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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, SWITZERLAND) 2024; 13:1030. [PMID: 38611559 PMCID: PMC11013090 DOI: 10.3390/plants13071030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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.
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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
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Reutemann AV, Honfi AI, Karunarathne P, Eckers F, Hojsgaard DH, Martínez EJ. Comparative analysis of molecular and morphological diversity in two diploid Paspalum species (Poaceae) with contrasting mating systems. PLANT REPRODUCTION 2024; 37:15-32. [PMID: 37566236 DOI: 10.1007/s00497-023-00478-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/22/2023] [Indexed: 08/12/2023]
Abstract
KEY MESSAGE Interspecific comparison of two Paspalum species has demonstrated that mating systems (selfing and outcrossing) contribute to variation (genetically and morphologically) within species through similar but mutually exclusive processes. Mating systems play a key role in the genetic dynamics of populations. Studies show that populations of selfing plants have less genetic diversity than outcrossing plants. Yet, many such studies have ignored morphological diversity. Here, we compared the morphological and molecular diversity patterns in populations of two phylogenetically-related sexual diploids that differ in their mating system: self-sterile Paspalum indecorum and self-fertile P. pumilum. We assessed the morphological variation using 16 morpho-phenological characters and the molecular diversity using three combinations of AFLPs. We compared the morphological and molecular diversity within and among populations in each mating system. Contrary to expectations, selfers showed higher morphological variation within populations, mainly in vegetative and phenological traits, compared to outcrossers. The high morphological variation within populations of selfers led to a low differentiation among populations. At molecular level, selfing populations showed lower levels of genotypic and genetic diversity than outcrossing populations. As expected, selfers showed higher population structure than outcrossers (PhiST = 0.301 and PhiST = 0.108, respectively). Increased homozygous combinations for the same trait/locus enhance morphological variation and reduce molecular variation within populations in selfing P. pumilum. Thus, selfing outcomes are opposite when comparing morphological and molecular variation in P. pumilum. Meanwhile, pollen flow in obligate outcrossing populations of P. indecorum increases within-population molecular variation, but tends to homogenize phenotypes within-population. Pollen flow in obligate outcrossers tends to merge geographically closer populations; but isolation by distance can lead to a weak differentiation among distant populations of P. indecorum.
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Affiliation(s)
- A Verena Reutemann
- Instituto de Botánica del Nordeste (IBONE-CONICET-UNNE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), 3400, Corrientes, Argentina
| | - Ana I Honfi
- Programa de Estudios Florísticos y Genética Vegetal, Instituto de Biología Subtropical (PEFyGV, IBS-UNaM-CONICET), 3300, Posadas, Argentina
| | - Piyal Karunarathne
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-Von-Haller Institute for Plant Sciences, University of Goettingen, 37073, Goettingen, Germany
- Institute for Population Genetics, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Fabiana Eckers
- Programa de Estudios Florísticos y Genética Vegetal, Instituto de Biología Subtropical (PEFyGV, IBS-UNaM-CONICET), 3300, Posadas, Argentina
| | - Diego H Hojsgaard
- Taxonomy and Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Eric J Martínez
- Instituto de Botánica del Nordeste (IBONE-CONICET-UNNE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), 3400, Corrientes, Argentina.
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Kandarkar K, Palaniappan V, Satpathy S, Vemula A, Rajasekaran R, Jeyakumar P, Sevugaperumal N, Gupta SK. Understanding genetic diversity in drought-adaptive hybrid parental lines in pearl millet. PLoS One 2024; 19:e0298636. [PMID: 38394324 PMCID: PMC10890771 DOI: 10.1371/journal.pone.0298636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Information on genetic diversity and population structure is helpful to strategize enhancing the genetic base of hybrid parental lines in breeding programs. The present study determined the population structure and genetic diversity of 109 pearl millet hybrid parental lines, known for their better adaptation and performance in drought-prone environments, using 16,472 single nucleotide polymorphic (SNP) markers generated from GBS (genotyping-by-sequencing) platforms. The SNPs were distributed uniformly across the pearl millet genome and showed considerable genetic diversity (0.337), expected heterozygosity (0.334), and observed heterozygosity (0.031). Most of the pairs of lines (78.36%) had Identity-by-State (IBS) based genetic distances of more than 0.3, indicating a significant amount of genetic diversity among the parental lines. Bayesian model-based population stratification, neighbor-joining phylogenetic analysis, and principal coordinate analysis (PCoA) differentiated all hybrid parental lines into two clear-cut major groups, one each for seed parents (B-lines) and pollinators (R-lines). Majority of parental lines sharing common parentages were found grouped in the same cluster. Analysis of molecular variance (AMOVA) revealed 7% of the variation among subpopulations, and 93% of the variation was attributable to within sub-populations. Chromosome 3 had the highest number of LD regions. Genomic LD decay distance was 0.69 Mb and varied across the different chromosomes. Genetic diversity based on 11 agro-morphological and grain quality traits also suggested that the majority of the B- and R-lines were grouped into two major clusters with few overlaps. In addition, the combined analysis of phenotypic and genotypic data showed similarities in the population grouping patterns. The present study revealed the uniqueness of most of the inbred lines, which can be a valuable source of new alleles and help breeders to utilize these inbred lines for the development of hybrids in drought-prone environments.
