreign genetic elements in plant tissues. To test if this approach is a viable technique for in planta transformation, CNT-mediated plasmid DNA delivery into rice tissues was performed using leaf and excised-embryo infiltration with reporter genes. Quantitative and qualitative data indicate that CNTs facilitate plasmid DNA delivery in rice leaf and embryo tissues, resulting in transient GFP, YFP, and GUS expression. Experiments were also initiated with CRISPR-Cas vectors targeting the phytoene desaturase (PDS) gene for CNT delivery into mature embryos to create heritable genetic edits. Overall, the results suggest that CNT-based delivery of plasmid DNA appears promising for in planta transformation, and further optimization can enable high-throughput gene editing to accelerate functional genomics and crop improvement activities. [ABSTRACT FROM AUTHOR]

Apparent amylose and protein concentrations (AAC and PC) affect the milling, cooking, and eating quality of rice. This study was conducted to assess the phenotypic and genotypic variation and to identify genomic regions and putative candidate genes associated with AAC and PC in milled rice grain. Two hundred and seventeen and 207 diverse rice accessions were grown at the Texas A&M AgriLife Research Center in 2018 and 2019, respectively. Milled rice samples were analyzed for AAC and PC using the iodine colorimetry and Dumas method, respectively. Genome-wide association studies (GWAS) for AAC and PC were conducted using 872,556 single nucleotide polymorphism (SNP) markers following the mixed linear model. Significant variation among the accessions was found for both variables each year. Associations between 32 SNPs with PC and seven SNPs with AAC were detected. Gene models linked to these SNPs have a wide range of biological functions, including protein and carbohydrate metabolism, DNA methylation, and response to abiotic and biotic stresses. Seven of the identified SNPs colocalized with previously reported quantitative trait loci (QTL) for protein concentration. Fine-mapping of significant genomic regions and gene validation are necessary for this information to aid in marker-assisted breeding for improved grain quality. [ABSTRACT FROM AUTHOR]

Key message: Novel mutations of OsCOP1 were identified to be responsible for yellowish pericarp and embryo lethal phenotype, which revealed that OsCOP1 plays a crucial role in flavonoid biosynthesis and embryogenesis in rice seed. Successful production of viable seeds is a major component of plant life cycles, and seed development is a complex, highly regulated process that affects characteristics such as seed viability and color. In this study, three yellowish-pericarp embryo lethal (yel) mutants, yel-hc, yel-sk, and yel-cc, were produced from three different japonica cultivars of rice (Oryza sativa L). Mutant seeds had yellowish pericarps and exhibited embryonic lethality, with significantly reduced grain size and weight. Morphological aberrations were apparent by 5 days after pollination, with abnormal embryo development and increased flavonoid accumulation observed in the yel mutants. Genetic analysis and mapping revealed that the phenotype of the three yel mutants was controlled by a single recessive gene, LOC_Os02g53140, an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). The yel-hc, yel-sk, and yel-cc mutants carried mutations in the RING finger, coiled-coil, and WD40 repeat domains, respectively, of OsCOP1. CRISPR/Cas9-targeted mutagenesis was used to knock out OsCOP1 by targeting its functional domains, and transgenic seed displayed the yel mutant phenotype. Overexpression of OsCOP1 in a homozygous yel-hc mutant background restored pericarp color, and the aberrant flavonoid accumulation observed in yel-hc mutant was significantly reduced in the embryo and endosperm. These results demonstrate that OsCOP1 is associated with embryo development and flavonoid biosynthesis in rice grains. This study will facilitate a better understanding of the functional roles of OsCOP1 involved in early embryogenesis and flavonoid biosynthesis in rice seeds. [ABSTRACT FROM AUTHOR]

Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 trait-specific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the C7AIR provides valuable information that can be used to select informative and reliable SNP markers for conversion to lower-cost genotyping platforms for genomic selection and other downstream applications in breeding. [ABSTRACT FROM AUTHOR]

