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Arsenic (As) is naturally present in all soils and can accumulate to toxic levels in rice (Oryza sativa L.) grains under some production conditions. It can also reduce grain yields, posing a double threat to global food security. Plant genetics can affect the amount of As accumulated in grains. A growing body of evidence suggests that one mechanism plants use to detoxify As and limit As concentrations in grains (grain‐As) is to sequester As in vegetative tissues. We evaluated 17 rice cultivars previously shown to have contrastingly high or low grain‐As. Cultivars high in grain‐As commonly transferred As out of their flag leaves during grain fill, while all eight cultivars having low grain‐As retained As in flag leaves, effectively excluding it from transfer to developing grains. Sequestration of As in cell vacuoles involves several sulfur (S)‐containing compounds. We hypothesized that enhanced leaf concentration of S via foliar fertilization could further reduce grain‐As. Effect of foliar‐S on grain‐As was studied in field‐scale and plot experiments. The plot study included cultivars known to contrastingly retain As in flag leaves during grain fill grown in both As‐enriched and Native (non‐enriched) soils, and included severity ratings for rice straighthead, an As‐induced disorder. Contrary to the hypothesis, while foliar‐S did increase grain‐S concentrations, it did not prove useful for reducing grain‐As, nor did it reduce straighthead severity, possibly because soil was not deficient in S or plants used a biochemical mechanism other than S‐related As chelation and sequestration to retain As in leaves. Core Ideas: Some rice cultivars accumulate less arsenic in their grains than other rice cultivars.Cultivars with lower grain arsenic continue accumulating arsenic in flag leaves during grain fill.Cultivars with higher grain arsenic remobilize arsenic out of flag leaves during grain fill.Results suggest grain arsenic is reduced by increasing leaf sequestration, involving sulfur‐containing compounds.Foliar‐applied sulfur fertilizer did not reduce grain arsenic concentrations under study conditions. [ABSTRACT FROM AUTHOR]

Tillering and plant biomass are key determinants of rice crop productivity. Tillering at the vegetative stage is associated with weed competition, nutrient uptake, and methane emissions. However, little information is available on quantitative trait loci (QTLs) associated with tiller number (qTN), root biomass (qRB), and shoot biomass (qSB) at the active tillering stage which occurs approximately 6 weeks after planting. Here, we mapped tiller and biomass QTLs with ~ 250 recombinant inbred lines derived from a 'Francis' by 'Rondo' cross using data collected at the maximum tillering stage from two years of greenhouse study, and further compared these QTLs with those mapped at the harvest stage from a field study. Across these three studies, we discovered six qTNs, two qRBs, and three qSBs. Multiple linear regression further indicated that qTN1-2, qTN3-3, qTN4-1, qRB3-1, and qRB5-1 were significant at the maximum tillering stage while qTN3-2 was detected only at the harvest stage. Moreover, qTN3-1 was consistently significant across different developmental stages and growing environments. The genes identified from the peak target qTN regions included a carotenoid metabolism enzyme, a MYB transcription factor, a CBS domain-containing protein, a SAC3/GANP family protein, a TIFY motif containing protein, and an ABC transporter protein. Two genes in the qRB peak target regions included an expressed protein and a WRKY gene. This knowledge of the QTLs, associated markers, candidate genes, and germplasm resources with high TN, RB and SB is of value to rice cultivar improvement programs. [ABSTRACT FROM AUTHOR]