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Affiliation(s)
- Kuldeep Kandarkar
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Viswanathan Palaniappan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Subhrajit Satpathy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Anilkumar Vemula
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Ravikesavan Rajasekaran
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Prabhakaran Jeyakumar
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Nakkeeran Sevugaperumal
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Shashi Kumar Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
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Choudhary M, Singh A, Das MM, Kumar P, Naliath R, Singh V, Kumar B, Rakshit S. Morpho-physiological traits and SSR markers-based analysis of relationships and genetic diversity among fodder maize landraces in India. Mol Biol Rep 2023; 50:6829-6841. [PMID: 37392281 DOI: 10.1007/s11033-023-08602-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/15/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND Maize is an excellent fodder crop due to its high biomass, better palatability, succulency, and nutrition. Studies on morpho-physiological and biochemical characterization of fodder maize are limited. The present study aimed to explore the genetic variation in fodder maize landraces for various morpho-physiological traits and estimation of genetic relationship and population structure. METHODS AND RESULTS The study on 47 fodder maize landraces revealed significant variation for all morpho-physiological traits except leaf-stem ratio. Plant height, stem girth, leaf-width and number of leaves showed positive correlation with green fodder yield. Morpho-physiological traits-based clustering grouped the landraces into three major clusters, whereas neighbour joining cluster and population structure analysis using 40 SSR markers revealed four and five major groups, respectively. Most landraces of Northern Himalaya-Kashmir and Ludhiana fall into a single group, whereas rest groups mainly had landraces from North-Eastern Himalaya. A total of 101 alleles were generated with mean polymorphic information content value of 0.36 and major allele frequency of 0.68. The pair wise genetic dissimilarity between genotypes ranged from 0.21 to 0.67. Mantel test revealed weak but significant correlation between morphological and molecular distance. Biochemical characterisation of superior landraces revealed significant variation for neutral detergent fibre, acid detergent fibre, cellulose and lignin content. CONCLUSION Interestingly, significant, and positive correlation of SPAD with lignin content can be explored to bypass the costly affair of invitro quality assessment for digestibility parameters. The study identified superior landraces and demonstrated the use of molecular markers in genetic diversity assessment and grouping of genotypes for fodder maize improvement.
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Affiliation(s)
- Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
- School of Agriculture and Environment, Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Alla Singh
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
| | - M M Das
- ICAR-Indian Grassland and Forage Research Institute, Jhansi, 284003, Uttar Pradesh, India
| | - Pardeep Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India.
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, 84322, USA.
| | - Ritu Naliath
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
| | - Vishal Singh
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010, Jharkhand, India
| | - Bhupender Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010, Jharkhand, India
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Lezzi A, Stagnati L, Madormo F, Chabloz D, Lanubile A, Letey M, Marocco A, Bassignana M, Busconi M. Characterization and Valorization of Maize Landraces from Aosta Valley. PLANTS (BASEL, SWITZERLAND) 2023; 12:2674. [PMID: 37514288 PMCID: PMC10383193 DOI: 10.3390/plants12142674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
While there is a rich collection of maize germplasm from Italy, it lacks genetic resources from the Aosta Valley, an isolated mountain region where landraces have been preserved in the absence of modern germplasm introductions. These local materials, which are still cultivated mainly at household level, can have high importance from a genetic and historical point of view. In the present study, five landraces named, after the collecting sites, Arnad, Arnad-Crest, Châtillon, Entrebin and Perloz, were sampled in Aosta Valley and subjected to historic, morphologic and genetic characterization. This study provided evidence for the landraces' long presence in Aosta Valley, a significant genetic variability and differentiation among the investigated landraces. Globally, 67 different alleles were detected ranging from 4 for markers phi127 and p-bnlg176 to 10 for phi031, with a mean of 6.7 alleles per locus. Observed heterozygosity levels were comprised from 0.16 to 0.51 and are generalkly lower than expected heterozigosity supporting fixation at some loci. STRUCTURE analysis revealed clear separation between accessions revealing the presence of four ancestral populations. This may be explained by the long reproductive isolation experienced by these materials. Finally, morphological observations confirm the high diversity between landraces revealing that they generally have flint kernels, variable color from yellow to dark red (Châtillon) while Perloz showed kernels with an apical beak. The present work confirms the importance of mountain areas in conserving biodiversity and increases the rich Italian maize germplasm with materials well adapted to marginal areas. Such new genetic variability may be used to breed new materials for more resilient agriculture.
