1
|
Di Pasquale GM, Stagnati L, Lezzi A, Lanubile A, Marocco A, Rossi G, Busconi M. Morphological and Genetic Characterization of Maize Landraces Adapted to Marginal Hills in North-West Italy. Plants (Basel) 2024; 13:1030. [PMID: 38611559 PMCID: PMC11013090 DOI: 10.3390/plants13071030] [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: 03/05/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
The growing interest in maize landraces over the past two decades has led to the need to characterize the Italian maize germplasm. In Italy, hundreds of maize landraces have been developed, but only a few of them have been genetically characterized, and even fewer are currently employed in agriculture or for breeding purposes. In the present study, 13 maize landraces of the west Emilia-Romagna region were morphologically and genetically characterized. These accessions were sampled in 1954 from three provinces, Modena, Parma, and Piacenza, during the characterization project of Italian maize landraces. The morphological characterization of these 13 accessions was performed according to the UPOV protocol CPVO/TP2/3, examining 34 phenotypic traits. A total of 820 individuals were genotyped with 10 SSR markers. The genetic characterization revealed 74 different alleles, a FST mean value of 0.13, and a Nm mean of 1.73 over all loci. Moreover, AMOVA analysis disclosed a low degree of differentiation among accessions, with only 13% of genetic variability found between populations, supporting PCoA analysis results, where the first two coordinates explained only 16% of variability. Structure analysis, supported by PCoA, showed that only four accessions were clearly distinguished for both K = 4 and 6. Italian landraces can be useful resources to be employed in maize breeding programs for the development of new varieties, adapted to different environmental conditions, in order to increase crop resilience and expand the maize cultivation area.
Collapse
Affiliation(s)
- Giovanni Maria Di Pasquale
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Lorenzo Stagnati
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
- Research Centre for Biodiversity and Ancient DNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Alessandra Lezzi
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Alessandra Lanubile
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
- Research Centre for Biodiversity and Ancient DNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Adriano Marocco
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
- Research Centre for Biodiversity and Ancient DNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Graziano Rossi
- Department of Earth and Environmental Sciences, Università di Pavia, Via S. Epifanio 14, 27100 Pavia, Italy
| | - Matteo Busconi
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| |
Collapse
|
2
|
Sorokhaibam SS, Chandra A, Baishya R, Barik SK, Goel S, Tandon R. Contradistinctive floral attributes, pollination guilds and their consequence on the outcrossing rate in two elevational morphs of Rhododendron arboreum Sm. Front Plant Sci 2024; 15:1355680. [PMID: 38606073 PMCID: PMC11007036 DOI: 10.3389/fpls.2024.1355680] [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: 12/14/2023] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
Infraspecific floral trait variations may appear in response to elevational differences in alpine plant species. There is enormous information on the selection of such morphs mediated by biotic and/or abiotic variables. Whether such differences contribute to differences in reproductive strategy and mating outcomes is rarely investigated. We investigated these aspects in two distinct elevational floral morphs (Red and Pink) of Rhododendron arboreum Sm. in Western Himalaya. The red morphs occupy the lower elevations while pink morphs the higher elevations. The two morphs differ in floral traits like phenology, dimension, display, quality of floral rewards, and pollinators that happen to influence interaction with available pollinator pool at each elevation. The pink morph exhibits entomophily, while the red ones show ornithophily. Although experimental pollinations established that both the morphs are self-compatible, selfing results in significantly lower fruit-set than either cross- or open-pollinations. The outcrossing rate in the red morph, as determined by using simple sequence repeat (SSR) markers, was higher (tm=0.82) than that in the pink morph (tm=0.76), with a tendency of the latter to be shifting towards mixed-mating strategy. However, the extent of biparental inbreeding was comparable among the two morphs. It is inferred that the differences in the mating outcomes among the morphs in the tree species are linked to those emerging from floral traits and the pollination by different functional groups of floral visitors.
Collapse
Affiliation(s)
| | - Atika Chandra
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Ratul Baishya
- Department of Botany, University of Delhi, New Delhi, India
| | - Saroj Kanta Barik
- Department of Botany, Centre for Advanced Studies in Botany, North-Eastern Hill University, Shillong, India
| | | | - Rajesh Tandon
- Department of Botany, University of Delhi, New Delhi, India
| |
Collapse
|
3
|
Guizani A, Babay E, Askri H, Sialer MF, Gharbi F. Screening for drought tolerance and genetic diversity of wheat varieties using agronomic and molecular markers. Mol Biol Rep 2024; 51:432. [PMID: 38520570 DOI: 10.1007/s11033-024-09340-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/09/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND The future predictions for frequent and severe droughts will represent a significant threat to wheat yield and food security. In this context, breeding has proven to be the most efficient approach to enhance wheat productivity in dry environments. METHODS AND RESULTS In this study, both agronomic and molecular-based approaches were used to evaluate the response of twenty-eight Tunisian wheat varieties to drought stress. The primary objective was to screen these varieties for drought tolerance using molecular and agro-morphological markers. All varieties were significantly affected by drought stress regarding various traits including total dry matter, straw length, flag leaf area, number of senescent leaves, SPAD value, grain yield and grain number. Furthermore, substantial variability in drought-stress tolerance was observed among wheat genotypes. The cluster analysis and principal component analyses confirmed the existence of genotypic variation in growth and yield impairments induced by drought. The stress susceptibility index (SSI) and tolerance index (TOL) proved to be the most effective indices and were strongly correlated with the varying levels of genotypic tolerance. The genotyping evaluation resulted in the amplification of 101 alleles using highly polymorphic 12 SSR markers, showed an average polymorphism of 74%. CONCLUSIONS Taken together, the combination of agronomic and molecular approaches revealed that Karim, Td7, D117 and Utique are the most drought-tolerant wheat varieties. These varieties are particularly promising candidates for genetic improvements and can be utilized as potential genitors for future breeding programs in arid and semi-arid regions.
Collapse
Affiliation(s)
- Asma Guizani
- Laboratory of Mycology, Pathologies and Biomarkers LR16ES05, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia.
| | - Elyes Babay
- Agricultural Applied Biotechnology Laboratory (LR16INRAT06), Institut National de la Recherche Agronomique de Tunisie (INRAT), University of Carthage, Tunis, Tunisia
| | - Hend Askri
- Laboratory of Valorization of Non-Conventional Water (LR16INRGREF02), Water and Forestry, National Institute of Rural Engineering, Carthage University, Tunis, Tunisia
| | | | - Fatma Gharbi
- Laboratory of Mycology, Pathologies and Biomarkers LR16ES05, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| |
Collapse
|
4
|
Ricciardi V, Crespan M, Maddalena G, Migliaro D, Brancadoro L, Maghradze D, Failla O, Toffolatti SL, De Lorenzis G. Novel loci associated with resistance to downy and powdery mildew in grapevine. Front Plant Sci 2024; 15:1386225. [PMID: 38584944 PMCID: PMC10998452 DOI: 10.3389/fpls.2024.1386225] [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: 02/14/2024] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
Among the main challenges in current viticulture, there is the increasing demand for sustainability in the protection from fungal diseases, such as downy mildew (DM) and powdery mildew (PM). Breeding disease-resistant grapevine varieties is a key strategy for better managing fungicide inputs. This study explores the diversity of grapevine germplasm (cultivated and wild) from Caucasus and neighboring areas to identify genotypes resistant to DM and PM, based on 13 Simple Sequence Repeat (SSR) loci and phenotypical (artificial pathogen inoculation) analysis, and to identify loci associated with DM and PM resistance, via Genome-Wide Association Analysis (GWAS) on Single Nucleotide Polymorphism (SNP) profiles. SSR analysis revealed resistant alleles for 16 out of 88 genotypes. Phenotypic data identified seven DM and 31 PM resistant genotypes. GWAS identified two new loci associated with DM resistance, located on chromosome 15 and 16 (designated as Rpv36 and Rpv37), and two with PM resistance, located on chromosome 6 and 17 (designated as Ren14 and Ren15). The four novel loci identified genomic regions rich in genes related to biotic stress response, such as genes involved in pathogen recognition, signal transduction and resistance response. This study highlights potential candidate genes associated with resistance to DM and PM, providing valuable insights for breeding programs for resistant varieties. To optimize their utilization, further functional characterization studies are recommended.
Collapse
Affiliation(s)
- Valentina Ricciardi
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Manna Crespan
- Centro di Ricerca per la Viticoltura e l'Enologia, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Conegliano, Italy
| | - Giuliana Maddalena
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Daniele Migliaro
- Centro di Ricerca per la Viticoltura e l'Enologia, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Conegliano, Italy
| | - Lucio Brancadoro
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - David Maghradze
- Faculty of Viticulture-Winemaking, Caucasus International University, Tbilisi, Georgia
- Faculty of Agricultural Sciences and Biosystems Engineering, Georgian Technical University, Tbilisi, Georgia
| | - Osvaldo Failla
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Silvia Laura Toffolatti
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Gabriella De Lorenzis
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| |
Collapse
|
5
|
Huang Y, Cao A, Zhang B, Li S, He C, Gao J, Cao X. Identification of polymorphic markers for germplasm conservation of three precious Chinese palace goldfish using whole-genome sequencing. Anim Genet 2024. [PMID: 38500412 DOI: 10.1111/age.13419] [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: 07/26/2023] [Revised: 01/31/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
China was the first country in the world to breed goldfish and has generated many unique goldfish varieties, including the most aristocratic Chinese palace goldfish. Due to the lack of scientific research on Chinese palace goldfish, their selection and breeding are mainly carried out through traditional hybridization, leading to serious inbreeding and the degradation of germplasm resources. To this end, whole-genome resequencing was performed to understand the genetic variation among three different varieties (eggpompons, goosehead, and tigerhead) from nine core conserved populations in China. A total of 15 polymorphic SSRs were developed for population genetics, and all tested populations were considered moderately polymorphic with an average polymorphism information content value of 0.4943. Genetic diversity in different varieties showed that all conserved populations were well protected with the potential for continued exploitation. This study provides reliable molecular tools and a basis for designing conservation and management programs in Chinese palace goldfish.
Collapse
Affiliation(s)
- Yuwei Huang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Aiying Cao
- Beijing Fisheries Technology Promotion Station, Beijing, China
| | - Beiyuan Zhang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Sen Li
- Beijing Fisheries Technology Promotion Station, Beijing, China
| | - Chuan He
- Beijing Fisheries Technology Promotion Station, Beijing, China
| | - Jian Gao
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xiaojuan Cao
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
6
|
Patel R, Memon J, Kumar S, Patel DA, Sakure AA, Patel MB, Das A, Karjagi CG, Patel S, Patel U, Roychowdhury R. Genetic Diversity and Population Structure of Maize ( Zea mays L.) Inbred Lines in Association with Phenotypic and Grain Qualitative Traits Using SSR Genotyping. Plants (Basel) 2024; 13:823. [PMID: 38592835 PMCID: PMC10975177 DOI: 10.3390/plants13060823] [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: 01/27/2024] [Revised: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Maize (Zea mays L.) is an important cereal and is affected by climate change. Therefore, the production of climate-smart maize is urgently needed by preserving diverse genetic backgrounds through the exploration of their genetic diversity. To achieve this, 96 maize inbred lines were used to screen for phenotypic yield-associated traits and grain quality parameters. These traits were studied across two different environments (Anand and Godhra) and polymorphic simple sequence repeat (SSR) markers were employed to investigate the genetic diversity, population structure, and trait-linked association. Genotype-environment interaction (GEI) reveals that most of the phenotypic traits were governed by the genotype itself across the environments, except for plant and ear height, which largely interact with the environment. The genotypic correlation was found to be positive and significant among protein, lysine and tryptophan content. Similarly, yield-attributing traits like ear girth, kernel rows ear-1, kernels row-1 and number of kernels ear-1 were strongly correlated to each other. Pair-wise genetic distance ranged from 0.0983 (1820194/T1 and 1820192/4-20) to 0.7377 (IGI-1101 and 1820168/T1). The SSRs can discriminate the maize population into three distinct groups and shortlisted two genotypes (IGI-1101 and 1820168/T1) as highly diverse lines. Out of the studied 136 SSRs, 61 were polymorphic to amplify a total of 131 alleles (2-3 per loci) with 0.46 average gene diversity. The Polymorphism Information Content (PIC) ranged from 0.24 (umc1578) to 0.58 (umc2252). Similarly, population structure analysis revealed three distinct groups with 19.79% admixture among the genotypes. Genome-wide scanning through a mixed linear model identifies the stable association of the markers umc2038, umc2050 and umc2296 with protein, umc2296 and umc2252 with tryptophan, and umc1535 and umc1303 with total soluble sugar. The obtained maize lines and SSRs can be utilized in future maize breeding programs in relation to other trait characterizations, developments, and subsequent molecular breeding performances for trait introgression into elite genotypes.
