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Park S, Zhang D, Ali GS. Assessing the genetic integrity of sugarcane germplasm in the USDA-ARS National Plant Germplasm System collection using single-dose SNP markers. FRONTIERS IN PLANT SCIENCE 2024; 14:1337736. [PMID: 38239228 PMCID: PMC10794611 DOI: 10.3389/fpls.2023.1337736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, FL, is one of the largest sugarcane germplasm repositories in the world. However, the genetic integrity of the Saccharum spp. germplasm in this collection has not been fully analyzed. In this study, we employed a single-dose SNP panel to genotype 901 sugarcane accessions, representing six Saccharum species and various hybrids. Our analysis uncovered a high rate of clone mislabeling in the collection. Specifically, we identified 86 groups of duplicates, characterized by identical SNP genotypes, which encompassed 211 accessions (23% of the total clones), while 135 groups, constituting 471 clones (52% of the total), exhibited near-identical genotypes. In addition, twenty-seven homonymous groups were detected, which shared the same clone name but differed in SNP genotypes. Hierarchical analysis of population structure partitioned the Saccharum germplasm into five clusters, corresponding to S. barberi, S. sinense, S. officinarum, S. spontaneum and S. robustum/S. edule. An assignment test, based on the five Saccharum species, enabled correcting 141 instances of mislabeled species memberships and inaccuracies. Moreover, we clarified the species membership and parentage of 298 clones that had ambiguous passport records (e.g., 'Saccharum spp', 'unknown', and 'hybrid'). Population structure and genetic diversity in these five species were further supported by Principal Coordinate Analysis and neighbor-joining clustering analysis. Analysis of Molecular Variance revealed that within-species genetic variations accounted for 85% of the total molecular variance, with the remaining 15% attributed to among-species genetic variations. The single-dose SNP markers developed in this study offer a robust tool for characterizing sugarcane germplasm worldwide. These findings have important implications for sugarcane genebank management, germplasm exchange, and crop genetic improvement.
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Affiliation(s)
- Sunchung Park
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Gul Shad Ali
- Subtropical Horticulture Research Station, United States Department of Agriculture, Agriculture Research Service, Miami, FL, United States
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Elumalai K, Srinivasan A. Genetic diversity and population structure of sugarcane introgressed hybrids by SSR markers. 3 Biotech 2023; 13:399. [PMID: 37974927 PMCID: PMC10645997 DOI: 10.1007/s13205-023-03823-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/19/2023] [Indexed: 11/19/2023] Open
Abstract
One hundred and seventy two introgressed hybrids from four different introgression groups and in three nobilized stages (F1, BC1,and BC2) involving two genera viz., Sugarcane (Saccharum spp) and Erianthusl (E.arundinaceus),and Coimbatore (Commercials) clones were studied for yield and quality traits, and as well with 30 SSR markers (simple sequence repeats) for diversity and population structure. The yield and quality components of the introgressed hybrids from improved S. spontaneum, improved S. robustum, S. barberi (Pathri) and E. arundinaceus (IK-76-76) showed significant variation. The traits viz., cane height, single cane weight and cane yield showed the highest level of phenotypic and genotypic variation. 456 polymorphic alleles in all with values ranging from 6 (SMC 863-GC) to 24 (NKS 43) with an average of 15 alleles per primer were studied. Polymorphism information content (PIC) generated by 30 SSR primers varied from 0.57 (NKS 1) to 0.94 (NKS 34) and the highest average PIC (0.93) was observed in hybrids of S. spontaneum (SSH). The highest number of observed and effective alleles, and Shannon's index were also registered by introgressed hybrids of SSH and the lowest variability was observed with hybrids of Co canes x S. barberi. SSR-based population genetic measures identified three mating groups involving improved S.officinarum, improved S.robustum and Coimbatore canes with maximum variability. Structure analysis identified 51 introgressed hybrids with abundant genetic variation and low gene flow as a new germplasm source for future sugarcane breeding programmes. Fifty-nine rare alleles were detected, and structure analysis revealed a low degree of admixture between the generated hybrids. Low gene flow estimates from group I (Nm: 1.052, where mostly F1 and BC1 hybrids were grouped together) explained that the maximum variability from parental clones was inherited until the BC1 generation, and high values of Nm in group III also indicated that most of the wild alleles were fixed in the BC1 population. Structure and cluster analysis (PCoA, UPGMA) explained that the grouping of introgressed hybrids is highly correlated to different stages of nobilization. UPGMA and PCoA methods grouped the individuals into three major clusters, with a clear differentiation of F1 and backcross hybrids grouped under different internal sub-clusters. The occurrence of wide genetic variability in the population and elite hybrids with a unique genetic base can be exploited in breeding programmes to develop trait specific donors for genetic enhancement and to mitigate climate change.
