cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17704690.v1
title: An extended phenotype of <i>RP1L1</i> maculopathy – case report

description: To report the ophthalmological findings of a new phenotypical variant of <i>RP1L1</i> maculopathy in an Indian patient with a homozygous variant in the <i>RP1L1</i> gene A 39-year-old male presented with complaints of disturbance in the central field of vision in both eyes (BE) for a duration of 6 months. He underwent ophthalmic examinations and diagnostic imaging. A complete retinal degeneration panel consisting of 228 genes was evaluated for pathologic variations using next-generation sequencing (NGS), which showed a variant in the <i>RP1L1</i> gene. On fundus examination, he was found to have ill-defined foveal mottling in BE. Spectral domain optical coherence tomography (SD-OCT) showed sub-foveal hyper-reflective deposits and outer retinal layer disruption. A provisional diagnosis of the atypical variant of adult-onset foveomacular vitelliform dystrophy (AOFVD) was made on the basis of clinical, OCT, Fundus autofluorescence (FAF) and electrophysiological features. Genetic assessment of the proband revealed the presence of a homozygous base pair deletion in exon 4 of <i>RP1L1</i> gene (chr8:g.10468194_10468195del), which results in frameshift and premature truncation of the protein 24 amino acids downstream to codon 1138 (p.Lys1138SerfsTer24). This variant was confirmed in the proband’s parents by Sanger sequencing. The diagnosis was revised to <i>RP1L1</i> maculopathy, as the <i>RP1L1</i> gene variant is most commonly associated with this entity. This report presents the multimodal imaging of a previously unreported phenotype of <i>RP1L1</i> maculopathy associated with a genetic variant of <i>RP1L1</i> gene, thereby expanding the spectrum associated with <i>RP1L1</i> maculopathy.
DOI: 10.6084/m9.figshare.18393669
title: Clinical course of a Japanese girl with Leber congenital amaurosis associated with a novel nonsense pathogenic variant in <i>NMNAT1</i>: a case report and mini review

description: Leber congenital amaurosis (LCA), although rare, is one of the most severe forms of early-onset inherited retinal dystrophy (IRD). Here, we review the molecular genetics and phenotypic characteristics of patients with <i>NMNAT1-</i>associated IRD. The longitudinal clinical and molecular findings of a Japanese girl diagnosed with LCA associated with pathogenic variants in <i>NMNAT1</i> c.648delG, (p.Trp216Ter*) and c.709C&gt;T (p.Arg237Cys) have been described to highlight the salient clinical features of <i>NMNAT1</i>-associated IRD.
DOI: 10.6084/m9.figshare.18393669.v2
title: Clinical course of a Japanese girl with Leber congenital amaurosis associated with a novel nonsense pathogenic variant in <i>NMNAT1</i>: a case report and mini review

description: Leber congenital amaurosis (LCA), although rare, is one of the most severe forms of early-onset inherited retinal dystrophy (IRD). Here, we review the molecular genetics and phenotypic characteristics of patients with <i>NMNAT1-</i>associated IRD. The longitudinal clinical and molecular findings of a Japanese girl diagnosed with LCA associated with pathogenic variants in <i>NMNAT1</i> c.648delG, (p.Trp216Ter*) and c.709C&gt;T (p.Arg237Cys) have been described to highlight the salient clinical features of <i>NMNAT1</i>-associated IRD.
DOI: 10.6084/m9.figshare.20003699
title: Sample 11719 - Read1 - Metagenomic Reads Pescadero

description: Sample 11719 - Read1 - Metagenomic Reads Pescadero
DOI: 10.6084/m9.figshare.20003699.v1
title: Sample 11719 - Read1 - Metagenomic Reads Pescadero

description: Sample 11719 - Read1 - Metagenomic Reads Pescadero
DOI: 10.6084/m9.figshare.9871625
title: A leaf bud technique for rapid propagation of cassava (Manihot esculenta Crantz)