Collapse
Affiliation(s)
- Rumit Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand 388110, India
| | - Juned Memon
- Department of Genetics and Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand 388110, India
| | - Sushil Kumar
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand 388110, India
| | - Dipak A. Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand 388110, India
| | - Amar A. Sakure
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand 388110, India
| | - Manish B. Patel
- Main Maize Research Station, Anand Agricultural University, Godhra 389001, India
| | - Arna Das
- Department of Genetics and Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand 388110, India
| | | | - Swati Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand 388110, India
| | - Ujjaval Patel
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari 396450, India
| | - Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO)—Volcani Center, Rishon Lezion 7505101, Israel
| |
Collapse
|
7
|
Fandade V, Singh P, Singh D, Sharma H, Thakur G, Saini S, Kumar P, Mantri S, Bishnoi OP, Roy J. Genome-wide identification of microsatellites for mapping, genetic diversity and cross-transferability in wheat (Triticum spp). Gene 2024; 896:148039. [PMID: 38036075 DOI: 10.1016/j.gene.2023.148039] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
Wheat (Triticum aestivum L.) is a crucial global staple crop, and is consistently being improved to enhance yield, disease resistance, and quality traits. However, the development of molecular markers is a challenging task due to its hexaploid genome. Molecular marker system such as simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) are helpful for breeding, but SNP has limitations due to its development cost and its conversion to breeder markers. The study proposed an in-silico approach, by utilizing the low-cost transcriptome sequencing of two parental lines, 'TAC 75' and 'WH 1105', to identify polymorphic SSRs for mapping in a recombinant inbred line (RIL) population. This study introduces a new approach to bridge wheat genetics intricacies and next-generation sequencing potential. It presents a comprehensive genome-wide SSR distribution using IWGSC CS RefSeq v2.1 genome assembly and to identify 189 polymorphic loci through in-silico strategy. Of these, 54.76% showed polymorphism between parents, surpassing the traditional low polymorphic success rate. A RIL population screening validated these markers, demonstrating the fitness of identified markers through chi-square tests. The designed SSRs were also validated for genetic diversity analysis in a subset of 37 Indian wheat genotypes and cross-transferability in the wild/relative wheat species. In diversity analysis, a subset of 38 markers revealed 95 alleles (2.5 allele/locus), indicating substantial genetic variation. Population structure analysis unveiled three distinct groups, supported by phylogenetic and PCoA analyses. Further the polymorphic SSRs were also analyzed for SSR-gene association using gene ontology analysis. By utilizing the developing seed transcriptome data within parental lines, the study has enhanced the polymorphic SSR identification precision and facilitated in the RIL population. The undertaken study pioneers the use of transcriptome sequencing and genetic mapping to overcome challenges posed by the intricate wheat genome. This approach offers a cost-effective, less labour-intensive alternative to conventional methods, providing a platform for advancing wheat breeding research.
Collapse
Affiliation(s)
- Vikas Fandade
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.
| | - Pradeep Singh
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - Dalwinder Singh
- Department of Anatomy and cell biology, University of Western Ontario, London, Canada.
| | - Himanshu Sharma
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - Garima Thakur
- Protection for Plant Varieties and Farmers Rights Authority, New Delhi, India.
| | - Shivangi Saini
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - Prashant Kumar
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.
| | - Shrikant Mantri
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - O P Bishnoi
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar- 125004, India.
| | - Joy Roy
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| |
Collapse
|
8
|
Boussou CK, Das SP, Mohanty M, Das G, Verma DK, Sahoo L, Routray P, Das P. Morphometric and genetic characterization of cultured and wild populations of tilapia, Oreochromis niloticus in India. 3 Biotech 2024; 14:51. [PMID: 38274848 PMCID: PMC10805755 DOI: 10.1007/s13205-023-03895-3] [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: 03/07/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
To study genetic variation in Indian populations of tilapia, Oreochromis niloticus, both truss morphometrics and genetic characterization have been performed. In the present study, 88 individuals from two farm populations (GIFT and West Bengal) and one reservoir population (Gujarat) were selected to analyse variations at ten morphometric landmarks and eight microsatellite loci. Truss morphometric analysis showed PCI, PCII, and PCIII expressing 29.1%, 21.36%, and 15.48% of the variance, respectively. Results showed no clear shift in shape between the studied populations of O. niloticus, indicating low morphological variability among them. The number of microsatellite alleles ranged from 3 to 9, while expected heterozygosity (HE) and observed heterozygosity (HO) values ranged from 0.56 (WB) to 0.68 (Guj) and 0.59 (GIFT) to 0.72 (Guj), respectively. The Gujarat and West Bengal populations had the smallest pairwise distance (0.0123) between them, indicating that they were genetically closer. Individuals from GIFT, however, showed the largest distance from the other populations. DNA marker variations revealed the highest genetic variability in the Gujarat population and the lowest variability in the GIFT population. The results of this study will help establish a base population for genetic improvement program and conservation of wild populations.
Collapse
Affiliation(s)
| | - Sofia P. Das
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Mausumee Mohanty
- Barcode Biosciences, Dr. Shivaram Karanth Nagar, Bengaluru, 560077 India
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Gargee Das
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Dhananjay K. Verma
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Lakshman Sahoo
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Padmanava Routray
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Paramananda Das
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| |
Collapse
|
9
|
Yao H, Sun J, Chen M, Dong Y, Wang P, Xu J, Shao Q, Wang Z. The impact of non-environmental factors on the chemical variation of Radix S crophulariae. Heliyon 2024; 10:e24468. [PMID: 38304803 PMCID: PMC10831622 DOI: 10.1016/j.heliyon.2024.e24468] [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: 10/05/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 02/03/2024] Open
Abstract
Radix Scrophulariae is a commonly used Chinese herb derived from the dried root of Scrophularia ningpoesis Hemsl. (S. ningpoensis). It is difficult to accurately estimate the dosage of Chinese medicinal materials used in the prescription because of the chemical variation caused by various factors. To analyze the non-environmental factors affecting the chemical variation of Radix Scrophulariae, we planted nine different cultivated varieties of S. ningpoensis in the same plantation. Based on sequence-related amplified polymorphism (SRAP), simple sequence repeats (SSR) markers and high-performance liquid chromatography (HPLC) analysis, we found that the materials from the cultivated varieties could be divided into two groups, the Zhejiang group, and the southwest China group. The genetic distance based on molecular data between the two groups was above 0.3882, and the Euclidean distance based on chemical data between the two groups was above 5.312. The correlation analysis between the genetic distance matrix based on SRAP and the Euclidean distance matrix based on 18 HPLC peaks of the whole underground part revealed that the genetic differentiation and chemical variation were positively related, r = 0.7196 (p < 0.05). The genetic background, different part of the roots and the different development of the roots are the three non-environmental factors causing the chemical variation. The coefficient of variation (C.V) of chemical composition of Radix Scrophulariae with different genetic background reached to 93.62 %, the C.V of the chemical composition of Radix Scrophulariae derived from the same variety reached to 64.21 %, the C.V of the chemical composition of Radix Scrophulariae derived from the middle part of the roots of S. ningpoensis from the same variety reached to 45.55 %. The C.V of chemical composition of Radix Scrophulairae produced in the same plantation could be controlled to 38.43 % by using the same variety of roots with the approximate mass derived from the middle part of the roots under 20 g. Our findings provided insights to decrease the chemical variation of Chinese medicinal materials by controlling non-environmental factors.
Collapse
Affiliation(s)
- Hui Yao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jian Sun
- Zhejiang Research Institute of Traditional Chinese Medicine Co., Ltd., Hangzhou, 310023, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang Agriculture & Forest University, Hangzhou, 311300, China
| | - Mengying Chen
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang Agriculture & Forest University, Hangzhou, 311300, China
| | - Yu Dong
- Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, 310007, China
| | - Pan Wang
- Institute of Traditional Chinese Medicine Industry Innovation of Pan'an, Pan'an, 322300, China
| | - Jianzhong Xu
- Zhejiang Research Institute of Traditional Chinese Medicine Co., Ltd., Hangzhou, 310023, China
| | - Qingsong Shao
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang Agriculture & Forest University, Hangzhou, 311300, China
| | - Zhian Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
- Zhejiang Research Institute of Traditional Chinese Medicine Co., Ltd., Hangzhou, 310023, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang Agriculture & Forest University, Hangzhou, 311300, China
| |
Collapse
|
10
|
Zhou X, Ren H, Zhang J, Xu D, Xiao W, Huang H, Li G, Zhang H, Zheng Y. The complete chloroplast genome of Brassica rapa var. purpuraria (L.H.Bailey) Kitam 1950 and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:143-147. [PMID: 38274856 PMCID: PMC10810650 DOI: 10.1080/23802359.2024.2305403] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
Zicaitai (Brassica rapa var. purpuraria (L.H.Bailey) Kitam 1950) is a vegetable crop that boasts a high nutritional value and unique flavor. It originated from Central China and was formed after long-term cultivation and domestication. In this study, we obtained the complete sequence of the chloroplast genome of zicaitai, a circular molecule of 153,483 bp in length. This chloroplast genome consists of a large single-copy (LSC) region (83,282 bp), a small single-copy (SSC) region (17,775 bp), and a pair of inverted repeats (IRs) (26,213 bp). By sequence annotation, 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes were identified in the zicaitai chloroplast. A total of 315 simple sequence repeats (SSRs) were found located in LSC (197), SSC (72), and IR (46), respectively. Phylogenetic analysis based on chloroplast genomes indicated the relationship of zicaitai and the Brassicaceae family, which supports zicaitai as a variety of B. rapa in taxonomy. The results obtained in this study provide insight into further research on Brassica chloroplasts and their phylogeny.
Collapse
Affiliation(s)
- Xianyu Zhou
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Hailong Ren
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Jing Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Donglin Xu
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Wanyu Xiao
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Hongdi Huang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Guangguang Li
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Yansong Zheng
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| |
Collapse
|
11
|
Fu X, Meyer-Rochow VB, Ballantyne L, Zhu X, Zhang Q. Sperm Competition and Paternity in the Endangered Firefly Pyrocoelia pectoralis (Coleoptera: Lampyridae: Lampyrinae). Insects 2024; 15:66. [PMID: 38249072 PMCID: PMC10817000 DOI: 10.3390/insects15010066] [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: 11/25/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
The endangered terrestrial firefly Pyrocoelia pectoralis (Olivier) is endemic to China. Populations of P. pectoralis have decreased dramatically due to urbanization and pollution. Breeding and re-introduction to a suitable habitat may save the species from becoming extinct. Because of its polyandrous character, an investigation into the possibility of sperm competition and paternity outcomes from multiple matings was initiated to better understand its reproductive physiology. To achieve these goals, 13 SSR markers were developed. The results of paternity experiments indicate there is a significant difference between P3 and P1 or P2. The female reproductive system has three spermathecae which accept sperm from different matings, and no bursa or spermatophore-digesting organ is developed. Our research established that multiple inseminations with sperm from different males occur, leading to competition between ejaculates. The benefits of such competition include an increasing number of sperm in the ejaculates of competing males and the consequential increase in fertilized eggs (thus, fecundity), and thereby a higher chance of genetic diversity and fitness in the offspring of the firefly P. pectoralis.
Collapse
Affiliation(s)
- Xinhua Fu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Firefly Conservation Research Centre, Wuhan 430070, China;
| | - Victor Benno Meyer-Rochow
- Department of Ecology and Genetics, Oulu University, SF-90140 Oulu, Finland;
- Agricultural Science and Technology Research Institute, Andong National University, Andong 36729, Republic of Korea
| | - Lesley Ballantyne
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, P.O. Box 588, Wagga Wagga 2678, Australia;
| | - Xinlei Zhu
- Firefly Conservation Research Centre, Wuhan 430070, China;
| | - Qiyulu Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| |
Collapse
|
12
|
Orazov A, Yermagambetova M, Myrzagaliyeva A, Mukhitdinov N, Tustubayeva S, Turuspekov Y, Almerekova S. Plant height variation and genetic diversity between Prunus ledebouriana (Schlecht.) YY Yao and Prunus tenella Batsch based on using SSR markers in East Kazakhstan. PeerJ 2024; 12:e16735. [PMID: 38223754 PMCID: PMC10788089 DOI: 10.7717/peerj.16735] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024] Open
Abstract
Background Genetic differences between isolated endemic populations of plant species and those with widely known twin species are relevant for conserving the biological diversity of our planet's flora. Prunus ledebouriana (Schlecht.) YY Yao is an endangered and endemic species of shrub almond from central Asia. Few studies have explored this species, which is closely related and morphologically similar to the well-known Prunus tenella Batsch. In this article, we present a comparative analysis of studies of three P. ledebouriana populations and one close population of P. tenella in Eastern Kazakhstan in order to determine the particular geographic mutual replacement of the two species. Methods The populations were collected from different ecological niches, including one steppe population near Ust-Kamenogorsk (P. tenella) and three populations (P. ledebouriana) in the mountainous area. Estimation of plant height using a t-test suggested a statistically significant difference between the populations and the two species (P < 0.0001). DNA simple sequence repeat (SSR) markers were applied to study the two species' genetic diversity and population structure. Results A total of 19 polymorphic SSR loci were analyzed, and the results showed that the population collected in mountainous areas had a lower variation level than steppe populations. The highest level of Nei's genetic diversity index was demonstrated in the 4-UK population (0.622) of P. tenella. The lowest was recorded in population 3-KA (0.461) of P. ledebouriana, collected at the highest altitude of the four populations (2,086 meters above sea level). The total genetic variation of P. ledebouriana was distributed 73% within populations and 27% between populations. STRUCTURE results showed that two morphologically similar species diverged starting at step K = 3, with limited population mixing. The results confirmed the morphological and genetic differences between P. tenella and P. ledebouriana and described the level of genetic variation for P. ledebouriana. The study's results proved that the steppe zone and mountain altitude factor between P. tenella and isolated mountain samples of P. ledebouriana.
