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Jara FM, García-Martínez MDLM, López-Córcoles H, Carrión ME, Zalacain A, Carmona M. Evaluating Guayule (Parthenium argentatum A. Gray) Germplasm Grown in Spain: Rubber and Resin along Three Production Cycles. Plants (Basel) 2024; 13:1092. [PMID: 38674500 PMCID: PMC11054728 DOI: 10.3390/plants13081092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 03/30/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024]
Abstract
Rubber and resin are potentially important products of guayule (Parthenium argentatum A. Gray) that can assure the profitability of this crop as an agricultural alternative for the semi-arid areas of central and eastern Spain. This study analyzes, for the first time, the changes in rubber and resin production across 27 guayule accessions (traditional and modern) and along three cycles under the agroclimatic conditions of Castilla-La Mancha, simulating industrial management with a biannual harvest. The rubber content (% of dry mass) increased from 4.2% in one-year-old plants to 6.6% in two-year-old plants, but decreased after harvesting. Contrastingly, the rubber yield doubled in contiguous sampling, reaching a mean of 303.6 kg ha-1, with a maximum yield of 341.2 kg ha-1 after the first harvest. Three patterns of rubber production were established based on the production periods. A similar analysis was performed for resin production, which was heterogeneous across accessions belonging to the same rubber groups. In this case, three independent groups were established to classify the resin accumulation profiles following the same criteria of production periods. Here, we demonstrate that biannual harvesting has the potential to enhance rubber accumulation in summer, although more research is needed for its adaption to current harvesting techniques in this area.
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Affiliation(s)
- Francisco Miguel Jara
- Instituto Técnico Agronómico Provincial (ITAP), S.A. Polígono Industrial Campollano, Avenida 2, 42 B, 02007 Albacete, Spain; (F.M.J.); (M.d.l.M.G.-M.); (H.L.-C.)
| | - María de las Mercedes García-Martínez
- Instituto Técnico Agronómico Provincial (ITAP), S.A. Polígono Industrial Campollano, Avenida 2, 42 B, 02007 Albacete, Spain; (F.M.J.); (M.d.l.M.G.-M.); (H.L.-C.)
- Cátedra de Química Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, de Montes y Biotecnología (ETSIAMB), Universidad de Castilla-La Mancha, Avda. de España s/n, 02071 Albacete, Spain;
| | - Horacio López-Córcoles
- Instituto Técnico Agronómico Provincial (ITAP), S.A. Polígono Industrial Campollano, Avenida 2, 42 B, 02007 Albacete, Spain; (F.M.J.); (M.d.l.M.G.-M.); (H.L.-C.)
| | - María Engracia Carrión
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain;
| | - Amaya Zalacain
- Cátedra de Química Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, de Montes y Biotecnología (ETSIAMB), Universidad de Castilla-La Mancha, Avda. de España s/n, 02071 Albacete, Spain;
| | - Manuel Carmona
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain;
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Shivute FN, Zhong Y, Wu J, Bao Y, Wang W, Liu X, Lu Z, Yu H. Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen. Front Plant Sci 2024; 15:1345708. [PMID: 38650702 PMCID: PMC11033514 DOI: 10.3389/fpls.2024.1345708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
Introduction Oryza alta Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource. Methods A new wild rice line, Huaye 5, was developed from Oryza alta Swallen in our lab. Whole genome re-sequencing and pan-genomic analysis were employed to analyze its genomic variations and novel genes. Results and Discussion More than ten million genomic variations were detected when compared with Asian cultivar. Among the variational genes, 724, 197 and 710 genes coded protein kinase, synthetase and transcription factor, respectively. A total of 353, 131 and 135 variational genes were associated with morphological trait, physiological trait, resistance or tolerance, respectively. A total of 62 were NBS-LRR genes were detected, in which 11 NBS-LRR genes expressed in sheath and mature stem, and 26 expressed in young and mature roots expressed. The pan-genome sequences of wild rice species with CCDD genome were constructed by integrating 8 Oryza alta (OA), 2 Oryza grandiglumis (OG) and 18 Oryza latifolia (OL) accessions. A total of 28 non-reference NBS-LRR genes were revealed, and 7 of which were mainly expressed in mature roots. This research demonstrated rich DNA variation in the Oryza alta Swallen that may provide a new germplasm for rice resistance breeding.
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Affiliation(s)
- Fimanekeni Ndaitavela Shivute
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yi Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yueming Bao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Wei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Zijun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Zhao D, Sapkota M, Lin M, Beil C, Sheehan M, Greene S, Irish BM. Genetic diversity, population structure, and taxonomic confirmation in annual medic ( Medicago spp.) collections from Crimea, Ukraine. Front Plant Sci 2024; 15:1339298. [PMID: 38633467 PMCID: PMC11021755 DOI: 10.3389/fpls.2024.1339298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
Annual medic (Medicago spp.) germplasm was collected from the Crimean Peninsula of Ukraine in 2008 to fill gaps in geographic coverage in the United States department of Agriculture, Agricultural Research Service, National Plant Germplasm System (NPGS) temperate-adapted forage legume collection. A total of 102 accessions across 10 Medicago species were collected. To assess genetic diversity, population structure, and to confirm taxonomic identities, the collections were phenotypically and genetically characterized. Phenotyping included the use of 24 descriptor traits while genetic characterization was accomplished using a 3K Diversity Array Technologies (DArTag) panel developed for alfalfa (Medicago sativa L.). For both field and molecular characterizations, a reference set of 92 geographically diverse and species-representative accessions were obtained from the NPGS collection. Phenotypic descriptors showed consistency among replicated plants within accessions, some variation across accessions within species, and evident distinctions between species. Because the DArTag panel was developed for cultivated alfalfa, the transferability of markers to the species being evaluated was limited, resulting in an average of ~1,500 marker loci detected per species. From these loci, 448 markers were present in 95% of the samples. Principal component and phylogenetic analysis based on a larger set of 2,396 selected markers clustered accessions by species and predicted evolutionary relationships among species. Additionally, the markers aided in the taxonomic identity of a few accessions that were likely mislabeled. The genotyping results also showed that sampling individual plants for these mostly self-pollinating species is sufficient due to high reproducibility between single (n=3) and pooled (n=7) biological replicate leaf samples. The phenotyping and the 2,396 Single Nucleotide Polymorphism (SNP) marker set were useful in estimating population structure in the Crimean and reference accessions, highlighting novel and unique genetic diversity captured in the Crimean accessions. This research not only demonstrated the utility of the DArTag marker panel in evaluating the Crimean germplasm but also highlighted its broader application in assessing genetic resources within the Medicago genus. Furthermore, we anticipate that our findings will underscore the importance of leveraging genetic resources and advanced genotyping tools for sustainable crop improvement and biodiversity conservation in annual medic species.
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Affiliation(s)
- Dongyan Zhao
- Breeding Insight, Cornell University, Ithaca, NY, United States
| | - Manoj Sapkota
- Breeding Insight, Cornell University, Ithaca, NY, United States
| | - Meng Lin
- Breeding Insight, Cornell University, Ithaca, NY, United States
| | - Craig Beil
- Breeding Insight, Cornell University, Ithaca, NY, United States
| | - Moira Sheehan
- Breeding Insight, Cornell University, Ithaca, NY, United States
| | - Stephanie Greene
- Agricultural Genetic Resources Preservation Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Prosser, WA, United States
| | - Brian M. Irish
- Plant Germplasm Introduction and Testing Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Prosser, WA, United States
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Yang T, Amanullah S, Li S, Gao P, Bai J, Li C, Ma J, Luan F, Wang X. Deciphering the Genomic Characterization of the GGP Gene Family and Expression Verification of CmGGP1 Modulating Ascorbic Acid Biosynthesis in Melon Plants. Antioxidants (Basel) 2024; 13:397. [PMID: 38671845 PMCID: PMC11047344 DOI: 10.3390/antiox13040397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Ascorbic acid (AsA), also known as vitamin C, is a well-known antioxidant found in living entities that plays an essential role in growth and development, as well as in defensive mechanisms. GDP-L-galactose phosphorylase (GGP) is a candidate gene regulating AsA biosynthesis at the translational and transcriptional levels in plants. In the current study, we conducted genome-wide bioinformatic analysis and pinpointed a single AsA synthesis rate-limiting enzyme gene in melon (CmGGP1). The protein prediction analysis depicted that the CmGGP1 protein does not have a signaling peptide or transmembrane structure and mainly functions in the chloroplast or nucleus. The constructed phylogenetic tree analysis in multispecies showed that the CmGGP1 protein has a highly conserved motif in cucurbit crops. The structural variation analysis of the CmGGP1 gene in different domesticated melon germplasms showed a single non-synonymous type-base mutation and indicated that this gene was selected by domestication during evolution. Wild-type (WT) and landrace (LDR) germplasms of melon depicted close relationships to each other, and improved-type (IMP) varieties showed modern domestication selection. The endogenous quantification of AsA content in both the young and old leaves of nine melon varieties exhibited the major differentiations for AsA synthesis and metabolism. The real-time quantitative polymerase chain reaction (qRT-PCR) analysis of gene co-expression showed that AsA biosynthesis in leaves was greater than AsA metabolic consumption, and four putative interactive genes (MELO3C025552.2, MELO3C007440.2, MELO3C023324.2, and MELO3C018576.2) associated with the CmGGP1 gene were revealed. Meanwhile, the CmGGP1 gene expression pattern was noticed to be up-regulated to varying degrees in different acclimated melons. We believe that the obtained results would provide useful insights for an in-depth genetic understanding of the AsA biosynthesis mechanism, aimed at the development of improving crop plants for melon.
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Affiliation(s)
- Tiantian Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (P.G.); (J.B.); (C.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Sikandar Amanullah
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (P.G.); (J.B.); (C.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Shenglong Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (P.G.); (J.B.); (C.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (P.G.); (J.B.); (C.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Junyu Bai
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (P.G.); (J.B.); (C.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Chang Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (P.G.); (J.B.); (C.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Jie Ma
- Bayannur Institute of Agriculture and Animal Husbandry Science, Inner Mongolia Autonomous Region, Bayannur 015000, China;
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (P.G.); (J.B.); (C.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (P.G.); (J.B.); (C.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
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Spina A, De Benedetti S, Heinzl GC, Ceravolo G, Magni C, Emide D, Castorina G, Consonni G, Canale M, Scarafoni A. Biochemical Characterization of the Seed Quality of a Collection of White Lupin Landraces from Southern Italy. Plants (Basel) 2024; 13:785. [PMID: 38592821 PMCID: PMC10974116 DOI: 10.3390/plants13060785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 04/11/2024]
Abstract
Lupin species provide essential nutrients and bioactive compounds. Within pulses, they have one of the highest contents of proteins and fibers and are among the poorest in carbohydrates. The Mediterranean region is an important cradle area of the origin and domestication of cultivated white lupin (Lupinus albus L.). In this work, we present the characterization of 19 white lupin landraces collected from several sites in southern Italy, characterized by different pedoclimatic conditions. The protein contents and electrophoretic patterns, total polyphenols, phytic acid, lipids and phosphorous content, and reducing and anti-tryptic activities have been determined for each landrace. The relationships of the compositional characteristics, the area of origin of landraces and between compositional characteristics and thermo-pluviometric trends that occurred in the genotype comparison field during the two-year period between 2019 and 2020 are compared and discussed. From a nutritional point of view, some of the analyzed landraces differ from the commercial reference. The panel of molecular analyses performed can help in building an identity card for the grain to rapidly identify those varieties with the desired characteristics.
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Affiliation(s)
- Alfio Spina
- Council for Agricultural Research and Economics (CREA), Centro di Ricerca Cerealicoltura e Colture Industriali, Corso Savoia 190, 95024 Acireale, Italy; (A.S.); (M.C.)
| | - Stefano De Benedetti
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133 Milan, Italy; (S.D.B.); (G.C.H.); (G.C.); (C.M.); (D.E.)
| | - Giuditta Carlotta Heinzl
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133 Milan, Italy; (S.D.B.); (G.C.H.); (G.C.); (C.M.); (D.E.)
| | - Giulia Ceravolo
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133 Milan, Italy; (S.D.B.); (G.C.H.); (G.C.); (C.M.); (D.E.)
| | - Chiara Magni
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133 Milan, Italy; (S.D.B.); (G.C.H.); (G.C.); (C.M.); (D.E.)
| | - Davide Emide
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133 Milan, Italy; (S.D.B.); (G.C.H.); (G.C.); (C.M.); (D.E.)
| | - Giulia Castorina
- Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via G. Celoria 2, 20133 Milan, Italy; (G.C.); (G.C.)
| | - Gabriella Consonni
- Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via G. Celoria 2, 20133 Milan, Italy; (G.C.); (G.C.)
| | - Michele Canale
- Council for Agricultural Research and Economics (CREA), Centro di Ricerca Cerealicoltura e Colture Industriali, Corso Savoia 190, 95024 Acireale, Italy; (A.S.); (M.C.)
| | - Alessio Scarafoni
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133 Milan, Italy; (S.D.B.); (G.C.H.); (G.C.); (C.M.); (D.E.)