description: ABSTRACT The slow rate of multiplication is one of the main constraints on the production of cassava (Manihot esculenta Crantz). This work aimed to evaluate the use of leaf buds for rapid propagation of cassava varieties. Leaf buds were excised from three cassava varieties (BRS Kiriris, 98150-06 and 9624-09) for plantlet generation. The experiment was completely randomized with a 5 (age of mother plant) × 3 (position of the leaf buds on the stems) × 2 (agrochemical treatments) factorial design. Data were collected on leaf sprouting percentage (Spro.Per), plantlet height (Plant.Hei) and total dry mass of plantlets (Dry.Mass.Plant). There was a difference between the three traits for most of the varieties, demonstrating significant effects on the agronomic attributes evaluated. Better agronomic performance (higher sprouting percentage, plantlet height and total dry mass) in plantlets was observed in leaf buds of: i) maturing plants up to six months old; ii) more herbaceous (upper) parts; and iii) plants treated with agrochemicals (fungicides and insecticides). Considering four-month-old plants, three annual cycles, and an 81 % average sprouting, it would be possible to reach an annual multiplication rate of 1:72, which is much higher than that achieved by traditional methods using mature stem cuttings from 12-month-old plants (around 1:5). These results are important because they demonstrate the possibility of using cassava leaf buds to produce high-quality plantlets rapidly for greater multiplication and diffusion of new varieties and cultivation on a larger scale.
DOI: 10.6084/m9.figshare.9871625.v1
title: A leaf bud technique for rapid propagation of cassava (Manihot esculenta Crantz)

description: ABSTRACT The slow rate of multiplication is one of the main constraints on the production of cassava (Manihot esculenta Crantz). This work aimed to evaluate the use of leaf buds for rapid propagation of cassava varieties. Leaf buds were excised from three cassava varieties (BRS Kiriris, 98150-06 and 9624-09) for plantlet generation. The experiment was completely randomized with a 5 (age of mother plant) × 3 (position of the leaf buds on the stems) × 2 (agrochemical treatments) factorial design. Data were collected on leaf sprouting percentage (Spro.Per), plantlet height (Plant.Hei) and total dry mass of plantlets (Dry.Mass.Plant). There was a difference between the three traits for most of the varieties, demonstrating significant effects on the agronomic attributes evaluated. Better agronomic performance (higher sprouting percentage, plantlet height and total dry mass) in plantlets was observed in leaf buds of: i) maturing plants up to six months old; ii) more herbaceous (upper) parts; and iii) plants treated with agrochemicals (fungicides and insecticides). Considering four-month-old plants, three annual cycles, and an 81 % average sprouting, it would be possible to reach an annual multiplication rate of 1:72, which is much higher than that achieved by traditional methods using mature stem cuttings from 12-month-old plants (around 1:5). These results are important because they demonstrate the possibility of using cassava leaf buds to produce high-quality plantlets rapidly for greater multiplication and diffusion of new varieties and cultivation on a larger scale.
DOI: 10.6084/m9.figshare.9871709
title: Yield, quality and drought sensitivity of tomato to water deficit during different growth stages

description: ABSTRACT In areas where the supply of water for irrigation is limited, tomato production is often subject to drought stress. In order to investigate the drought sensitivity of tomato (Lycopersicon esculentum Mill.) yield and quality during different growth stages, field and pot experiments were conducted in a high tunnel in southern China during the 2013 and 2016 growing seasons. The experiments consisted of four treatments. Crops were drip-irrigated to 100 % of field capacity at all growth stages divided into treatment T1 (control) and the treatment group T2, T3 and T4 receiving half the amount of irrigation as T1 when the soil water content reached 70 % of field capacity, the vegetative phase (stage I) T2, the flowering and fruit development phase (stage II) T3, and the fruit ripening phase (stage III) T4. Compared to the control treatment, drought stress at stages II and III caused a decrease in yield of 13 % and 26 %, respectively. Fruit firmness and color index were positively affected by drought stress, while fruit water content and shape index did not show any differences between treatments. Taste and nutritional quality parameters, such as total soluble solids, soluble sugar, organic acids and vitamin C improved in response to limited water supply (p ≤ 0.05). Despite having a negative effect on fruit yield, drought stress applied at stage III tended to enhance fruit quality traits. This study found that applying drought stress at stage I can be a positive management approach as it saves water and has fewer negative effects compared to applying drought stress at the other critical growth stages, thereby minimizing the adverse effects of drought stress.
DOI: 10.6084/m9.figshare.9871709.v1
title: Yield, quality and drought sensitivity of tomato to water deficit during different growth stages