Low temperature significantly affects rice growth and yield. Temperatures lower than 15°C are generally detrimental for germination and uniform seedling stand. To investigate the genetic architecture underlying cold tolerance during germination in rice, we conducted a genome-wide association study using a novel diversity panel of 257 rice accessions from around the world and the 7K SNP marker array. Phenotyping was conducted in controlled growth chambers under dark conditions at 13°C. The rice accessions were measured for low-temperature germinability, germination index, coleoptile length under cold stress, plumule length at 4-day recovery, and plumule length recovery rate. A total of 51 QTLs were identified at p < 0.001 and 17 QTLs were identified using an FDR < 0.05 across the different chilling indices with the whole panel of accessions. At the threshold of p < 0.001, a total of 20 QTLs were identified in the subset of japonica accessions, while 9 QTLs were identified in the subset of indica accessions. Considering the recurring SNPs and linked SNPs across different chilling indices, we identified 31 distinct QTL regions in the whole panel, 13 QTL regions in the japonica subset, and 7 distinct QTL regions in the indica subset. Among these QTL regions, three regions were common between the whole panel and japonica , three regions were common between the whole panel and indica , and one region was common between indica and japonica. A subset of QTL regions was potentially colocalized with previously identified genes and QTLs, including 10 from the japonica subset, 4 from the indica subset, and 6 from the whole panel. On the other hand, a total of 21 potentially novel QTL regions from the whole panel, 10 from the japonica subset, and 1 from the indica subset were identified. The results of our study provide useful information on the genetic architecture underlying cold tolerance during germination in rice, which in turn can be used for further molecular study and crop improvement for low-temperature stressed environments. [ABSTRACT FROM AUTHOR]

With 3 figures and 5 tables Abstract To identify quantitative trait loci (QTL) controlling heat tolerance in rice, the progeny of BC1F1 and F2 populations derived from an IR64 × N22 cross were exposed to 38/24°C for 14 days at the flowering stage, and spikelet fertility was assessed. A custom 384-plex Illumina GoldenGate genotyping assay was used to genotype the F2 and selected BC1F1 plants. Four single nucleotide polymorphisms were associated with heat tolerance in the BC1F1 population using selective genotyping and single marker analysis, and four putative QTL were found to be associated with heat tolerance in the F2 population. Two major QTL were located on chromosome 1 (qHTSF1.1) and chromosome 4 (qHTSF4.1). These two major QTL could explain 12.6% (qHTSF1.1) and 17.6% (qHTSF4.1) of the variation in spikelet fertility under high temperature. Tolerant allele of qHTSF1.1 was from the susceptible parent IR64, and that of qHTSF4.1 was from tolerant parent N22. The effect of qHTSF4.1 on chromosome 4 was confirmed in selected BC2F2 progeny from the same IR64 × N22 cross, and the plants with qHTSF4.1 showed significantly higher spikelet fertility than other genotypes. [ABSTRACT FROM AUTHOR]

With 2 figures and 5 tables Abstract A population of BC3F4 rice lines derived from a cross of salt-tolerant Pokkali and sensitive IR29 was developed for validation of the Saltol QTL and comparison of this QTL effect with background QTLs. Specific BC3F4 progenies from the advanced backcross population were found to have similar salinity tolerance at the seedling stage even without the Saltol alleles. Therefore, additional QTLs responsible for seedling-stage salinity tolerance were investigated by screening and genotyping with markers at multiple loci throughout the 12 rice chromosomes. Single marker regression (SMR) using Q-Gene detected seven QTLs above the threshold logarithm of the odds of 3.0. Single marker analysis using IciMapping detected the same markers linked to the seven QTLs identified by SMR. Likelihood ratio test-based on stepwise regression (LRT-RSTEP) analysis using IciMapping, more suitable for BC3F4 introgression lines located six QTLs, of which two were common with SMR and included two significant segments within Saltol. The new non- Saltol QTLs represent targets for further study to evaluate their usefulness in breeding for higher levels of seedling-stage salinity tolerance in rice. [ABSTRACT FROM AUTHOR]