There is global concern that rice grains and foods can contain harmful amounts of arsenic (As), motivating breeders to produce cultivars that restrict As accumulation in grains to protect human health. Arsenic is also toxic to plants, with straighthead disorder (StHD), causing panicle sterility, being observed in rice. The genetic variation in StHD resistance suggests that plants have evolved mechanisms that reduce As toxicity, possibly via regulation of As uptake, transport, or detoxification/sequestration. Because these mechanisms could also underlie the wide (3- to 100-fold) differences in grain As concentration (grain-As) observed among diverse rice genotypes, it was hypothesized that some genes reduce both grain-As content and StHD susceptibility and may be detectable as co-located StDH and As quantitative trait loci (QTL). We used a machine-learning Bayesian network approach plus high-resolution genome-wide association study (GWAS) to identify QTL for grain-As and StHD resistance within the USDA Rice Minicore Collection (RMC). Arsenic enters roots through phosphorus (P) and silica (Si) transporters, As detoxification involves sulfur (S), and cell signaling to activate stress tolerance mechanisms is impacted by Si, calcium (Ca), and copper (Cu). Therefore, concentrations of Si, P, S, Ca, and Cu were included in this study to elucidate physiological mechanisms underlying grain-As and StHD QTL. Multiple QTL (from 9 to 33) were identified for each of the investigated As-associated traits. Although the QTL for StHD, Si, and grain-As did not overlap as heavily as our hypothesis predicted (4/33 StHD and 4/15 As QTL co-located), they do provide useful guidance to future research. Furthermore, these are the first StHD and Si QTL to be identified using high-density mapping, resulting in their being mapped to shorter, more precise genomic regions than previously reported QTL. The candidate genes identified provide guidance for future research, such as gene editing or mutation studies to further investigate the role of antioxidants and ROS scavenging to StHD resistance, as indicated by candidate genes around the commonly reported qStHD8-2 QTL. Other genes indicated for future study for improving grain-As and StHD include several multidrug and toxic compound extrusion (MATE) genes, F-box genes, and NIPs not documented to date to transport As. [ABSTRACT FROM AUTHOR]

Root system architecture (RSA) is a crucial factor in resource acquisition and plant productivity. Roots are difficult to phenotype in the field, thus new tools for predicting phenotype from genotype are particularly valuable for plant breeders aiming to improve RSA. This study identifies quantitative trait loci (QTLs) for RSA and agronomic traits in a rice (Oryza sativa) recombinant inbred line (RIL) population derived from parents with contrasting RSA traits (PI312777 X Katy). The lines were phenotyped for agronomic traits in the field, and separately grown as seedlings on agar plates which were imaged to extract RSA trait measurements. QTLs were discovered from conventional linkage analysis and from a machine learning approach using a Bayesian network (BN) consisting of genome-wide SNP data and phenotypic data. The genomic prediction abilities (GPAs) of multi-QTL models and the BN analysis were compared with the several standard genomic prediction (GP) methods. We found GPAs were improved using multitrait (BN) compared to single trait GP in traits with low to moderate heritability. Two groups of individuals were selected based on GPs and a modified rank sum index (GSRI) indicating their divergence across multiple RSA traits. Selections made on GPs did result in differences between the group means for numerous RSA. The ranking accuracy across RSA traits among the individual selected RILs ranged from 0.14 for root volume to 0.59 for lateral root tips. We conclude that the multitrait GP model using BN can in some cases improve the GPA of RSA and agronomic traits, and the GSRI approach is useful to simultaneously select for a desired set of RSA traits in a segregating population. [ABSTRACT FROM AUTHOR]

Rice provides more than one fifth of daily calories for half of the world's human population, and is a major dietary source of both essential mineral nutrients and toxic elements. Rice grains are generally poor in some essential nutrients but may contain unsafe levels of some toxic elements under certain conditions. Identification of quantitative trait loci (QTLs) controlling the concentrations of mineral nutrients and toxic trace metals (the ionome) in rice will facilitate development of nutritionally improved rice varieties. However, QTL analyses have traditionally considered each element separately without considering their interrelatedness. In this study, we performed principal component analysis (PCA) and multivariate QTL analyses to identify the genetic loci controlling the covariance among mineral elements in the rice ionome. We resequenced the whole genomes of a rice recombinant inbred line (RIL) population, and performed univariate and multivariate QTL analyses for the concentrations of 16 elements in grains, shoots and roots of the RIL population grown in different conditions. We identified a total of 167 unique elemental QTLs based on analyses of individual elemental concentrations as separate traits, 53 QTLs controlling covariance among elemental concentrations within a single environment/tissue (PC-QTLs), and 152 QTLs which determined covariation among elements across environments/tissues (aPC-QTLs). The candidate genes underlying the QTL clusters with elemental QTLs, PC-QTLs and aPC-QTLs co-localized were identified, including OsHMA4 and OsNRAMP5. The identification of both elemental QTLs and PC QTLs will facilitate the cloning of underlying causal genes and the dissection of the complex regulation of the ionome in rice. [ABSTRACT FROM AUTHOR]