description: ABSTRACT In areas where the supply of water for irrigation is limited, tomato production is often subject to drought stress. In order to investigate the drought sensitivity of tomato (Lycopersicon esculentum Mill.) yield and quality during different growth stages, field and pot experiments were conducted in a high tunnel in southern China during the 2013 and 2016 growing seasons. The experiments consisted of four treatments. Crops were drip-irrigated to 100 % of field capacity at all growth stages divided into treatment T1 (control) and the treatment group T2, T3 and T4 receiving half the amount of irrigation as T1 when the soil water content reached 70 % of field capacity, the vegetative phase (stage I) T2, the flowering and fruit development phase (stage II) T3, and the fruit ripening phase (stage III) T4. Compared to the control treatment, drought stress at stages II and III caused a decrease in yield of 13 % and 26 %, respectively. Fruit firmness and color index were positively affected by drought stress, while fruit water content and shape index did not show any differences between treatments. Taste and nutritional quality parameters, such as total soluble solids, soluble sugar, organic acids and vitamin C improved in response to limited water supply (p ≤ 0.05). Despite having a negative effect on fruit yield, drought stress applied at stage III tended to enhance fruit quality traits. This study found that applying drought stress at stage I can be a positive management approach as it saves water and has fewer negative effects compared to applying drought stress at the other critical growth stages, thereby minimizing the adverse effects of drought stress.
DOI: 10.6084/m9.figshare.9870461
title: A lima bean core collection based on molecular markers

description: ABSTRACT Some germplasm collections have a high number of accessions, which makes it difficult to explore the genetic variability present in the germplasm bank due to the redundancy and the difficulty of detailed analysis of all conserved accessions. Therefore, our study aimed to analyze the genetic diversity of 153 lima bean (Phaseolus lunatus) accessions for the purpose of constructing a core collection. Eleven SSRs were used for this purpose. The 153 lima bean accessions can be represented by low redundancy using a minimum of 34 accessions, thus representing 22 % of the size of the entire germplasm bank. The core collection had a higher Shannon diversity index and expected heterozygosity (1.906 and 0.811, respectively) than those presented by the entire germplasm bank (1.605 and 0.713, respectively), indicating a higher polymorphism of the representative cultivars in relation to the entire collection. The accessions selected for the core collection may be used in future studies of genome association as well as in genetic crosses in breeding programs aimed at developing improved cultivars with high genetic diversity which can meet current and future market needs.
DOI: 10.6084/m9.figshare.9870461.v1
title: A lima bean core collection based on molecular markers

description: ABSTRACT Some germplasm collections have a high number of accessions, which makes it difficult to explore the genetic variability present in the germplasm bank due to the redundancy and the difficulty of detailed analysis of all conserved accessions. Therefore, our study aimed to analyze the genetic diversity of 153 lima bean (Phaseolus lunatus) accessions for the purpose of constructing a core collection. Eleven SSRs were used for this purpose. The 153 lima bean accessions can be represented by low redundancy using a minimum of 34 accessions, thus representing 22 % of the size of the entire germplasm bank. The core collection had a higher Shannon diversity index and expected heterozygosity (1.906 and 0.811, respectively) than those presented by the entire germplasm bank (1.605 and 0.713, respectively), indicating a higher polymorphism of the representative cultivars in relation to the entire collection. The accessions selected for the core collection may be used in future studies of genome association as well as in genetic crosses in breeding programs aimed at developing improved cultivars with high genetic diversity which can meet current and future market needs.
DOI: 10.6084/m9.figshare.9870380
title: Association mapping of drought tolerance indices in wheat: QTL-rich regions on chromosome 4A