Collapse
Affiliation(s)
- Aidyn Orazov
- School of Natural Sciences, Astana International University, Astana, Kazakhstan
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Moldir Yermagambetova
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anar Myrzagaliyeva
- School of Natural Sciences, Astana International University, Astana, Kazakhstan
| | - Nashtay Mukhitdinov
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Shynar Tustubayeva
- School of Natural Sciences, Astana International University, Astana, Kazakhstan
| | - Yerlan Turuspekov
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Shyryn Almerekova
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| |
Collapse
|
13
|
Truong HTH, Ho NTH, Ho HN, Nguyen BLQ, Le MHD, Duong TT. Morphological, phytochemical and genetic characterization of Centella asiatica accessions collected throughout Vietnam and Laos. Saudi J Biol Sci 2024; 31:103895. [PMID: 38173443 PMCID: PMC10761913 DOI: 10.1016/j.sjbs.2023.103895] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Pennywort (Centella asiatica L.) is commonly grown in the tropical world for its nutritional and medicinal values. Valuable saponins in pennywort are extensively investigated for their anti-tumour activities. The diversity in morphology, phytochemical contents and genetics among pennywort accessions has been extensively studied to identify elite landraces for large-scale production. While pennywort is widely consumed in Vietnam, a systematic characterization of their diverse morphology, secondary metabolites and genetics is lacking. In this work, 26 pennywort accessions were collected across Vietnam and Laos. Their morphological features and yields were characterized under uniform agro-climatic conditions at Hue city in central Vietnam. The highest yield was obtained with HUIB_CA20 (478 g per tray), compared to the lowest yield in HUIB_CA19 (107 g per tray). Furthermore, a range of phytochemical markers, including vitamin C, reducing sugar, carotenoid, tannin, phenolic, flavonoid and saponin contents, were determined. Based on yield, phenolic and flavonoid contents, HUIB_CA20 and HUIB_CA27 were determined to be elite cultivars in this germplasm. Finally, microsatellite analysis was performed to explore the genetic diversity within the germplasm. Using fourteen SSR primer pairs, a total of 47 alleles were identified with 45 alleles (96 %) being polymorphic. These results will be useful for breeding programs aiming to create elite pennywort cultivars with enhanced properties.
Collapse
Affiliation(s)
| | - Nhi Thi Hoang Ho
- The Institute of Biotechnology, Hue University, Thua Thien Hue, Viet Nam
| | - Han Ngoc Ho
- The Institute of Biotechnology, Hue University, Thua Thien Hue, Viet Nam
| | - Bao Le Quy Nguyen
- The Institute of Biotechnology, Hue University, Thua Thien Hue, Viet Nam
| | - Minh Hoang Duy Le
- The Institute of Biotechnology, Hue University, Thua Thien Hue, Viet Nam
| | - Thuy Thanh Duong
- Hue University of Agriculture and Forestry, Hue University, Thua Thien Hue, Viet Nam
| |
Collapse
|
14
|
Tseng MC, Lee YH, Yen TB, Li SM. Genome-wide characterization of microsatellites in cobia Rachycentron canadum (Linnaeus, 1766): Survey and analysis of their abundance and diversity. J Fish Biol 2024; 104:44-55. [PMID: 37658731 DOI: 10.1111/jfb.15552] [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] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/23/2023] [Accepted: 08/31/2023] [Indexed: 09/05/2023]
Abstract
The cobia Rachycentron canadum, mainly distributed in the warm waters of tropical and subtropical regions around the world, remains a fish of considerable economic importance. Detailed diversity and the number of microsatellite sequences in the cobia genome are still unintelligible. The primary aim of this work was to identify and quantify the miscellaneous SSR sequences in the cobia genome. More than 280,000 sequences were sequenced and screened using next-generation sequencing technology and microsatellite identification. Perfect mononucleotide repeats, dinucleotide microsatellites, and trinucleotide microsatellites contain (A)10 /(T)10 , (AC)6 /(TG)6 , and (AAT)5-32 as the largest number of motifs in each type of microsatellite, respectively. The tetranucleotide and pentanucleotide microsatellites (TTM and PTM) consist of the largest number of motifs of both (ATCT)5-32 and (TCAT)5-31 in TTMs, and (CTCTC)5-9 in PTMs, whereas the hexanucleotide microsatellites are rarely observed in the cobia genome. All c. 38000 sequences of composite microsatellites are extremely diverse, including compound (11.71%), interrupted compound (71.77%), complex (0.45%), and interrupted complex (16.07%). In this study, we developed a convenient and useful recording system for writing down and categorizing diverse composite microsatellite types. This system will provide great support for exploring repeat origins, evolutionary mechanisms, and the application of polymorphic microsatellites.
Collapse
Affiliation(s)
- Mei-Chen Tseng
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan, R.O.C
| | - Yen-Hung Lee
- Tungkang Aquaculture Research Center, Fisheries Research Institute, MOA, Pingtung 928, Taiwan, R.O.C
| | - Tsair-Bor Yen
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Pingtung 912, Taiwan, R.O.C
| | - Shu-Ming Li
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan, R.O.C
| |
Collapse
|
15
|
Manthos I, Sotiropoulos T, Karapetsi L, Ganopoulos I, Pratsinakis ED, Maloupa E, Madesis P. Molecular Characterization of Local Walnut ( Juglans regia) Genotypes in the North-East Parnon Mountain Region of Greece. Int J Mol Sci 2023; 24:17230. [PMID: 38139058 PMCID: PMC10743642 DOI: 10.3390/ijms242417230] [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: 10/31/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Walnut is one of the most important nuts regarding their production and consumption. The available but uncharacterized genetic resources of walnut are important for the development and breeding of local varieties. Greece holds an important number of genetically uncharacterized walnut landraces, especially within the area of Parnon, which is considered to play a significant role as an in situ gene bank, due to its unique location traits. However, the genetic characterization and further use of these resources has been insufficient, due to the absence of genetic studies. In this study, we implemented SSR molecular markers, both to genetically characterize the walnut tree genetic diversity of the Parnon area and to identify its unique genetic structure, which will form the starting material for subsequent breeding programs. Overall, high levels of genetic variation were found among the individual walnut accessions that were collected in the Parnon mountain region.
Collapse
Affiliation(s)
- Ioannis Manthos
- Department of Nut Trees, Institute of Plant Breeding & Genetic Resources, Hellenic Agricultural Organization (ELGO)-DIMITRA, Neo Krikello, 35100 Lamia, Greece;
| | - Thomas Sotiropoulos
- Department of Deciduous Fruit Trees, Institute of Plant Breeding & Genetic Resources, Hellenic Agricultural Organization (ELGO)-DIMITRA, 59200 Naousa, Greece;
| | - Lefkothea Karapetsi
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece;
- Institute of Applied Biosciences, Centre for Research & Technology-Hellas, 57001 Thessaloniki, Greece;
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, 57001 Thessaloniki, Greece; (I.G.); (E.M.)
| | - Emmanouil D. Pratsinakis
- Institute of Applied Biosciences, Centre for Research & Technology-Hellas, 57001 Thessaloniki, Greece;
| | - Eleni Maloupa
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, 57001 Thessaloniki, Greece; (I.G.); (E.M.)
| | - Panagiotis Madesis
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece;
- Institute of Applied Biosciences, Centre for Research & Technology-Hellas, 57001 Thessaloniki, Greece;
| |
Collapse
|
16
|
Shukre VM, Tahakik R, Kumar KG, Tarte SH, Kore G. In Vitro Screening of Molecular Diversity Among Sorghums (Sorghum bicolor (L.) Landraces in Marathwada Region by Molecular Markers. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04724-2. [PMID: 38051406 DOI: 10.1007/s12010-023-04724-2] [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] [Accepted: 09/15/2023] [Indexed: 12/07/2023]
Abstract
Allelic variation is a valuable tool for displaying high levels of polymorphism within species and is closely correlated with crop productivity. In Marathawada, there is a significant amount of phenotypic heterogeneity among sorghum landraces. However, molecular variability needs to be reevaluated in order to identify any potential barriers that can interfere with current improvement initiatives. In the current work, we used 5 SSR markers to categorize 20 genotypes of elite (Sorghum bicolor L. Moench) accession from the Marathwada region, including one standard cultivar from various agro-economic zones. According to the results of this study, 14 alleles were found among the 20 genotypes, with a PIC value that ranged from 0.37 to 0.70 and a mean of 0.44 per locus. Each locus had anything from 1 (gpsb089) and 5 (mSbCIR223), with an average of 2.80 alleles per locus. A neighbor-joining tree was constructed and showed clustering of genotypes into two groups; this indicates that there is considerable diversity in genotypes compared with advanced cultivar for desired genotype (IS1042) by using SSR markers. Results show that most diverse cultivars were IS-4564, IS18357, and IS-18381, and significant variation was also reported in IS4566 and IS18379.
Collapse
Affiliation(s)
- Vikas Manikrao Shukre
- Dept. of Plant Biotechnology, MGM College of Agricultural Biotechnology, Vasantrao Naik Marathwada Krishi Vidyapeeth, Gandheli, Aurangabad, India, Maharashtra.
| | - Rushikesh Tahakik
- Dept. of Plant Biotechnology, MGM College of Agricultural Biotechnology, Vasantrao Naik Marathwada Krishi Vidyapeeth, Gandheli, Aurangabad, India, Maharashtra
| | - Kunvar Gyanendra Kumar
- Dept. of Plant Biotechnology, MGM College of Agricultural Biotechnology, Vasantrao Naik Marathwada Krishi Vidyapeeth, Gandheli, Aurangabad, India, Maharashtra
| | - Shilpa Hanmatrao Tarte
- Dept. of Plant Biotechnology, MGM College of Agricultural Biotechnology, Vasantrao Naik Marathwada Krishi Vidyapeeth, Gandheli, Aurangabad, India, Maharashtra
| | - Ganesh Kore
- Dept. of Plant Biotechnology, MGM College of Agricultural Biotechnology, Vasantrao Naik Marathwada Krishi Vidyapeeth, Gandheli, Aurangabad, India, Maharashtra
| |
Collapse
|
17
|
Heck DW, Hay F, Pethybridge SJ. Enabling Population Biology Studies of Stemphylium vesicarium from Onion with Microsatellites. Plant Dis 2023; 107:3886-3895. [PMID: 37330630 DOI: 10.1094/pdis-04-23-0706-re] [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] [Indexed: 06/19/2023]
Abstract
Stemphylium leaf blight (SLB), caused by the fungus Stemphylium vesicarium, is dominant within the foliar disease complex affecting onion production in New York (NY). The disease causes premature defoliation and significant reductions in bulb weight and quality. Foliar diseases of onion are usually managed by an intensive fungicide program, but SLB management is complicated by resistance to multiple single-site modes of action. The design of integrated disease management strategies is limited by incomplete knowledge surrounding the dominant sources of S. vesicarium inoculum. To facilitate genomic-based studies of S. vesicarium populations, nine microsatellite markers were developed. The markers were multiplexed into two PCR assays containing four and five fluorescently labeled microsatellite markers. Initial testing of the S. vesicarium isolates found the markers were highly polymorphic and reproducible with an average of 8.2 alleles per locus. The markers were used to characterize 54 S. vesicarium isolates from major NY onion production regions in 2016 (n = 27) and 2018 (n = 27). Fifty-two multilocus genotypes (MLGs) were identified between these populations. Genotypic and allelic diversities were high in both the 2016 and 2018 populations. A greater degree of genetic variation was observed within populations than between years. No distinct pattern of MLGs according to population was identified and some MLGs were closely related between 2016 and 2018. The lack of evidence for linkage among loci also was strongly suggestive of clonal populations with only minor differences between the two populations. These microsatellite markers will be a foundational resource for the testing of hypotheses surrounding the population biology of S. vesicarium and therefore informing disease management.
Collapse
Affiliation(s)
- Daniel W Heck
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Frank Hay
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Sarah J Pethybridge
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| |
Collapse
|
18
|
Hinze A, Pelletier J, Ghaninia M, Marois E, Hill SR, Ignell R. Knockout of OR39 reveals redundancy in the olfactory pathway regulating the acquisition of host seeking in Anopheles coluzzii. Proc Biol Sci 2023; 290:20232092. [PMID: 38018099 PMCID: PMC10685123 DOI: 10.1098/rspb.2023.2092] [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: 09/14/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
The attraction of anthropophilic mosquitoes to human host cues, such as body odour and carbon dioxide, gradually increases during adult maturation. This acquisition of host-seeking behaviour correlates with age-dependent changes in odorant receptor (OR) transcript abundance and sensitivity of olfactory sensory neurons (OSNs). One OR gene of the human malaria vector, Anopheles coluzzii, AcolOR39, is significantly downregulated in mature females, and a cognate ligand of AcolOR39, sulcatone, a major component of human emanations, mediates the observed behavioural inhibition of newly emerged (teneral) females to human body odour. Knockout of AcolOR39, using CRISPR-Cas9 mutagenesis, selectively abolished sulcatone detection in OSNs, housed in trichoid sensilla. However, knockout of AcolOR39 altered neither the response rate nor the flight behaviour of teneral females in a wind tunnel, indicating the involvement of other genes, and thus a redundancy, in regulating the acquisition of host seeking in mosquitoes.
Collapse
Affiliation(s)
- Annika Hinze
- Disease Vector Group, Unit of Chemical Ecology, Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp 750 07, Sweden
| | - Julien Pelletier
- Disease Vector Group, Unit of Chemical Ecology, Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp 750 07, Sweden
| | - Majid Ghaninia
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Eric Marois
- Inserm, CNRS, Université de Strasbourg, Strasbourg 67070, France
| | - Sharon Rose Hill
- Disease Vector Group, Unit of Chemical Ecology, Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp 750 07, Sweden
| | - Rickard Ignell
- Disease Vector Group, Unit of Chemical Ecology, Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp 750 07, Sweden
| |
Collapse
|
19
|
An Y, Xia X, Zheng H, Yu S, Jing T, Zhang F. Multi-genome comprehensive identification of SSR/SV and development of molecular markers database to serve Sorghum bicolor (L.) breeding. BMC Genom Data 2023; 24:62. [PMID: 37924022 PMCID: PMC10625204 DOI: 10.1186/s12863-023-01165-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND As an important food and cash crop, identification of DNA molecular markers is of great significance for molecular marker-assisted breeding of Sorghum (Sorghum bicolor (L.) moench). Although some sorghum-related mutation databases have been published, the special SSR and SV databases still need to be constructed and updated. RESULTS In this study, the quality of 18 different sorghum genomes was evaluated, and two genomes were assembled at chromosome level. Through the identification and comparative analysis of SSR loci in these genomes, the distribution characteristics of SSR in the above sorghum genomes were initially revealed. At the same time, five representative reference genomes were selected to identify the structural variation of sorghum. Finally, a convenient SSR/SV database of sorghum was constructed by integrating the above results ( http://www.sorghum.top:8079/ ; http://43.154.129.150:8079/ ; http://47.106.184.91:8079/ ). Users can query the information of related sites and primer pairs. CONCLUSIONS Anyway, our research provides convenience for sorghum researchers and will play an active role in sorghum molecular marker-assisted breeding.