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Affiliation(s)
- Alessandra Lezzi
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Lorenzo Stagnati
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
- Centro di Ricerca BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | | | - Denise Chabloz
- Institut Agricole Régional, Reg. La Rochère 1/A, 11100 Aosta, Italy
| | - Alessandra Lanubile
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
- Centro di Ricerca BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Marilisa Letey
- Institut Agricole Régional, Reg. La Rochère 1/A, 11100 Aosta, Italy
| | - Adriano Marocco
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
- Centro di Ricerca BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Mauro Bassignana
- Institut Agricole Régional, Reg. La Rochère 1/A, 11100 Aosta, Italy
| | - Matteo Busconi
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
- Centro di Ricerca BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
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Cornea-Cipcigan M, Pamfil D, Sisea CR, Margaoan R. Characterization of Cyclamen genotypes using morphological descriptors and DNA molecular markers in a multivariate analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1100099. [PMID: 36778673 PMCID: PMC9909266 DOI: 10.3389/fpls.2023.1100099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Morphological and molecular characterization of germplasm is essential for the improvement of cultivated plants efforts. This study investigated the genetic diversity of 32 Cyclamen genotypes comprising 16 C. persicum varieties and 16 Cyclamen species using multivariate analysis for 36 morphological traits (19 quantitative and 17 qualitative) and molecular characterization (SRAP and SCoT markers). The color CIELab parameters were collected via PCE-CSM7 that separately measured the leaves dark and silvery patterns and the flower's slip (region of the petal top), eye (the region of the petal base) and sepal. Genetic diversity was also evaluated using Shannon Wiener (H') and Simpson's (λ) Indices, and Pilou evenness (J) using the library vegan from R software. According to the principal component analysis, the variables that contributed the most were leaf pattern color, leaf abaxial surface color, pedicel coiling, leaf and stem number. The color indicators of Cyclamen leaves showed decreased L* values in darker colored genotypes, whereas increased a* values were noticed in flower eye and lower in slip. Molecular characterization was based on 26 SRAP and 12 SCoT markers that produced clearly repeatable DNA bands and exhibited significant levels of polymorphism. Based on the morphological traits and molecular markers data, the UPGMA method for hierarchical clustering technique was used to generate the dendrograms, and their entanglement was obtained using the Tanglegram algorithm from the dendextend package with the R software. Entanglement analysis (0.30) between dendrograms obtained from the morphological and genetic analysis using SRAP markers showed a high association. Comparison between color measurements of flowers (entanglement=0.45) and leaves (entanglement=0.47) with SCoT analysis revealed differences at species level, discriminating between similar genotypes. Combined phenotypic and molecular analysis improved the comprehensive estimation of real diversity in the investigated Cyclamen genotypes. The findings of the present study are useful for quantifying diversity and genetic variability in Cyclamen breeding and genetic investigations.
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Affiliation(s)
- Mihaiela Cornea-Cipcigan
- Department of Horticulture and Business in Rural Development, Faculty of Horticulture, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Doru Pamfil
- Research Centre for Biotechnology in Agriculture Affiliated to Romanian Academy, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Cristian Radu Sisea
- Department of Horticulture and Business in Rural Development, Faculty of Horticulture, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Rodica Margaoan
- Laboratory of Cell Analysis and Spectrometry, Advanced Horticultural Research Institute of Transylvania, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
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Chaturvedi T, Gupta AK, Shanker K, Dubey BK, Tiwari G. Maximizing genetic gain through unlocking genetic variation in different ecotypes of kalmegh ( Andrographis paniculata (Burm. f.) Nee). FRONTIERS IN PLANT SCIENCE 2022; 13:1042222. [PMID: 36420038 PMCID: PMC9677111 DOI: 10.3389/fpls.2022.1042222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Andrographis paniculata, commonly known as kalmegh is among the most popular medicinal herbs in Southeast Asia. It is widely cultivated for medicinal purposes. The bioactive molecule, Andrographolide accumulated in herb leaves has immense therapeutic and economic potential. However, comprehensive information regarding genetic diversity is very limited in this species. The present study assessed genetic diversity between and within the six populations (ecotypes) of twenty-four kalmegh accessions using multiple datasets (agro-morphological traits, phytochemical traits, and genic markers). This is the established report where EST-SSR (Expressed sequence tags-Simple Sequence Repeat) markers have been used to unlock genetic variation in kalmegh. Here, we identified and developed ninety-one metabolic pathway-specific EST-SSR markers. Finally, 32 random EST-SSR primer pairs were selected for genetic diversity assessment. Multivariate analysis to unveil the agro-morphological, phytochemical and genotypic variability was helpful in discriminating various germplasms studied in the present study. Among all the morphological discriptors used in present study, days to fifty percent flowering and dry herb yield were found as potential selection index for AP genetic improvement. Hierarchical cluster analysis built with agro-morphological data identified three major groups. However, corresponding analysis with phytochemical and molecular data generated two clear-cut groups among the studied individuals. Moreover, the grouping of individuals into different clusters using multiple datasets was geographically independent, and also showed inconsistency in grouping among agromorphological, phytochemical and molecular dataset based clusters. However, joint analysis using agro-morphological, phytochemical and genotypic information generated two genetic groups, which could be a valuable resource for identifying complementary crossing panels in the kalmegh breeding program. The accessions AP7, AP13, AP5, AP3 belong to cluster I and accessions AP17, AP18 belong to cluster II could be utilized as potential donors for high dry herb yield and andrographolide content, respectively in different selective breeding programs of AP. Thus, our results provided useful information about the overall genetic diversity and variation in economic traits useful for initiating selective breeding programs for contrasting traits of interest and maximizing genetic gain in kalmegh.
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Affiliation(s)
- Trishna Chaturvedi
- Division of Plant Breeding and Genetic Resource Conservation, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, Uttar Pradesh, India
| | - Anil Kumar Gupta
- Division of Plant Breeding and Genetic Resource Conservation, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, Uttar Pradesh, India
| | - Karuna Shanker
- Phytochemistry Division, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, Uttar Pradesh, India
| | - Basant Kumar Dubey
- Biotechnology Division, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, Uttar Pradesh, India
| | - Gunjan Tiwari
- Division of Plant Breeding and Genetic Resource Conservation, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, Uttar Pradesh, India
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de Faria SV, Zuffo LT, Rezende WM, Caixeta DG, Pereira HD, Azevedo CF, DeLima RO. Phenotypic and molecular characterization of a set of tropical maize inbred lines from a public breeding program in Brazil. BMC Genomics 2022; 23:54. [PMID: 35030994 PMCID: PMC8759194 DOI: 10.1186/s12864-021-08127-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022] Open
Abstract
Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08127-7.