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Affiliation(s)
- Karpagam Elumalai
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - Alarmelu Srinivasan
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
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Zhang B, Huang Y, Zhang L, Zhou Z, Zhou S, Duan W, Yang C, Gao Y, Li S, Chen M, Li Y, Yang X, Zhang G, Huang D. Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16815-16826. [PMID: 37856846 DOI: 10.1021/acs.jafc.3c02935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Sugarcane, a major sugar and energy crop worldwide faces an increasing demand for higher yields. Identifying yield-related markers and candidate genes is valuable for breeding high-yield varieties using molecular techniques. In this work, seven yield-related traits were evaluated in a diversity panel of 159 genotypes, derived from Tripidium arundinaceum, Saccharum spontaneum, and modern sugarcane genotypes. All traits exhibited significant genetic variance with high heritability and high correlations. Genetic diversity analysis reveals a genomic decay of 23 kb and an average single nucleotide polymorphism (SNP) number of 25,429 per genotype. These 159 genotypes were divided into 4 subgroups. Genome-wide association analysis identified 47 SNPs associated with brix, spanning 36 quantitative trait loci (QTLs), and 138 SNPs for other traits across 104 QTLs, covering all 32 chromosomes. Interestingly, 12 stable QTLs associated with yield-related traits were identified, which contained 35 candidate genes. This work provides markers and candidate genes for marker-assisted breeding to improve sugarcane yields.
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Affiliation(s)
- Baoqing Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Yuxin Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Lijun Zhang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Zhongfeng Zhou
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Shan Zhou
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Weixing Duan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Cuifang Yang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Yijing Gao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Sicheng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Meiyan Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Yangrui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Gemin Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Dongliang Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
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Riggins CW. Crop diversity: Breadfruit's checkered past bears fruit for food security. Curr Biol 2023; 33:R75-R77. [PMID: 36693314 DOI: 10.1016/j.cub.2022.11.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
New interdisciplinary research on breadfruit helps reconcile cultivar names with genotypic and phenotypic diversity across time, continents, and cultures. The findings will advance breeding and conservation initiatives for this underutilized crop, but also highlight methodological challenges commonplace in crop evolutionary studies.
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Affiliation(s)
- Chance W Riggins
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.
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Wijma M, Lembke CG, Diniz AL, Santini L, Zambotti-Villela L, Colepicolo P, Carneiro MS, Souza GM. Planting Season Impacts Sugarcane Stem Development, Secondary Metabolite Levels, and Natural Antisense Transcription. Cells 2021; 10:cells10123451. [PMID: 34943959 PMCID: PMC8700069 DOI: 10.3390/cells10123451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
To reduce the potentially irreversible environmental impacts caused by fossil fuels, the use of renewable energy sources must be increased on a global scale. One promising source of biomass and bioenergy is sugarcane. The study of this crop's development in different planting seasons can aid in successfully cultivating it in global climate change scenarios. The sugarcane variety SP80-3280 was field grown under two planting seasons with different climatic conditions. A systems biology approach was taken to study the changes on physiological, morphological, agrotechnological, transcriptomics, and metabolomics levels in the leaf +1, and immature, intermediate and mature internodes. Most of the variation found within the transcriptomics and metabolomics profiles is attributed to the differences among the distinct tissues. However, the integration of both transcriptomics and metabolomics data highlighted three main metabolic categories as the principal sources of variation across tissues: amino acid metabolism, biosynthesis of secondary metabolites, and xenobiotics biodegradation and metabolism. Differences in ripening and metabolite levels mainly in leaves and mature internodes may reflect the impact of contrasting environmental conditions on sugarcane development. In general, the same metabolites are found in mature internodes from both "one-year" and "one-and-a-half-year sugarcane", however, some metabolites (i.e., phenylpropanoids with economic value) and natural antisense transcript expression are only detected in the leaves of "one-year" sugarcane.