Summary: Molybdenum (Mo) is an essential micronutrient for most living organisms, including humans. Cereals such as rice (Oryza sativa) are the major dietary source of Mo. However, little is known about the genetic basis of the variation in Mo content in rice grain.We mapped a quantitative trait locus (QTL) qGMo8 that controls Mo accumulation in rice grain by using a recombinant inbred line population and a backcross introgression line population.We identified a molybdate transporter, OsMOT1;1, as the causal gene for this QTL. OsMOT1;1 exhibits transport activity for molybdate, but not sulfate, when heterogeneously expressed in yeast cells. OsMOT1;1 is mainly expressed in roots and is involved in the uptake and translocation of molybdate under molybdate‐limited condition. Knockdown of OsMOT1;1 results in less Mo being translocated to shoots, lower Mo concentration in grains and higher sensitivity to Mo deficiency. We reveal that the natural variation of Mo concentration in rice grains is attributed to the variable expression of OsMOT1;1 due to sequence variation in its promoter.Identification of natural allelic variation in OsMOT1;1 may facilitate the development of rice varieties with Mo‐enriched grain for dietary needs and improve Mo nutrition of rice on Mo‐deficient soils. [ABSTRACT FROM AUTHOR]

Arsenic (As) occurs naturally in the environment, and is present in all edible and nonedible plant tissues. Plants have multiple mechanisms to prevent plant injury by heavy metals such as As. These same mechanisms could be used to reduce accumulation of As in rice (Oryza sativa L.) grains. From previous study of 1765 international rice accessions, specific accessions were identified as having exceptionally high grain As concentrations (grain As accumulators) and others low grain As (grain As excluders). This study investigated As uptake, transport, and metabolism in six previously identified lines to determine which physiological responses, if any, were associated with accumulation or exclusion of As in grains. Hydroponically grown seedlings were treated with 0 (controls) or 100 μM arsenite [As(III)], and then whole seedlings were analyzed for concentrations of As plus key compounds involved in heavy metal metabolism. Both grain accumulators and grain excluders actively concentrated As within their roots, and both groups had 10-fold higher As concentrations in roots than leaves. In response to As(III), roots of both grain excluders and grain accumulators increased in cysteine and phytochelatin (PC) production, which suggests PC sequestration of As. In contrast, only grain excluders doubled in leaf glutathione (GSH) concentration by 72 h after As(III) addition. Because PC concentrations remained constant in leaves, it appears that the additional leaf GSH in the grain excluders was not used to produce more PC but may instead be forming As-GSH adducts, which also aid in As sequestration. [ABSTRACT FROM AUTHOR]