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Affiliation(s)
| | - Leandro Tonello Zuffo
- Department of Agronomy, Universidade Federal de Viçosa, Minas Gerais, Viçosa, Brazil
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Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers. Sci Rep 2020; 10:13191. [PMID: 32764649 PMCID: PMC7413250 DOI: 10.1038/s41598-020-69925-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 07/16/2020] [Indexed: 11/11/2022] Open
Abstract
Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome resequencing platform. Various diversity matrices and clustering methods were evaluated for a comprehensive characterization of genetic diversity in white Guinea yam from West Africa at phenotypic and molecular levels. The translation of the different diversity matrices from the phenotypic and genomic information into distinct groups varied with the hierarchal clustering methods used. Gower distance matrix based on phenotypic data and identity by state (IBS) distance matrix based on SNP data with the UPGMA clustering method found the best fit to dissect the genetic relationship in current set materials. However, the grouping pattern was inconsistent (r = − 0.05) between the morphological and molecular distance matrices due to the non-overlapping information between the two data types. Joint analysis for the phenotypic and molecular information maximized a comprehensive estimate of the actual diversity in the evaluated materials. The results from our study provide valuable insights for measuring quantitative genetic variability for breeding and genetic studies in yam and other root and tuber crops.
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Aci MM, Lupini A, Mauceri A, Morsli A, Khelifi L, Sunseri F. Genetic variation and structure of maize populations from Saoura and Gourara oasis in Algerian Sahara. BMC Genet 2018; 19:51. [PMID: 30068292 PMCID: PMC6090932 DOI: 10.1186/s12863-018-0655-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 07/12/2018] [Indexed: 11/14/2022] Open
Abstract
Background The ability of maize populations/landraces to tolerate drastically extreme environments over the past four centuries in Algeria leads to characterize these genetic resources for germplasm management as well as the identification of the best landraces useful for genetic improvement. Thus, the aim of the present work was a fingerprinting of an Algerian maize collection (47 landraces) from Saharan oasis by using 24 agro-morphological traits and18 Simple Sequence Repeats to evaluate genetic diversity and population structure. Results Phenotypic traits showed large significant variation in which earliness, plant size, ear and kernel features and crop yield appeared the most discriminant traits among landraces by using principal component analysis (PCA). One hundred ninety-seven different alleles were detected with a high mean number of allele per locus (10.9). The selected SSR were highly informative with PIC values > 0.65 as well as an overall genetic diversity (0.47) highlighting a broad genetic variability in the analyzed landraces. Genetic structure analysis revealed a high genetic differentiation among the 47 maize landraces with an overall Fst value (0.33). Cluster analysis for morphological traits as well as for SSR markers grouped the 47 Algerian populations regardless their geographic origin. Conclusions Maize from Algerian desert harbors a wide genetic diversity offering a source of novel/unique alleles useful for maize breeding programs to face the ongoing and future major challenge, the climate changes. Electronic supplementary material The online version of this article (10.1186/s12863-018-0655-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miyassa Meriem Aci
- LRGB, École Nationale Supérieure Agronomique (ENSA : ES1603), Avenue Pasteur, Hassan Badi, 16200, Algiers, El Harrach, Algeria
| | - Antonio Lupini
- Dipartimento AGRARIA, Università Mediterranea di Reggio Calabria, Località Feo di Vito snc, 89121, Reggio Calabria, Italy
| | - Antonio Mauceri
- Dipartimento AGRARIA, Università Mediterranea di Reggio Calabria, Località Feo di Vito snc, 89121, Reggio Calabria, Italy
| | - Abdelkader Morsli
- LRGB, École Nationale Supérieure Agronomique (ENSA : ES1603), Avenue Pasteur, Hassan Badi, 16200, Algiers, El Harrach, Algeria
| | - Lakhdar Khelifi
- LRGB, École Nationale Supérieure Agronomique (ENSA : ES1603), Avenue Pasteur, Hassan Badi, 16200, Algiers, El Harrach, Algeria.
| | - Francesco Sunseri
- Dipartimento AGRARIA, Università Mediterranea di Reggio Calabria, Località Feo di Vito snc, 89121, Reggio Calabria, Italy.