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Hiraoka Y, Ferrante SP, Wu GA, Federici CT, Roose ML. Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives. Plants (Basel) 2024; 13:691. [PMID: 38475537 DOI: 10.3390/plants13050691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, "PolyHighResolution" (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.
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Affiliation(s)
- Yoko Hiraoka
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Sergio Pietro Ferrante
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Guohong Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Claire T Federici
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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Park S, Zhang D, Ali GS. Assessing the genetic integrity of sugarcane germplasm in the USDA-ARS National Plant Germplasm System collection using single-dose SNP markers. Front Plant Sci 2024; 14:1337736. [PMID: 38239228 PMCID: PMC10794611 DOI: 10.3389/fpls.2023.1337736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, FL, is one of the largest sugarcane germplasm repositories in the world. However, the genetic integrity of the Saccharum spp. germplasm in this collection has not been fully analyzed. In this study, we employed a single-dose SNP panel to genotype 901 sugarcane accessions, representing six Saccharum species and various hybrids. Our analysis uncovered a high rate of clone mislabeling in the collection. Specifically, we identified 86 groups of duplicates, characterized by identical SNP genotypes, which encompassed 211 accessions (23% of the total clones), while 135 groups, constituting 471 clones (52% of the total), exhibited near-identical genotypes. In addition, twenty-seven homonymous groups were detected, which shared the same clone name but differed in SNP genotypes. Hierarchical analysis of population structure partitioned the Saccharum germplasm into five clusters, corresponding to S. barberi, S. sinense, S. officinarum, S. spontaneum and S. robustum/S. edule. An assignment test, based on the five Saccharum species, enabled correcting 141 instances of mislabeled species memberships and inaccuracies. Moreover, we clarified the species membership and parentage of 298 clones that had ambiguous passport records (e.g., 'Saccharum spp', 'unknown', and 'hybrid'). Population structure and genetic diversity in these five species were further supported by Principal Coordinate Analysis and neighbor-joining clustering analysis. Analysis of Molecular Variance revealed that within-species genetic variations accounted for 85% of the total molecular variance, with the remaining 15% attributed to among-species genetic variations. The single-dose SNP markers developed in this study offer a robust tool for characterizing sugarcane germplasm worldwide. These findings have important implications for sugarcane genebank management, germplasm exchange, and crop genetic improvement.
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Affiliation(s)
- Sunchung Park
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Gul Shad Ali
- Subtropical Horticulture Research Station, United States Department of Agriculture, Agriculture Research Service, Miami, FL, United States
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Ding X, Shi J, Gui J, Zhou H, Yan Y, Zhu X, Xie B, Liu X, He J. Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study. Plants (Basel) 2024; 13:134. [PMID: 38202442 PMCID: PMC10780921 DOI: 10.3390/plants13010134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024]
Abstract
The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only qPP2 was detected repeatedly two times. The candidate gene analysis showed that LOC_Os02g57530 (ETR3), LOC_Os01g57610 (GH3.1) and LOC_Os04g0425 (CTB2) were the candidate genes for qPP2, qPP1 and qPP4, respectively. The haplotype (Hap) analysis revealed that Hap1 of ETR3, Hap1 and 3 of GH3.1 and Hap2 and 5 of CTB2 are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of ETR3 is a favorable allele for the germination percentage; Hap3 of GH3.1 is an elite allele for seed germination; and Hap5 of CTB2 is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice.
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Affiliation(s)
| | | | | | | | | | | | | | - Xionglun Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (X.D.); (J.S.); (J.G.); (Y.Y.); (X.Z.); (B.X.)
| | - Jiwai He
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (X.D.); (J.S.); (J.G.); (Y.Y.); (X.Z.); (B.X.)
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Kim SH, Ochar K, Hwang A, Lee YJ, Kang HJ. Variability of Glucosinolates in Pak Choy (Brassica rapa subsp. chinensis) Germplasm. Plants (Basel) 2023; 13:9. [PMID: 38202314 PMCID: PMC10780573 DOI: 10.3390/plants13010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Glucosinolates are sulfur-containing phytochemicals generally abundant in cruciferous vegetables such as pak choy. Glucosinolates participate in a range of biological activities essential for promoting a healthy human body. In this study, we aimed to elucidate glucosinolate variability present in pak choy germplasm that are under conservation at the Rural Development Administration Genebank, Jeonju, Republic of Korea. The Acquity Ultra-Performance Liquid Chromatography (UHPLC) analytical system was used in profiling the glucosinolate content in leaf samples of various accessions. We identified a total of 17 glucosinolates in the germplasm. Based on principal compoment analysis performed, three separate groups of the accessions were obtained. Group 1 contained the cultivar cheongsacholong which recorded high content of glucobrassicin (an indole), glucoerucin (aliphatic), gluconasturtiin (aromatic) and glucoberteroin (aliphatic). Group 2 consisted of six accessions, BRA77/72, Lu ling gaogengbai, 9041, Wuyueman, RP-75 and DH-10, predominatly high in aliphatic compounds including glucoiberin, glucocheirolin, and sinigrin. Group 3 comprised the majority of the accessions which were characterized by high content of glucoraphanin, epiprogoitrin, progoitrin, and glucotropaeolin. These results revealed the presence of variability among the pak choy germplasm based on their glucosinolate content, providing an excellent opprtunity for future breeding for improved glucosinolate content in the crop.
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Affiliation(s)
- Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 5487, Republic of Korea; (K.O.); (A.H.); (Y.-J.L.)
| | - Kingsley Ochar
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 5487, Republic of Korea; (K.O.); (A.H.); (Y.-J.L.)
- Council for Scientific and Industrial Research, Plant Genetic Resources Research Institute, Bunso P.O. Box 7, Ghana
| | - Aejin Hwang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 5487, Republic of Korea; (K.O.); (A.H.); (Y.-J.L.)
| | - Yoon-Jung Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 5487, Republic of Korea; (K.O.); (A.H.); (Y.-J.L.)
| | - Hae Ju Kang
- Department of Agrofood Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea;
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10
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Washburn JD, LaFond HF, Lapadatescu MC, Pereira AE, Erb M, Hibbard BE. GWAS analysis of maize host plant resistance to western corn rootworm (Coleoptera: Chrysomelidae) reveals candidate small effect loci for resistance breeding. J Econ Entomol 2023; 116:2184-2192. [PMID: 37816495 DOI: 10.1093/jee/toad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023]
Abstract
Western corn rootworm, Diabrotica virgifera virgifera (LeConte) (Coleoptera: Chrysomelidae), is the most serious economic pest of maize, Zea mays (L.) (Poales: Poaceae), in the U.S. Corn Belt and also threatens production in Europe. Traditional management options have repeatedly failed over time as western corn rootworm rapidly develops resistance to insecticides, transgenic maize and even crop rotation. Traits that improve host plant resistance and tolerance are highly sought after by plant breeders for crop protection and pest management. However, maize resistance to western corn rootworm appears to be highly complex and despite over 75 yr of breeding efforts, there are no naturally resistant hybrids available commercially. Using phenotypic data from field and greenhouse experiments on a highly diverse collection of 282 inbred lines, we screened and genetically mapped western corn rootworm-related traits to identify genetic loci which may be useful for future breeding or genetic engineering efforts. Our results confirmed that western corn rootworm resistance is complex with relatively low heritability due in part to strong genotype by environment impacts and the inherent difficulties of phenotyping below ground root traits. The results of the Genome Wide Associated Study identified 29 loci that are potentially associated with resistance to western corn rootworm. Of these loci, 16 overlap with those found in previous transcription or mapping studies indicating a higher likelihood they are truly involved in maize western corn rootworm resistance. Taken together with previous studies, these results indicate that breeding for natural western corn rootworm resistance will likely require the stacking of multiple small effect loci.
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Affiliation(s)
- Jacob D Washburn
- United States Department of Agriculture - Agricultural Research Service, Plant Genetics Research Unit, 519 S College Avenue, Columbia, MO 65211, USA
| | - Harper F LaFond
- United States Department of Agriculture - Agricultural Research Service, Plant Genetics Research Unit, 519 S College Avenue, Columbia, MO 65211, USA
| | - Martian C Lapadatescu
- Division of Plant Science & Technology, University of Missouri, 2-64 Agriculture Building, Columbia, MO 65211, USA
| | - Adriano E Pereira
- United States Department of Agriculture - Agricultural Research Service, Plant Genetics Research Unit, 519 S College Avenue, Columbia, MO 65211, USA
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Bruce E Hibbard
- United States Department of Agriculture - Agricultural Research Service, Plant Genetics Research Unit, 519 S College Avenue, Columbia, MO 65211, USA
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11
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Sun M, Ma J, Cai Z, Yan J, Ma R, Yu M, Xie Y, Shen Z. Sensory Determination of Peach and Nectarine Germplasms with Instrumental Analysis. Foods 2023; 12:4444. [PMID: 38137247 PMCID: PMC10743018 DOI: 10.3390/foods12244444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The flavour and mouthfeel of peaches are crucial qualities of peach germplasm resources that significantly influence consumer preferences. In this study, we utilized 212 peach germplasm resources from the Nanjing Peach Resource Repository, National Fruit Germplasm facility, Jiangsu Academy of Agricultural Sciences as materials for sensory analysis, electronic nose analysis, and composition analysis via high-performance liquid chromatography (HPLC). In the sensory analysis, we divided 212 peach germplasms into three clusters based on hierarchical cluster analysis (d = 5). No.27, No.151, and No.46 emerged as the most representative of these clusters. The electronic nose was used to conduct an evaluation of the aroma profiles of the 212 peach germplasms, revealing that the primary distinguishing factors of peach aroma can be attributed to three sensors: W1S (methane), W1W (terpenes and organosulfur compounds), and W5S (hydrocarbons and aromatic compounds). The primary differences in the aromatic substances were characterized by sensors W2W (aromatic compounds, sulphur, and chlorine compounds) and W1C (aromatic benzene). The HPLC analysis indicated that the persistence of peach sensory characteristics was positively correlated with acids and sourness and negatively correlated with sweetness and the ratio of sugar to acids. The overall impression of the 212 peach germplasms revealed a negative correlation with acids, while a positive correlation was observed between the overall impression and the ratio of sugar to acids. Therefore, this study substantially contributes to the preliminary screening of the analysed specific characteristics of peach germplasms such as No.27, No.46, No.151, and No.211. These selections may provide valuable information for the potential creation of superior germplasm resources.
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Affiliation(s)
- Meng Sun
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China; (M.S.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China
| | - Julin Ma
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China; (M.S.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zhixiang Cai
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China; (M.S.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China
| | - Juan Yan
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China; (M.S.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China
| | - Ruijuan Ma
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China; (M.S.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China
| | - Mingliang Yu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China; (M.S.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China
| | - Yinfeng Xie
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zhijun Shen
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China; (M.S.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing 210014, China
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12
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Boczkowska M, Puchta-Jasińska M, Bolc P, Moskal K, Puła S, Motor A, Bączek K, Groszyk J, Podyma W. Characterization of the Moroccan Barley Germplasm Preserved in the Polish Genebank as a First Step towards Selecting Forms with Increased Drought Tolerance. Int J Mol Sci 2023; 24:16350. [PMID: 38003539 PMCID: PMC10671370 DOI: 10.3390/ijms242216350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
In marginal, arid, and semi-arid areas of Morocco, crops are often exposed to multiple abiotic and biotic stresses that have a major impact on yield. Farmer-maintained Moroccan landraces have been shaped by the impact of very strong selection pressures, gradually adapting to the local ecosystem and obsolete low-input agricultural practices without improvement towards high yield and quality. Considering the increasing threat of drought in Poland, it is necessary to introduce germplasm with tolerance to water deficit into barley breeding programs. The aim of this research was a DArTseq-based genetic characterization of a collection of germplasm of Moroccan origin, conserved in the Polish genebank. The results showed that all conserved landraces have a high level of heterogeneity and their gene pool is different from the material developed by Polish breeders. Based on the analysis of eco-geographical data, locations with extremely different intensities of drought stress were selected. A total of 129 SNPs unique to accessions from these locations were identified. In the neighborhood of the clusters of unique SNPs on chromosomes 5H and 6H, genes that may be associated with plant response to drought stress were identified. The results obtained may provide a roadmap for further research to support Polish barley breeding for increased drought tolerance.
