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Grosser MR, Sites SK, Murata MM, Lopez Y, Chamusco KC, Love Harriage K, Grosser JW, Graham JH, Gmitter FG, Chase CD. Plant mitochondrial introns as genetic markers - conservation and variation. FRONTIERS IN PLANT SCIENCE 2023; 14:1116851. [PMID: 37021319 PMCID: PMC10067590 DOI: 10.3389/fpls.2023.1116851] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Plant genomes are comprised of nuclear, plastid and mitochondrial components characterized by different patterns of inheritance and evolution. Genetic markers from the three genomes provide complementary tools for investigations of inheritance, genetic relationships and phenotypic contributions. Plant mitochondrial genomes are challenging for universal marker development because they are highly variable in terms of size, gene order and intergenic sequences and highly conserved with respect to protein-coding sequences. PCR amplification of introns with primers that anneal to conserved, flanking exons is effective for the development of polymorphic nuclear genome markers. The potential for plant mitochondrial intron polymorphisms to distinguish between congeneric species or intraspecific varieties has not been systematically investigated and is possibly constrained by requirements for intron secondary structure and interactions with co-evolved organelle intron splicing factors. To explore the potential for broadly applicable plant mitochondrial intron markers, PCR primer sets based upon conserved sequences flanking 11 introns common to seven angiosperm species were tested across a range of plant orders. PCR-amplified introns were screened for indel polymorphisms among a group of cross-compatible Citrus species and relatives; two Raphanus sativus mitotypes; representatives of the two Phaseolus vulgaris gene pools; and congeneric pairs of Cynodon, Cenchrus, Solanum, and Vaccinium species. All introns were successfully amplified from each plant entry. Length polymorphisms distinguishable by gel electrophoresis were common among genera but infrequent within genera. Sequencing of three introns amplified from 16 entries identified additional short indel polymorphisms and nucleotide substitutions that separated Citrus, Cynodon, Cenchrus and Vaccinium congeners, but failed to distinguish Solanum congeners or representatives of the Phaseolus vulgaris major gene pools. The ability of primer sets to amplify a wider range of plant species' introns and the presence of intron polymorphisms that distinguish congeners was confirmed by in silico analysis. While mitochondrial intron variation is limited in comparison to nuclear introns, these exon-based primer sets provide robust tools for the amplification of mitochondrial introns across a wide range of plant species wherein useful polymorphisms can be identified.
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Affiliation(s)
- Melinda R. Grosser
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Samantha K. Sites
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Mayara M. Murata
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Yolanda Lopez
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Karen C. Chamusco
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Kyra Love Harriage
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Jude W. Grosser
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - James H. Graham
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Fred G. Gmitter
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Christine D. Chase
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
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Singh RB, Mahenderakar MD, Jugran AK, Singh RK, Srivastava RK. Assessing genetic diversity and population structure of sugarcane cultivars, progenitor species and genera using microsatellite (SSR) markers. Gene 2020; 753:144800. [PMID: 32454179 DOI: 10.1016/j.gene.2020.144800] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/13/2020] [Accepted: 05/19/2020] [Indexed: 01/15/2023]
Abstract
Sugarcane is one among the most important commercial crops used to produce sugar, ethanol, and other byproducts, which significantly contributes in the GDP of India and many other countries around the world. Genetic diversity is a platform for any breeding program of a plant species. Estimation of the genetic variability and population structure play a vital role for conservation planning and management of plant genetic resources. Genetic variability serves as a source of noble alleles responsible for key agronomic and quality traits, which ultimately form basis for identification and selection of promising parents for breeding programs. In the present study genetic diversity and population structure of 139 accessions of the genus Saccharum, allied genera of family Poaceae and cultivars were assessed using informative microsatellite (SSR) markers. A sum of 427 alleles was produced using 61 polymorphic primers and number of alleles generated was ranged from 2 to 13 with an average of 7 alleles per locus. PIC values were ranged from 0.35 to 0.90, with a mean value of 0.66 for all the markers evaluated. Cluster analysis based on UPGMA method revealed three major clusters which were further subdivided into nine subclusters. Population structure analysis also established three subpopulations of used accession set, however there were no correlation of sub-groupings with that of place of origin. AMOVA analysis also confirmed that 83% and 17% of total variations were attributed to the within- and between-populations, correspondingly, demonstrating greater exchange of gene pool across places of origin. The principal component analysis (PCA) demonstrated the distribution of accessions in the scatter-plot was substantially dispersed, revealing rich genetic diversity among accessions of different species. The findings from this study will be useful in breeding programs for introgression of noble alleles into modern cultivars by exploiting natural genetic variation existing in sugarcane genetic resources.