Collapse
Affiliation(s)
- Yanlin An
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Xiaobo Xia
- College of Plant Protection , Nanjing Agricultural University, Nanjing, 210095, China
| | - Huayan Zheng
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Shirui Yu
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China.
| | - Feng Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China.
| |
Collapse
|
20
|
Zhang X, Zhang Y, Wang L, Wu G, Pan C. Three novel simple sequence repeats ( SSRs) identified by MALDI-TOF-MS method were associated with backfat in pig. Anim Biotechnol 2023; 34:1014-1021. [PMID: 35048796 DOI: 10.1080/10495398.2021.2009845] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Backfat trait is an important economic trait and highly heritable, but difficult to evaluate. Thus, it is of great significance to explore optimal backfat thickness of pigs by using marker-assisted selection (MAS) to speed up its breeding process and improve economic efficiency. This study aimed to investigate the relationship between genetic variations (e.g., SSRs) and backfat of Qinghai Bamei pigs using MALDI-TOF Mass Spectrometry (MALDI-TOF-MS). Herein, five alternative SSR loci (namely V1, V2, V3, V4 and V5) were selected for subsequent detection. The results suggested that 3 (141-, 143- and 145-), 3 (128-, 130- and 132-), 2 (160- and 162-), 2 (136- and 139-) and 3 (170-, 184- and 192-) alleles of V1, V2, V3, V4 and V5 were found, respectively. Subsequent analysis showed that there was linkage equilibrium among five SSRs and Hap19 (13.1%) (141-/132-/160-/139-/192-) had the highest haplotype frequency. Among these five SSR loci, V1, V2 and V3 loci were significantly associated to the backfat of Qinghai Bamei sows. These findings enriched the study of SSRs in Qinghai Bamei pigs, and (AC)n (Chr15:85485851-85485995), (AC)n (Chr10:52724583-52724713) and (TG)n (Chr4:90732644-90732802) could be utilized as the candidate locus for MAS in pig industry.HIGHLIGHTSFive novel SSR loci was identified in pigs through MALDI-TOF MS.V1, V2 and V3 loci was were significantly associated to the backfat of pigs.
Collapse
Affiliation(s)
- Xuelian Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yanghai Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Meat Science and Muscle Biology Laboratory, Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Lei Wang
- College of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Guofang Wu
- College of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| |
Collapse
|
21
|
Safaa H, Khaled R, Isaac S, Mostafa R, Ragab M, Elsayed DAA, Helal M. Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks. J Genet Eng Biotechnol 2023; 21:105. [PMID: 37856056 PMCID: PMC10587045 DOI: 10.1186/s43141-023-00556-z] [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: 07/05/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Microsatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers. RESULTS The total number of the detected microsatellites using chromosome-wise was 250,053 and 226,417 loci compared to 260,059 and 238,462 loci using whole genome in Mallards and Muscovies. The frequencies of different motifs had similar patterns using the two approaches. Dinucleotide motifs were predominant (> 50%) in both Mallards and Muscovies. The amplification of the genomes revealed an average number of alleles of 5.08 and 4.96 in Mallards and Muscovies. One locus was monographic in Mallards, and two were monomorphic in Muscovies. The average expected heterozygosity was higher in Muscovy than in Mallards (0.45 vs. 0.43) with no significant difference between the two primer sets, which indicated the usefulness of cross-species amplification of different primers. CONCLUSION The current study developed a whole-genome SSR panel for ducks for the first time, and the results could prove that using chromosome-wise mining did not generate different results compared to the whole-genome approach.
Collapse
Affiliation(s)
- Hosam Safaa
- Department of Biology, College of Science, University of Bisha, P.O. Box 551, 61922, Bisha, Saudi Arabia.
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Rawan Khaled
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Suzy Isaac
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Rofida Mostafa
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Mohamed Ragab
- Poultry Production Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
- Animal Breeding and Genetics Department, National Institute for Agricultural and Food Research and Technology (INIA), 28040, Madrid, Spain
| | - Dalia A A Elsayed
- Department of Poultry Breeding, Agriculture Research Center, Animal Production Research Institute, Dokki, Giza, Egypt
| | - Mostafa Helal
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| |
Collapse
|
22
|
Xu X, Wang N, Feng L, Wang J. Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing Rosa rugosa via High-Resolution Melting (HRM) Analysis. Biomolecules 2023; 13:1468. [PMID: 37892150 PMCID: PMC10605111 DOI: 10.3390/biom13101468] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Oil-bearing Rosa rugosa are popular in the essential oil and perfume markets. The similar botanical characteristics between high-oil-yield or low-oil-yield cultivars are confusing and it is hard for farmers or breeders to identify the high-oil-yield cultivar by phenotype difference. High-resolution melting (HRM) analysis of simple sequence repeats (SSRs) can construct accurate DNA fingerprints quickly, which was shown to be effective for identification of closely related cultivars of R. rugosa. Optimization of HRM-SSR indicated that the 10 µL HRM reaction mixture containing 20 ng of genomic DNA of R. rugosa and 0.75 µL of 10 µmol/L of each primer with an annealing temperature of 64 °C was a robust SSR genotyping protocol. Using this protocol, 9 polymorphic SSR markers with 3-9 genotypes among the 19 R. rugosa cultivars were identified. The top three polymorphic makers SSR9, SSR12 and SSR19 constructed a fingerprint of all cultivars, and the rare insertion in the flanking sequences of the repeat motif of SSR19 generated three characteristic genotypes of three high-oil-yield cultivars. These results may be economical and practical for the identification of high-oil-yield R. rugosa and be helpful for the selection and breeding of oil-bearing roses.
Collapse
Affiliation(s)
| | | | - Liguo Feng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (X.X.); (N.W.)
| | - Jianwen Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (X.X.); (N.W.)
| |
Collapse
|
23
|
Fabritius MP, Soltani V, Cyran CC, Ricke J, Bartenstein P, Auernhammer CJ, Spitzweg C, Schnitzer ML, Ebner R, Mansournia S, Hinterberger A, Lohse A, Sheikh GT, Winkelmann M, Knösel T, Ingenerf M, Schmid-Tannwald C, Kunz WG, Rübenthaler J, Grawe F. Diagnostic accuracy of SSR-PET/CT compared to histopathology in the identification of liver metastases from well-differentiated neuroendocrine tumors. Cancer Imaging 2023; 23:92. [PMID: 37770958 PMCID: PMC10537814 DOI: 10.1186/s40644-023-00614-2] [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] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Histopathology is the reference standard for diagnosing liver metastases of neuroendocrine tumors (NETs). Somatostatin receptor-positron emission tomography / computed tomography (SSR-PET/CT) has emerged as a promising non-invasive imaging modality for staging NETs. We aimed to assess the diagnostic accuracy of SSR-PET/CT in the identification of liver metastases in patients with proven NETs compared to histopathology. METHODS Histopathologic reports of 139 resected or biopsied liver lesions of patients with known NET were correlated with matching SSR-PET/CTs and the positive/negative predictive value (PPV/NPV), sensitivity, specificity, and diagnostic accuracy of SSR-PET/CT were evaluated. PET/CT reading was performed by one expert reader blinded to histopathology and clinical data. RESULTS 133 of 139 (95.7%) liver lesions showed malignant SSR-uptake in PET/CT while initial histopathology reported on 'liver metastases of NET´ in 127 (91.4%) cases, giving a PPV of 91.0%. Re-biopsy of the initially histopathologically negative lesions (reference standard) nevertheless diagnosed 'liver metastases of NET' in 6 cases, improving the PPV of PET/CT to 95.5%. Reasons for initial false-negative histopathology were inadequate sampling in the sense of non-target biopsies. The 6 (4.3%) SSR-negative lesions were all G2 NETs with a Ki-67 between 2-15%. CONCLUSION SSR-PET/CT is a highly accurate imaging modality for the diagnosis of liver metastases in patients with proven NETs. However, we found that due to the well-known tumor heterogeneity of NETs, specifically in G2 NETs approximately 4-5% are SSR-negative and may require additional imaging with [18F]FDG PET/CT.
Collapse
Affiliation(s)
- M P Fabritius
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - V Soltani
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - C C Cyran
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - J Ricke
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - P Bartenstein
- Department of Nuclear Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - C J Auernhammer
- Department of Internal Medicine 4, University Hospital, LMU Munich, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - C Spitzweg
- Department of Internal Medicine 4, University Hospital, LMU Munich, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - M L Schnitzer
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - R Ebner
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - S Mansournia
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - A Hinterberger
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - A Lohse
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - G T Sheikh
- Department of Nuclear Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - M Winkelmann
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - T Knösel
- Department of Pathology, University Hospital, LMU Munich, 81377, Munich, Germany
| | - M Ingenerf
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - C Schmid-Tannwald
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - W G Kunz
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - J Rübenthaler
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - Freba Grawe
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.
- Department of Nuclear Medicine, University Hospital, LMU Munich, 81377, Munich, Germany.
| |
Collapse
|
24
|
Zhuo J, Vasupalli N, Wang Y, Zhou G, Gao H, Zheng Y, Li B, Hou D, Lin X. Molecular identification of Bambusa changningensis is the natural bamboo hybrid of B. rigida × Dendrocalamus farinosus. Front Plant Sci 2023; 14:1231940. [PMID: 37727859 PMCID: PMC10505617 DOI: 10.3389/fpls.2023.1231940] [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: 05/31/2023] [Accepted: 08/09/2023] [Indexed: 09/21/2023]
Abstract
Bamboo is one of the fastest-growing plants commonly used in food, fibre, paper, biofuel, ornamental and medicinal industries. Natural hybridization in bamboo is rare due to its long vegetative period followed by gregarious flowering and death of the entire population. In the current study, a new bamboo species, Bambusa changningensis, shows intermediate characteristics of Dendrocalamus farinosus and B. rigida morphologically, but it is unknown whether B. changningensis is a natural hybrid. Moreover, B. changningensis has been identified as a superior variety of Sichuan Province with high pulping yield, fibre length and width. Therefore, we analyzed the morphological characteristics, DNA markers, DNA barcoding and chloroplast genomes to identify the hybrid origin of B. changningensis and possible maternal parent. We have developed the transcriptomic data for B. changningensis and mined the SSR loci. The putative parental lines and hybrid were screened for 64 SSR makers and identified that SSR14, SSR28, SSR31 and SSR34 markers showed both alleles of the parental species in B. changningensis, proving heterozygosity. Sequencing nuclear gene GBSSI partial regions and phylogenetic analysis also confirm the hybrid nature of B. changningensis. Further, we have generated the complete chloroplast genome sequence (139505 bp) of B. changningensis. By analyzing the cp genomes of both parents and B. changningensis, we identified that B. rigida might be the female parent. In conclusion, our study identified that B. changningensis is a natural hybrid, providing evidence for bamboo's natural hybridization. This is the first report on confirming a natural bamboo hybrid and its parents through SSR and chloroplast genome sequence.
Collapse
Affiliation(s)
- Juan Zhuo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Naresh Vasupalli
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Yong Wang
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Guoqiang Zhou
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Huibin Gao
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Ying Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Benxiang Li
- Sichuan Changning Century Bamboo Garden, Yibin, Sichuan, China
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| |
Collapse
|
25
|
Li R, Huang Y, Yang X, Su M, Xiong H, Dai Y, Wu W, Pei X, Yuan Q. Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers. Plants (Basel) 2023; 12:2876. [PMID: 37571029 PMCID: PMC10421310 DOI: 10.3390/plants12152876] [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: 06/18/2023] [Revised: 07/15/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023]
Abstract
Shanlan upland rice (Oryza sativa L.) is a unique upland rice variety cultivated by the Li nationality for a long time, which has good drought resistance and high utilization value in drought resistance breeding. To explore the origin of Shanlan upland rice and its genetic relationship with upland rice from other geographical sources, 214 upland rice cultivars from Southeast Asia and five provinces (regions) in southern China were used to study genetic diversity by using SSR markers. Twelve SSR primers were screened and 164 alleles (Na) were detected, with the minimum number of alleles being 8 and the maximum number of alleles being 23, with an average of 13.667. The analysis of genetic diversity and analysis of molecular variance (AMOVA) showed that the differences among the materials mainly came from the individuals of upland rice. The results of gene flow and genetic differentiation revealed the relationship between the upland rice populations, and Hainan Shanlan upland rice presumably originated from upland rice in Guangdong province, and some of them were genetically differentiated from Hunan upland rice. It can be indirectly proved that the Li nationality in Hainan is a descendant of the ancient Baiyue ethnic group, which provides circumstantial evidence for the migration history of the Li nationality in Hainan, and also provides basic data for the advanced protection of Shanlan upland rice, and the innovative utilization of germplasm resources.