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Affiliation(s)
- Maja Boczkowska
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (M.P.-J.); (P.B.); (K.M.); (S.P.); (A.M.); (J.G.); (W.P.)
| | - Marta Puchta-Jasińska
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (M.P.-J.); (P.B.); (K.M.); (S.P.); (A.M.); (J.G.); (W.P.)
| | - Paulina Bolc
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (M.P.-J.); (P.B.); (K.M.); (S.P.); (A.M.); (J.G.); (W.P.)
| | - Kinga Moskal
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (M.P.-J.); (P.B.); (K.M.); (S.P.); (A.M.); (J.G.); (W.P.)
| | - Szymon Puła
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (M.P.-J.); (P.B.); (K.M.); (S.P.); (A.M.); (J.G.); (W.P.)
| | - Adrian Motor
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (M.P.-J.); (P.B.); (K.M.); (S.P.); (A.M.); (J.G.); (W.P.)
| | - Katarzyna Bączek
- Department of Vegetable and Medicinal Plants, Institute of Horticultural Sciences, Warsaw University of Life Sciences SGGW, 159 Nowoursynowska Str., 02-776 Warsaw, Poland;
| | - Jolanta Groszyk
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (M.P.-J.); (P.B.); (K.M.); (S.P.); (A.M.); (J.G.); (W.P.)
| | - Wiesław Podyma
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (M.P.-J.); (P.B.); (K.M.); (S.P.); (A.M.); (J.G.); (W.P.)
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13
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Blackburn HD, Azevedo HC, Purdy PH. Incorporation of Biotechnologies into Gene Banking Strategies to Facilitate Rapid Reconstitution of Populations. Animals (Basel) 2023; 13:3169. [PMID: 37893893 PMCID: PMC10603745 DOI: 10.3390/ani13203169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
National animal gene banks that are responsible for conserving livestock, poultry, and aquatic genetic resources need to be capable of utilizing a broad array of cryotechnologies coupled with assisted reproductive technologies to reconstitute either specific animals or populations/breeds as needed. This capability is predicated upon having sufficient genetic diversity (usually encapsulated by number of animals in the collection), units of germplasm or tissues, and the ability to reconstitute animals. While the Food and Agriculture Organization of the United Nations (FAO 2012, 2023) developed a set of guidelines for gene banks on these matters, those guidelines do not consider applications and utilization of newer technologies (e.g., primordial germ cells, cloning from somatic cells, embryo transfer, IVF, sex-sorted semen), which can radically change how gene banks collect, store, and utilize genetic resources. This paper reviews the current status of using newer technologies, explores how gene banks might make such technologies part of their routine operations, and illustrates how combining newer assisted reproductive technologies with older approaches enables populations to be reconstituted more efficiently.
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Affiliation(s)
- Harvey D. Blackburn
- USDA ARS National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO 80521-4500, USA
| | | | - Phillip H. Purdy
- USDA ARS National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO 80521-4500, USA
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14
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dos Santos CC, de Andrade LRB, do Carmo CD, de Oliveira EJ. The Development of Thematic Core Collections in Cassava Based on Yield, Disease Resistance, and Root Quality Traits. Plants (Basel) 2023; 12:3474. [PMID: 37836214 PMCID: PMC10574880 DOI: 10.3390/plants12193474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023]
Abstract
Thematic collections (TCs), which are composed of genotypes with superior agronomic traits and reduced size, offer valuable opportunities for parental selection in plant breeding programs. Three TCs were created to focus on crucial attributes: root yield (CC_Yield), pest and disease resistance (CC_Disease), and root quality traits (CC_Root_quality). The genotypes were ranked using the best linear unbiased predictors (BLUP) method, and a truncated selection was implemented for each collection based on specific traits. The TCs exhibited minimal overlap, with each collection comprising 72 genotypes (CC_Disease), 63 genotypes (CC_Root_quality), and 64 genotypes (CC_Yield), representing 4%, 3.5%, and 3.5% of the total individuals in the entire collection, respectively. The Shannon-Weaver Diversity Index values generally varied but remained below 10% when compared to the entire collection. Most TCs exhibited observed heterozygosity, genetic diversity, and the inbreeding coefficient that closely resembled those of the entire collection, effectively retaining 90.76%, 88.10%, and 88.99% of the alleles present in the entire collection (CC_Disease, CC_Root_quality, and CC_Disease, respectively). A PCA of molecular and agro-morphological data revealed well-distributed and dispersed genotypes, while a discriminant analysis of principal components (DAPC) displayed a high discrimination capacity among the accessions within each collection. The strategies employed in this study hold significant potential for advancing crop improvement efforts.
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Affiliation(s)
- Caroline Cardoso dos Santos
- Centro de Ciências Agrárias, Ambientais e Biológicas, Universidade Federal do Recôncavo da Bahia, Cruz das Almas 44380-000, BA, Brazil
| | | | - Cátia Dias do Carmo
- Embrapa Mandioca e Fruticultura, Nugene, Cruz das Almas 44380-000, BA, Brazil
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15
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Mattos LM, Reis FC, Racanicci AMC, Pivato I, Tonelli GSSS, Báo SN, Martins CF. Freezing for the Future: Obtaining Fibroblast Samples from Deceased Wild Mammals for the Brazilian Cerrado Germplasm Bank. Biopreserv Biobank 2023; 21:504-509. [PMID: 35904947 DOI: 10.1089/bio.2022.0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
We isolated and further characterized fibroblasts obtained from postmortem skin biopsies of three different Brazilian wild species (Chrysocyon brachyurus-maned wolf, Cerdocyon thous-crab-eating fox, Mazama gouazoubira-brown brocket deer). The effects of two cryoprotectants, 10% dimethyl sulfoxide (DMSO) and 5% dimethylformamide (DMF), were assessed to determine the most efficient cryopreservation protocol. Such an investigation promotes the creation of germplasm banks, using samples that would otherwise be rejected and permanently lost following the death of the animals. We utilized animal corpses that were involved in highway accidents, found dead in the natural environment, or referred to us from the veterinary hospital at the Brasília Zoo. Fibroblasts from C. brachyurus specimens presented a delay in cell growth in Dulbecco's modified Eagle's medium in relation to other species. This observation is a limiting factor for the future storage of cells from this species. Differences in cellular morphology were observed between C. brachyurus, C. thous, and M. gouazoubira, presenting branched, fusiform, and spherical forms, respectively. The cryoprotective solution containing 10% DMSO was more efficient than 5% DMF medium in preserving the viability of fibroblasts of the three species (p < 0.05). After defining the best cryopreservation solution, a germplasm bank was successfully formed. This biological reservoir is configured as the first germplasm bank containing somatic cells and gametes of wild mammals of the Cerrado biome of Brazil. This material will be used for future characterization of the species and multiplication by means of nuclear transfer cloning.
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Affiliation(s)
- Luciana Miranda Mattos
- Brazilian Agricultural Research Corporation (Embrapa Cerrados), Brasília, Brazil
- University of Brasília, Brasília, Brazil
| | - Filipe Carneiro Reis
- Brazilian Agricultural Research Corporation (Embrapa Cerrados), Brasília, Brazil
- Brasília Zoo, Brasília, Brazil
| | | | - Ivo Pivato
- University of Brasília, Brasília, Brazil
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16
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Ochar K, Kim SH. Conservation and Global Distribution of Onion ( Allium cepa L.) Germplasm for Agricultural Sustainability. Plants (Basel) 2023; 12:3294. [PMID: 37765458 PMCID: PMC10535454 DOI: 10.3390/plants12183294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Onion (Allium cepa L.) is recognized globally as a crucial vegetable crop, prized not only for its culinary applications but also for its numerous health-promoting properties. With climate change relentlessly exerting mounting challenges to agriculture, the preservation and deployment of onion germplasm has become critical to ensuring sustainable agriculture and safeguarding food security. Global onion germplasm collections function as repositories of genetic diversity, holding within them an extensive array of valuable traits or genes. These can be harnessed to develop varieties resilient to climate adversities. Therefore, detailed information concerning onion germplasm collections from various geographical regions can bolster their utility. Furthermore, an amplified understanding of the importance of fostering international and inter-institutional collaborations becomes essential. Sharing and making use of onion genetic resources can provide viable solutions to the looming agricultural challenges of the future. In this review, we have discussed the preservation and worldwide distribution of onion germplasm, along with its implications for agricultural sustainability. We have also underscored the importance of international and interinstitutional collaboration in onion germplasm collecting and conservation for agricultural sustainability.
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Affiliation(s)
- Kingsley Ochar
- Council for Scientific and Industrial Research, Plant Genetic Resources Research Institute, Bunso P.O. Box 7, Ghana;
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 5487, Republic of Korea
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17
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dos Santos CC, de Andrade LRB, do Carmo CD, de Oliveira EJ. Development of cassava core collections based on morphological and agronomic traits and SNPS markers. Front Plant Sci 2023; 14:1250205. [PMID: 37745996 PMCID: PMC10511765 DOI: 10.3389/fpls.2023.1250205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023]
Abstract
Cassava (Manihot esculenta Crantz) holds significant importance as one of the world's key starchy crop species. This study aimed to develop core collections by utilizing both phenotypic data (15 quantitative and 33 qualitative descriptors) and genotypic data (20,023 single-nucleotide polymorphisms) obtained from 1,486 cassava accessions. Six core collections were derived through two optimization strategies based on genetic distances: Average accession-to-nearest-entry and Average entry-to-nearest-entry, along with combinations of phenotypic and genotypic data. The quality of the core collections was evaluated by assessing genetic parameters such as genetic diversity Shannon-Weaver Index, inbreeding (Fis), observed (Ho), and expected (Hs) heterozygosity. While the selection of accessions varied among the six core collections, a seventh collection (consolidated collection) was developed, comprising accessions selected by at least two core collections. Most collections exhibited genetic parameters similar to the complete collection, except for those developed by the Average accession-to-nearest-entry algorithm. However, the variations in the maximum and minimum values of Ho, Hs, and Fis parameters closely resembled the complete collection. The consolidated collection and the collection constructed using genotypic data and the Average entry-to-nearest-entry algorithm (GenEN) retained the highest number of alleles (>97%). Although the differences were not statistically significant (above 5%), the consolidated collection demonstrated a distribution profile and mean trait values most similar to the complete collection, with a few exceptions. The Shannon-Weaver Index of qualitative traits exhibited variations exceeding ±10% when compared to the complete collection. Principal component analysis revealed that the consolidated collection selected cassava accessions with a more uniform dispersion in all four quadrants compared to the other core collections. These findings highlight the development of optimized and valuable core collections for efficient breeding programs and genomic association studies.
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Affiliation(s)
- Caroline Cardoso dos Santos
- Centro de Ciências Agrárias, Ambientais e Biológicas, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Bahia, Brazil
| | | | - Cátia Dias do Carmo
- Centro de Ciências Agrárias, Ambientais e Biológicas, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Bahia, Brazil
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18
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Tang Q, Wang X, Jin X, Peng J, Zhang H, Wang Y. CRISPR/Cas Technology Revolutionizes Crop Breeding. Plants (Basel) 2023; 12:3119. [PMID: 37687368 PMCID: PMC10489799 DOI: 10.3390/plants12173119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
Crop breeding is an important global strategy to meet sustainable food demand. CRISPR/Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm and promoting the development of a series of new breeding techniques, which will certainly lead to the transformation of agricultural innovation. In this review, we summarize recent advances of CRISPR/Cas technology in gene function analyses and the generation of new germplasms with increased yield, improved product quality, and enhanced resistance to biotic and abiotic stress. We highlight their applications and breakthroughs in agriculture, including crop de novo domestication, decoupling the gene pleiotropy tradeoff, crop hybrid seed conventional production, hybrid rice asexual reproduction, and double haploid breeding; the continuous development and application of these technologies will undoubtedly usher in a new era for crop breeding. Moreover, the challenges and development of CRISPR/Cas technology in crops are also discussed.