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Affiliation(s)
- Ram Baran Singh
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Patancheru-503 324, Hyderabad, Telangana State, India; Uttar Pradesh Council of Sugarcane Research (UPCSR), Shahjahanpur-242 001, Uttar Pradesh, India.
| | - Mahesh D Mahenderakar
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Patancheru-503 324, Hyderabad, Telangana State, India
| | - Arun K Jugran
- G.B. Pant National Institute of Himalayan Environment & Sustainable Development, Almora 243 643, Uttarakhand, India
| | - Ram Kushal Singh
- Uttar Pradesh Council of Sugarcane Research (UPCSR), Shahjahanpur-242 001, Uttar Pradesh, India
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Patancheru-503 324, Hyderabad, Telangana State, India
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Medeiros AH, Mingossi FB, Dias RO, Franco FP, Vicentini R, Mello MO, Moura DS, Silva-Filho MC. Sugarcane Serine Peptidase Inhibitors, Serine Peptidases, and Clp Protease System Subunits Associated with Sugarcane Borer (Diatraea saccharalis) Herbivory and Wounding. Int J Mol Sci 2016; 17:E1444. [PMID: 27598134 PMCID: PMC5037723 DOI: 10.3390/ijms17091444] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/16/2016] [Accepted: 08/25/2016] [Indexed: 11/16/2022] Open
Abstract
Sugarcane's (Saccharum spp.) response to Diatraea saccharalis (F.) (Lepidoptera: (Crambidae) herbivory was investigated using a macroarray spotted with 248 sugarcane Expressed Sequence Tags (ESTs) encoding serine peptidase inhibitors, serine peptidases. and Clp protease system subunits. Our results showed that after nine hours of herbivory, 13 sugarcane genes were upregulated and nine were downregulated. Among the upregulated genes, nine were similar to serine peptidase inhibitors and four were similar to Bowman-Birk Inhibitors (BBIs). Phylogenetic analysis revealed that these sequences belong to a phylogenetic group of sugarcane BBIs that are potentially involved in plant defense against insect predation. The remaining four upregulated genes included serine peptidases and one homolog to the Arabidopsis AAA+ chaperone subunit ClpD, which is a member of the Clp protease system. Among the downregulated genes, five were homologous to serine peptidases and four were homologous to Arabidopsis Clp subunits (three homologous to Clp AAA+ chaperones and one to a ClpP-related ClpR subunit). Although the roles of serine peptidase inhibitors in plant defenses against herbivory have been extensively investigated, the roles of plant serine peptidases and the Clp protease system represent a new and underexplored field of study. The up- and downregulated D. saccharalis genes presented in this study may be candidate genes for the further investigation of the sugarcane response to herbivory.
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Affiliation(s)
- Ane H Medeiros
- Departamento de Ciências da Natureza, Matemática e Educação, Universidade Federal de São Carlos, Araras, 13600-970 São Paulo, Brazil.
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
| | - Fabiana B Mingossi
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
| | - Renata O Dias
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
| | - Flávia P Franco
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
| | - Renato Vicentini
- Systems Biology Laboratory, Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, 13083-970 São Paulo, Brazil.
| | - Marcia O Mello
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
- Monsanto do Brasil, Campinas, 13069-380 São Paulo, Brazil.
| | - Daniel S Moura
- Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13400-918 São Paulo, Brazil.
| | - Marcio C Silva-Filho
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
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Nayak SN, Song J, Villa A, Pathak B, Ayala-Silva T, Yang X, Todd J, Glynn NC, Kuhn DN, Glaz B, Gilbert RA, Comstock JC, Wang J. Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction. PLoS One 2014; 9:e110856. [PMID: 25333358 PMCID: PMC4205016 DOI: 10.1371/journal.pone.0110856] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/25/2014] [Indexed: 12/22/2022] Open
Abstract
Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance.
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Affiliation(s)
- Spurthi N. Nayak
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Jian Song
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
- College of Life Sciences, Dezhou University, Dezhou, Shandong, China
| | - Andrea Villa
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Bhuvan Pathak
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Tomas Ayala-Silva
- Subtropical Horticulture Research Station, USDA-ARS, Miami, Florida, United States of America
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - James Todd
- Everglades Research and Education Center, University of Florida, Belle Glade, Florida, United States of America
| | - Neil C. Glynn
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - David N. Kuhn
- Subtropical Horticulture Research Station, USDA-ARS, Miami, Florida, United States of America
| | - Barry Glaz
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - Robert A. Gilbert
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Jack C. Comstock
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
- Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, Florida, United States of America
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Chandra A, Grisham MP, Pan YB. Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane. Genome 2014; 57:363-72. [PMID: 25247737 DOI: 10.1139/gen-2014-0072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Though sugarcane cultivars (Saccharum spp. hybrids) are complex aneupolyploid hybrids, genetic evaluation and tracking of clone- or cultivar-specific alleles become possible through capillary electrophoresis (CE) using fluorescence-labeled SSR markers. Twenty-four sugarcane cultivars, 12 each from India and the USA, were genetically assessed using 21 fluorescence-labeled polymorphic SSR markers. These markers primed the amplification of 213 alleles. Of these alleles, 161 were common to both Indian and US cultivars, 25 were specific to the Indian cultivars, and 27 were observed only in the US cultivars. Only 10 alleles were monomorphic. A high level of heterozygosity was observed in both Indian (82.4%) and US (91.1%) cultivars resulting in average polymorphism information content (PIC) values of 0.66 and 0.77 and marker index (MI) values of 5.07 and 5.58, respectively. Pearson correlation between PIC and MI was significant in both sets of cultivars (r = 0.58 and 0.69). UPGMA clustering separated cultivars into three distinct clusters at 59% homology level. These results propose the potential utility of six Indian cultivar-specific SSR alleles (mSSCIR3_182, SMC486CG_229, SMC36BUQ_125, mSSCIR74_216, SMC334BS_154, and mSSCIR43_238) in sugarcane breeding, vis a vis transporting CE-based evaluation in clone or variety identity testing, cross fidelity assessments, and genetic relatedness among species of the genus Saccharum and related genera.
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Affiliation(s)
- Amaresh Chandra
- a USDA-ARS, MSA, Sugarcane Research Laboratory, Houma, LA 70360, USA
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