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Öner F. Ordu İli Yerel Mısır (Zea mays L.) Genotiplerinin Morfolojik Karakterizasyonu. ULUSLARARASI TARIM VE YABAN HAYATI BILIMLERI DERGISI 2017. [DOI: 10.24180/ijaws.344833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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El Kharrassi Y, Mazri M, Sedra M, Mabrouk A, Nasser B., El Mzouri E. Characterization of genetic diversity of cactus species (Opuntia spp.) in Morocco by morphological traits and molecular markers. ACTA ACUST UNITED AC 2017. [DOI: 10.12944/carj.5.2.01] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The genetic diversity within and among 124 accessions of Opuntia spp. collected from different regions of Morocco was assessed using morphological descriptors and molecular markers. Based on 10 morphological traits, the accessions were separated into 3 main clusters; each cluster was containing accessions from different regions and species. Polymerase chain reaction (PCR) was then performed on 22 accessions from different regions and species, with 10 inter-simple sequence repeat (ISSR) primers and one random amplified polymorphic DNA (RAPD) primer. ISSR primers produced 66 bands overall, 64 (96.9 %) of which were polymorphic while 6 bands were generated by the RAPD marker, all polymorphic. The polymorphic information content (PIC) values ranged from 0.62 to 0.97, with an average of 0.82. The dendrogram of genetic differences generated using the unweighted pair-group method using arithmetic averages (UPGMA) method showed 7 different clusters at a similarity of 0.76, which was confirmed by the principal component analysis (PCA). The main conclusion of our work is the high genetic similarity between Opuntia ficus indica and Opuntia megacantha species in Morocco. Our results will be useful for plant breeding and genetic resource conservation programs.
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Affiliation(s)
- Y. El Kharrassi
- Institut National de la Recherche Agronomique, CRRA de Settat, Service de Recherche et Développement, Route tertiaire 1406, Km 5, Settat, Morocco
| | - M.A. Mazri
- Institut National de la Recherche Agronomique, CRRA de Marrakech, UR Agro-Biotechnologie, Avenue Mohammed 6, BP 533, Marrakech, Morocco
| | - M.H. Sedra
- Institut National de la Recherche Agronomique, CRRA de Marrakech, UR Protection des Plantes, Avenue Mohammed 6, BP 533, Marrakech, Morocco
| | - A. Mabrouk
- Université Hassan I, Faculté des Sciences et Techniques, Laboratoire d’Agro-alimentaire et Santé, Settat, Morocco, 26000
| | - B . Nasser
- Université Hassan I, Faculté des Sciences et Techniques, Laboratoire de Biochimie et Neurosciences, BP 577, 26000 Settat, Morocco
| | - E. El Mzouri
- Institut National de la Recherche Agronomique, CRRA de Settat, Service de Recherche et Développement, Route tertiaire 1406, Km 5, Settat, Morocco
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da Silva MJ, Pastina MM, de Souza VF, Schaffert RE, Carneiro PCS, Noda RW, Carneiro JEDS, Damasceno CMB, Parrella RADC. Phenotypic and molecular characterization of sweet sorghum accessions for bioenergy production. PLoS One 2017; 12:e0183504. [PMID: 28817696 PMCID: PMC5560702 DOI: 10.1371/journal.pone.0183504] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/04/2017] [Indexed: 11/18/2022] Open
Abstract
Sweet sorghum [Sorghum bicolor (L.) Moench] is a type of cultivated sorghum characterized by the accumulation of high levels of sugar in the stems and high biomass accumulation, making this crop an important feedstock for bioenergy production. Sweet sorghum breeding programs that focus on bioenergy have two main goals: to improve quantity and quality of sugars in the juicy stem and to increase fresh biomass productivity. Genetic diversity studies are very important for the success of a breeding program, especially in the early stages, where understanding the genetic relationship between accessions is essential to identify superior parents for the development of improved breeding lines. The objectives of this study were: to perform phenotypic and molecular characterization of 100 sweet sorghum accessions from the germplasm bank of the Embrapa Maize and Sorghum breeding program; to examine the relationship between the phenotypic and the molecular diversity matrices; and to infer about the population structure in the sweet sorghum accessions. Morphological and agro-industrial traits related to sugar and biomass production were used for phenotypic characterization, and single nucleotide polymorphisms (SNPs) were used for molecular diversity analysis. Both phenotypic and molecular characterizations revealed the existence of considerable genetic diversity among the 100 sweet sorghum accessions. The correlation between the phenotypic and the molecular diversity matrices was low (0.35), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and the molecular diversity analyses. Furthermore, the clusters obtained by the molecular diversity analysis were more consistent with the genealogy and the historic background of the sweet sorghum accessions than the clusters obtained through the phenotypic diversity analysis. The low correlation observed between the molecular and the phenotypic diversity matrices highlights the complementarity between the molecular and the phenotypic characterization to assist a breeding program.
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Affiliation(s)
- Michele Jorge da Silva
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brasil
| | | | - Vander Fillipe de Souza
- Departamento de Engenharia de Biossistemas, Universidade Federal de São João del-Rei, São João del-Rei, Minas Gerais, Brasil
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Ali Al-Somain BH, Migdadi HM, Al-Faifi SA, Alghamdi SS, Muharram AA, Mohammed NA, Refay YA. Assessment of genetic diversity of sesame accessions collected from different ecological regions using sequence-related amplified polymorphism markers. 3 Biotech 2017; 7:82. [PMID: 28500406 DOI: 10.1007/s13205-017-0680-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/27/2017] [Indexed: 11/30/2022] Open
Abstract
Sequence-related amplified polymorphism (SRAP) markers were used to assess the genetic diversity among a collection of 52 sesame accessions representing different geographical environments, including eight Saudi landraces. A combination of seventeen primers generated a high number of alleles (365) with 100% polymorphism. The polymorphic information content (PIC) and primer discrimination power (DP) recorded overall means of 0.88 and 5.88, respectively. Genetic similarity values based on Jaccard coefficients ranged from 0.12 to 0.49, with an average similarity value of 0.30, indicating both high genetic distance and a wide genetic basis of the investigated accessions. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram grouped 48 of 52 accessions into seven main clusters, and five accessions failed to form clusters and were separated individually. However, subclusters separated the accessions and, considering the relatedness of accessions and their geographical origin, formed distinct diversity among groups. Saudi landraces showed the widest genetic basis compared with other introduced accessions that were distributed throughout the dendrogram, indicating that agro-ecological zones were indistinguishable by cluster analysis. SRAP analysis revealed a high degree of genetic polymorphism in sesame accessions investigated and showed weak association between geographical origin and SRAP patterns. This wide genetic variability should be considered for sesame breeding programs.