A radio-controlled unmanned helicopter-based low-altitude remote sensing (LARS) platform was used to acquire quality images of high spatial and temporal resolution in order to estimate yield and total biomass of a rice crop (Oriza sativa L.). Fifteen rice field plots with five N treatments (0, 33, 66, 99, and 132 kg ha-1) having three replicates each were arranged in a randomized complete block design for estimating yield and biomass as a function of applied N. Images were obtained by image acquisition sensors mounted on the LARS platform operating at the height of 20 m over experimental plots. The rice yield and total biomass for the five N treatments were found to be significantly different at the 0.05 and 0.1 levels of significance, respectively, and normalized difference vegetation index (NDVI) values at panicle initiation stage were highly correlated with yield and total biomass with regression coefficients (r²) of 0.728 (RMSE = 0.458 ton ha-1) and 0.760 (RMSE = 0.598 ton ha-1), respectively. The study demonstrated the suitability of using LARS images as a substitute for satellite images for estimating leaf chlorophyll content in terms of NDVI values (r² = 0.897, RMSE = 0.012). The LARS system described has potential to evaluate areas that require additional nutrients at critical growth stages to improve final yield in rice cropping. [ABSTRACT FROM AUTHOR]

A quantitative trait locus (QTL), dth1.1, was associated with transgressive variation for days to heading in an advanced backcross population derived from the Oryza sativa variety Jefferson and an accession of the wild rice relative Oryza rufipogon. A series of near-isogenic lines (NILs) containing different O. rufipogon introgressions across the target region were constructed to dissect dth1.1 using substitution mapping. In contrast to the late-flowering O. rufipogon parent, O. rufipogon alleles in the substitution lines caused early flowering under both short- and long-day lengths and provided evidence for at least two distinct sub-QTL: dth1.1a and dth1.1b. Potential candidate genes underlying these sub-QTL include genes with sequence similarity to Arabidopsis GI, FT SOC1, and EMF1, and Pharbitis nil PNZIP. Evidence from families with nontarget O. rufipogon introgressions in combination with dth1.1 alleles also detected an early flowering QTL on chromosome 4 and a late-flowering QTL on chromosome 6 and provided evidence for additional sub-QTL in the dth1.1 region. The availability of a series of near-isogenic lines with alleles introgressed from a wild relative of rice provides an opportunity to better understand the molecular basis of transgressive variation in a quantitative trait. [ABSTRACT FROM AUTHOR]

Rc is a domestication-related gene required for red pericarp in rice (Oryza sativa). The red grain color is ubiquitous among the wild ancestors of O. sativa, in which it is closely associated with seed shattering and dormancy. Rc encodes a basic helix-loop-helix (bHLH) protein that was fine-mapped to an 18.5-kb region on rice chromosome 7 using a cross between Oryza rufipogon (red pericarp) and O. sativa cv Jefferson (white pericarp). Sequencing of the alleles from both mapping parents as well as from two independent genetic stocks of Rc revealed that the dominant red allele differed from the recessive white allele by a 14-bp deletion within exon 6 that knocked out the bHLH domain of the protein. A premature stop codon was identified in the second mutant stock that had a light red pericarp. RT-PCR experiments confirmed that the Rc gene was expressed in both red- and white-grained rice but that a shortened transcript was present in white varieties. Phylogenetic analysis, supported by comparative mapping in rice and maize (Zea mays), showed that Rc, a positive regulator of proanthocyanidin, is orthologous with INTENSIFIER1, a negative regulator of anthocyanin production in maize, and is not in the same clade as rice bHLH anthocyanin regulators. [ABSTRACT FROM AUTHOR]

In order to encourage the involvement of the private sector in importing rice, the Iranian government plans to relax the system of multiple foreign exchange rates applied to importers wishing to supply the domestic market. In this article, the welfare effects of removing the current controls on the rice trade, and a domestic rice coupon program, are evaluated by applying a partial equilibrium analysis to 1961–1999 data. The results show that, as far as foreign exchange is concerned, liberalization of the rice market causes an increase in rice imports, mainly due to a decrease in domestic supply. In welfare terms, the loss in producer surplus from rice market liberalization is relatively high, but most rice consumers, and the Iranian taxpayer, would gain. Overall, gains to consumers and taxpayers are estimated to be higher than the losses incurred by domestic suppliers, and therefore net social welfare at national level can be improved by rice market liberalization in Iran. Issues for further discussion include residual food security roles for the state, and supply-side adjustments in terms of resource use and higher-quality production. [ABSTRACT FROM AUTHOR]