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Affiliation(s)
- Qiaoling Tang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Xujing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Xi Jin
- Hebei Technology Innovation Center for Green Management of Soi-Borne Diseases, Baoding University, Baoding 071000, China;
| | - Jun Peng
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
| | - Haiwen Zhang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Youhua Wang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
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19
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Sharma V, Ankita, Karnwal A, Sharma S, Kamal B, Jadon VS, Gupta S, Sivanasen I. A Comprehensive Review Uncovering the Challenges and Advancements in the In Vitro Propagation of Eucalyptus Plantations. Plants (Basel) 2023; 12:3018. [PMID: 37687265 PMCID: PMC10490407 DOI: 10.3390/plants12173018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023]
Abstract
The genus Eucalyptus is a globally captivated source of hardwood and is well known for its medicinal uses. The hybrid and wild species of Eucalyptus are widely used as exotic plantations due to their renowned potential of adapting to various systems and sites, and rapid large-scale propagation of genetically similar plantlets, which further leads to the extensive propagation of this species. Tissue culture plays a crucial role in the preservation, propagation, and genetic improvement of Eucalyptus species. Despite unquestionable progression in biotechnological and tissue culture approaches, the productivity of plantations is still limited, often due to the low efficiency of clonal propagation from cuttings. The obtained F1 hybrids yield high biomass and high-quality low-cost raw material for large-scale production; however, the development of hybrid, clonal multiplication, proliferation, and post-developmental studies are still major concerns. This riveting review describes the problems concerning the in vitro and clonal propagation of Eucalyptus plantation and recent advances in biotechnological and tissue culture practices for massive and rapid micropropagation of Eucalyptus, and it highlights the Eucalyptus germplasm preservation techniques.
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Affiliation(s)
- Vikas Sharma
- School of Bioengineering and Bioscience, Lovely Professional University, Phagwara 144411, Punjab, India; (V.S.); (A.); (A.K.); (S.S.)
| | - Ankita
- School of Bioengineering and Bioscience, Lovely Professional University, Phagwara 144411, Punjab, India; (V.S.); (A.); (A.K.); (S.S.)
| | - Arun Karnwal
- School of Bioengineering and Bioscience, Lovely Professional University, Phagwara 144411, Punjab, India; (V.S.); (A.); (A.K.); (S.S.)
| | - Shivika Sharma
- School of Bioengineering and Bioscience, Lovely Professional University, Phagwara 144411, Punjab, India; (V.S.); (A.); (A.K.); (S.S.)
| | - Barkha Kamal
- DBS (PG) College, Dehradun 248001, Uttarakhand, India;
| | - Vikash S. Jadon
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant Dehradun 248016, Uttarakhand, India; (V.S.J.); (S.G.)
| | - Sanjay Gupta
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant Dehradun 248016, Uttarakhand, India; (V.S.J.); (S.G.)
| | - Iyyakkannu Sivanasen
- Department of Bioresource and Food Science, Institute of Natural Science and Agriculture, Konkuk University, Seoul 05029, Republic of Korea
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20
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Li H, Song K, Zhang X, Wang D, Dong S, Liu Y, Yang L. Application of Multi-Perspectives in Tea Breeding and the Main Directions. Int J Mol Sci 2023; 24:12643. [PMID: 37628823 PMCID: PMC10454712 DOI: 10.3390/ijms241612643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/29/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Tea plants are an economically important crop and conducting research on tea breeding contributes to enhancing the yield and quality of tea leaves as well as breeding traits that satisfy the requirements of the public. This study reviews the current status of tea plants germplasm resources and their utilization, which has provided genetic material for the application of multi-omics, including genomics and transcriptomics in breeding. Various molecular markers for breeding were designed based on multi-omics, and available approaches in the direction of high yield, quality and resistance in tea plants breeding are proposed. Additionally, future breeding of tea plants based on single-cellomics, pangenomics, plant-microbe interactions and epigenetics are proposed and provided as references. This study aims to provide inspiration and guidance for advancing the development of genetic breeding in tea plants, as well as providing implications for breeding research in other crops.
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Affiliation(s)
| | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China
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21
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Doyle DA, Burian FN, Aharoni B, Klinder AJ, Menzel MM, Nifras GCC, Shabazz-Henry AL, Palma BU, Hidalgo GA, Sottolano CJ, Ortega BM, Niepielko MG. Germ Granule Evolution Provides Mechanistic Insight into Drosophila Germline Development. Mol Biol Evol 2023; 40:msad174. [PMID: 37527522 PMCID: PMC10414811 DOI: 10.1093/molbev/msad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023] Open
Abstract
The copackaging of mRNAs into biomolecular condensates called germ granules is a conserved strategy to posttranscriptionally regulate germline mRNAs. In Drosophila melanogaster, mRNAs accumulate in germ granules by forming homotypic clusters, aggregates containing multiple transcripts from the same gene. Nucleated by Oskar (Osk), homotypic clusters are generated through a stochastic seeding and self-recruitment process that requires the 3' untranslated region (UTR) of germ granule mRNAs. Interestingly, the 3' UTR belonging to germ granule mRNAs, such as nanos (nos), have considerable sequence variations among Drosophila species and we hypothesized that this diversity influences homotypic clustering. To test our hypothesis, we investigated the homotypic clustering of nos and polar granule component (pgc) in four Drosophila species and concluded that clustering is a conserved process used to enrich germ granule mRNAs. However, we discovered germ granule phenotypes that included significant changes in the abundance of transcripts present in species' homotypic clusters, which also reflected diversity in the number of coalesced primordial germ cells within their embryonic gonads. By integrating biological data with computational modeling, we found that multiple mechanisms underlie naturally occurring germ granule diversity, including changes in nos, pgc, osk levels and/or homotypic clustering efficacy. Furthermore, we demonstrated how the nos 3' UTR from different species influences nos clustering, causing granules to have ∼70% less nos and increasing the presence of defective primordial germ cells. Our results highlight the impact that evolution has on germ granules, which should provide broader insight into processes that modify compositions and activities of other classes of biomolecular condensate.
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Affiliation(s)
- Dominique A Doyle
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Florencia N Burian
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Benjamin Aharoni
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Annabelle J Klinder
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Melissa M Menzel
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | | | | | - Bianca Ulrich Palma
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Gisselle A Hidalgo
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Christopher J Sottolano
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, USA
| | - Bianca M Ortega
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Matthew G Niepielko
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
- Department of Biological Sciences, Kean University, Union, NJ, USA
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22
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Anuradha, Kumari M, Zinta G, Chauhan R, Kumar A, Singh S, Singh S. Genetic resources and breeding approaches for improvement of amaranth ( Amaranthus spp.) and quinoa ( Chenopodium quinoa). Front Nutr 2023; 10:1129723. [PMID: 37554703 PMCID: PMC10405290 DOI: 10.3389/fnut.2023.1129723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/03/2023] [Indexed: 08/10/2023] Open
Abstract
Nowadays, the human population is more concerned about their diet and very specific in choosing their food sources to ensure a healthy lifestyle and avoid diseases. So people are shifting to more smart nutritious food choices other than regular cereals and staple foods they have been eating for a long time. Pseudocereals, especially, amaranth and quinoa, are important alternatives to traditional cereals due to comparatively higher nutrition, essential minerals, amino acids, and zero gluten. Both Amaranchaceae crops are low-input demanding and hardy plants tolerant to stress, drought, and salinity conditions. Thus, these crops may benefit developing countries that follow subsistence agriculture and have limited farming resources. However, these are underutilized orphan crops, and the efforts to improve them by reducing their saponin content remain ignored for a long time. Furthermore, these crops have very rich variability, but the progress of their genetic gain for getting high-yielding genotypes is slow. Realizing problems in traditional cereals and opting for crop diversification to tackle climate change, research should be focused on the genetic improvement for low saponin, nutritionally rich, tolerant to biotic and abiotic stresses, location-specific photoperiod, and high yielding varietal development of amaranth and quinoa to expand their commercial cultivation. The latest technologies that can accelerate the breeding to improve yield and quality in these crops are much behind and slower than the already established major crops of the world. We could learn from past mistakes and utilize the latest trends such as CRISPR/Cas, TILLING, and RNA interference (RNAi) technology to improve these pseudocereals genetically. Hence, the study reviewed important nutrition quality traits, morphological descriptors, their breeding behavior, available genetic resources, and breeding approaches for these crops to shed light on future breeding strategies to develop superior genotypes.
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Affiliation(s)
- Anuradha
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Manisha Kumari
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Gaurav Zinta
- Division of Biotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Ramesh Chauhan
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Ashok Kumar
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Sanatsujat Singh
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Satbeer Singh
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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23
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Heslop AD, Jahufer Z, Hofmann RW. Responses to water stress extremes in diverse red clover germplasm accessions. Front Plant Sci 2023; 14:1195058. [PMID: 37426971 PMCID: PMC10325626 DOI: 10.3389/fpls.2023.1195058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023]
Abstract
Red clover (Trifolium pratense L.), a key perennial pastoral species used globally, can strengthen pastural mixes to withstand increasingly disruptive weather patterns from climate change. Breeding selections can be refined for this purpose by obtaining an in-depth understanding of key functional traits. A replicated randomized complete block glasshouse pot trial was used to observe trait responses critical to plant performance under control (15% VMC), water deficit (5% VMC) and waterlogged conditions (50% VMC) in seven red clover populations and compared against white clover. Twelve morphological and physiological traits were identified as key contributors to the different plant coping mechanisms displayed. Under water deficit, the levels of all aboveground morphological traits decreased, highlighted by a 41% decrease in total dry matter and 50% decreases in both leaf number and leaf thickness compared to the control treatment. An increase in root to shoot ratio indicated a shift to prioritizing root maintenance by sacrificing shoot growth, a trait attributed to plant water deficit tolerance. Under waterlogging, a reduction in photosynthetic activity among red clover populations reduced several morphological traits including a 30% decrease in root dry mass and total dry matter, and a 34% decrease in leaf number. The importance of root morphology for waterlogging was highlighted with low performance of red clover: there was an 83% decrease in root dry mass compared to white clover which was able to maintain root dry mass and therefore plant performance. This study highlights the importance of germplasm evaluation across water stress extremes to identify traits for future breeding programs.
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Affiliation(s)
- Angus D. Heslop
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
- AgResearch Limited, Lincoln Research Centre, Christchurch, New Zealand
| | - Zulfi Jahufer
- AgResearch Limited, Lincoln Research Centre, Palmerston North, New Zealand
| | - Rainer W. Hofmann
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
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24
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Sapkota D, Zhang D, Park S, Meinhardt LW, Yao S. Genotyping of Jujube ( Ziziphus spp.) Germplasm in New Mexico and Southwestern Texas. Plants (Basel) 2023; 12:2405. [PMID: 37446967 DOI: 10.3390/plants12132405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/15/2023]
Abstract
Since the early 19th century, a substantial amount of jujube (Ziziphus spp.) germplasm has been introduced from China and Europe into the United States. However, due to a lack of passport data, cultivar mislabeling is common and the genetic background of the introduced germplasm remains unknown. In the present study, a low-density SNP array was employed to genotype 204 jujube trees sampled from multiple locations in New Mexico, Texas, Missouri, and Kentucky. Multilocus matching of SNP profiles revealed a significant rate of genetic redundancy among these jujube samples. A total of 14 synonymous groups were detected, comprising 48 accessions. Bayesian clustering analysis and neighbor-joining tree partitioned the US jujube germplasm into two major clusters. The first cluster included cultivated genotypes (Ziziphus jujuba Mill.), whereas the other major cluster comprised the wild/sour jujube (Ziziphus spinosa Hu.). The results also revealed a unique jujube population at Fabens/Tornillo, Texas, and a semi-naturalized population at Tucumcari, NM. These findings will provide valuable guidance to jujube growers and researchers on the effective utilization of jujube germplasm in the horticultural industry.
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Affiliation(s)
- Dikshya Sapkota
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Sunchung Park
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Shengrui Yao
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
- Sustainable Agriculture Sciences Center, New Mexico State University, Alcalde, NM 87511, USA
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25
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Kim SH, Subramanian P, Hahn BS. Glucosinolate Diversity Analysis in Choy Sum (Brassica rapa subsp. chinensis var. parachinensis) Germplasms for Functional Food Breeding. Foods 2023; 12:2400. [PMID: 37372611 DOI: 10.3390/foods12122400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
The aim of this study was to analyze glucosinolates (GSLs) in germplasm that are currently conserved at the RDA-Genebank. The analysis focused on the glucosinolate diversity among the analyzed germplasms, with the goal of identifying those that would be most useful for future breeding efforts to produce nutritionally rich Choy sum plants. In total, 23 accessions of Choy sums that possessed ample background passport information were selected. On analyzing the glucosinolate content for 17 different glucosinolates, we observed aliphatic GSLs to be the most common (89.45%) and aromatic GSLs to be the least common (6.94%) of the total glucosinolates detected. Among the highly represented aliphatic GSLs, gluconapin and glucobrassicanapin were found to contribute the most (>20%), and sinalbin, glucoraphanin, glucoraphasatin, and glucoiberin were detected the least (less than 0.05%). We identified one of the accessions, IT228140, to synthesize high quantities of glucobrassicanapin and progoitrin, which have been reported to contain several therapeutic applications. These conserved germplasms are potential bioresources for breeders, and the availability of information, including therapeutically important glucosinolate content, can help produce plant varieties that can naturally impact public health.