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Affiliation(s)
- Bazel H Ali Al-Somain
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Hussein M Migdadi
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia.
| | - Sulieman A Al-Faifi
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Salem S Alghamdi
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Abdulmalek A Muharram
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Nabil A Mohammed
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Yahya A Refay
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
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15
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Stephen A, Antonia YT, Patrick T, Kingsley BA, Richard AA. Genetic diversity in lowland, midaltitude and highland African maize landraces by morphological trait evaluation. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajps2016.1448] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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16
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Liu L, Chen W, Zheng X, Li J, Yan DT, Liu L, Liu X, Wang YL. Genetic diversity of Ulmus lamellosa by morphological traits and sequence-related amplified polymorphism (SRAP) markers. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.04.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Analysis of the genetic diversity of garlic (Allium sativum L.) by simple sequence repeat and inter simple sequence repeat analysis and agro-morphological traits. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.03.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Șuteu D, Băcilă I, Haș V, Haș I, Miclăuș M. Romanian maize (Zea mays) inbred lines as a source of genetic diversity in SE Europe, and their potential in future breeding efforts. PLoS One 2014; 8:e85501. [PMID: 24392016 PMCID: PMC3877385 DOI: 10.1371/journal.pone.0085501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 11/27/2013] [Indexed: 11/24/2022] Open
Abstract
Maize has always been under constant human selection ever since it had been domesticated. Intensive breeding programs that resulted in the massive use of hybrids nowadays have started in the 60s. That brought significant yield increases but reduced the genetic diversity at the same time. Consequently, breeders and researchers alike turned their attention to national germplasm collections established decades ago in many countries, as they may hold allelic variations that could prove useful for future improvements. These collections are mainly composed of inbred lines originating from well-adapted local open pollinated varieties. However, there is an overall lack of data in the literature about the genetic diversity of maize in SE Europe, and its potential for future breeding efforts. There are no data, whatsoever, on the nutritional quality of the grain, primarily dictated by the zein proteins. We therefore sought to use the Romanian maize germplasm as an entry point in understanding the molecular make-up of maize in this part of Europe. By using 80 SSR markers, evenly spread throughout the genome, on 82 inbred lines from various parts of the country, we were able to decipher population structure and the existing relationships between those and the eight international standards used, including the reference sequenced genome B73. Corroborating molecular data with a standardized morphological, physiological, and biochemical characterization of all 90 inbred lines, this is the first comprehensive such study on the existing SE European maize germplasm. The inbred lines we present here are an important addition to the ever-shrinking gene pool that the breeding programs are faced-with, because of the allelic richness they hold. They may serve as parental lines in crosses that will lead to new hybrids, characterized by a high level of heterosis, nationwide and beyond, due to their existing relationship with the international germplasm.
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Affiliation(s)
- Dana Șuteu
- National Institute of Research and Development for Biological Sciences, Cluj-Napoca, Romania
| | - Ioan Băcilă
- National Institute of Research and Development for Biological Sciences, Cluj-Napoca, Romania
| | - Voichița Haș
- Agricultural Research and Development Station, Turda, Romania
| | - Ioan Haș
- Agricultural Research and Development Station, Turda, Romania
- University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Mihai Miclăuș
- National Institute of Research and Development for Biological Sciences, Cluj-Napoca, Romania
- * E-mail:
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19
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Next generation characterisation of cereal genomes for marker discovery. BIOLOGY 2013; 2:1357-77. [PMID: 24833229 PMCID: PMC4009793 DOI: 10.3390/biology2041357] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/29/2013] [Accepted: 11/08/2013] [Indexed: 12/30/2022]
Abstract
Cereal crops form the bulk of the world’s food sources, and thus their importance cannot be understated. Crop breeding programs increasingly rely on high-resolution molecular genetic markers to accelerate the breeding process. The development of these markers is hampered by the complexity of some of the major cereal crop genomes, as well as the time and cost required. In this review, we address current and future methods available for the characterisation of cereal genomes, with an emphasis on faster and more cost effective approaches for genome sequencing and the development of markers for trait association and marker assisted selection (MAS) in crop breeding programs.