Bottlenecks in plant transformation and regeneration have slowed progress in applying CRISPR/Cas-based genome editing for crop improvement. Rice (Oryza sativa L.) has highly efficient temperate japonica transformation protocols, along with reasonably efficient indica protocols using immature embryos. However, rapid and efficient protocols are not available for transformation and regeneration in tropical japonica varieties, even though they represent the majority of rice production in the U.S. and South America. The current study has optimized a protocol using callus induction from mature seeds with both Agrobacterium-mediated and biolistic transformation of the high-yielding U.S. tropical japonica cultivar Presidio. Gene editing efficiency was tested by evaluating knockout mutations in the phytoene desaturase (PDS) and young seedling albino (YSA) genes, which provide a visible phenotype at the seedling stage for successful knockouts. Using the optimized protocol, transformation of 648 explants with particle bombardment and 532 explants with Agrobacterium led to a 33% regeneration efficiency. The YSA targets had ambiguous phenotypes, but 60% of regenerated plants for PDS showed an albino phenotype. Sanger sequencing of edited progeny showed a number of insertions, deletions, and substitutions at the gRNA target sites. These results pave the way for more efficient gene editing of tropical japonica rice varieties. [ABSTRACT FROM AUTHOR]

Responses of two genotypes of wheat (Triticum aestivum cvs. Gamenya and Kite) and one genotype of triticale (Triticosecale cv. Muir) were evaluated in stagnant solution culture and in waterlogged soil, using 23- to 36-d-old plants. Stagnant nutrient solutions decreased shoot fresh with of Gemenya by 21% compared with aerated plants, while shoot fresh weight of Muir was unaffected. Reductions in nodal root fresh weight under stagnant conditions were also less for Muir than Gamenya. Aerenchyma in nodal roots of stagnantly grown plants accounted for 6.7 and 12.7% of the root cross sectional area for Gamenya and Muir, respectively, Oxygen supplied via this aerenchyma was substantially greater for Muir than Gamenya, and greatest for nodal roots of Kite. Elongation rates of stagnantly grown nodal roots in an O2- free medium reflected the amount of O2 supplied via the aerenchyma, and were 0.11, 0.17 and 0.27 mm h&sup-1; for Gamenya, Muir and Kite, respectively. Waterlogging in soil decreased the redox potential from +600 to -200 mV after 35d. Waterlogging decreased shoot fresh wight of Gamenya, Kite and Muir by 63-82% compared with drained plants, with similar reductions in growth of seminal roots. Nodal root growth was little affected by waterlogging in soil, although Muir had a 1.6-2.4-fold greater nodal root mass than Gamenya and Kite. Furthermore, after two cycles of 7 d waterlogging and 7 d drainage the seminal roots of Muir were at least double the length of Gamenya and Kite. Under the same waterlogged conditions, the shoot growth of rice (Oryza sativa cv. Calrose) was much greater than for wheat and triticale, and this reflected differences in morphology and anatomy of the root systems. Nodal root/shoot ratios indicated the major factor limiting shoot growth of wheat was the small mass of nodal roots per plant. However, aposible additional factor is the poor function of nodal root of wheat and triticale in waterlogged soil. [ABSTRACT FROM AUTHOR]

Digital farming is a modern agricultural concept that aims to maximize the crop yield while simultaneously minimizing the environmental impact of farming. Successful implementation of digital farming requires development of sensors to detect and identify diseases and abiotic stresses in plants, as well as to probe the nutrient content of seeds and identify plant varieties. Experimental evidence of the suitability of Raman spectroscopy (RS) for confirmatory diagnostics of plant diseases was previously provided by our team and other research groups. In this study, we investigate the potential use of RS as a label-free, non-invasive and non-destructive analytical technique for the fast and accurate identification of nutrient components in the grains from 15 different rice genotypes. We demonstrate that spectroscopic analysis of intact rice seeds provides the accurate rice variety identification in ~86% of samples. These results suggest that RS can be used for fully automated, fast and accurate identification of seeds nutrient components. [ABSTRACT FROM AUTHOR]