Collapse
Affiliation(s)
- Rongju Li
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Yinling Huang
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Xinsen Yang
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Meng Su
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Huaiyang Xiong
- Hainan Guangling High-Tech Industrial Co., Ltd., Lingshui 572400, China; (H.X.); (Y.D.)
| | - Yang Dai
- Hainan Guangling High-Tech Industrial Co., Ltd., Lingshui 572400, China; (H.X.); (Y.D.)
| | - Wei Wu
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qianhua Yuan
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| |
Collapse
|
26
|
Giancaspro A, Giove SL, Marcotuli I, Ferrara G, Gadaleta A. Datasets for genetic diversity assessment in a collection of wild and cultivated pomegranates ( Punica granatum L.) by microsatellite markers. Data Brief 2023; 49:109346. [PMID: 37456114 PMCID: PMC10344663 DOI: 10.1016/j.dib.2023.109346] [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: 04/26/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
Data described in this article refer to molecular characterization and assessment of genetic diversity within a wide collection of pomegranate genotypes including both selections and cultivars from different geographical origin/disseminations by using microsatellite (SSR, Simple Sequence Repeats) markers. Supplied datasets refer to a set of 63 genotypes including 55 accessions (landraces) from Italy, Turkmenistan, Japan, and USA and 8 cultivars from Israel, established at the pomegranate repository of the Fruit Tree Unit of the Department of Soil, Plant and Food Science at University of Bari "Aldo Moro", Italy. Pomegranate accessions differed for end-use purpose (edible, ornamental) and some morpho-pomological traits including juice taste, inner tegmen hardness, and skin/seed color. Molecular data were opportunely employed to build a similarity matrix to establish phylogenetic relationships (genetic similarity and distances) among pomegranate accessions and compare genetic clustering to morpho-pomological classification. The present data article provides detailed information and methodological protocols on SSR markers, PCR amplification and banding profiling aimed to molecular characterization of pomegranate collection. This latter was conducted by amplifying a set of informative polymorphic SSR markers on the genomic DNA of each pomegranate accession, and then comparing the different molecular profiles by capillary electrophoresis. The banding patterns obtained from microsatellite markers were used to build a binary matrix containing the scores for each individual SSR fragment, which was transformed into a similarity matrix and finally used for cluster analysis and dendrogram building based on the UPGMA algorithm. This paper supplies data potentially useful for the identification of polymorphic markers suitable for varietal identification and traceability, or discrimination between tightly related pomegranate accessions with very high morphological similarity and/or geographical identity. Data described in this paper support the published original research article titled "Exploiting DNA-based molecular tools to assess genetic diversity in pomegranate (Punica granatum L.) selections and cultivars" [1].
Collapse
|
27
|
Nagpal S, Sirari A, Sharma P, Singh S, Mandahal KS, Singh H, Singh S. Marker trait association for biological nitrogen fixation traits in an interspecific cross of chickpea ( Cicer arietinum × Cicer reticulatum). Physiol Mol Biol Plants 2023; 29:1005-1018. [PMID: 37649881 PMCID: PMC10462594 DOI: 10.1007/s12298-023-01335-3] [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: 11/17/2022] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 09/01/2023]
Abstract
A set of 165 Recombinant inbred lines (RILs) derived from an interspecific cross of chickpea was used to identify QTLs for key biological nitrogen fixation (BNF) traits. The phenotyping of BNF and related traits was done at two different agroclimatic zones viz., Central plain zone (Ludhiana) and Sub-Mountainous undulating zone (Gurdaspur) for 2 consecutive rabi seasons (2018-2020). Wild parent C. reticulatum ILWC292 showed significantly high performance in terms of biological nitrogen fixation (BNF) traits over the cultivated C. arietinum GPF-2. The triple interaction of genotypes × locations × years was significant (p 0.05) for all BNF traits in parental lines. Highly significant positive correlation was obtained between grain yield and key growth and symbiotic parameters at both the sites. Phenotypic analysis revealed nodule dry weight and leghaemoglobin content as key traits for BNF efficiency and contrasting DNA bulks were constituted on the basis of these traits. Out of 535 SSR markers, 139 exhibited polymorphism between the parental lines on polyacrylamide gel electrophoresis. A total of 30 SSR markers showed polymorphism between the higher and lower bulks for nodule dry weight and leghaemoglobin content. Out of these, 20 SSRs did not show any segregation distortion in RIL population as determined by chi square analysis (p < 0.05) and were used for quantitative trait loci (QTL) analysis. Using QTL cartographer, markers- CAGM02697, CAGM09835, CAGM09777, CAGM09227, CAGM09021, CAGM08679 were found linked with QTLs for BNF. These markers can be validated further for identification of genes for BNF traits and marker assisted selection in chickpea. To the best of our knowledge this is the first report on identification of genomic regions associated with key BNF traits in chickpea across different agro-climatic zones. Supplementary information The online version contains supplementary material available at 10.1007/s12298-023-01335-3.
Collapse
Affiliation(s)
- Sharon Nagpal
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Asmita Sirari
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Poonam Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Satinder Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | | | - Harpreet Singh
- Regional Research Station, Punjab Agricultural University, Gurdaspur, 143521 India
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| |
Collapse
|
28
|
Aslam F, Mohti W, Ali H, Ferreira P. Interplay of multifractal dynamics between shadow policy rates and stock markets. Heliyon 2023; 9:e18114. [PMID: 37483712 PMCID: PMC10362331 DOI: 10.1016/j.heliyon.2023.e18114] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023] Open
Abstract
Stock markets are generally perceived as a barometer of the economy and respond to international monetary policies even before economic activities. Many central banks have turned to unconventional policy measures in response to various financial crises such as the global financial crisis of 2007-2009 or the recent crisis caused by COVID-19. To examine the cross-correlation of overall international monetary policies with stock markets, we employ the daily shadow short rate (SSR), which has the advantage of allowing comparison across unconventional and conventional regimes. The analysis is made through a multifractal context using multifractal detrended cross correlation analysis (MF-DXA), considering daily data from 1st January 2000 to 31st March 2022 and country specific SSR and the stock markets of eight developed economies. The main empirical findings are the following: (i) all the country specific pairs of SSR with stock markets have significant multifractal characteristics (ii) the pairs of NZ-SSR/NZX50, US-SSR/DJIA, and CN-SSR/S&P TSX have the highest multifractal patterns while EU-SSR/Euro-area Index has the lowest multifractal patterns (iii) Australian and New Zealand stock markets exhibit anti-persistent cross-correlation with SSR while the remainder have persistent cross-correlation in their multifractality. Lastly, the findings of this study have several important implications for central banks and stock market participants.
Collapse
Affiliation(s)
- Faheem Aslam
- Department of Management Sciences, COMSATS University Islamabad, Park Road, 45550 Islamabad, Pakistan
| | - Wahbeeah Mohti
- Department of Business Administration, Iqra University Islamabad Campus Pakistan
| | - Haider Ali
- Department of Management Sciences, COMSATS University Islamabad, Park Road, 45550 Islamabad, Pakistan
| | - Paulo Ferreira
- VALORIZA—Research Center for Endogenous Resource Valorization, 7300-555 Portalegre, Portugal Department of Economic Sciences and Organizations, Polytechnic Institute of Portalegre
| |
Collapse
|
29
|
Dey P, Ray SD, Pramod P, Singh RP. Dataset from genome sequencing, assembly and mining of microsatellite markers in barred-button quail ( Turnix suscitator). Data Brief 2023; 48:109288. [PMID: 37383822 PMCID: PMC10294100 DOI: 10.1016/j.dib.2023.109288] [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: 04/12/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023] Open
Abstract
Turnix suscitator (barred-button quail) is a member of the primitive genus Turnix in the highly diverse order of shore birds Charadriiformes. Absence of genome scale data of T. suscitator has limited our understanding about its systematics, taxonomic and evolutionary history as well has hindered the characterization of genome wide microsatellite markers of the same. Hence we generated whole genome short read sequences of T. suscitator, created a high quality assembly and mined genome-wide microsatellite markers from the same. A total of 34142524 reads were sequenced with an estimated genome size of 817 mb. SPAdes assembly consisted of 320761 total contigs and an estimated N50 value of 907 base pairs. Krait identified a total of 77028 microsatellite motifs covering 0.64% of the total sequences in the SPAdes assembly. Further the whole genome sequence and genome wide microsatellites dataset of T. suscitator will facilitate future genomic/evolutionary studies of Turnix species.
Collapse
Affiliation(s)
- Prateek Dey
- Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu 641108, India
- Bharathiar University, Coimbatore, Tamil Nadu 641046, India
| | - Swapna Devi Ray
- Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu 641108, India
- Bharathiar University, Coimbatore, Tamil Nadu 641046, India
| | - Padmanabhan Pramod
- Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu 641108, India
| | - Ram Pratap Singh
- Department of Life Science, Central University of South Bihar, Gaya 824236, India
| |
Collapse
|
30
|
Xiao Y, Chen X, Yin Y, Zheng J, Yi H, Song L. Comparative genetic and epigenetic of the Sphagneticola trilobata (L.) Pruski from different regions in China. BMC Plant Biol 2023; 23:289. [PMID: 37254044 DOI: 10.1186/s12870-023-04277-w] [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] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/09/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Sphagneticola trilobata (L.) Pruski is a prevalent and widely distributed invasive plant in South China. To investigate the molecular mechanisms underlying its rapid adaptation, we employed DNA methylation-sensitive amplified polymorphism (MSAP) and simple sequence repeat (SSR) analysis to study 60 S. trilobata individuals collected from Fuzhou (FZ), Haikou (HK), Jinghong (JH) and Guangzhou (GZ). RESULTS In this study, we computed the Shannon diversity index (I) of SSR and MSAP as 0.354 and 0.303, respectively. The UPGMA phylogenetic tree and PCoA analyses showed that MSAP had a better discriminatory power to distinguish populations from different regions. Notably, the GZ population was found to be the most distinct from the other three populations. Moreover, Mantel analysis revealed a significantly higher correlation between epigenetic distance and geographic distance as compared to genetic distance and geographic distance. Consequently, the correlation between epigenetic distance and geographic distance observed to be markedly stronger than that between genetic distance and geographical distance on Mantel analysis. CONCLUSIONS The S. trilobata populations in various regions displayed a high of complementary genetic and epigenetic diversity, which was a key feature contributing to their rapid invasion. Interestingly, the correlation between epigenetics and geographical distance was significantly stronger than that observed for genetics and geographical distance. These findings indicated that the epigenetic mechanism of S. trilobar exhibited high plasticity, leading to significant differences in methylation pattern across different populations.
Collapse
Affiliation(s)
- Yusha Xiao
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Xiuqing Chen
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yuhan Yin
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Jiening Zheng
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Huixian Yi
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Liying Song
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
| |
Collapse
|
31
|
Türkoğlu A, Haliloğlu K, Mohammadi SA, Öztürk A, Bolouri P, Özkan G, Bocianowski J, Pour-Aboughadareh A, Jamshidi B. Genetic Diversity and Population Structure in Türkiye Bread Wheat Genotypes Revealed by Simple Sequence Repeats ( SSR) Markers. Genes (Basel) 2023; 14:1182. [PMID: 37372362 DOI: 10.3390/genes14061182] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Wheat genotypes should be improved through available germplasm genetic diversity to ensure food security. This study investigated the molecular diversity and population structure of a set of Türkiye bread wheat genotypes using 120 microsatellite markers. Based on the results, 651 polymorphic alleles were evaluated to determine genetic diversity and population structure. The number of alleles ranged from 2 to 19, with an average of 5.44 alleles per locus. Polymorphic information content (PIC) ranged from 0.031 to 0.915 with a mean of 0.43. In addition, the gene diversity index ranged from 0.03 to 0.92 with an average of 0.46. The expected heterozygosity ranged from 0.00 to 0.359 with a mean of 0.124. The unbiased expected heterozygosity ranged from 0.00 to 0.319 with an average of 0.112. The mean values of the number of effective alleles (Ne), genetic diversity of Nei (H) and Shannon's information index (I) were estimated at 1.190, 1.049 and 0.168, respectively. The highest genetic diversity (GD) was estimated between genotypes G1 and G27. In the UPGMA dendrogram, the 63 genotypes were grouped into three clusters. The three main coordinates were able to explain 12.64, 6.38 and 4.90% of genetic diversity, respectively. AMOVA revealed diversity within populations at 78% and between populations at 22%. The current populations were found to be highly structured. Model-based cluster analyses classified the 63 genotypes studied into three subpopulations. The values of F-statistic (Fst) for the identified subpopulations were 0.253, 0.330 and 0.244, respectively. In addition, the expected values of heterozygosity (He) for these sub-populations were recorded as 0.45, 0.46 and 0.44, respectively. Therefore, SSR markers can be useful not only in genetic diversity and association analysis of wheat but also in its germplasm for various agronomic traits or mechanisms of tolerance to environmental stresses.
Collapse
Affiliation(s)
- Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, 42310 Konya, Turkey
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Seyyed Abolgahasem Mohammadi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz 5166616471, Iran
| | - Ali Öztürk
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Parisa Bolouri
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Güller Özkan
- Department of Biology, Faculty of Science, Ankara University, 06100 Ankara, Turkey
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
| | - Alireza Pour-Aboughadareh
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31585-854, Iran
| | - Bita Jamshidi
- Department of Food Security and Public Health, Khabat Technical Institute, Erbil Polytechnic University, Erbil 44001, Iraq
| |
Collapse
|
32
|
Ibrahimi M, Brhadda N, Ziri R, Fokar M, Iraqi D, Gaboun F, Labhilili M, Habach A, Meziani R, Elfadile J, Abdelwahd R, Diria G. Analysis of genetic diversity and population structure of Moroccan date palm (Phoenix dactylifera L.) using SSR and DAMD molecular markers. J Genet Eng Biotechnol 2023; 21:66. [PMID: 37217693 DOI: 10.1186/s43141-023-00516-7] [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: 01/17/2023] [Accepted: 05/06/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Date palm, oasis pivot, plays a vital socio-economic part in the southern area of Morocco. However, with climate change and drought intensity and frequency increasing, the Moroccan palm grove is threatened with significant genetic degradation. Genetic characterization of this resource is key element for the development of effective conservation and management strategies in the current circumstances of climate change and various biotic and abiotic stresses. To evaluate the genetic diversity of date palm populations collected from different Moroccan oases, we used simple sequence repeats (SSR) and directed amplification of mini-satellite DNA (DAMD) markers. Our results showed that used markers could efficiently assess genetic diversity in Phoenix dactylifera L. RESULTS A total of 249 and 471 bands were respectively scored for SSR and DAMD, of which 100% and 92.9% were polymorphic. The polymorphic information content (PIC = 0.95), generated by the SSR primer was nearly identical to that generated by the DAMD primer (PIC = 0.98). The resolving power (Rp) was higher in DAMD than SSR (29.46 and 19.51, respectively). Analysis of the molecular variance (AMOVA) based on the combined data sets for both markers revealed a higher variance within populations (75%) than among populations (25%). Principal coordinate analysis (PCoA) and the ascendant hierarchical classification showed that the population of Zagora and Goulmima regions were the closest populations. The STRUCTURE analysis clustering of the 283 tested samples into seven clusters based on their genetic composition. CONCLUSION The results drawn from this study will orient genotypes selection strategies for a successful future breeding and conservation program, particularly under climate change context.
