cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28279922
title: Phenotypic analysis of sorghum [<i>Sorghum bicolor</i> (L) Moench] genotypes for drought responsive traits

description: Sorghum (<i>Sorghum bicolor</i> L.) production in Ethiopia is often affected by a range of abiotic factors, mainly drought. This study aimed to evaluate the genetic variation and heritability of shoot and root traits that contribute to drought tolerance in sorghum genotypes. A total of 158 genotypes were analyzed using a high-throughput phenotyping platform. Highly significant (<i>p</i> &lt; .001) variations were observed for all traits considered, with strong and positive correlations among root-related traits at <i>p</i> &lt; .001 (<i>r</i> = 0.76–0.99) and shoot traits at <i>p</i> &lt; .001 (r = 0.27–0.98). The observed range of the root angles varied from 7.75° to 25.17°, with an average of 14.81°. The heritability estimates ranged from 35.51% to 76.25%, with an average of 62.40%. At an eigenvalue of greater than 1, four principal components explained 87.20% of the variability of the data sets, with PC1 and PC2 accounting for 38.10% and 34.10% of the total variability. Cluster analysis grouped the genotypes into four genetic groups. We believe that this study provides valuable insights into the genetic diversity and heritability of root and shoot-related traits in sorghum. In addition, these findings can assist in decision-making regarding the prioritization of sorghum genotypes in breeding programs targeting drought.
DOI: 10.6084/m9.figshare.28279922.v1
title: Phenotypic analysis of sorghum [<i>Sorghum bicolor</i> (L) Moench] genotypes for drought responsive traits

description: Sorghum (<i>Sorghum bicolor</i> L.) production in Ethiopia is often affected by a range of abiotic factors, mainly drought. This study aimed to evaluate the genetic variation and heritability of shoot and root traits that contribute to drought tolerance in sorghum genotypes. A total of 158 genotypes were analyzed using a high-throughput phenotyping platform. Highly significant (<i>p</i> &lt; .001) variations were observed for all traits considered, with strong and positive correlations among root-related traits at <i>p</i> &lt; .001 (<i>r</i> = 0.76–0.99) and shoot traits at <i>p</i> &lt; .001 (r = 0.27–0.98). The observed range of the root angles varied from 7.75° to 25.17°, with an average of 14.81°. The heritability estimates ranged from 35.51% to 76.25%, with an average of 62.40%. At an eigenvalue of greater than 1, four principal components explained 87.20% of the variability of the data sets, with PC1 and PC2 accounting for 38.10% and 34.10% of the total variability. Cluster analysis grouped the genotypes into four genetic groups. We believe that this study provides valuable insights into the genetic diversity and heritability of root and shoot-related traits in sorghum. In addition, these findings can assist in decision-making regarding the prioritization of sorghum genotypes in breeding programs targeting drought.
DOI: 10.6084/m9.figshare.30760829
title: MiR-3594-3p regulates proliferation and differentiation in myoblasts of chickens by targeting APOBEC2

description: MicroRNAs (miRNAs) play a pivotal role in muscle development. To identify miRNAs associated with myofiber formation during chicken embryogenesis, two chicken strains with distinct genetic backgrounds were selected—Rose-comb chicken and Cobb chicken for our experiments. Leg muscles from Rose-comb and Cobb chicken embryos at days 8 (E8) and 14 (E14) of incubation were collected for immunohistochemical analysis and small RNA sequencing to screen for differentially expressed miRNAs, which were subsequently validated by qRT-PCR. Softwares were employed to predict miRNA target genes, and miRNA-mRNA co-analysis was conducted to identify miRNA-mRNA interaction pairs related to myofiber formation. The differentially expressed miRNA-3594-3p and its target gene, APOBEC2, were identified. Subsequently, functional validation of the gene was conducted. Results demonstrated that miR-3594-3p overexpression during the proliferation phase significantly inhibited myoblast growth, a phenotype recapitulated by APOBEC2 knockdown. During differentiation, miR-3594-3p upregulation enhanced expression of myogenic regulatory factors (MYOG, MYOD, MYHC) and slow-twitch muscle markers (TNNT1, TNNC1), while markedly repressing fast-twitch muscle genes (TNNC2, TNNT3). Notably, APOBEC2 suppression mirrored these effects, confirming miR-3594-3p’s role in modulating myoblast proliferation, differentiation, and muscle fibrin isoform switching through APOBEC2 regulation. This work elucidated miRNA-mediated regulatory networks governing embryonic muscle development in poultry, offering mechanistic insights with translational potential for improving meat quality traits in agricultural genetics.
DOI: 10.6084/m9.figshare.30760829.v1
title: MiR-3594-3p regulates proliferation and differentiation in myoblasts of chickens by targeting APOBEC2