description: ABSTRACT Drought is likely the main abiotic stress that affects wheat yield. The identification of drought-tolerant genotypes represents an effective way of dealing with the continuous decrease in water resources as well as the increase in world population. The aim of this study was to identify single nucleotide polymorphisms (SNP) associated with drought tolerance indices in wheat by using a genome-wide association study (GWAS) under fully irrigated and rain-fed conditions. The drought tolerance indices (i.e., Stress Susceptibility Index, Stress Tolerance Index, Tolerance Index and Yield Stability Index) were calculated based on grain yield, 1,000-kernel weight and kernels per spike. The association panel was genotyped using genotyping-by-sequencing (GBS). A total of 175 SNPs exhibited statistical evidence of association with at least one drought tolerance index, explaining up to 6 % of the phenotypic variation. Forty-five SNPs were associated with more than one tolerance index (up to 4 agronomic traits). Most associations were located on chromosome 4A, supporting the hypothesis that this chromosome has a key role in drought tolerance which should be exploited for wheat improvement. In addition, statistical analysis detected SNPs associated with tolerance indices in both growing seasons, providing information about genetic regions with stable effects under different environmental conditions. This GWAS experiment serves as one of the few studies on association mapping for drought tolerance indices in wheat, which could increase the efficiency of rain-fed and irrigated crop production.
DOI: 10.6084/m9.figshare.9870380.v1
title: Association mapping of drought tolerance indices in wheat: QTL-rich regions on chromosome 4A

description: ABSTRACT Drought is likely the main abiotic stress that affects wheat yield. The identification of drought-tolerant genotypes represents an effective way of dealing with the continuous decrease in water resources as well as the increase in world population. The aim of this study was to identify single nucleotide polymorphisms (SNP) associated with drought tolerance indices in wheat by using a genome-wide association study (GWAS) under fully irrigated and rain-fed conditions. The drought tolerance indices (i.e., Stress Susceptibility Index, Stress Tolerance Index, Tolerance Index and Yield Stability Index) were calculated based on grain yield, 1,000-kernel weight and kernels per spike. The association panel was genotyped using genotyping-by-sequencing (GBS). A total of 175 SNPs exhibited statistical evidence of association with at least one drought tolerance index, explaining up to 6 % of the phenotypic variation. Forty-five SNPs were associated with more than one tolerance index (up to 4 agronomic traits). Most associations were located on chromosome 4A, supporting the hypothesis that this chromosome has a key role in drought tolerance which should be exploited for wheat improvement. In addition, statistical analysis detected SNPs associated with tolerance indices in both growing seasons, providing information about genetic regions with stable effects under different environmental conditions. This GWAS experiment serves as one of the few studies on association mapping for drought tolerance indices in wheat, which could increase the efficiency of rain-fed and irrigated crop production.
DOI: 10.6084/m9.figshare.9871073
title: Soil-applied Zn effect on soil fractions

description: ABSTRACT The interaction of Zn with soil compartments influences its bioavailability and uptake by plants. In this study, rice and soybean were cultivated under greenhouse conditions with the aim of evaluating Zn bioavailability and fractionation in a clayey-textured Typic Hapludox as a function of Zn rates (4 or 8 mg kg –1 Zn). The experiment was conducted until grain filling. Two soil subsamples (t 1 and t 2 ) that referred to the seeding and flowering stages, were collected and compared with two single extraction schemes, DTPA (Zn DTPAt1 and Zn DTPAt2 ) and Mehlich-1 (Zn Mt1 and Zn Mt2 ) for Zn available contents. Zn fractionation was carried out with t 2 soil subsamples for the testing of the following fractions: exchangeable Zn (Zn Exc ), Zn bound to carbonates (Zn Carb ), Zn bound to organic matter (Zn OM ), Zn bound to oxides (Zn Oxi ) and residual Zn (Zn res ). Zn applied to soil increased the Zn concentration in labile fractions in decreasing order as follows: Zn Exc &gt; Zn OM &gt; Zn Carb . There was no difference between the lesser or unavailable fractions, Zn Oxi and Zn res, when there was no correlation between the rates either with total accumulated Zn in plants (Zna total ), or the contents extracted by DTPA or Mehlich-1. Total cumulative Zn content in rice and soybean affected by the ZnCl 2 rates applied were positively correlated with Zn content extracted by both solutions. Both extractant solutions presented positive correlation between available contents of Zn with Zn bound to labile fractions.
DOI: 10.6084/m9.figshare.9871073.v1
title: Soil-applied Zn effect on soil fractions