Collapse
Affiliation(s)
- Maha Ibrahimi
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
- Laboratory of Plant, Animal and Agro-Industry Productions, Faculty of Sciences, University of Ibn Tofail, Kenitra, Morocco
| | - Najiba Brhadda
- Laboratory of Plant, Animal and Agro-Industry Productions, Faculty of Sciences, University of Ibn Tofail, Kenitra, Morocco
| | - Rabea Ziri
- Laboratory of Plant, Animal and Agro-Industry Productions, Faculty of Sciences, University of Ibn Tofail, Kenitra, Morocco
| | - Mohamed Fokar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
| | - Driss Iraqi
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Fatima Gaboun
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Mustapha Labhilili
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Aicha Habach
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Reda Meziani
- UR Oasis Systems, National Laboratory of Date Palm Tissues Culture, Regional Center of Agricultural Research of Errachidia, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Jamal Elfadile
- UR Oasis Systems, National Laboratory of Date Palm Tissues Culture, Regional Center of Agricultural Research of Errachidia, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Rabha Abdelwahd
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Ghizlane Diria
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco.
| |
Collapse
|
33
|
López-López N, Rojas JC, Cruz-López L, Ulloa-García A, Malo EA. Dog hair volatiles attract Rhipicephalus sanguineus sensu lato (Acari: Ixodidae) females. J Med Entomol 2023; 60:432-442. [PMID: 36893033 DOI: 10.1093/jme/tjad019] [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: 08/30/2022] [Revised: 11/30/2022] [Accepted: 02/06/2023] [Indexed: 05/13/2023]
Abstract
Rhipicephalus sanguineus sensu lato (s.l.) (Latreille) feeds on domestic dogs worldwide. This tick species uses dog volatiles during host-seeking behavior. In this study, we identified volatile compounds from dog hairs involved in the host location of R. sanguineus s.l. The R. sanguineus s.l. females, but not males, were attracted to hair samples and Super Q extracts from Schnauzer dogs in Y-tube olfactometer bioassays. A total of 54 compounds from dog hair extracts were identified by gas chromatography coupled to mass spectrometry, including hydrocarbons, aldehydes, alcohols, ketones, and carboxylic acids. Screening the identified compounds by the single sensillum recording technique showed that isovaleric acid, hexanal, heptanal, and sucaltone (6-methyl-5-hepten-2-one) significantly stimulated the olfactory receptor neurons of the basiconic, chaeticum, and trichodeum sensilla of female ticks. When synthetic compounds were evaluated alone, or in binary, tertiary, or quaternary mixtures, female ticks were only attracted to isovaleric acid and 1 tertiary mixture (hexanal, heptanal, and isovaleric acid). We conclude that isovaleric acid functions as an attractant for R. sanguineus s.l. These findings contribute to the understanding of the chemical ecology of ticks during host location.
Collapse
Affiliation(s)
- Noe López-López
- Grupo de Ecología de Artrópodos y Manejo de Plagas, Departamento de Agricultura, Sociedad y Ambiente, El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto Km 2.5, Tapachula, Chiapas 30700, Mexico
| | - Julio C Rojas
- Grupo de Ecología de Artrópodos y Manejo de Plagas, Departamento de Agricultura, Sociedad y Ambiente, El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto Km 2.5, Tapachula, Chiapas 30700, Mexico
| | - Leopoldo Cruz-López
- Grupo de Ecología de Artrópodos y Manejo de Plagas, Departamento de Agricultura, Sociedad y Ambiente, El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto Km 2.5, Tapachula, Chiapas 30700, Mexico
| | - Armando Ulloa-García
- Facultad de Ciencias Químicas, Universidad Autónoma de Chiapas, Carretera a Puerto Madero Km. 1.5, Centro, Tapachula, Chiapas 30580, Mexico
| | - Edi A Malo
- Grupo de Ecología de Artrópodos y Manejo de Plagas, Departamento de Agricultura, Sociedad y Ambiente, El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto Km 2.5, Tapachula, Chiapas 30700, Mexico
| |
Collapse
|
34
|
Figueroa D, Corredor FA, Mamani-Cato RH, Gallegos-Acero RF, Condori-Rojas N, Estrada R, Heredia L, Salazar W, Quilcate C, Arbizu CI. Microsatellite-Based Genetic Diversity and Population Structure of Huacaya Alpacas ( Vicugna pacos) in Southern Peru. Animals (Basel) 2023; 13:ani13091552. [PMID: 37174589 PMCID: PMC10177232 DOI: 10.3390/ani13091552] [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: 12/29/2022] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 05/15/2023] Open
Abstract
The alpaca population mostly consists of the Huacaya phenotype and is widely distributed in Southern Peru. This study aimed to estimate the genetic diversity and population structure of two Huacaya alpaca populations (Ajoyani and Quimsachata) using fourteen and twelve microsatellite markers for each population, respectively. A total of 168 alpaca biological samples were outsourced to Peruvian laboratories for DNA extraction and genotyping. For genetic diversity, observed heterozygosity (Ho), expected heterozygosity (He), polymorphism information content (PIC), and fixation indices values were estimated. An admixture analysis was performed for the population structure analysis. Different programs were used for these estimations. In total, 133 (Ajoyani) and 129 (Quimsachata) alleles were found, with a range of 4 to 17 by locus. The mean HO, HE, and PIC per marker for Ajoyani were 0.764 ± 0.112, 0.771 ± 0.1, and 0.736; for Quimsachata, they were 0.783 ± 0.087, 0.773 ± 0.095, and 0.738, respectively. The population structure showed no structure with K = 2. This study provides useful indicators for the creation of appropriate alpaca conservation programs.
Collapse
Affiliation(s)
- Deyanira Figueroa
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Flor-Anita Corredor
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Ruben H Mamani-Cato
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Estación Experimental Agraria Illpa, Puno 21002, Peru
| | - Roberto F Gallegos-Acero
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional del Altiplano, Av. Floral 1153, Puno 21001, Peru
| | - Nicoll Condori-Rojas
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Estación Experimental Agraria Illpa, Puno 21002, Peru
| | - Richard Estrada
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Lizeth Heredia
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Wilian Salazar
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Carlos Quilcate
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Carlos I Arbizu
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
- Facultad de Ingeniería y Ciencias Agrarias, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Cl. Higos Urco 342, Chachapoyas 01001, Peru
| |
Collapse
|
35
|
Hu J, Duan Y, Yang J, Gan L, Chen W, Yang J, Xiao G, Guan L, Chen J. Transcriptome Analysis Reveals Genes Associated with Flooding Tolerance in Mulberry Plants. Life (Basel) 2023; 13:life13051087. [PMID: 37240733 DOI: 10.3390/life13051087] [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: 03/14/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Mulberry (Morus alba), a widely distributed economic plant, can withstand long-term flooding stress. However, the regulatory gene network underlying this tolerance is unknown. In the present study, mulberry plants were subjected to submergence stress. Subsequently, mulberry leaves were collected to perform quantitative reverse-transcription PCR (qRT-PCR) and transcriptome analysis. Genes encoding ascorbate peroxidase and glutathione S-transferase were significantly upregulated after submergence stress, indicating that they could protect the mulberry plant from flood damage by mediating ROS homeostasis. Genes that regulate starch and sucrose metabolism; genes encoding pyruvate kinase, alcohol dehydrogenase, and pyruvate decarboxylase (enzymes involved in glycolysis and ethanol fermentation); and genes encoding malate dehydrogenase and ATPase (enzymes involved in the TCA cycle) were also obviously upregulated. Hence, these genes likely played a key role in mitigating energy shortage during flooding stress. In addition, genes associated with ethylene, cytokinin, abscisic acid, and MAPK signaling; genes involved in phenylpropanoid biosynthesis; and transcription factor genes also showed upregulation under flooding stress in mulberry plants. These results provide further insights into the adaptation mechanisms and genetics of submergence tolerance in mulberry plants and could aid in the molecular breeding of these plants.
Collapse
Affiliation(s)
- Jingtao Hu
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Yanyan Duan
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Junnian Yang
- College of Teacher Education, Chongqing Three Gorges University, Chongqing 404100, China
| | - Liping Gan
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Wenjing Chen
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Jin Yang
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Guosheng Xiao
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Lingliang Guan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jingsheng Chen
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| |
Collapse
|
36
|
Grawe F, Rosenberger N, Ingenerf M, Beyer L, Eschbach R, Todica A, Seidensticker R, Schmid-Tannwald C, Cyran CC, Ricke J, Bartenstein P, Auernhammer CJ, Ruebenthaler J, Fabritius MP. Diagnostic performance of PET/CT in the detection of liver metastases in well-differentiated NETs. Cancer Imaging 2023; 23:41. [PMID: 37098632 PMCID: PMC10131442 DOI: 10.1186/s40644-023-00556-9] [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: 01/14/2023] [Accepted: 04/13/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND The aim of this retrospective study was to compare the diagnostic accuracy of somatostatin receptor (SSR)-PET/CT to liver MRI as reference standard in the evaluation of hepatic involvement in neuroendocrine tumors (NET). METHODS An institutional database was screened for "SSR" imaging studies between 2006 and 2021. 1000 NET Patients (grade 1/2) with 2383 SSR-PET/CT studies and matching liver MRI in an interval of +3 months were identified. Medical reports of SSR-PET/CT and MRI were retrospectively evaluated regarding hepatic involvement and either confirmed by both or observed in MRI but not in SSR-PET/CT (false-negative) or in SSR-PET but not in MRI (false-positive). RESULTS Metastatic hepatic involvement was reported in 1650 (69.2%) of the total 2383 SSR-PET/CT imaging studies, whereas MRI detected hepatic involvement in 1685 (70.7%) cases. There were 51 (2.1%) false-negative and 16 (0.7%) false-positive cases. In case of discrepant reports, MRI and PET/CT were reviewed side by side for consensus reading. SSR-PET/CT demonstrated a sensitivity of 97.0% (95%CI: 96.0%, 97.7%), a specificity of 97.7% (95%CI: 96.3%, 98.7%), a PPV of 99.0% (95%CI: 98.4%, 99.4%) and NPV of 93.0% (95%CI: 91.0, 94.8%) in identifying hepatic involvement. The most frequent reason for false-negative results was the small size of lesions with the majority < 0.6 cm. CONCLUSION This study confirms the high diagnostic accuracy of SSR-PET/CT in the detection of hepatic involvement in NET patients based on a patient-based analysis of metastatic hepatic involvement with a high sensitivity and specificity using liver MRI imaging as reference standard. However, one should be aware of possible pitfalls when a single imaging method is used in evaluating neuroendocrine liver metastases in patients.
Collapse
Affiliation(s)
- Freba Grawe
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Department of Nuclear Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Natalie Rosenberger
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Maria Ingenerf
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Leonie Beyer
- Department of Nuclear Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - Ralf Eschbach
- Department of Nuclear Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Andrei Todica
- Department of Nuclear Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - Ricarda Seidensticker
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - Christine Schmid-Tannwald
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - Clemens C Cyran
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - Jens Ricke
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - Peter Bartenstein
- Department of Nuclear Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - Christoph J Auernhammer
- Department of Internal Medicine 4, University Hospital, LMU Munich, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - Johannes Ruebenthaler
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System (GEPNET-KUM, ENETS certified Center of Excellence), University Hospital, LMU Munich, 81377, Munich, Germany
| | - Matthias P Fabritius
- Department of Radiology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.
| |
Collapse
|
37
|
Ogiso-Tanaka E, Chankaew S, Yoshida Y, Isemura T, Marubodee R, Kongjaimun A, Baba-Kasai A, Okuno K, Ehara H, Tomooka N. Unique Salt-Tolerance-Related QTLs, Evolved in Vigna riukiuensis (Na + Includer) and V. nakashimae (Na + Excluder), Shed Light on the Development of Super-Salt-Tolerant Azuki Bean ( V. angularis) Cultivars. Plants (Basel) 2023; 12:1680. [PMID: 37111908 PMCID: PMC10146836 DOI: 10.3390/plants12081680] [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: 03/04/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
Wild relatives of crops have the potential to improve food crops, especially in terms of improving abiotic stress tolerance. Two closely related wild species of the traditional East Asian legume crops, Azuki bean (Vigna angularis), V. riukiuensis "Tojinbaka" and V. nakashimae "Ukushima" were shown to have much higher levels of salt tolerance than azuki beans. To identify the genomic regions responsible for salt tolerance in "Tojinbaka" and "Ukushima", three interspecific hybrids were developed: (A) azuki bean cultivar "Kyoto Dainagon" × "Tojinbaka", (B) "Kyoto Dainagon" × "Ukushima" and (C) "Ukushima" × "Tojinbaka". Linkage maps were developed using SSR or restriction-site-associated DNA markers. There were three QTLs for "percentage of wilt leaves" in populations A, B and C, while populations A and B had three QTLs and population C had two QTLs for "days to wilt". In population C, four QTLs were detected for Na+ concentration in the primary leaf. Among the F2 individuals in population C, 24% showed higher salt tolerance than both wild parents, suggesting that the salt tolerance of azuki beans can be further improved by combining the QTL alleles of the two wild relatives. The marker information would facilitate the transfer of salt tolerance alleles from "Tojinbaka" and "Ukushima" to azuki beans.