description: MicroRNAs (miRNAs) play a pivotal role in muscle development. To identify miRNAs associated with myofiber formation during chicken embryogenesis, two chicken strains with distinct genetic backgrounds were selected—Rose-comb chicken and Cobb chicken for our experiments. Leg muscles from Rose-comb and Cobb chicken embryos at days 8 (E8) and 14 (E14) of incubation were collected for immunohistochemical analysis and small RNA sequencing to screen for differentially expressed miRNAs, which were subsequently validated by qRT-PCR. Softwares were employed to predict miRNA target genes, and miRNA-mRNA co-analysis was conducted to identify miRNA-mRNA interaction pairs related to myofiber formation. The differentially expressed miRNA-3594-3p and its target gene, APOBEC2, were identified. Subsequently, functional validation of the gene was conducted. Results demonstrated that miR-3594-3p overexpression during the proliferation phase significantly inhibited myoblast growth, a phenotype recapitulated by APOBEC2 knockdown. During differentiation, miR-3594-3p upregulation enhanced expression of myogenic regulatory factors (MYOG, MYOD, MYHC) and slow-twitch muscle markers (TNNT1, TNNC1), while markedly repressing fast-twitch muscle genes (TNNC2, TNNT3). Notably, APOBEC2 suppression mirrored these effects, confirming miR-3594-3p’s role in modulating myoblast proliferation, differentiation, and muscle fibrin isoform switching through APOBEC2 regulation. This work elucidated miRNA-mediated regulatory networks governing embryonic muscle development in poultry, offering mechanistic insights with translational potential for improving meat quality traits in agricultural genetics.
DOI: 10.3535/p9t-b0x-ekz
title: Rhinocerotidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z17-489-c5d
title: Castor fiber Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5re-wcy-fyl
title: Carcharias

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kf7-fqk-q9q
title: Salamandridae Goldfuss, 1820

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.29912279
title: Determinants of improved seed adoption and intensity in lentil farming: evidence from Terai region of Nepal

description: The prevailing dominance of the informal seed system and dramatically low seed replacement rate (SRR) are the potent evidence of poor adoption of improved lentil seed in Nepal. In this study, we used a logit model to identify the determinants of farmers’ decisions regarding the adoption of improved lentil seed in Nepal. A total of 300 participants, selected using stratified random sampling, were interviewed using a pretested questionnaire. Focus group discussions and key informant interviews were also conducted. The empirical results showed that owned land (<i>p</i> ≤ .047), number of economically active household members (<i>p</i> ≤ .018), improved seed knowledge (<i>p</i> ≤ .001), training (<i>p</i> ≤ .045), technical assistance (<i>p</i> ≤ .005), demonstration visits (<i>p</i> ≤ .001) and subsidies (<i>p</i> ≤ .035) had a significantly positive effect on the adoption of improved lentil seed, while waterlogging low land (<i>p</i> ≤ .049) and seed cost (<i>p</i> ≤ .032) had a significantly negative effect. The level of recommended technology adoption by improved seed adopters was calculated using the adoption index. The low adoption index (0.38) revealed the underutilization of recommended lentil production technologies by the improved seed adopters. The proportion of land with improved seed and the rate of seed used were satisfactory, but fertilizer and pesticide use were dramatically lower than the recommended level. To facilitate the sustainable adoption of improved seed, the government must place emphasis on holistic and robust research and extension services, technical assistance and demonstration visits, along with the implementation of targeted subsidy programs.
DOI: 10.6084/m9.figshare.29912279.v1
title: Determinants of improved seed adoption and intensity in lentil farming: evidence from Terai region of Nepal