An increase in early tiller production is desired in rice (Oryza sativa L.) to increase yield potential and enhance ability to shade and suppress weeds. Unfortunately, tiller production and survival are sensitive to many environmental cues, making tillering pattern a difficult trait to reliably evaluate in field plots. The present objective was to use pot-grown plants where seeding depth and the environment could be controlled to identify quantitative trait loci (QTLs) associated with rate of seedling development (seedling leaf number, SLN) and tiller production (tiller number, TN) as well as the node from which the first tiller originated (N1T).The QTLs were identified in two related mapping populations, the first being a set of 280 'Lemont' × 'TeQing' recombinant inbred lines (RILs) observed over four trials, in which nine QTLs associated with TN, three for SLN, and two for N1T were detected. Eight of the TN QTLs were verified in a second population consisting of 123 TeQing-into-Lemont backcross introgression lines (TILs). Each SLN and N1T QTL was colocated with a TN QTL, and all nine detected TN QTLs were located in genomic regions previously reported to contain TN major genes or QTLs, demonstrating their robustness under diverse genetic backgrounds and growth conditions. Early tillering was associated with rapid seedling development as detected by an increased number of leaves and nodes on 8-wk-old seedlings. The present data indicated that breeders could effectively select for enhanced early tiller production among segregating genotypes based on tiller counts conducted at a single time point approximately 8 to 9 wk after germination under greenhouse conditions. Marker-trait linkages reported here can support marker-assisted selection of these nine TN QTLs. [ABSTRACT FROM AUTHOR]

The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA) mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of ∼300 accessions and 36.9 k single nucleotide polymorphisms (SNPs). The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel). This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel. [ABSTRACT FROM AUTHOR]

Summary [ABSTRACT FROM AUTHOR]

Most commercial cultivars of rice (Oryza sativa L.) are susceptible to sheath blight (SB), a devastating fungal disease causing significant losses in grain yield and quality. There are limited sources of genetic resistance adapted to U.S. growing conditions, and no commercial long grain cultivar of rice is currently available in the United States with a high level of SB resistance. Sheath blight resistance has been reported to be horizontal and quantitative. A population of 279 F2.3 progeny rows derived from a cross between two tropical japonica U.S. rice cultivars, Rosemont (semi-dwarf, SB susceptible) and Pecos (tall, SB resistant), was used to map SB resistance. Progeny families were evaluated for disease reactions, plant height (PH), and heading date (HD) in replicated field trials for 2 yr and genotyped with 149 simple sequence repeat markers. Correlation analysis between SB ratings with PH and HD showed that both agronomic traits were significantly correlated with SB resistance. Four significant (logarithm of odds ratio ≥ 3.6) quantitative trait loci (QTL5) were identified for SB resistance, with individual effects explaining 5.6 to 33.4% of the total phenotypic variation. Plant height appears to have a direct influence on SB resistance, with QTLs for these traits colocated on chromosome 1. Consistent results across years indicate the stability of the identified QTLs and their potential for improving rice SB resistance using marker-assisted selection. [ABSTRACT FROM AUTHOR]

Abstract: Associations between RVA pasting properties and three single nucleotide polymorphism (SNP) sites in the Waxy gene intron 1, exon 6, and exon 10 were determined using rice genotypes of diverse geographic origin. A total of four SNP-haplotypes (combination of SNP alleles) were identified that explained high proportions of the variation in RVA pasting properties (R 2 =0.574–0.704). A haplotype containing DNA sequence variation in exon 10 (exon 10 cytosine nucleotide) was exclusively found in high-apparent amylose content (AAC) genotypes with a higher RVA viscosity profile compared to the high AAC genotypes with a different haplotype. The exon 10 SNP explained variances in coolpaste and setback (coolpaste–hotpaste) to 0.642 and 0.499, respectively. Across three haplotypes, which contained exon 10 adenine nucleotide, AAC was correlated with peak, hotpaste, breakdown and setback (coolpaste–hotpaste) at r =−0.85, −0.75, −0.79, and 0.49, respectively. Therefore, the exon 10 SNP differentiates high AAC types with a strong RVA profile and thus can be used by molecular breeding programs focused on quality improvement. Additionally, characterizing genotypes by their functional SNPs allowed us to better understand the relationship between the Waxy gene, its chemical product (i.e., AAC) and the functionality created by the product (i.e., pasting properties). [Copyright &y& Elsevier]