Collapse
Affiliation(s)
- Eri Ogiso-Tanaka
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba 305-8602, Ibaraki, Japan
| | - Sompong Chankaew
- Program in Plant Breeding, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
| | - Yutaro Yoshida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennohdai 1-1-1, Tsukuba 305-8571, Ibaraki, Japan
| | - Takehisa Isemura
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba 305-8602, Ibaraki, Japan
| | - Rusama Marubodee
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu 514-0102, Mie, Japan
| | - Alisa Kongjaimun
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba 305-8602, Ibaraki, Japan
| | - Akiko Baba-Kasai
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba 305-8602, Ibaraki, Japan
| | - Kazutoshi Okuno
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennohdai 1-1-1, Tsukuba 305-8571, Ibaraki, Japan
| | - Hiroshi Ehara
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu 514-0102, Mie, Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba 305-8602, Ibaraki, Japan
| |
Collapse
|
38
|
Wu Y, Wu W, Zhang C, Lyu L, Li W. Breeding and Growth Performance of 'Ningzhi 4', a New Blackberry Cultivar with High Yield Potential and Good Quality in China. Plants (Basel) 2023; 12:1661. [PMID: 37111883 PMCID: PMC10147019 DOI: 10.3390/plants12081661] [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: 02/28/2023] [Revised: 04/12/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
The thornless blackberry cultivar 'Ningzhi 4' was developed by the Institute of Botany, Jiangsu Province and the Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen). The new blackberry cultivar was selected from the 'Kiowa' (female parent) and 'Hull Thornless' (male parent) F1 hybrid. 'Ningzhi 4' had excellent plant characteristics, including thornlessness, semi-erect to erect canes, vigorous growth and good disease resistance. 'Ningzhi 4' had large fruit and high yield. In addition, the parents of the superior hybrid plant were further identified by SSR markers, which provided the basis for the fingerprint of the new blackberry cultivar 'Ningzhi 4'. This is a commercial cultivar to be grown for fruit production for either shipping or local sales. It also has value as a home-garden plant. This unique type of blackberry fruit was a traditional summer fruit. This new cultivar has thornless semi-erect to erect canes and produces high-quality berries with large size, good firmness, excellent flavor, and potential for shipping and postharvest storage. The new blackberry cultivar 'Ningzhi 4' is adapted to all areas of southern China and is expected to replace or complement 'Kiowa', 'Hull Thornless', 'Chester Thornless' and 'Triple Crown'. A local cultivar patent has been approved by the Jiangsu Variety Approval Committee as 'Rubus spp. Ningzhi 4' in 2020 (S-SV-RS-014-2020). In the future, 'Ningzhi 4' could be promoted as an advantageous thornless blackberry cultivar in the main production regions of China.
Collapse
Affiliation(s)
- Yaqiong Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (L.L.)
| | - Wenlong Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (L.L.)
| | - Chunhong Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (L.L.)
| | - Lianfei Lyu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (L.L.)
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| |
Collapse
|
39
|
Fanelli V, Dellino M, Taranto F, De Giovanni C, Sabetta W, De Vita P, Montemurro C. Varietal identification in pasta through an SSR-based approach: a case study. J Sci Food Agric 2023. [PMID: 37058574 DOI: 10.1002/jsfa.12631] [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: 01/18/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Pasta is a worldwide popular Italian food made exclusively of durum wheat. The choice of variety to be used to produce pasta is at the discretion of the producer based on the peculiar characteristics of each cultivar. The availability of analytical approaches for the tracking of specific varieties along the productive chain is becoming increasingly important to authenticate the pasta products and distinguish between fraudulent activities and cross-contaminations during the production process. Among the different methods, molecular approaches based on DNA markers are the most used for these purposes because of their ease of use and high reproducibility. RESULTS In the present study, we used an easy simple sequence repeats-based method to identify the durum wheat varieties used to produce 25 samples of semolina and commercial pasta comparing their molecular profile with those of the four varieties declared by the producer and other 10 durum wheat cultivars commonly used in pasta production. All of the samples showed the expected molecular profile; however, most of them present also a foreign allele indicating a possible cross-contamination. Moreover, we evaluated the accuracy of the proposed approach through the analysis of 27 hand-made mixtures with increasing amounts of a specific contaminant variety, allowing the estimation of the limit of detection of 5% (w/w). CONCLUSION We demonstrated the feasibility of the proposed method and its effectiveness in the detection of not declared varieties when these are present in a percentage equal to or higher than 5%. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Collapse
Affiliation(s)
- Valentina Fanelli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Maria Dellino
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Francesca Taranto
- Institute of Biosciences and BioResources, National Research Council of Italy (IBBR-CNR), Bari, Italy
| | - Claudio De Giovanni
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Wilma Sabetta
- Institute of Biosciences and BioResources, National Research Council of Italy (IBBR-CNR), Bari, Italy
- Spin off Sinagri s.r.l., University of Bari Aldo Moro, Bari, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- Spin off Sinagri s.r.l., University of Bari Aldo Moro, Bari, Italy
- Institute for Sustainable Plant Protection-Support Unit Bari, National Research Council of Italy (IPSP-CNR), Bari, Italy
| |
Collapse
|
40
|
Boiko SM. The trends in the spread of simple sequence repeats in the genomes of Schizophyllum commune. Mycologia 2023; 115:288-298. [PMID: 37039602 DOI: 10.1080/00275514.2023.2186742] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Due to their high number and variety, simple sequence repeats in DNA are a valuable source of genetic markers widely used in population genetics, genetic diversity, and fingerprinting. Schizophyllum commune is a cosmopolitan basidiomycete and a valuable object for biotechnology and mycology. It is often used as a model organism in genetic and population studies. Numerous genome sequences of S. commune are available in the National Center for Biotechnology Information (NCBI) database, allowing for a meticulous study of the distribution of simple tandem nucleotide repeats in the genomes of different strains, based on their origin. Analysis of the average density of simple tandem repeats in the genomes of S. commune fungi reveals the division of cultures into groups based on the USA, Ru (Russian Federation), and EA (South Korea, Japan, China) populations. Intensive point mutations lead to the accumulation and dominance of mononucleotide (C)n and dinucleotide (CG)n motifs in fungal genomes. Results show that the GCT motif contributes more to the divergence of the Ru population, whereas CTC, GAG, and GGA motifs contribute to the divergence of the USA population. Strains MG53 (China) and IUM1114-SS01 (South Korea: Incheon) from the EA population occupy a separate position, mainly because of the CGA motif. The divergence in quantitative traits of motifs between populations provides evidence of the evolutionary transformation of fungal genomes under environmental factors.
Collapse
Affiliation(s)
- Sergiy M Boiko
- Department of Phytoecology, Institute for Evolutionary Ecology, National Academy of Sciences of Ukraine, 37 Lebedeva Str., Kyiv 03143, Ukraine
| |
Collapse
|
41
|
Zheng S, Zhang T, Tu K, Li L, Liu Z, Wu B, Zhou L, Sun X. Population Genetics of Manila Clam ( Ruditapes philippinarum) in China Inferred from Microsatellite Markers. Biology (Basel) 2023; 12:biology12040557. [PMID: 37106757 PMCID: PMC10135866 DOI: 10.3390/biology12040557] [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: 02/18/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023]
Abstract
The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (Ne). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (Ho) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (He) was calculated to be varying from 0.587 to 0.700. Fst values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all Fst values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams.
Collapse
Affiliation(s)
- Sichen Zheng
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Tianshi Zhang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Kang Tu
- Putian Institute of Aquaculture Science of Fujian Province, Putian 351100, China
| | - Li Li
- National Oceanographic Center, Marine Science Research Institute of Shandong Province, Qingdao 266104, China
| | - Zhihong Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Biao Wu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Liqing Zhou
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiujun Sun
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| |
Collapse
|
42
|
Zhang J, Hieno A, Otsubo K, Feng W, Kageyama K. Population Genetic Analysis of Phytophthora colocasiae from Taro in Japan Using SSR Markers. J Fungi (Basel) 2023; 9:jof9040391. [PMID: 37108846 PMCID: PMC10145753 DOI: 10.3390/jof9040391] [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: 02/27/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Phytophthora colocasiae is an important pathogen that causes great economic losses in taro production in tropical and subtropical regions, especially in Japan. Understanding the genetic variations in P. colocasiae populations and their transmission patterns in Japan is essential for effective disease control. Here, the genetic diversity of 358 P. colocasiae isolates, including 348 from Japan, 7 from China, and 3 from Indonesia, was assessed using 11 simple sequence repeat (SSR) primer pairs with high polymorphism. The phylogenetic tree of the SSR locus showed that the isolates from Japan could be divided into 14 groups, with group A being the dominant group. Among foreign isolates, only six from mainland China were similar to those from Japan and clustered in groups B and E. Analysis of molecular variance (AMOVA), principal components analysis (PCA), and cluster analysis (K = 3) results revealed a moderate level of genetic diversity, mainly within individuals. Populations showed high heterozygosity, a lack of regional differentiation, and frequent gene flow. Analysis of mating types and ploidy levels revealed that A2 and self-fertile (SF) A2 types and tetraploids were dominant across populations. Explanations and hypotheses for the results can provide more effective strategies for disease management of taro leaf blight.
Collapse
Affiliation(s)
- Jing Zhang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Kayoko Otsubo
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Wenzhuo Feng
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| |
Collapse
|
43
|
Nemati Z, Dadkhodaie A, Mostowfizadeh-Ghalamfarsa R, Mehrabi R, Cacciola SO. Genetic Variation of Puccinia triticina Populations in Iran from 2010 to 2017 as Revealed by SSR and ISSR Markers. J Fungi (Basel) 2023; 9:jof9030388. [PMID: 36983556 PMCID: PMC10056552 DOI: 10.3390/jof9030388] [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: 01/22/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Puccinia triticina is a major wheat pathogen worldwide. Although Iran is within the Fertile Crescent, which is supposed to be the center of origin of both wheat and P. triticina, the knowledge of the genetic variability of local populations of this basidiomycete is limited. We analyzed 12 inter simple sequence repeats (ISSRs) and 18 simple sequence repeats (SSRs) of 175 P. triticina isolates sampled between 2010 and 2017 from wheat and other Poaceae in 14 provinces of Iran. SSRs revealed more polymorphisms than ISSRs, indicating they were more effective in differentiating P. triticina populations. Based on a dissimilarity matrix with a variable mutation rate for SSRs and a Dice coefficient for ISSRs, the isolates were separated into three large groups, each including isolates from diverse geographic origins and hosts. The grouping of SSR genotypes in UPGMA dendrograms was consistent with the grouping inferred from the Bayesian approach. However, isolates with a common origin clustered into separate subgroups within each group. The high proportion of heterozygous alleles suggests that in Iran clonal reproduction prevails over sexual reproduction of the pathogen. A significant correlation was found between SSR and ISSR genotypes and the virulence phenotypes of the isolates, as determined in a previous study.
Collapse
Affiliation(s)
- Zahra Nemati
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ali Dadkhodaie
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | | | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 81431-53784, Iran
| | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy
| |
Collapse
|
44
|
Ternjak T, Barreneche T, Šiško M, Ivančič A, Šušek A, Quero-García J. Genetic diversity and structure of Slovenian native germplasm of plum species ( P. domestica L., P. cerasifera Ehrh. and P. spinosa L.). Front Plant Sci 2023; 14:1150459. [PMID: 37025128 PMCID: PMC10070851 DOI: 10.3389/fpls.2023.1150459] [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: 01/24/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Slovenia has particular climatic, soil, geographic and historical conditions that lead to long tradition of plum cultivation and use. In this work, a set of 11 SSR and three universal cpDNA markers, as well as flow cytometry, were used to (1) evaluate the genetic diversity of 124 accessions of the three Prunus species (P. domestica L., P. cerasifera Ehrh., and P. spinosa L.), (2) investigate the possible involvement of P. cerasifera and P. spinosa species in P. domestica origin, (3) study the genetic relationships and variability among the most typical P. domestica accessions present in Slovenia. Ten haplotypes of cpDNA were identified and clustered into three groups according to the Neighbor-Joining analysis (NJ). All 11 SSR primer pairs were polymorphic, revealing 116 unique genotypes. A total of 328 alleles were detected with an average value of 29.82 alleles per locus, showing relatively high diversity. Bayesian analysis of genetic structure was used to identify two ancestral populations in the analyses of all three species as well as in a separate set consisting of P. domestica material only. Principal Coordinate Analysis (PCoA) showed that accessions clustered largely in agreement with Bayesian analysis. Neighbor-Joining analysis grouped 71 P. domestica accessions into three clusters with many subgroups that exhibited complex arrangement. Most accessions clustered in agreement with traditional pomological groups, such as common prunes, mirabelle plums and greengages. In this study, the analyses revealed within P. domestica pool valuable local landraces, such as traditional prunes or bluish plums, which seem to be highly interesting from a genetic point of view. Moreover, complementary approaches allowed us to distinguish between the three species and to gain insights into the origin of plum. The results will be instrumental in understanding the diversity of Slovenian plum germplasm, improving the conservation process, recovering local genotypes and enriching existing collections of plant genetic resources.