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20
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Molin D, Coelho CJ, Máximo DS, Ferreira FS, Gardingo JR, Matiello RR. Genetic diversity in the germplasm of tropical maize landraces determined using molecular markers. GENETICS AND MOLECULAR RESEARCH 2013; 12:99-114. [PMID: 23359029 DOI: 10.4238/2013.january.22.8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Maize landraces derived from tropical germplasm represent an important source of genetic variability, which is currently poorly understood and under-exploited by Brazilian crop breeding programs. The aims of our study were to a) estimate the genetic diversity across 48 varieties of maize landraces cultivated at different locations in the States of Rio Grande do Sul (RS) and Paraná (PR) by means of random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), and amplified fragment length polymorphism (AFLP) markers; b) cluster these varieties based on their genetic similarity estimates, and c) establish possible correlations between genetic similarity and germplasm collection sites. Maize landrace accessions were genotyped through the 30 RAPD, 47 SSR, and 25 combinations of AFLP primers. The results revealed high levels of variability across landraces within and between collection sites. AFLP analysis resulted in amplification of 762 polymorphic fragments and a polymorphic index of 40.3%, followed by RAPD with 335 fragments (81.9%) and SSR with 105 fragments (78.3%). The genetic similarity estimates of the investigated landraces ranged from 41 (SSR) to 74% (AFLP), and the amplitudes of these indices were notably similar between RAPD and SSR, as well as between AFLP and joint analysis. Regarding the RAPD and AFLP dendrograms, groups comprising accessions from RS prevailed, whereas SSR comprised varieties from both collection sites. Groups exclusive to RS or PR support the hypothesis that divergence between groups is possible owing to the fixation of regional adaptation alleles and to spatial barriers hindering genetic flow between locations.
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Affiliation(s)
- D Molin
- Pós-Graduação em Ciências Biológicas, Biologia Evolutiva, Ponta Grossa, PR, Brasil
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21
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da Cunha KS, Pereira MG, Gonçalves LSA, Berilli APCG, de Oliveira EC, Ramos HCC, do Amaral Júnior AT. Full-sib reciprocal recurrent selection in the maize populations Cimmyt and Piranão. GENETICS AND MOLECULAR RESEARCH 2012; 11:3398-408. [PMID: 23079833 DOI: 10.4238/2012.september.25.8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We estimated the genetic gains of the 12th cycle of reciprocal recurrent selection for maize traits of agronomic interest. We used 23 ISSR molecular markers in an attempt to maximize genetic variability among and within populations based on selection of S(1) progenies. To this end, 138 full-sib families were evaluated in a randomized block design in two environments (the municipalities of Campos dos Goytacazes and Itaocara, in the State of Rio de Janeiro, Brazil), with replications within sets. Direct selection for grain yield was used for the selection of the families. To assess genetic diversity among and within populations, we examined plants produced from part of the S(1s) seeds from the parents that originated the 42 full-sib families that were selected from the agronomic traits. Direct selection for grain yield provided good gains for the traits evaluated, with estimated improvement of -0.87 days for days to flowering, 0.35 plants, 1.79 ears per plot, 0.58 g per 100-grain weight, 308.21 g ear weight per plot, and 261.83 kg/ha grain yield. Application of molecular markers at the stage of superior progeny selection led to increased genetic distance among populations, which is a very important factor for utilization of heterosis and providing greater longevity to the reciprocal recurrent selection program.
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Affiliation(s)
- K S da Cunha
- Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brasil
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22
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Pino Del Carpio D, Basnet RK, De Vos RCH, Maliepaard C, Visser R, Bonnema G. The patterns of population differentiation in a Brassica rapa core collection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1105-18. [PMID: 21193901 PMCID: PMC3057009 DOI: 10.1007/s00122-010-1516-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 12/08/2010] [Indexed: 05/02/2023]
Abstract
With the recent advances in high throughput profiling techniques the amount of genetic and phenotypic data available has increased dramatically. Although many genetic diversity studies combine morphological and genetic data, metabolite profiling has yet to be integrated into these studies. For our study we selected 168 accessions representing the different morphotypes and geographic origins of Brassica rapa. Metabolite profiling was performed on all plants of this collection in the youngest expanded leaves, 5 weeks after transplanting and the same material was used for molecular marker profiling. During the same season a year later, 26 morphological characteristics were measured on plants that had been vernalized in the seedling stage. The number of groups and composition following a hierarchical clustering with molecular markers was highly correlated to the groups based on morphological traits (r = 0.420) and metabolic profiles (r = 0.476). To reveal the admixture levels in B. rapa, comparison with the results of the programme STRUCTURE was needed to obtain information on population substructure. To analyze 5546 metabolite (LC-MS) signals the groups identified with STRUCTURE were used for random forests classification. When comparing the random forests and STRUCTURE membership probabilities 86% of the accessions were allocated into the same subgroup. Our findings indicate that if extensive phenotypic data (metabolites) are available, classification based on this type of data is very comparable to genetic classification. These multivariate types of data and methodological approaches are valuable for the selection of accessions to study the genetics of selected traits and for genetic improvement programs, and additionally provide information on the evolution of the different morphotypes in B. rapa.