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Affiliation(s)
- Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 5487, Republic of Korea
| | - Parthiban Subramanian
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 5487, Republic of Korea
- Department of Physiology, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha Dental College & Hospitals, Saveetha University, Chennai 600077, India
| | - Bum-Soo Hahn
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 5487, Republic of Korea
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26
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Singh L, Wu Y, McCurdy JD, Stewart BR, Warburton ML, Baldwin BS, Dong H. Genetic diversity and population structure of bermudagrass ( Cynodon spp.) revealed by genotyping-by-sequencing. Front Plant Sci 2023; 14:1155721. [PMID: 37360708 PMCID: PMC10285298 DOI: 10.3389/fpls.2023.1155721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023]
Abstract
Bermudagrass (Cynodon spp.) breeding and cultivar development is hampered by limited information regarding its genetic and phenotypic diversity. To explore diversity in bermudagrass, a total of 206 Cynodon accessions consisting of 193 common bermudagrass (C. dactylon var. dactylon) and 13 African bermudagrass (C. transvaalensis) accessions of worldwide origin were assembled for genetic characterization. Genotyping-by-sequencing (GBS) was employed for genetic marker development. With a minor allele frequency of 0.05 and a minimum call rate of 0.5, a total of 37,496 raw single nucleotide polymorphisms (SNPs) were called de novo and were used in the genetic diversity characterization. Population structure analysis using ADMIXTURE revealed four subpopulations in this germplasm panel, which was consistent with principal component analysis (PCA) and phylogenetic analysis results. The first three principal components explained 15.6%, 10.1%, and 3.8% of the variance in the germplasm panel, respectively. The first subpopulation consisted of C. dactylon accessions from various continents; the second subpopulation was comprised mainly of C. transvaalensis accessions; the third subpopulation contained C. dactylon accessions primarily of African origin; and the fourth subpopulation represented C. dactylon accessions obtained from the Oklahoma State University bermudagrass breeding program. Genetic diversity parameters including Nei's genetic distance, inbreeding coefficient, and Fst statistic revealed substantial genetic variation in the Cynodon accessions, demonstrating the potential of this germplasm panel for further genetic studies and cultivar development in breeding programs.
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Affiliation(s)
- Lovepreet Singh
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Yanqi Wu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
| | - James D. McCurdy
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Barry R. Stewart
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Marilyn L. Warburton
- United States Department of Agriculture – Agricultural Research Service (USDA ARS) Western Regional Plant Introduction Station, Pullman, WA, United States
| | - Brian S. Baldwin
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Hongxu Dong
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
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Iacono R, Slavov GT, Davey CL, Clifton-Brown J, Allison G, Bosch M. Variability of cell wall recalcitrance and composition in genotypes of Miscanthus from different genetic groups and geographical origin. Front Plant Sci 2023; 14:1155188. [PMID: 37346113 PMCID: PMC10279889 DOI: 10.3389/fpls.2023.1155188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/05/2023] [Indexed: 06/23/2023]
Abstract
Miscanthus is a promising crop for bioenergy and biorefining in Europe. The improvement of Miscanthus as a crop relies on the creation of new varieties through the hybridization of germplasm collected in the wild with genetic variation and suitable characteristics in terms of resilience, yield and quality of the biomass. Local adaptation has likely shaped genetic variation for these characteristics and is therefore important to quantify. A key biomass quality parameter for biorefining is the ease of conversion of cell wall polysaccharides to monomeric sugars. Thus far, the variability of cell wall related traits in Miscanthus has mostly been explored in accessions from limited genetic backgrounds. Here we analysed the soil and climatic conditions of the original collection sites of 592 Miscanthus genotypes, which form eight distinct genetic groups based on discriminant analysis of principal components of 25,014 single-nucleotide polymorphisms. Our results show that species of the genus Miscanthus grow naturally across a range of soil and climate conditions. Based on a detailed analysis of 49 representative genotypes, we report generally minor differences in cell wall characteristics between different genetic groups and high levels of genetic variation within groups, with less investigated species like M. floridulus showing lower recalcitrance compared to the other genetic groups. The results emphasize that both inter- and intra- specific variation in cell wall characteristics and biomass recalcitrance can be used effectively in Miscanthus breeding programmes, while also reinforcing the importance of considering biomass yield when quantifying overall conversion efficiency. Thus, in addition to reflecting the complexity of the interactions between compositional and structural cell wall features and cell wall recalcitrance to sugar release, our results point to traits that could potentially require attention in breeding programmes targeted at improving the Miscanthus biomass crop.
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Affiliation(s)
- Rosario Iacono
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, United Kingdom
| | - Gancho T. Slavov
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, United Kingdom
- Radiata Pine Breeding Company, Rotorua, New Zealand
| | - Christopher L. Davey
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, United Kingdom
| | - John Clifton-Brown
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, United Kingdom
- Department of Agronomy and Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Gordon Allison
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, United Kingdom
| | - Maurice Bosch
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, United Kingdom
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Bibi S, Awan MA, Rakha BA, Ejaz R, Qadeer S, Arshad J, Anjum MZ, Akhter S. Evaluation of carboxylated poly l-lysine for cryopreservation of Labeo rohita sperm. Reprod Domest Anim 2023. [PMID: 37191551 DOI: 10.1111/rda.14391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/16/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023]
Abstract
Carboxylated poly l-lysine (CPLL) is an anti-freeze agent having pronounced non-permeating yet membrane stabilizing cryoprotective capabilities. The objective was to evaluate the CPLL supplementation in extender in terms of post thaw quality (sperm), total antioxidant activity (milt) and fertilization potential of cryopreserved Labeo rohita sperm. For this purpose, male brood fish reared at fish seed hatchery, Rawal Town Islamabad, Pakistan were captured from different rearing ponds and acclimatized in hatchery ponds for 6 hours. The brooder were injected with Ovaprim (0.2 ml/kg), milt was collected after 8 hours in cooled sterilized falcon tubes, maintained at 4°C and evaluated for sperm motility. The milt collected from three brooders (n=3) was diluted in extenders viz., modified Kurokura-2 extender having 10% methanol (control); experimental extenders with CPLL supplementation at the rate of 0.5%, 1% and 1.5%. Diluted milt was filled in 0.5ml straws, exposed to liquid nitrogen vapors and cryopreserved. Cryopreserved milt was thawed at 250 C and assessed for post-thaw sperm quality. Sperm motility, motility duration, viability, total antioxidant capacity and DNA integrity was significantly higher (P<0.05) in extender having 1.5% CPLL than control. To evaluate the fertilization rates, male and female brooders were injected with Ovaprim at 0.2ml/Kg and 0.5ml/Kg body weight respectively. Fresh eggs and milt were collected through abdominal stripping. Batches of 10g of eggs from each female (n=2) were fertilized with one straw, each from frozen sperm with KE+methanol (control), KE+methanol+1.5% CPLL and 50 μl fresh milt (negative control). After 1.5 hours of fertilization, eggs were collected from all jars and a total of 200 eggs were counted. The fertilized eggs appeared clear and transparent while unfertilized eggs looked opaque with disintegrated nucleus. Sperm fertilization rate (%) was higher (P<0.05) in extender KE+methanol+1.5%CPLL (78.7±0.5) compared to control (KE+methanol) (52.0±0.4) however, it was lower compared to that of negative control, the fresh milt (85.2±0.6). In conclusion, supplementation of carboxylated poly l-lysine (1.5%) to modified Kurokura-2 extender having 10% methanol improves post thaw motility, motility duration, viability, DNA integrity, anti-oxidant capacity (milt) and fertilizing ability of cryopreserved L. rohita sperm.
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Affiliation(s)
- Shaista Bibi
- Department of Zoology, Wildlife and Fisheries, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi-46300, Pakistan
- Department of Fisheries, Government of Punjab, Pakistan
| | - Muhammad Amjad Awan
- Department of Zoology, Wildlife and Fisheries, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi-46300, Pakistan
| | - Bushra Allah Rakha
- Department of Zoology, Wildlife and Fisheries, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi-46300, Pakistan
| | - Rabea Ejaz
- Department of Zoology, Rawalpindi Women University, Rawalpindi, Pakistan
| | - Saima Qadeer
- Department of Zoology, University of Education, Jauharabad Campus Khushab, Pakistan
| | - Javeria Arshad
- Department of Zoology, Wildlife and Fisheries, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi-46300, Pakistan
| | - Muhammad Zubair Anjum
- Department of Zoology, Wildlife and Fisheries, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi-46300, Pakistan
| | - Shamim Akhter
- Department of Zoology, Wildlife and Fisheries, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi-46300, Pakistan
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Ashfaq M, Rasheed A, Zhu R, Ali M, Javed MA, Anwar A, Tabassum J, Shaheen S, Wu X. Genome-Wide Association Mapping for Yield and Yield-Related Traits in Rice ( Oryza Sativa L.) Using SNPs Markers. Genes (Basel) 2023; 14:genes14051089. [PMID: 37239449 DOI: 10.3390/genes14051089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Rice (Oryza sativa L.) is a staple food for more than 50% of the world's population. Rice cultivar improvement is critical in order to feed the world's growing population. Improving yield is one of the main aims of rice breeders. However, yield is a complex quantitative trait controlled by many genes. The presence of genetic diversity is the key factor to improve the yield hence, the presence of diversity in any germplasm is important for yield improvement. In the current study, the rice germplasm was collected from Pakistan and the United States of America and a panel of 100 diverse genotypes was utilized to identify important yield and yield-related traits. For this, a genome-wide association study (GWAS) was performed to identify the genetic loci related to yield. The GWAS on the diverse germplasm will lead to the identification of new genes which can be utilized in the breeding program for improvement of yield. For this reason, firstly, the germplasm was phenotypically evaluated in two growing seasons for yield and yield-related traits. The analysis of variance results showed significant differences among traits which showed the presence of diversity in the current germplasm. Secondly, the germplasm was also genotypically evaluated using 10K SNP. Genetic structure analysis showed the presence of four groups which showed that enough genetic diversity was present in the rice germplasm to be used for association mapping analysis. The results of GWAS identified 201 significant marker trait associations (MTAs. 16 MTAs were identified for plant height, 49 for days to flowering, three for days to maturity, four for tillers per plant, four for panicle length, eight for grains per panicle, 20 unfilled grains per panicle, 81 for seed setting %, four for thousand-grain weight, five for yield per plot and seven for yield per hectare. Apart from this, some pleiotropic loci were also identified. The results showed that panicle length (PL) and thousand-grain weight (TGW) were controlled by a pleiotropic locus OsGRb23906 on chromosome 1 at 10,116,371 cM. The loci OsGRb25803 and OsGRb15974 on chromosomes 4 and 8 at the position of 14,321,111 cM and 6,205,816 cM respectively, showed pleiotropic effects for seed setting % (SS) and unfilled grain per panicle (UG/P). A locus OsGRb09180 on chromosome 4 at 19,850,601 cM was significantly linked with SS and yield/ha. Furthermore, gene annotation was performed, and results indicated that the 190 candidate genes or QTLs that closely linked with studied traits. These candidate genes and novel significant markers could be useful in marker-assisted gene selection and QTL pyramiding to improve rice yield and the selection of potential parents, recombinants and MTAs which could be used in rice breeding programs to develop high-yielding rice varieties for sustainable food security.
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Affiliation(s)
- Muhammad Ashfaq
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Abdul Rasheed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Renshan Zhu
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Muhammad Ali
- Department of Entomology, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Alia Anwar
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Javaria Tabassum
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Shabnum Shaheen
- Department of Botany, Lahore College for Women University, Lahore 54590, Pakistan
| | - Xianting Wu
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Wang X, Bai S, Zhang Z, Zheng F, Song L, Wen L, Guo M, Cheng G, Yao W, Gao Y, Li J. Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution. Front Plant Sci 2023; 14:1179009. [PMID: 37229122 PMCID: PMC10203424 DOI: 10.3389/fpls.2023.1179009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023]
Abstract
In order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and intron, inverted repeat regions, and repeat sequences among the 29 cp genomes. Moreover, single-nucleotide polymorphism (SNP) loci with high polymorphism located at 17 fragments were selected as candidate SNP markers for future studies. In the phylogenetic tree, the cp genomes of tomatoes were clustered into two major clades, and the genetic relationship between S. pimpinellifolium and S. lycopersicum was very close. In addition, only rps15 showed the highest average K A/K S ratio in the analysis of adaptive evolution, which was strongly positively selected. It may be very important for the study of adaptive evolution and breeding of tomato. In general, this study provides valuable information for further study of phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.