description: The prevailing dominance of the informal seed system and dramatically low seed replacement rate (SRR) are the potent evidence of poor adoption of improved lentil seed in Nepal. In this study, we used a logit model to identify the determinants of farmers’ decisions regarding the adoption of improved lentil seed in Nepal. A total of 300 participants, selected using stratified random sampling, were interviewed using a pretested questionnaire. Focus group discussions and key informant interviews were also conducted. The empirical results showed that owned land (<i>p</i> ≤ .047), number of economically active household members (<i>p</i> ≤ .018), improved seed knowledge (<i>p</i> ≤ .001), training (<i>p</i> ≤ .045), technical assistance (<i>p</i> ≤ .005), demonstration visits (<i>p</i> ≤ .001) and subsidies (<i>p</i> ≤ .035) had a significantly positive effect on the adoption of improved lentil seed, while waterlogging low land (<i>p</i> ≤ .049) and seed cost (<i>p</i> ≤ .032) had a significantly negative effect. The level of recommended technology adoption by improved seed adopters was calculated using the adoption index. The low adoption index (0.38) revealed the underutilization of recommended lentil production technologies by the improved seed adopters. The proportion of land with improved seed and the rate of seed used were satisfactory, but fertilizer and pesticide use were dramatically lower than the recommended level. To facilitate the sustainable adoption of improved seed, the government must place emphasis on holistic and robust research and extension services, technical assistance and demonstration visits, along with the implementation of targeted subsidy programs.
DOI: 10.6084/m9.figshare.30340979
title: Prebiotic effects of <i>Amorphophallus muelleri</i> on growth performance and gut microbiota in broilers

description: The global poultry industry is shifting towards sustainable practices, necessitating alternatives to antibiotic growth promoters (AGPs) to enhance broiler performance and gut health. This study evaluated the effects of <i>Amorphophallus muelleri</i> (Porang) powder supplementation as a functional feed additive. A randomized controlled trial was conducted in which 300 broilers were assigned to one of four diets supplemented with 0, 0.25, 0.50, or 0.75% <i>A. muelleri</i> powder. Growth performance metrics were recorded, and gut microbiota were analyzed using metagenomic techniques. Supplementation improved final body weight (BW), feed conversion ratio (FCR), and performance index. These benefits were achieved without altering feed intake, indicating enhanced nutrient utilization. Gut microbiota analysis revealed that supplementation modulated microbial composition, enriching beneficial taxa such as <i>Lactobacillus crispatus</i> and <i>Lactobacillus johnsonii</i>. These findings suggest the prebiotic activity of glucomannan in A. muelleri powder modulates the gut microbiota and improves growth performance. This study supports the use of <i>A. muelleri</i> powder as a sustainable feed additive for enhancing broiler growth performance without antibiotics.
DOI: 10.6084/m9.figshare.30340979.v1
title: Prebiotic effects of <i>Amorphophallus muelleri</i> on growth performance and gut microbiota in broilers

description: The global poultry industry is shifting towards sustainable practices, necessitating alternatives to antibiotic growth promoters (AGPs) to enhance broiler performance and gut health. This study evaluated the effects of <i>Amorphophallus muelleri</i> (Porang) powder supplementation as a functional feed additive. A randomized controlled trial was conducted in which 300 broilers were assigned to one of four diets supplemented with 0, 0.25, 0.50, or 0.75% <i>A. muelleri</i> powder. Growth performance metrics were recorded, and gut microbiota were analyzed using metagenomic techniques. Supplementation improved final body weight (BW), feed conversion ratio (FCR), and performance index. These benefits were achieved without altering feed intake, indicating enhanced nutrient utilization. Gut microbiota analysis revealed that supplementation modulated microbial composition, enriching beneficial taxa such as <i>Lactobacillus crispatus</i> and <i>Lactobacillus johnsonii</i>. These findings suggest the prebiotic activity of glucomannan in A. muelleri powder modulates the gut microbiota and improves growth performance. This study supports the use of <i>A. muelleri</i> powder as a sustainable feed additive for enhancing broiler growth performance without antibiotics.
DOI: 10.3535/26c-2yl-vvx
title: Chordata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/505-p71-plw
title: †Catopygus L. Agassiz, 1835