description: ABSTRACT The interaction of Zn with soil compartments influences its bioavailability and uptake by plants. In this study, rice and soybean were cultivated under greenhouse conditions with the aim of evaluating Zn bioavailability and fractionation in a clayey-textured Typic Hapludox as a function of Zn rates (4 or 8 mg kg –1 Zn). The experiment was conducted until grain filling. Two soil subsamples (t 1 and t 2 ) that referred to the seeding and flowering stages, were collected and compared with two single extraction schemes, DTPA (Zn DTPAt1 and Zn DTPAt2 ) and Mehlich-1 (Zn Mt1 and Zn Mt2 ) for Zn available contents. Zn fractionation was carried out with t 2 soil subsamples for the testing of the following fractions: exchangeable Zn (Zn Exc ), Zn bound to carbonates (Zn Carb ), Zn bound to organic matter (Zn OM ), Zn bound to oxides (Zn Oxi ) and residual Zn (Zn res ). Zn applied to soil increased the Zn concentration in labile fractions in decreasing order as follows: Zn Exc &gt; Zn OM &gt; Zn Carb . There was no difference between the lesser or unavailable fractions, Zn Oxi and Zn res, when there was no correlation between the rates either with total accumulated Zn in plants (Zna total ), or the contents extracted by DTPA or Mehlich-1. Total cumulative Zn content in rice and soybean affected by the ZnCl 2 rates applied were positively correlated with Zn content extracted by both solutions. Both extractant solutions presented positive correlation between available contents of Zn with Zn bound to labile fractions.
DOI: 10.6084/m9.figshare.10258472
title: Sample size and prediction of weight and yield of individual cuts from Braford steers pistol hindquarters

description: ABSTRACT Two hundred seventeen grass-finished Braford steers were assessed by ultrasonic scanning and subsequently harvested with their pistol hindquarters fabricated into boneless wholesale cuts. The Longissimus thoracis muscle area and subcutaneous fat depths were measured. The objectives of this study were: 1) to develop prediction equations for weights of the pistol hindquarter and high-value commercial cuts, and 2) to estimate sample size needed for experiments comparing pistol hindquarter retail product weight using either physically or ultrasonically measured carcass traits. Carcass measurements explained 44 % to 94 % of the variation in weights of individual cuts, whereas, measurements that were made using ultrasound explained 42 % to 90 % of the variation in the weights. Models used to predict the weight of pistol hindquarter retail product with carcass measures and ultrasound measures showed high coefficient of determination (R 2 = 0.92 and 0.97, respectively). Whether based on carcass or ultrasound measures, models used to estimate weight percentage of fat trimmed from the pistol hindquarter had lack of fit. In general, models for individual cuts weights that used traits measured with ultrasound as independent variables approached the accuracy of models using carcass traits. Thus, only slightly greater samples sizes were required to have equivalent power to detect differences in retail product weights using ultrasound measures. For experiments of equivalent power, differences in the number of animals required may be offset by avoiding costs for slaughter and fabrication.
DOI: 10.6084/m9.figshare.10258472.v1
title: Sample size and prediction of weight and yield of individual cuts from Braford steers pistol hindquarters

description: ABSTRACT Two hundred seventeen grass-finished Braford steers were assessed by ultrasonic scanning and subsequently harvested with their pistol hindquarters fabricated into boneless wholesale cuts. The Longissimus thoracis muscle area and subcutaneous fat depths were measured. The objectives of this study were: 1) to develop prediction equations for weights of the pistol hindquarter and high-value commercial cuts, and 2) to estimate sample size needed for experiments comparing pistol hindquarter retail product weight using either physically or ultrasonically measured carcass traits. Carcass measurements explained 44 % to 94 % of the variation in weights of individual cuts, whereas, measurements that were made using ultrasound explained 42 % to 90 % of the variation in the weights. Models used to predict the weight of pistol hindquarter retail product with carcass measures and ultrasound measures showed high coefficient of determination (R 2 = 0.92 and 0.97, respectively). Whether based on carcass or ultrasound measures, models used to estimate weight percentage of fat trimmed from the pistol hindquarter had lack of fit. In general, models for individual cuts weights that used traits measured with ultrasound as independent variables approached the accuracy of models using carcass traits. Thus, only slightly greater samples sizes were required to have equivalent power to detect differences in retail product weights using ultrasound measures. For experiments of equivalent power, differences in the number of animals required may be offset by avoiding costs for slaughter and fabrication.