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Affiliation(s)
- Xiaomin Wang
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Shengyi Bai
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Fushun Zheng
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Lina Song
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Lu Wen
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Meng Guo
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Guoxin Cheng
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Wenkong Yao
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Yanming Gao
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Jianshe Li
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
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Wang Q, Ban J, Cai R, Zhang X, Lai C, Chen Y, Li X, Chen C, Chen Y, Zhang Z, Lai Z, Lin Y. Metabolic Composition and Quality Traits of Polygonatum cyrtonema Hua from Different Germplasms and Age Sections Based on Widely Targeted Metabolomics Analysis. Int J Mol Sci 2023; 24:ijms24076077. [PMID: 37047050 PMCID: PMC10094609 DOI: 10.3390/ijms24076077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Polygonatum rhizomes are rich in various compounds with many biological activities and are widely used in functional foods and pharmaceutical products. In order to screen for superior Polygonatum cyrtonema Hua (P. cyrtonema) germplasm and also to elucidate the nutritional and medicinal values of rhizomes, the metabolic composition and quality traits of rhizomes from different germplasms and age sections of P. cyrtonema were analysed by widely targeted metabolomics, and the molecular mechanism of triacylglycerol synthesis was explored. The results showed that the different germplasms and age sections of P. cyrtonema were rich in different nutritional and medicinal components. Of these, the broad-leaved green stem (GK) germplasm is rich in polysaccharides, alkaloids, and lipids; the pointed-leaved green stem (JL) germplasm is rich in flavonoids, steroids, and amino acids, while the pointed-leaved purple stem (JZ) germplasm contains more phenolic acids. The one-year (AT) age section is rich in polysaccharides, steroids, organic acids, and lipids; the three years (CT) age section contains more flavonoids, alkaloids, and amino acid metabolites. Lipids were significantly enriched in the broad-leaved green stem germplasm and the one-year age section. Interestingly, the highest accumulation of triacylglycerols, an important component of lipids, was also found in the GK germplasm and the AT age section. Nineteen, 14, and 13 members of the glycerol-3-phosphate acyltransferase (GPAT), lysophosphatidic acid acyltransferase (LPAT), and diacylglycerol acyltransferase (DGAT) gene families, respectively, involved in triacylglycerol synthesis were also identified. The quantitative real-time PCR (qRT-PCR) results further suggested that the differentially expressed PcDGAT1, PcDGAT2.4, PcGPAT9.1, PcLPAT2.9, and PcLPAT4.3 genes may play important roles in triacylglycerol synthesis in P. cyrtonema. Therefore, this study provides a new theoretical reference for product development and the breeding of new varieties of Polygonatum species.
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Affiliation(s)
- Qingshuang Wang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingjie Ban
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Roudi Cai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunwang Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoli Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuirong Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Hernandez CO, Labate J, Reitsma K, Fabrizio J, Bao K, Fei Z, Grumet R, Mazourek M. Characterization of the USDA Cucurbita pepo, C. moschata, and C. maxima germplasm collections. Front Plant Sci 2023; 14:1130814. [PMID: 36993863 PMCID: PMC10040574 DOI: 10.3389/fpls.2023.1130814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
The Cucurbita genus is home to a number of economically and culturally important species. We present the analysis of genotype data generated through genotyping-by-sequencing of the USDA germplasm collections of Cucurbita pepo, C. moschata, and C. maxima. These collections include a mixture of wild, landrace, and cultivated specimens from all over the world. Roughly 1,500 - 32,000 high-quality single nucleotide polymorphisms (SNPs) were called in each of the collections, which ranged in size from 314 to 829 accessions. Genomic analyses were conducted to characterize the diversity in each of the species. Analysis revealed extensive structure corresponding to a combination of geographical origin and morphotype/market class. Genome-wide associate studies (GWAS) were conducted using both historical and contemporary data. Signals were observed for several traits, but the strongest was for the bush (Bu) gene in C. pepo. Analysis of genomic heritability, together with population structure and GWAS results, was used to demonstrate a close alignment of seed size in C. pepo, maturity in C. moschata, and plant habit in C. maxima with genetic subgroups. These data represent a large, valuable collection of sequenced Cucurbita that can be used to direct the maintenance of genetic diversity, for developing breeding resources, and to help prioritize whole-genome re-sequencing.
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Affiliation(s)
- Christopher O. Hernandez
- Department of Agriculture Nutrition and Food Systems, University of New Hampshire, Durham, NH, United States
| | - Joanne Labate
- Plant Genetic Resource Conservation Unit, United States Department of Agricultural Research Service, Geneva, NY, United States
| | - Kathleen Reitsma
- North Central Regional Plant Introduction Station, Iowa State University, Ames, IA, United States
| | - Jack Fabrizio
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Kan Bao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
- U.S. Department of Agriculture-Agriculture Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Michael Mazourek
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
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Cortés AJ, Barnaby JY. Editorial: Harnessing genebanks: High-throughput phenotyping and genotyping of crop wild relatives and landraces. Front Plant Sci 2023; 14:1149469. [PMID: 36968416 PMCID: PMC10036837 DOI: 10.3389/fpls.2023.1149469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria – AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Jinyoung Y. Barnaby
- U.S. Department of Agriculture, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, MD, United States
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Cice D, Ferrara E, Magri A, Adiletta G, Capriolo G, Rega P, Di Matteo M, Petriccione M. Autochthonous Apple Cultivars from the Campania Region (Southern Italy): Bio-Agronomic and Qualitative Traits. Plants (Basel) 2023; 12:1160. [PMID: 36904021 PMCID: PMC10007192 DOI: 10.3390/plants12051160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Apple (Malus × domestica Borkh.) is an important fruit crop widely spread in the cold and mild climates of temperate regions in the world, with more than 93 million tons harvested worldwide in 2021. The object of this work was to analyze thirty-one local apple cultivars of the Campania region (Southern Italy) using agronomic, morphological (UPOV descriptors) and physicochemical (solid soluble content, texture, pH and titratable acidity, skin color, Young's modulus and browning index) traits. UPOV descriptors highlighted similarities and differences among apple cultivars with a depth phenotypic characterization. Apple cultivars showed significant differences in fruit weight (31.3-236.02 g) and physicochemical trait ranging from 8.0 to 14.64° Brix for solid soluble content, 2.34-10.38 g malic acid L-1 for titratable acidity, and 15-40% for browning index. Furthermore, different percentages in apple shape and skin color have been detected. Similarities among the cultivars based on their bio-agronomic and qualitative traits have been evaluated by cluster analyses and principal component analyses. This apple germplasm collection represents an irreplaceable genetic resource with considerable morphological and pomological variabilities among several cultivars. Nowadays, some local cultivars, widespread only in restricted geographical areas, could be reintroduced in cultivation contribution to improving the diversity of our diets and contemporary to preserve knowledge on traditional agricultural systems.
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Affiliation(s)
- Danilo Cice
- CREA, Council for Agricultural Research and Economics, Research Centre for Olive, Fruits and Citrus Crops, Via Torrino 3, 81100 Caserta, Italy
| | - Elvira Ferrara
- CREA, Council for Agricultural Research and Economics, Research Centre for Olive, Fruits and Citrus Crops, Via Torrino 3, 81100 Caserta, Italy
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Anna Magri
- CREA, Council for Agricultural Research and Economics, Research Centre for Olive, Fruits and Citrus Crops, Via Torrino 3, 81100 Caserta, Italy
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Giuseppina Adiletta
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 84084 Fisciano, Italy
| | - Giuseppe Capriolo
- CREA, Council for Agricultural Research and Economics, Research Centre for Olive, Fruits and Citrus Crops, Via Torrino 3, 81100 Caserta, Italy
| | - Pietro Rega
- CREA, Council for Agricultural Research and Economics, Research Centre for Olive, Fruits and Citrus Crops, Via Torrino 3, 81100 Caserta, Italy
| | - Marisa Di Matteo
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 84084 Fisciano, Italy
| | - Milena Petriccione
- CREA, Council for Agricultural Research and Economics, Research Centre for Olive, Fruits and Citrus Crops, Via Torrino 3, 81100 Caserta, Italy
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Nicolao R, Gaiero P, Castro CM, Heiden G. Solanum malmeanum, a promising wild relative for potato breeding. Front Plant Sci 2023; 13:1046702. [PMID: 36891130 PMCID: PMC9986444 DOI: 10.3389/fpls.2022.1046702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Crop wild relatives are gaining increasing attention. Their use in plant breeding is essential to broaden the genetic basis of crops as well as to meet industrial demands, for global food security and sustainable production. Solanum malmeanum (Solanum sect. Petota, Solanaceae) is a wild relative of potatoes (S. tuberosum) from Southern South America, occurring in Argentina, Brazil, Paraguay and Uruguay. This wild potato has been largely mistaken for or historically considered as conspecific with S. commersonii. Recently, it was reinstated at the species level. Retrieving information on its traits and applied uses is challenging, because the species name has not always been applied correctly and also because species circumscriptions and morphological criteria applied to recognize it have not been consistent. To overcome these difficulties, we performed a thorough literature reference survey, herbaria specimens' identification revision and genebank database queries to review and update the information available on this potato wild relative, contributing to an increase in research on it to fully understand and explore its potential for potato breeding. Scarce studies have been carried out concerning its reproductive biology, resistance against pests and diseases as well as tolerance to abiotic stresses and evaluation of quality traits. The scattered information available makes it less represented in genebanks and genetic studies are missing. We compile, update and present available information for S. malmeanum on taxonomy, geographical distribution, ecology, reproductive biology, relationship with its closest relatives, biotic and abiotic stresses resistance and quality traits and discuss ways to overcome sexual barriers of hybridization and future perspectives for its use in potato breeding. As a final remark, we highlight that this species' potential uses have been neglected and must be unlocked. Thus, further studies on morphological and genetic variability with molecular tools are fundamental for an efficient conservation and applied use of this promising genetic resource.
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Affiliation(s)
- Rodrigo Nicolao
- Programa de Pós-Graduação em Agronomia/Fitomelhoramento - Universidade Federal de Pelotas (UFPel), Pelotas, RS, Brazil
| | - Paola Gaiero
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Caroline M. Castro
- Laboratório de Recursos Genéticos, Embrapa Clima Temperado, Pelotas, RS, Brazil
| | - Gustavo Heiden
- Laboratório de Recursos Genéticos, Embrapa Clima Temperado, Pelotas, RS, Brazil
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Rispail N, Wohor OZ, Osuna-Caballero S, Barilli E, Rubiales D. Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection. Int J Mol Sci 2023; 24:2470. [PMID: 36768792 PMCID: PMC9916889 DOI: 10.3390/ijms24032470] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Peas (Pisum sativum) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers. More than 90% of these markers mapped onto the pea reference genome, with an average of 2787 SilicoDArT and 1644 SNP markers per chromosome, and an average LD50 distance of 0.48 and 1.38 Mbp, respectively. The pea core collection clustered in three or six subpopulations depending on the pea subspecies. Many admixed accessions were also detected, confirming the frequent genetic exchange between populations. Our results support the classification of Pisum genus into two species, P. fulvum and P. sativum (including subsp. sativum, arvense, elatius, humile, jomardii and abyssinicum). In addition, the study showed that wild alleles were incorporated into the cultivated pea through the intermediate P. sativum subsp. jomardii and P. sativum subsp. arvense during pea domestication, which have important implications for breeding programs. The high genetic diversity found in the collection and the high marker coverage are also expected to improve trait discovery and the efficient implementation of advanced breeding approaches.
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Affiliation(s)
- Nicolas Rispail
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Osman Zakaria Wohor
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Savanna Agriculture Research Institute, CSIR, Nyankpala, Tamale P.O. Box TL52, Ghana
| | | | - Eleonora Barilli
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Diego Rubiales
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
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Lu-Irving P, Bragg JG, Rossetto M, King K, O’Brien M, van der Merwe MM. Capturing Genetic Diversity in Seed Collections: An Empirical Study of Two Congeners with Contrasting Mating Systems. Plants (Basel) 2023; 12:522. [PMID: 36771606 PMCID: PMC9921034 DOI: 10.3390/plants12030522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Plant mating systems shape patterns of genetic diversity and impact the long-term success of populations. As such, they are relevant to the design of seed collections aiming to maximise genetic diversity (e.g., germplasm conservation, ecological restoration). However, for most species, little is known empirically about how variation in mating systems and genetic diversity is distributed. We investigated the relationship between genetic diversity and mating systems in two functionally similar, co-occurring species of Hakea (Proteaceae), and evaluated the extent to which genetic diversity was captured in seeds. We genotyped hundreds of seedlings and mother plants via DArTseq, and developed novel implementations of two approaches to inferring the mating system from SNP data. A striking contrast in patterns of genetic diversity between H. sericea and H. teretifolia was revealed, consistent with a contrast in their mating systems. While both species had mixed mating systems, H. sericea was found to be habitually selfing, while H. teretifolia more evenly employed both selfing and outcrossing. In both species, seed collection schemes maximised genetic diversity by increasing the number of maternal lines and sites sampled, but twice as many sites were needed for the selfing species to capture equivalent levels of genetic variation at a regional scale.