Collapse
Affiliation(s)
- T. Ternjak
- Faculty of Agriculture and Life Sciences, University of Maribor, Hoče, Slovenia
| | - T. Barreneche
- INRAE, Univ. Bordeaux, UMR BFP, Villenave d’Ornon, France
| | - M. Šiško
- Faculty of Agriculture and Life Sciences, University of Maribor, Hoče, Slovenia
| | - A. Ivančič
- Faculty of Agriculture and Life Sciences, University of Maribor, Hoče, Slovenia
| | - A. Šušek
- Faculty of Agriculture and Life Sciences, University of Maribor, Hoče, Slovenia
| | | |
Collapse
|
45
|
Sun X, Wang G, Yang J, Yu W, Xu J, Tang B, Ding G, Zhang D. Whole genome evaluation analysis and preliminary Assembly of Oratosquilla oratoria (Stomatopoda: Squillidae). Mol Biol Rep 2023; 50:4165-4173. [PMID: 36894769 DOI: 10.1007/s11033-023-08356-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND As the dominant species of Stomatopoda, Oratosquilla oratoria has not been fully cultivated artificially, and the fishery production mainly depends on marine fishing. Due to the lack of stomatopod genome, the development of molecular breeding of mantis shrimps still lags behind. METHODS AND RESULTS A survey analysis was performed to obtain the genome size, GC content and heterozygosity ratio in order to provide a fundation for subsequent whole-genome sequencing. The results showed that the estimated genome size of the O. oratoria was about 2.56 G, and the heterozygosity ratio was 1.81%, indicating that it is a complex genome. Then the sequencing data was preliminarily assembled with k-mer = 51 by SOAPdenovo software to obtain a genome size of 3.01G and GC content of 40.37%. According to ReapeatMasker and RepeatModerler analysis, the percentage of repeats in O. oratoria was 45.23% in the total genome, similar to 44% in Survey analysis. The MISA tool was used to analyze the simple sequence repeat (SSR) characteristics of genome sequences including Oratosquilla oratoria, Macrobrachium nipponense, Fenneropenaeus chinensis, Eriocheir japonica sinensis, Scylla paramamosain and Paralithodes platypus. All crustacean genomes showed similar SSRs characteristics, with the highest proportion of di-nucleotide repeat sequences. And AC/GT and AGG/CCT repeats were the main types of di-nucleotide and tri-nucleotide repeats in O. oratoria. CONCLUSION This study provided a reference for the genome assembly and annotation of the O. oratoria, and also provided a theoretical basis for the development of molecular markers of O. oratoria.
Collapse
Affiliation(s)
- Xiaoli Sun
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Jie Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Wei Yu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Jiayue Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Ge Ding
- Chemical and Biological Engineering College, Yancheng Institute of Technology, Yancheng, 224003, China
| | - Daizhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China.
| |
Collapse
|
46
|
Pandita D, Mahajan R, Zargar SM, Nehvi FA, Dhekale B, Shafi F, Shah MUD, Sofi NR, Husaini AM. Trait specific marker-based characterization and population structure analysis in rice (Oryza sativa L.) germplasm of Kashmir Himalayas. Mol Biol Rep 2023; 50:4155-4163. [PMID: 36881341 DOI: 10.1007/s11033-023-08324-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND Rice is a key food grain contributor to the global food grain basket and is considered the main food crop in India with a large number of varieties released every year. SSR markers have proven to be an excellent tool for studying genetic diversity. As a result, the present study was done to characterize and assess genetic diversity as well as population structural aspects. METHODS AND RESULTS Fifty genotypes of rice were characterized using 40 SSR markers to assess the genetic diversity and genetic relationship. A total of 114 alleles were amplified with an average of 2.85 alleles per locus. The Polymorphism Information Content (PIC) values varied from 0.30 (RM162) to 0.58 (RM413) with an average of 0.44. Gene diversity was in the range of 0.35 (RM162) to 0.66 (RM413), with an average value of 0.52, while heterozygosity ranged from 0.18 (RM27) to 0.74 (RM55), with an average of 0.39. The population structure revealed a narrow genetic base with only three major subpopulations. Analysis of molecular variance revealed that 74% of the variation was attributed within individuals, 23% was among individuals, and 3% was among populations. Pairwise Fst value of population A & B is 0.024, population B & C is 0.120 and population A & C is 0.115. Dendrogram grouped the genotypes into three clusters with wide variation among the accessions. CONCLUSION Genotyping combined with phylogeny and population structure analysis proved to be a powerful method for characterizing germplasm in this study. There is significant gene flow within populations, as well as the presence of different combinations of alleles, and that allelic exchange rates within the populations are higher than among the populations. Assessing the genetic diversity among individual genotypes within populations is quite useful in selecting candidate parents for future breeding programs to improve the target traits in rice for the Himalayan region.
Collapse
Affiliation(s)
- Deepika Pandita
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, J&K, 190025, India
| | | | | | - Firdous A Nehvi
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, J&K, 190025, India
| | | | - Fouzia Shafi
- Division of Basic Sciences, SKUAST-K, Srinagar, India
| | | | | | - Amjad M Husaini
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, J&K, 190025, India.
| |
Collapse
|
47
|
Pardeshi P, Jadhav P, Sakhare S, Zunjare R, Rathod D, Sonkamble P, Saroj R, Varghese P. Morphological and microsatellite marker-based characterization and diversity analysis of novel vegetable soybean [Glycine max (L.) Merrill]. Mol Biol Rep 2023; 50:4049-4060. [PMID: 36869205 DOI: 10.1007/s11033-023-08328-1] [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: 11/13/2022] [Accepted: 02/09/2023] [Indexed: 03/05/2023]
Abstract
BACKGROUND Vegetable soybean seeds are among the most popular and nutrient-dense beans in the world due to their delicious flavor, high yield, superior nutritional value, and low trypsin content. There is significant potential for this crop that Indian farmers do not fully appreciate because of the limited germplasm range. Therefore, the current study aims to identify the diverse lines of vegetable soybean and explore the diversity produced by hybridizing grain and vegetable-type soybean varieties. Indian researchers have not yet published work describing and analysing novel vegetable soybean for microsatellite markers and morphological traits. METHODS AND RESULTS Sixty polymorphic SSR markers and 19 morphological traits were used to evaluate the genetic diversity of 21 newly developed vegetable soybean genotypes. A total of 238 alleles, ranging from 2 to 8, were found, with a mean of 3.97 alleles per locus. The polymorphism information content varied from 0.05 to 0.85, with an average of 0.60. A variation of 0.25-0.58 with a mean of 0.43 was observed for Jaccard's dissimilarity coefficient. CONCLUSION The diverse genotypes identified can be helpful to understand the genetics of vegetable soybean traits and can be used in improvement programs; study also explains the utility of SSR markers for diversity analysis of vegetable soybean. Here, we identified the highly informative SSRs with PIC > 0.80 (satt199, satt165, satt167, satt191, satt183, satt202, and satt126), which apply to genetic structure analysis, mapping strategies, polymorphic marker surveys, and background selection in genomics-assisted breeding.
Collapse
Affiliation(s)
| | - Pravin Jadhav
- Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, India
| | | | | | | | | | - Ranjit Saroj
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | |
Collapse
|
48
|
Yanfei N, Tai S, Chunhua W, Jia D, Fazhong Y. Complete chloroplast genome sequences of the medicinal plant Aconitum transsectum (Ranunculaceae): comparative analysis and phylogenetic relationships. BMC Genomics 2023; 24:90. [PMID: 36855055 PMCID: PMC9976445 DOI: 10.1186/s12864-023-09180-0] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Aconitum transsectum Diels. (Ranunculaceae) is an important medicinal plant that is widely used in traditional Chinese medicine, but its morphological traits make it difficult to recognize from other Aconitum species. No research has sequenced the chloroplast genome of A.transsectum, despite the fact that phylogenetic analysis based on chloroplast genome sequences provides essential evidence for plant classification. RESULTS In this study, the chloroplast (cp) genome of A. transsectum was sequenced, assembled, and annotated. A. transsectum cp genome is a 155,872 bp tetrameric structure including a large single copy (LSC, 87,671 bp) and a small single copy (SSC, 18,891 bp) section, as well as a pair of inverted repeat sequences (IRa and IRb, 25,894 bp each). 131 genes are encoded by the complete cp genome, comprising 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The most favored codon in the A. transsectum cp genome is AUG, and 46 repeats and 241 SSRs were also identified. The A. transsectum cp genome is similar in size, gene composition, and IR expansion and contraction to the cp genomes of seven Ranunculaceae species. Phylogenetic analysis of cp genomes of 28 plants from the Ranunculaceae family shows that A. transsectum is most closely related to A. vilmorinianum, A. episcopale, and A. forrestii of Subgen. Aconitum. CONCLUSIONS Overall, this study provides complete cp genome resources for A. transsectum that will be beneficial for identifying potential.
Collapse
Affiliation(s)
- Niu Yanfei
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China ,grid.506261.60000 0001 0706 7839Yunnan Institute of Materia Medica, Kunming, 650111 China ,Yunnan Baiyao Group Chinese Medicinal Resources Division, Kunming, 650500 China
| | - Su Tai
- grid.506261.60000 0001 0706 7839Yunnan Institute of Materia Medica, Kunming, 650111 China
| | - Wu Chunhua
- Key Laboratory of State Forestry and Grassland Administration On Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Kunming, 650224, China. .,College of Chemical Engineering, Southwest Forestry University, Kunming, 650224, China.
| | - Deng Jia
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China
| | - Yang Fazhong
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China ,Key Laboratory of State Forestry and Grassland Administration On Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Kunming, 650224 China
| |
Collapse
|
49
|
Ferrer V, Paymal N, Costantino G, Paoli M, Quinton C, Tomi F, Luro F. Correspondence between the Compositional and Aromatic Diversity of Leaf and Fruit Essential Oils and the Pomological Diversity of 43 Sweet Oranges ( Citrus x aurantium var sinensis L.). Plants (Basel) 2023; 12:990. [PMID: 36903852 PMCID: PMC10005092 DOI: 10.3390/plants12050990] [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: 12/09/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Orange (Citrus x aurantium var sinensis) is the most widely consumed citrus fruit, and its essential oil, which is made from the peel, is the most widely used in the food, perfume, and cosmetics industries. This citrus fruit is an interspecific hybrid that would have appeared long before our era and would result from two natural crosses between mandarin and pummelo hybrids. This single initial genotype was multiplied by apomictic reproduction and diversified by mutations to produce hundreds of cultivars selected by men essentially based on phenotypic characteristics of appearance, spread of maturity, and taste. Our study aimed to assess the diversity of essential oil composition and variability in the aroma profile of 43 orange cultivars representing all morphotypes. In agreement with the mutation-based evolution of orange trees, the genetic variability tested with 10 SSR genetic markers was null. The oils from peels and leaves extracted by hydrodistillation were analyzed for composition by GC (FID) and GC/MS and for aroma profile by the CATA (Check All That Apply) method by panelists. Oil yield varied between varieties by a factor of 3 for PEO and a factor of 14 for LEO between maximum and minimum. The composition of the oils was very similar between cultivars and was mainly dominated by limonene (>90%). However, small variations were observed as well as in the aromatic profile, with some varieties clearly distinguishing themselves from the others. This low chemical diversity contrasts with the pomological diversity, suggesting that aromatic variability has never been a selection criterion in orange trees.
Collapse
Affiliation(s)
- Vincent Ferrer
- INRAE, UMR AGAP Institut, INRAE, Institut Agro, Cirad, University Montpellier, 20230 San Giuliano, France
- Rémy Cointreau–Les Molières, 49124 Saint-Barthélemy-d’Anjou, France
| | - Noémie Paymal
- Rémy Cointreau–Les Molières, 49124 Saint-Barthélemy-d’Anjou, France
| | - Gilles Costantino
- INRAE, UMR AGAP Institut, INRAE, Institut Agro, Cirad, University Montpellier, 20230 San Giuliano, France
| | - Mathieu Paoli
- CNRS, Equipe Chimie et Biomasse, UMR SPE 6134, Université de Corse, 20000 Ajaccio, France
| | - Carole Quinton
- Rémy Cointreau–Les Molières, 49124 Saint-Barthélemy-d’Anjou, France
| | - Félix Tomi
- CNRS, Equipe Chimie et Biomasse, UMR SPE 6134, Université de Corse, 20000 Ajaccio, France
| | - François Luro
- INRAE, UMR AGAP Institut, INRAE, Institut Agro, Cirad, University Montpellier, 20230 San Giuliano, France
| |
Collapse
|
50
|
Aguirre NC, Filippi CV, Vera PA, Puebla AF, Zaina G, Lia VV, Marcucci Poltri SN, Paniego NB. Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq) Technology. Methods Mol Biol 2023; 2638:37-57. [PMID: 36781634 DOI: 10.1007/978-1-0716-3024-2_4] [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: 02/15/2023]
Abstract
Double digest restriction-site associated DNA sequencing (ddRADseq) technology combines genome reduced representation by digestion with two restriction enzymes and next generation sequencing (NGS) to obtain thousands of markers (SNP, SSR, and InDels) and genotype tens to hundreds of samples simultaneously. In this chapter, we describe a 96-plex derived ddRADseq protocol that can be set up to obtain different depth of coverage per locus and can be exploited to model and non-model plant species.
Collapse
Affiliation(s)
- Natalia Cristina Aguirre
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo), Unidad Ejecutora de Doble Dependencia Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Ciencia y Técnica (CONICET), Hurlingham, Argentina.
| | - Carla Valeria Filippi
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo), Unidad Ejecutora de Doble Dependencia Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Ciencia y Técnica (CONICET), Hurlingham, Argentina.,Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Pablo Alfredo Vera
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo), Unidad Ejecutora de Doble Dependencia Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Ciencia y Técnica (CONICET), Hurlingham, Argentina
| | - Andrea Fabiana Puebla
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo), Unidad Ejecutora de Doble Dependencia Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Ciencia y Técnica (CONICET), Hurlingham, Argentina
| | - Giusi Zaina
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Verónica Viviana Lia
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo), Unidad Ejecutora de Doble Dependencia Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Ciencia y Técnica (CONICET), Hurlingham, Argentina
| | - Susana Noemí Marcucci Poltri
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo), Unidad Ejecutora de Doble Dependencia Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Ciencia y Técnica (CONICET), Hurlingham, Argentina
| | - Norma Beatriz Paniego
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo), Unidad Ejecutora de Doble Dependencia Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Ciencia y Técnica (CONICET), Hurlingham, Argentina
| |
Collapse
|