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Affiliation(s)
- Dunia Pino Del Carpio
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Present Address: Institut für Genetik, Heinrich-Heine Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Ram Kumar Basnet
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands
| | - Ric C. H. De Vos
- Centre for Biosystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands
- Plant Research International, Business Unit Bioscience, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Chris Maliepaard
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands
| | - Richard Visser
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Guusje Bonnema
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands
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Jungmann L, Vigna BBZ, Boldrini KR, Sousa ACB, do Valle CB, Resende RMS, Pagliarini MS, Zucchi MI, de Souza AP. Genetic diversity and population structure analysis of the tropical pasture grass Brachiaria humidicola based on microsatellites, cytogenetics, morphological traits, and geographical origin. Genome 2011; 53:698-709. [PMID: 20924419 DOI: 10.1139/g10-055] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Brachiaria humidicola (Rendle) Schweick. is a warm-season grass commonly used as forage in the tropics. Accessions of this species were collected in eastern Africa and massively introduced into South America in the 1980s. Several of these accessions form a germplasm collection at the Brazilian Agricultural Research Corporation. However, apomixis, ploidy, and limited knowledge of the genetic basis of this germplasm collection have constrained breeding activities. The objectives of this work were to identify genetic variability in the Brazilian B. humidicola germplasm collection using microsatellite markers and to compare the results with information on the following: (1) collection sites of the accessions; (2) reproductive mode and ploidy levels; and (3) genetic diversity revealed by morphological traits. The evaluated germplasm population is highly structured into four major groups. The sole sexual accession did not group with any of the clusters. Genetic dissimilarities did not correlate with either geographic distances or genetic distances inferred from morphological descriptors. Additionally, the genetic structure identified in this collection did not correspond to differences in ploidy level. Alleles exclusive to either sexual or apomictic accessions were identified, suggesting that further evaluation of the association of these loci with apospory should be carried out.
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Affiliation(s)
- L Jungmann
- Brazilian Agricultural Research Corporation (Embrapa), Center for Beef Cattle Research, Plant Biotechnology Laboratory, CP 154, Campo Grande, MS 79002-970, Brazil
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Sharma L, Prasanna BM, Ramesh B. Analysis of phenotypic and microsatellite-based diversity of maize landraces in India, especially from the north east Himalayan region. Genetica 2010; 138:619-31. [PMID: 20107870 DOI: 10.1007/s10709-010-9436-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 01/11/2010] [Indexed: 10/19/2022]
Abstract
The maize landraces in the North East Himalayan (NEH) region in India, especially in the Sikkim state, are morphologically highly diverse. The present study provides details of phenotypic and molecular characterization of a set of 48 selected maize landrace accessions, including the 'Sikkim Primitives' which have a unique habit of prolificacy (5-9 ears on a single stalk). Multi-location phenotypic evaluation of these 48 accessions revealed significant genetic variability for grain yield and its components, leading to identification of several promising accessions. Cluster analysis and PCA using nine morpho-agronomic characters clearly separated 'Sikkim Primitives' from the rest of the accessions. PCA revealed two principal components describing 90% of the total variation, with hundred kernel weight, ear length, ear diameter, number of kernels per ear and flowering behaviour forming the most discriminatory traits. The accessions were genotyped using 42 microsatellite or simple sequence repeat (SSR) markers using a 'population bulk DNA fingerprinting strategy', with allele resolution using an automated DNA Sequencer. The study revealed a high mean number of alleles per SSR locus (13.0) and high Polymorphism Information Content (PIC) value of 0.60. The analysis also led to identification of 163 private/unique alleles, differentiating 44 out of 48 accessions. Six highly frequent SSR alleles were detected at different loci (phi014, phi062, phi090, umc1266, umc1367 and umc2250) with individual frequencies >/=0.75. Some of these SSR loci were reported to tag specific genes/QTL for some important traits, indicating that chromosomal regions harboring these SSR alleles were not selectively neutral. Cluster analysis using Rogers' genetic distance also revealed distinct genetic identity of the 'Sikkim Primitives' from the rest of the accessions in India, including Sikkim. Mantel's test revealed significant and positive correlation between the phenotypic and molecular genetic dissimilarity matrices. The study was the first to portray the patterns of phenotypic and molecular diversity in the maize landraces from the NEH region in India.
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Affiliation(s)
- Lata Sharma
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India
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25
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Berardo N, Mazzinelli G, Valoti P, Laganà P, Redaelli R. Characterization of maize germplasm for the chemical composition of the grain. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:2378-84. [PMID: 19249819 DOI: 10.1021/jf803688t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The aim of this research was the evaluation of food grain quality-related traits in a collection of maize populations of different origins, currently used in the framework of breeding and genetic programs. A total of 1245 maize samples were scanned by near-infrared (NIR) spectroscopy to develop calibration equations to evaluate the content of crude protein, crude lipid, starch, and floatation area. The performances of the NIR equations developed in our study were assessed using the determination coefficient of cross-validation r(2) (ranging from 0.66 to 0.91) and the ratio of performance deviation (1.71-3.31) in flour starch and grain crude protein, respectively. Among the genotypes considered, 93 landraces belonging to the European Union Maize Landraces Core Collection (EUMLCC) were also analyzed for their content of lutein, zeaxanthin, and total carotenoids. Among the populations of the collection, several accessions, interesting from a nutritional point of view, were identified: VA25, VA158, VA282, VA284, VA285, VA567, VA572, VA814, VA950, VA1057, and VA1179. They showed protein and lipid contents ranging between 12.52 and 15.16% and 5.26 and 7.17%. The range of variation observed for antioxidants in the EUMLCC was quite large. Lutein varied between 1.03 and 21.00 mg kg(-1) dm, zeaxanthin varied between 0.01 and 35.00 mg kg(-1) dm, and total carotenoids ranged from 1.09 to 61.10 mg kg(-1) dm. Recently, a single cross-hybrid was developed from the ITA0370005 population; this hybrid had a high carotenoids content and is currently being used by the Italian food industry.
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