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Affiliation(s)
- Patricia Lu-Irving
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Jason G. Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Kit King
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Mitchell O’Brien
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Innovation Quarter Westmead, Level 3, East Tower, 158-164 Hawkesbury Rd., Westmead, NSW 2145, Australia
| | - Marlien M. van der Merwe
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
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Dell'Olmo E, Zaccardelli M, Basile B, Corrado G, Sigillo L. Identification and Characterization of New Seedborne Pathogens in Phaseolus vulgaris Landraces of Southern Italy. Pathogens 2023; 12. [PMID: 36678456 DOI: 10.3390/pathogens12010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/28/2022] [Accepted: 01/03/2023] [Indexed: 01/10/2023] Open
Abstract
The diagnostic survey of seedborne fungal pathogens is fundamental for symptomless material stored in gene banks to avoid the diffusion of pathogens by germplasm distribution and propagation. In this work, seeds of Southern Italian landraces of the common bean (Phaseolus vulgaris L.) belonging to the gene bank at CREA (Italy) were inspected to assess their phytosanitary status. The phytopathological analysis revealed the presence of the most common pathogens associated with common bean seeds such as Fusarium spp., Macrophomina phaseolina, Rhizoctonia solani, Colletotrichum lindemuthianum and Diaporthe/Phomopsis complex. However, new fungi able to completely inhibit seed germination were also observed. The most aggressive were isolated, and the morpho-pathological characterization, DNA sequencing and phylogenetic analysis allowed us to define the strains as Botryosphaeria dothidea CREA OF 360.4 and Diplodia mutila CREA OF 420.36. These two plant pathogens are generally associated with grapevines and other fruit trees. Pathogenicity tests were carried out along with a transmissibility test in which the transmission of the pathogens to the seedlings was proven. Host range experiments revealed the ability of these pathogens to infect crops such as pepper and melon. To our knowledge, this is the first time that B. dothidea and D. mutila were detected on the common bean.
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Farneti B, Khomenko I, Ajelli M, Wells KE, Betta E, Aprea E, Giongo L, Biasioli F. Volatilomics of raspberry fruit germplasm by combining chromatographic and direct-injection mass spectrometric techniques. Front Mol Biosci 2023; 10:1155564. [PMID: 37122562 PMCID: PMC10133483 DOI: 10.3389/fmolb.2023.1155564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
The application of direct-injection mass spectrometric (DI-MS) techniques, like Proton Transfer Reaction Time of Flight Mass Spectrometry (PTR-ToF-MS) has been suggested as a reliable phenotyping tool for fruit volatilome assessment in both genetic and quality-related studies. In this study the complexity of raspberry aroma was investigated by a comprehensive untargeted VOC analysis, done by combining SPME-GC-MS and PTR-ToF-MS assessments with multi-block discriminant analysis using the DIABLO mixOmics framework. The aim was to acquire an exhaustive characterization of the raspberry volatilome according to different fruit ripening stages (pink, ripe, and overripe) and genetic variances (50 accessions), as well as to investigate the potential of PTR-ToF-MS as a rapid and high throughput VOC phenotyping tool to address issues related to raspberry fruit quality. Results of this study demonstrated the complementarity between SPME-GC-MS and PTR-ToF-MS techniques to evaluate the raspberry aroma composition. PTR-ToF-MS generates reliable raspberry VOC fingerprints mainly due to a reduced compound fragmentation and precise content estimation. In addition, the high collinearity between isomers of monoterpenes and norisoprenoids, discovered by GC analysis, reduces the main analytic limitation of PTR-ToF-MS of not being able to separate isomeric molecules. The high similarity between the VOC matrices obtained by applying PTR-ToF-MS and SPME-GC-MS confirmed the possibility of using PTR-ToF-MS as a reliable high throughput phenotyping tool for raspberry volatiolome assessment. In addition, results provided by the germplasm collection investigation enabled to distinguish the best performing accessions, based on VOCs composition, to be used as superior parental lines for future breeding programs.
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Affiliation(s)
- Brian Farneti
- Berries Genetics and Breeding Unit, Research and Innovation Centre of Fondazione Edmund Mach, Trento, Italy
- *Correspondence: Brian Farneti,
| | - Iuliia Khomenko
- Sensory Quality Unit, Research and Innovation Centre of Fondazione Edmund Mach, Trento, Italy
| | - Matteo Ajelli
- Berries Genetics and Breeding Unit, Research and Innovation Centre of Fondazione Edmund Mach, Trento, Italy
| | - Karen Elizabeth Wells
- Berries Genetics and Breeding Unit, Research and Innovation Centre of Fondazione Edmund Mach, Trento, Italy
| | - Emanuela Betta
- Sensory Quality Unit, Research and Innovation Centre of Fondazione Edmund Mach, Trento, Italy
| | - Eugenio Aprea
- Sensory Quality Unit, Research and Innovation Centre of Fondazione Edmund Mach, Trento, Italy
- Center Agriculture Food Environment C3A, University of Trento, Trento, Italy
| | - Lara Giongo
- Berries Genetics and Breeding Unit, Research and Innovation Centre of Fondazione Edmund Mach, Trento, Italy
| | - Franco Biasioli
- Sensory Quality Unit, Research and Innovation Centre of Fondazione Edmund Mach, Trento, Italy
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Chen T, Li G, Zhang H. Editorial: Advances in peanut research. Front Plant Sci 2023; 14:1180009. [PMID: 37082345 PMCID: PMC10111223 DOI: 10.3389/fpls.2023.1180009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Affiliation(s)
- Tingting Chen
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- *Correspondence: Tingting Chen,
| | - Guowei Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hong Zhang
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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Dudekula MV, Kandasamy V, Balaraman SS, Selvamani SB, Muthurajan R, Adhimoolam K, Manoharan B, Natesan S. Unlocking the genetic diversity of Indian turmeric ( Curcuma longa L.) germplasm based on rhizome yield traits and curcuminoids. Front Plant Sci 2022; 13:1036592. [PMID: 36589076 PMCID: PMC9797976 DOI: 10.3389/fpls.2022.1036592] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Turmeric is an important commercial crop widely grown in Asia due to its pharmacological and nutritional value. India is the centre of turmeric diversity and many turmeric accessions have good rhizome yield, varying curcuminoids content and are well-adapted to various agro-climatic zones. In the present study, we unravel the diversity among 200 Indian turmeric accessions based on rhizome yield traits and curcuminoids content. Clustering and correlation studies were also performed to group the turmeric accessions and to observe the relationship between the traits. Results revealed the presence of large variability among turmeric accessions including the major traits such as yield (24.77 g p-1 to 667.63 g p-1), dry recovery percentage (13.42% to 29.18%), curcumin (0.41% to 2.17%), demethoxycurcumin (0.38% to 1.45%), bisdemethoxycurcumin (0.37% to 1.24%) and total curcuminoid content (1.26% to 4.55%). The superior germplasm identified for curcuminoids content were as follows; curcumin (CL 157 - 2.17% and CL 272 - 2.13%), demethoxycurcumin (CL 253 - 1.45% and CL 157 - 1.31%), bisdemethoxycurcumin (CL 216 - 1.24% and CL 57 - 1.11%) and total curcuminoid content (CL 157 - 4.55% and CL 272 - 4.37%). Clustering based on dendrogram, grouped 200 accessions into seven clusters. Among seven clusters, the maximum number of accessions were grouped into cluster II while cluster VII showed maximum mean value for majority of the traits. Correlation analysis revealed a significant relationship between the traits where the total curcuminoid content is significantly and positively correlated with the primary rhizome core diameter and length of the secondary rhizome. The selection of these particular traits may result in the identification of germplasm with high total curcuminoid content. Taken together, it is the first report on the large screening of turmeric accessions for variation in the rhizome yield traits and curcuminoids content. The genetic diversity revealed in this study could be useful for further crop improvement programs in turmeric to develop new varieties with high rhizome yield coupled with high curcuminoids content.
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Affiliation(s)
- Mastan Vali Dudekula
- Department of Spices and Plantation Crops, Horticultural College and Research Institute, Tamil Nadu Agricultural University, Coimbatore, India
| | - Venkatesan Kandasamy
- Department of Spices and Plantation Crops, Horticultural College and Research Institute, Tamil Nadu Agricultural University, Coimbatore, India
| | - Senthamizh Selvi Balaraman
- Department of Spices and Plantation Crops, Horticultural College and Research Institute, Tamil Nadu Agricultural University, Coimbatore, India
| | - Selva Babu Selvamani
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Karthikeyan Adhimoolam
- Department of Biotechnology, Centre of Innovation, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, South Korea
| | - Bharani Manoharan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Senthil Natesan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Parashuram S, Singh NV, Gaikwad NN, Corrado G, Roopa Sowjanya P, Basile B, Devaraja NS, Chandra R, Babu KD, Patil PG, Kumar P, Singh A, Marathe RA. Morphological, Biochemical, and Molecular Diversity of an Indian Ex Situ Collection of Pomegranate ( Punica granatum L.). Plants (Basel) 2022; 11:3518. [PMID: 36559629 PMCID: PMC9781629 DOI: 10.3390/plants11243518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/21/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Pomegranate (Punica granatum, L.) is a fruit tree that is increasingly popular worldwide due to the health-related properties of the fruit juice. While several studies highlighted the rich phytochemical diversity, few efforts have been devoted to an integrative understanding of the level of diversity of this species. This study investigated the diversity of 40 pomegranate accessions in an Indian ex situ collection by using twenty-nine morphological traits, six biochemical parameters, and twenty-nine Simple Sequence Repeats (SSR) markers. Among the evaluated traits, fruit volume (23.34% CV), fruit weight (21.12% CV), and fruit color (*a) (22.69 % CV) largely contributed to the morphological classification. Based on Mahalanobis D2 distance and Tocher's clustering, the 40 pomegranate accessions were grouped into eight clusters, partly consistent with their origin. Specifically, cultivars introduced from foreign countries were present in distinct clusters. The SSR marker analysis generated 66 alleles. The observed heterozygosity values ranged from 0.05 to 0.63, with a mean value of 0.30. Maximum molecular genetic dissimilarity was observed between 'IC-318720' and 'Gul-e-Shah Red' (0.30). The neighbor-joining dendrogram separated wild accessions from cultivated varieties. The combination of morphological, biochemical, and molecular characterization allowed for comprehensively characterizing the pomegranate diversity and provided information on the relationships between the different aspects of the diversity. This work also suggests that the origin of the accessions is an important factor of discrimination and that the level of admixture between local and foreign material is currently limited.
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Affiliation(s)
- Shilpa Parashuram
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
| | - Nripendra Vikram Singh
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
| | | | - Giandomenico Corrado
- Department of Agricultural Sciences, University of Naples Federico II, 80138 Portici, NA, Italy
| | - P. Roopa Sowjanya
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
| | - Boris Basile
- Department of Agricultural Sciences, University of Naples Federico II, 80138 Portici, NA, Italy
| | - Nitesh Shirur Devaraja
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture & Technology, Kanpur 208002, Utter Pradesh, India
| | - Ram Chandra
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
| | | | - Prakash Goudappa Patil
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
| | - Pradeep Kumar
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, Rajasthan, India
| | - Akath Singh
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, Rajasthan, India
| | - Rajiv Arvind Marathe
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
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Larrea-Sarmiento AE, Olmedo-Velarde A, Wang X, Borth W, Domingo R, Matsumoto TK, Suzuki JY, Wall MM, Melzer MJ, Hu J. Genetic Diversity of Viral Populations Associated with Ananas Germplasm and Improvement of Virus Diagnostic Protocols. Pathogens 2022; 11. [PMID: 36558805 DOI: 10.3390/pathogens11121470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Pineapple (Ananas comosus L. [Merr.]) accessions from the U.S. Tropical Plant Genetic Resources and Disease Research (TPGRDR) in Hilo, Hawaii were subjected to RNA-sequencing to study the occurrence of viral populations associated with this vegetatively propagated crop. Analysis of high-throughput sequencing data obtained from 24 germplasm accessions and public domain transcriptome shotgun assembly (TSA) data identified two novel sadwaviruses, putatively named "pineapple secovirus C" (PSV-C) and "pineapple secovirus D" (PSV-D). They shared low amino acid sequence identity (from 34.8 to 41.3%) compared with their homologs in the Pro-pol region of the previously reported PSV-A and PSV-B. The complete genome (7485 bp) corresponding to a previously reported partial sequence of the badnavirus, pineapple bacilliform ER virus (PBERV), was retrieved from one of the datasets. Overall, we discovered a total of 69 viral sequences representing ten members within the Ampelovirus, Sadwavirus, and Badnavirus genera. Genetic diversity and recombination events were found in members of the pineapple mealybug wilt-associated virus (PMWaV) complex as well as PSVs. PMWaV-1, -3, and -6 presented recombination events across the quintuple gene block, while no recombination events were found for PMWaV-2. High recombination frequency of the RNA1 and RNA2 molecules from PSV-A and PSV-B were congruent with the diversity found by phylogenetic analyses. Here, we also report the development and improvement of RT-PCR diagnostic protocols for the specific identification and detection of viruses infecting pineapple based on the diverse viral populations characterized in this study. Given the high occurrence of recombination events, diversity, and discovery of viruses found in Ananas germplasm, the reported and validated RT-PCR assays represent an important advance for surveillance of viral infections of pineapple.