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/clr-q1f-6bs
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.29716846
title: Genetic diversity and population structure analysis of <i>Capsicum annuum</i> cultivated in the Northern region of Ghana using simple sequence repeat markers

description: Pepper (<i>Capsicum annuum</i>) is an essential spicy crop in sub-Saharan African, however, limited genetic improvement initiatives have been undertaken to enhance its productivity. This study characterized the genetic diversity and population structure of 40 <i>C. annuum</i> accessions using 24 simple sequence repeat (SSR) markers. Profiling <i>C. annuum</i> accessions with 24 SSR markers revealed a total of 39 alleles, with an overall mean of 1.63 alleles per locus. The polymorphic information content and observed heterozygosity of the markers ranged from 0.00 to 0.40 and 0.00 to 0.10, respectively. Phylogenetic analysis using the neighbor-joining method grouped the accessions into six clusters, with no clear pattern of distribution based on their collection locations. Genetic differentiation among sub-populations was high (FST = 0.34–0.71), with a mean FST of 0.57 and average expected heterozygosity of 0.06. Population structure analysis, using an admixture model at a 60% membership threshold, assigned 29 accessions to a single genetic cluster, indicating widespread similarity among the samples. The narrow genetic base observed likely reflects the repeated cultivation of locally adapted or recycled germplasm by farmers. These findings emphasize the need to broaden the genetic base of <i>C. annuum</i> through the introduction of diverse germplasm and structured breeding efforts.
DOI: 10.3535/45n-te0-gy7
title: Actinopterygii

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d1e-vyz-1xp
title: Chordata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x20-exq-drd
title: Equidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z95-ex4-wwl
title: Actinopterygii

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.28032536
title: Combining multi-criteria decision analysis with agro-morphological-biochemical-molecular traits of interest for use in breeding in promising common bean breeding lines (<i>Phaseolus vulgaris</i> L.)

description: Common bean is one of the most important legumes in the world. This study analyzed 26 promising breeding materials of <i>Phaseolus vulgaris</i> L. for 12 quantitative and 15 qualitative traits to identify elite lines for possible registration of new varieties. High variability was observed for most quantitative traits, with coefficients of variation (CV) from 8.87 to 67.04% and Shannon-Weaver diversity index (H’) values from 1.21 to 1.54. Qualitative traits had H’ values from 0.54 to 1.47. Seed yield per plant and total soluble solids showed considerable CVs (&gt;42%), indicating significant variability among breeding lines. The H’ value also illustrated diversity among quantitative traits, with 100 seed weight showing the highest diversity (H’=1.54). Factor analysis of mixed data (FAMD) and hierarchical clustering on principal components (HCPC) grouped the breeding materials into two clusters and subgroups. The number of seed colors and the main seed color were key differentiators. Using a Composite Performance Index (CPI) from multi-criteria decision analysis (MCDA), the breeding materials were ranked, and five elite breeding lines were selected: KIS6B, KIS23B, KIS22B, KIS8B and KIS7B (CPI = 44.5–53.1). These finings offer valuable insights into the diversity of promising common bean breeding lines and provide a solid basis for the final selection and registration of new varieties.
DOI: 10.6084/m9.figshare.28032536.v1
title: Combining multi-criteria decision analysis with agro-morphological-biochemical-molecular traits of interest for use in breeding in promising common bean breeding lines (<i>Phaseolus vulgaris</i> L.)

description: Common bean is one of the most important legumes in the world. This study analyzed 26 promising breeding materials of <i>Phaseolus vulgaris</i> L. for 12 quantitative and 15 qualitative traits to identify elite lines for possible registration of new varieties. High variability was observed for most quantitative traits, with coefficients of variation (CV) from 8.87 to 67.04% and Shannon-Weaver diversity index (H’) values from 1.21 to 1.54. Qualitative traits had H’ values from 0.54 to 1.47. Seed yield per plant and total soluble solids showed considerable CVs (&gt;42%), indicating significant variability among breeding lines. The H’ value also illustrated diversity among quantitative traits, with 100 seed weight showing the highest diversity (H’=1.54). Factor analysis of mixed data (FAMD) and hierarchical clustering on principal components (HCPC) grouped the breeding materials into two clusters and subgroups. The number of seed colors and the main seed color were key differentiators. Using a Composite Performance Index (CPI) from multi-criteria decision analysis (MCDA), the breeding materials were ranked, and five elite breeding lines were selected: KIS6B, KIS23B, KIS22B, KIS8B and KIS7B (CPI = 44.5–53.1). These finings offer valuable insights into the diversity of promising common bean breeding lines and provide a solid basis for the final selection and registration of new varieties.
DOI: 10.3535/fvf-z45-qqs
title: Proboscidea Illiger, 1811