Background: Salinity is one of the most widespread abiotic stresses affecting rice productivity worldwide. The purpose of this study was to establish the relative importance of different traits associated with salinity tolerance in rice and to identify new quantitative trait loci (QTL) conferring tolerance to salinity at seedling stage. A total of 231 F2:3 plants derived from a cross between a sensitive variety BRRI dhan29 (BR29 hereafter) and Capsule, a salt tolerant Bangladeshi indica landrace, were evaluated under salt stress in a phytotron. Results: Out of the 231 F2 plants, 47 highly tolerant and 47 most sensitive lines were selected, representing the two extreme tails of the phenotypic distribution. These 94 plants were genotyped for 105 simple sequence repeat (SSR) and insertion/deletion (InDel) markers. A genetic linkage map spanning approximately 1442.9 cM of the 12 linkage groups with an average marker distance of 13.7 cM was constructed. QTL were identified on the long arm of chromosome 1 for Na+ concentration, K+ concentration, Na+-K+ ratio and survival; chromosome 3 for Na+ concentration, survival and overall phenotypic evaluation using the Standard Evaluation system (SES); and chromosome 5 for SES. A total of 6 pairwise epistatic interactions were also detected between QTL-linked and QTL-unlinked regions. Graphical genotyping indicated an association between the phenotypes of the extreme families and their QTL genotypes. Path coefficient analysis revealed that Na+ concentration, survival, Na+-K+ ratio and the overall phenotypic performance (SES score) are the major traits associated with salinity tolerance of Capsule. Conclusions: Capsule provides an alternative source of salinity tolerance aside from Pokkali and Nona Bokra, the two Indian salt tolerant landraces traditionally used for breeding salt tolerant rice varieties. Pyramiding the new QTL identified in this study with previously discovered loci, such as Saltol, will facilitate breeding varieties that are highly tolerant of salt stress. [ABSTRACT FROM AUTHOR]

High-throughput genotyping using single-nucleotide polymorphisms (SNP) is one tool that can be used to study the genetic relationships between wild rice relatives and cultivated rice. In this study, a set of 96 indica–japonica SNP markers, which can differentiate indica and japonica subspecies of rice, were used to characterize 227 Oryza accessions including 93 AA genome accessions from seven wild Oryza species. A total of 72 markers of the 96 markers were selected for the phylogenetic study and allele polymorphism survey. A subset of SNP markers were present only in Oryza sativa and evolutionarily close species, Oryza nivara and Oryza rufipogon. These markers can be used for distinguishing cultivated rice from the other species and vice versa. Eight clusters were generated through phylogenetic analysis, and Oryza meridionalis and Oryza longistaminata appeared to be the most distantly related species to cultivated rice. In this study, Oryza barthii and Oryza glaberrima accessions were found to exhibit high genetic similarity. Across the wild species, more indica-type alleles were detected for most accessions. In this study, a set of markers selected to be informative across O. sativa accessions were used, but it will be interesting to compare the results of this study with SNP data obtained through next-generation sequencing in the future. [ABSTRACT FROM AUTHOR]

Heterotic groups are necessary for high vigor in hybrid rice. However, hybrids produced from crosses between parents from different rice subspecies (i.e., Indica x Japonica) have extensive incompatibility issues exhibited by low seed sets. The study objectives were to evaluate the heterosis in grain yield and yield-related traits between hybrids produced from low and high parental genetic distances (PGDs) and demonstrate the heterotic group approach in rice. From PGDs, eight and three hybrids were assigned to the low and high PGD hybrid groups, respectively. Neighbor-joining clustering and model-based population structure analyses classified the hybrid parents into four heterotic groups, with the low and high PGD hybrid groups found consisting of intra-subpopulation and intersubpopulation crosses, respectively. Replicated yield trials conducted at Beaumont, Texas, transpired in 2019 and 2020. The hybrids exhibited normal seed sets, with at least one of each hybrid's parents determined to possess the wide compatibility S5n allele necessary for normal seed sets in wide crosses. Trait and standard heterosis values estimates included the number of days to heading, plant height, tiller density, and grain yield. Higher trait values and heterosis for tiller density and grain yield occurred in the high than the low PGD hybrid group, especially in the inter-subpopulation crosses with indica rice. PGD had consistent positive correlations with heterosis for grain yield (r = 0.41 to 0.60) and tiller density (0.28 to 0.36) in both years. PGDs aid in determining highly heterotic cross combinations for tiller density and grain yield and in forming heterotic groups. Heterotic grouping is advisable through cluster and structure analyses of genome-wide markers instead of identifying genetically-distant crosses based on pedigree information. [ABSTRACT FROM AUTHOR]