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Sánchez E, Ali Z, Islam T, Mahfouz M. A CRISPR-based lateral flow assay for plant genotyping and pathogen diagnostics. Plant Biotechnol J 2022; 20:2418-2429. [PMID: 36072993 PMCID: PMC9674313 DOI: 10.1111/pbi.13924] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/14/2022] [Accepted: 08/28/2022] [Indexed: 05/27/2023]
Abstract
Efficient pathogen diagnostics and genotyping methods enable effective disease management and breeding, improve crop productivity and ensure food security. However, current germplasm selection and pathogen detection techniques are laborious, time-consuming, expensive and not easy to mass-scale application in the field. Here, we optimized a field-deployable lateral flow assay, Bio-SCAN, as a highly sensitive tool to precisely identify elite germplasm and detect mutations, transgenes and phytopathogens in <1 h, starting from sample isolation to result output using lateral flow strips. As a proof of concept, we genotyped various wheat germplasms for the Lr34 and Lr67 alleles conferring broad-spectrum resistance to stripe rust, confirmed the presence of synthetically produced herbicide-resistant alleles in the rice genome and screened for the presence of transgenic elements in the genome of transgenic tobacco and rice plants with 100% specificity. We also successfully applied this new assay to the detection of phytopathogens, including viruses and bacterial pathogens in Nicotiana benthamiana, and two destructive fungal pathogens (Puccinia striiformis f. sp. tritici and Magnaporthe oryzae Triticum) in wheat. Our results illustrate the power of Bio-SCAN in crop breeding, genetic engineering and pathogen diagnostics to enhance food security. The high sensitivity, simplicity, versatility and in-field deployability make the Bio-SCAN as an attractive molecular diagnostic tool for diverse applications in agriculture.
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Affiliation(s)
- Edith Sánchez
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE)Bangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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Baek SG, Park JJ, Kim S, Lee MJ, Paek JS, Choi J, Jang JY, Kim J, Lee T. Evaluation of Barley and Wheat Germplasm for Resistance to Head Blight and Mycotoxin Production by Fusarium asiaticum and F. graminearum. Plant Pathol J 2022; 38:637-645. [PMID: 36503192 PMCID: PMC9742790 DOI: 10.5423/ppj.oa.09.2022.0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Fusarium head blight (FHB) is one of the most serious diseases in barley and wheat, as it is usually accompanied by the production of harmful mycotoxins in the grains. To identify FHB-resistant breeding resources, we evaluated 60 elite germplasm accessions of barley (24) and wheat (36) for FHB and mycotoxin accumulation. Assessments were performed in a greenhouse and five heads per accession were inoculated with both Fusarium asiaticum (Fa73, nivalenol producer) and F. graminearum (Fg39, deoxynivalenol producer) strains. While the accessions varied in disease severity and mycotoxin production, four wheat and one barley showed <20% FHB severity repeatedly by both strains. Mycotoxin levels in these accessions ranged up to 3.9 mg/kg. FHB severity was generally higher in barley than in wheat, and Fa73 was more aggressive in both crops than Fg39. Fg39 itself, however, was more aggressive toward wheat and produced more mycotoxin in wheat than in barley. FHB severity by Fa73 and Fg39 were moderately correlated in both crops (r = 0.57/0.60 in barley and 0.42/0.58 in wheat). FHB severity and toxin production were also correlated in both crops, with a stronger correlation for Fa73 (r = 0.42/0.82 in barley, 0.70 in wheat) than for Fg39.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Theresa Lee
- Corresponding author: Phone) +82-63-238-3401, FAX) +82-63-238-3840, E-mail)
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Viteri DM, Linares-Ramírez AM. Screening a newly developed common bean germplasm with improved resistance to ashy stem blight in multiple environments. Front Plant Sci 2022; 13:1052398. [PMID: 36507399 PMCID: PMC9727294 DOI: 10.3389/fpls.2022.1052398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
Ashy stem blight (ASB) caused by the necrotrophic fungus Macrophomina phaseolina (Tassi) Goidanich is an important disease in common bean (Phaseolus vulgaris L.) in the Americas and worldwide. Low to intermediate levels of ASB resistance exist in cultivated and landrace genotypes of the common bean and the tertiary gene pool. However, cultivars with higher levels of resistance are not yet available. Our objectives were to 1) pyramid higher levels of resistance from multiple parent populations within the primary gene pool and 2) compare the response of the newly developed breeding lines (BL) with known sources of resistance. The BL UPR-Mp-22, UPR-Mp-34, UPR-Mp-42, and UPR-Mp-48, known sources of resistance, and susceptible checks were inoculated twice per plant with the PRI21 M. phaseolina isolate in the greenhouse and field trials conducted in Isabela and Lajas, Puerto Rico. None of the genotypes tested were resistant (mean scores 1-3). However, the new black UPR-Mp-42 and white UPR-Mp-48 BL had an intermediate response (mean scores 4-6) compared to white common bean genotypes 'Bella,' NY6020-4, and 'Verano' and black bean TARS-MST1 that were susceptible (scores ≥7) in all environments. Andean genotypes A 195, PRA154, PRA155, and UPR-Mp-22 were intermediate in the greenhouse. In contrast, UPR-Mp-34 had significantly lower scores than BAT 477 that had a susceptible reaction in the greenhouse in Isabela and in the field in Lajas and SEA 5 that was susceptible in all environments. These new BL possess an enhanced ASB resistance and may be used to improve common bean cultivars or germplasms of different market classes.
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Affiliation(s)
- Diego M. Viteri
- Department of Agro-environmental Sciences, University of Puerto Rico, Isabela Research Substation, Isabela, Puerto Rico
| | - Angela M. Linares-Ramírez
- Department of Agro-environmental Sciences, University of Puerto Rico, Lajas Research Substation, Lajas, Puerto Rico
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Yu R, Niu Y, Wang X, Yang K, Han X, Liu Z, Qi Z, Yang Y. Construction of a density mutant collection in bitter gourd via new germplasms innovation and gene functional study. Front Plant Sci 2022; 13:1069750. [PMID: 36483947 PMCID: PMC9724616 DOI: 10.3389/fpls.2022.1069750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Although a few studies have elucidated the creation of bitter gourd mutants, the suitable concentration and duration of ethyl methanesulfonate (EMS) mutagenesis have not been determined. In this study, mutant collection was conducted to create new germplasms and widen genetic diversity. By employing the seeds of the inbred line Y52 as the mutagenic material, EMS as the mutagen, and the suitable mutagenic conditions for bitter gourd seeds (EMS concentration 0.2%, mutagenic time 10 h), we mutated 10,000 seeds and acquired 3223 independent M1 lines. For the randomly selected 1000 M2 lines, 199 M2 lines with visible phenotypes were found, and 167 M2 lines were mutants of fruit shape, size, and tubercles. Furthermore, fourteen dwarf, eleven leaf color, five leaf shape, and eight meristem defect mutants were discovered in this mutant collection. In addition, three lines of 1253, 2284, and 3269 represented recessive mutants crossed with Y52. Furthermore, the yellow leaf lines of 2284 and 3269 were not mutated at the same gene locus. This study constructed a mutant collection through innovative new germplasms and provided valuable resources for bitter gourd breeding and functional gene research.
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Affiliation(s)
- Renbo Yu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
| | - Yu Niu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
| | - Xiaoyi Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Kaili Yang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
| | - Xu Han
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
| | - Zhaohua Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
| | - Zhiqiang Qi
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
| | - Yan Yang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
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Alavilli H, Poli Y, Verma KS, Kumar V, Gupta S, Chaudhary V, Jyoti A, Sahi SV, Kothari SL, Jain A. Miracle Tree Moringa oleifera: Status of the Genetic Diversity, Breeding, In Vitro Propagation, and a Cogent Source of Commercial Functional Food and Non-Food Products. Plants (Basel) 2022; 11:3132. [PMID: 36432862 PMCID: PMC9694164 DOI: 10.3390/plants11223132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Moringa oleifera Lam. (MO) is a fast-growing drought-resistant tree belonging to the family Moringaceae and native to the Indian subcontinent and cultivated and/or naturalized worldwide with a semi-arid climate. MO is also popularly known as a miracle tree for its repertoire of nutraceutical, pharmacological, and phytochemical properties. The MO germplasm is collected, conserved, and maintained by various institutions across the globe. Various morphological, biochemical, and molecular markers are used for determining the genetic diversity in MO accessions. A higher yield of leaves and pods is often desirable for making various products with commercial viability and amenable for trade in the international market. Therefore, breeding elite varieties adapted to local agroclimatic conditions and in vitro propagation are viable and sustainable approaches. Here, we provide a comprehensive overview of MO germplasm conservation and various markers that are employed for assessing the genetic diversity among them. Further, breeding and in vitro propagation of MO for various desirable agronomic traits are discussed. Finally, trade and commerce of various functional and biofortified foods and non-food products are enumerated albeit with a need for a rigorous and stringent toxicity evaluation.
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Affiliation(s)
- Hemasundar Alavilli
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Yugandhar Poli
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India
| | - Kumar Sambhav Verma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Vikram Kumar
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Swati Gupta
- Department of Biosciences, Manipal University Jaipur, Jaipur 303007, India
| | - Vigi Chaudhary
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Anupam Jyoti
- Biotechnology Department, Chandigarh University, National Highway-95, Ludhiana-Chandigarh State Highway, Chandigarh 160055, India
| | - Shivendra V. Sahi
- Department of Biology, Saint Joseph’s University (University City Campus), 600 South 43rd Street, Philadelphia, PA 19104, USA
| | - Shanker Lal Kothari
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
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Wang P, Mo Y, Wang Y, Fei Y, Huang J, Ni J, Xu ZF. Macadamia germplasm and genomic database (MacadamiaGGD): A comprehensive platform for germplasm innovation and functional genomics in Macadamia. Front Plant Sci 2022; 13:1007266. [PMID: 36388568 PMCID: PMC9646992 DOI: 10.3389/fpls.2022.1007266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
As an important nut crop species, macadamia continues to gain increased amounts of attention worldwide. Nevertheless, with the vast increase in macadamia omic data, it is becoming difficult for researchers to effectively process and utilize the information. In this work, we developed the first integrated germplasm and genomic database for macadamia (MacadamiaGGD), which includes five genomes of four species; three chloroplast and mitochondrial genomes; genome annotations; transcriptomic data for three macadamia varieties, germplasm data for four species and 262 main varieties; nine genetic linkage maps; and 35 single-nucleotide polymorphisms (SNPs). The database serves as a valuable collection of simple sequence repeat (SSR) markers, including both markers that are based on macadamia genomic sequences and developed in this study and markers developed previously. MacadamiaGGD is also integrated with multiple bioinformatic tools, such as search, JBrowse, BLAST, primer designer, sequence fetch, enrichment analysis, multiple sequence alignment, genome alignment, and gene homology annotation, which allows users to conveniently analyze their data of interest. MacadamiaGGD is freely available online (http://MacadamiaGGD.net). We believe that the database and additional information of the SSR markers can help scientists better understand the genomic sequence information of macadamia and further facilitate molecular breeding efforts of this species.
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Affiliation(s)
- Pan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Yi Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Yuchong Fei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Jianting Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Jun Ni
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Zeng-Fu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
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50
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Zeng L, Wilson I, Bourland FM. Editorial: Trends in cotton breeding: Meeting the challenges of the 21st century. Front Plant Sci 2022; 13:1019956. [PMID: 36262657 PMCID: PMC9574386 DOI: 10.3389/fpls.2022.1019956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Linghe Zeng
- United States Department of Agriculture (USDA), Agriculture Research Service, Crop Genetics Research Unit, Stoneville, MS, United States
| | - Iain Wilson
- CSIRO, Agriculture and Food, Canberra, ACT, Australia
| | - Fred M. Bourland
- University of Arkansas, Northeast Research & Extension Center, Keiser, AR, United States
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