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.30261129
title: Physiological growth of potato (<i>Solanum tuberosum</i> L.) following post-harvest seed treatment with 3-decen-2-one (SmartBlock<sup>®</sup>)

description: Seed producers may use transient sprout suppressants during post-harvest storage to control sprouting, allowing growth during field planting. Inadvertent exposure to 3-decen-2-one (SmartBlock<sup>®</sup>) may occur during commercial storage and handling; however, its long-term effect on seed potatoes is unknown. This study aimed to determine the dose effect of SmartBlock<sup>®</sup> on the emergence percentage and growth of potatoes in a controlled environment (completely randomized design with three replicates). ‘Mnandi’ and ‘Vanderplank’ seed potatoes with sprouts less than 3 mm were stored in 9 L plastic containers and treated with 0.100 and 0.135 mL/kg SmartBlock<sup>®</sup> dosages, compared to a control. Emergence percentage, plant height, leaf area, stomatal conductance, CO<sub>2</sub> assimilation, chlorophyll, transpiration rate, stem number and diameter and tuber number and weight were measured. At the high dosage (0.135 mL/kg), emergence percentage significantly reduced (<i>p</i> &lt; .05) in Mnandi cultivar compared to the control. Therefore, this indicated that SmartBlock<sup>®</sup> can delay and reduce emergence depending on a dosage applied. SmartBlock<sup>®</sup> significantly (<i>p</i> &lt; .05) reduced stomatal conductance, CO<sub>2</sub> assimilation, and tuber weight, with effects observed at specific dosages and differing among cultivars. These results suggest that SmartBlock<sup>®</sup> may influence photosynthetic processes and yield components in a limited manner, with some variation between cultivars.
DOI: 10.6084/m9.figshare.30261129.v1
title: Physiological growth of potato (<i>Solanum tuberosum</i> L.) following post-harvest seed treatment with 3-decen-2-one (SmartBlock<sup>®</sup>)

description: Seed producers may use transient sprout suppressants during post-harvest storage to control sprouting, allowing growth during field planting. Inadvertent exposure to 3-decen-2-one (SmartBlock<sup>®</sup>) may occur during commercial storage and handling; however, its long-term effect on seed potatoes is unknown. This study aimed to determine the dose effect of SmartBlock<sup>®</sup> on the emergence percentage and growth of potatoes in a controlled environment (completely randomized design with three replicates). ‘Mnandi’ and ‘Vanderplank’ seed potatoes with sprouts less than 3 mm were stored in 9 L plastic containers and treated with 0.100 and 0.135 mL/kg SmartBlock<sup>®</sup> dosages, compared to a control. Emergence percentage, plant height, leaf area, stomatal conductance, CO<sub>2</sub> assimilation, chlorophyll, transpiration rate, stem number and diameter and tuber number and weight were measured. At the high dosage (0.135 mL/kg), emergence percentage significantly reduced (<i>p</i> &lt; .05) in Mnandi cultivar compared to the control. Therefore, this indicated that SmartBlock<sup>®</sup> can delay and reduce emergence depending on a dosage applied. SmartBlock<sup>®</sup> significantly (<i>p</i> &lt; .05) reduced stomatal conductance, CO<sub>2</sub> assimilation, and tuber weight, with effects observed at specific dosages and differing among cultivars. These results suggest that SmartBlock<sup>®</sup> may influence photosynthetic processes and yield components in a limited manner, with some variation between cultivars.
DOI: 10.3535/6jt-yx9-t3e
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lz8-r10-6vx
title: Equidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.