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Affiliation(s)
- Maryke Wijma
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Luciane Santini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Leonardo Zambotti-Villela
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Pio Colepicolo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Monalisa Sampaio Carneiro
- Centro de Ciências Agrárias, Departamento de Biotecnologia e Produção Vegetal e Animal, Universidade Federal de São Carlos, São Paulo 13600-970, Brazil;
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
- Correspondence:
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6
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Baggett JP, Tillett RL, Cooper EA, Yerka MK. De novo identification and targeted sequencing of SSRs efficiently fingerprints Sorghum bicolor sub-population identity. PLoS One 2021; 16:e0248213. [PMID: 33684158 PMCID: PMC7939377 DOI: 10.1371/journal.pone.0248213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/22/2021] [Indexed: 11/21/2022] Open
Abstract
Recent plant breeding studies of several species have demonstrated the utility of combining molecular assessments of genetic distance into trait-linked SNP genotyping during the development of parent lines to maximize yield gains due to heterosis. SSRs (Short Sequence Repeats) are the molecular marker of choice to determine genetic diversity, but the methods historically used to sequence them have been burdensome. The ability to analyze SSRs in a higher-throughput manner independent of laboratory conditions would increase their utility in molecular ecology, germplasm curation, and plant breeding programs worldwide. This project reports simple bioinformatics methods that can be used to generate genome-wide de novo SSRs in silico followed by targeted Next Generation Sequencing (NGS) validation of those that provide the most information about sub-population identity of a breeding line, which influences heterotic group selection. While these methods were optimized in sorghum [Sorghum bicolor (L.) Moench], they were developed to be applied to any species with a reference genome and high-coverage whole-genome sequencing data of individuals from the sub-populations to be characterized. An analysis of published sorghum genomes selected to represent its five main races (bicolor, caudatum, durra, kafir, and guinea; 75 accessions total) identified 130,120 SSR motifs. Average lengths were 23.8 bp and 95% were between 10 and 92 bp, making them suitable for NGS. Validation through targeted sequencing amplified 188 of 192 assayed SSR loci. Results highlighted the distinctness of accessions from the guinea sub-group margaritiferum from all other sorghum accessions, consistent with previous studies of nuclear and mitochondrial DNA. SSRs that efficiently fingerprinted margaritiferum individuals (Xgma1 -Xgma6) are presented. Developing similar fingerprints of other sub-populations (Xunr1 -Xunr182) was not possible due to the extensive admixture between them in the data set analyzed. In summary, these methods were able to fingerprint specific sub-populations when rates of admixture between them are low.
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Affiliation(s)
- John P. Baggett
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, United States of America
| | - Richard L. Tillett
- Nevada Center for Bioinformatics, University of Nevada, Reno, NV, United States of America
| | - Elizabeth A. Cooper
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Melinda K. Yerka
- Department of Agriculture, Veterinary, and Rangeland Sciences, University of Nevada, Reno, NV, United States of America
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7
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de Oliveira GL, de Souza AP, de Oliveira FA, Zucchi MI, de Souza LM, Moura MF. Genetic structure and molecular diversity of Brazilian grapevine germplasm: Management and use in breeding programs. PLoS One 2020; 15:e0240665. [PMID: 33057449 PMCID: PMC7561202 DOI: 10.1371/journal.pone.0240665] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
The management of germplasm banks is complex, especially when many accessions are involved. Microsatellite markers are an efficient tool for assessing the genetic diversity of germplasm collections, optimizing their use in breeding programs. This study genetically characterizes a large collection of 410 grapevine accessions maintained at the Agronomic Institute of Campinas (IAC) (Brazil). The accessions were genotyped with 17 highly polymorphic microsatellite markers. Genetic data were analyzed to determine the genetic structure of the germplasm, quantify its allelic diversity, suggest the composition of a core collection, and discover cases of synonymy, duplication, and misnaming. A total of 304 alleles were obtained, and 334 unique genotypes were identified. The molecular profiles of 145 accessions were confirmed according to the literature and databases, and the molecular profiles of more than 100 genotypes were reported for the first time. The analysis of the genetic structure revealed different levels of stratification. The primary division was between accessions related to Vitis vinifera and V. labrusca, followed by their separation from wild grapevine. A core collection of 120 genotypes captured 100% of all detected alleles. The accessions selected for the core collection may be used in future phenotyping efforts, in genome association studies, and for conservation purposes. Genetic divergence among accessions has practical applications in grape breeding programs, as the choice of relatively divergent parents will maximize the frequency of progeny with superior characteristics. Together, our results can enhance the management of grapevine germplasm and guide the efficient exploitation of genetic diversity to facilitate the development of new grape cultivars for fresh fruits, wine, and rootstock.
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Affiliation(s)
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP) UNICAMP, Campinas, SP, Brazil
| | - Fernanda Ancelmo de Oliveira
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Maria Imaculada Zucchi
- Laboratory of Conservation Genetics and Genomics, Agribusiness Technological Development of São Paulo (APTA), Piracicaba, SP, Brazil
| | - Lívia Moura de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Mara Fernandes Moura
- Advanced Fruit Research Center, Agronomic Institute (IAC), Jundiaí, SP, Brazil
- * E-mail:
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Manimekalai R, Suresh G, Govinda Kurup H, Athiappan S, Kandalam M. Role of NGS and SNP genotyping methods in sugarcane improvement programs. Crit Rev Biotechnol 2020; 40:865-880. [PMID: 32508157 DOI: 10.1080/07388551.2020.1765730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Sugarcane (Saccharum spp.) is one of the most economically significant crops because of its high sucrose content and it is a promising biomass feedstock for biofuel production. Sugarcane genome sequencing and analysis is a difficult task due to its heterozygosity and polyploidy. Long sequence read technologies, PacBio Single-Molecule Real-Time (SMRT) sequencing, the Illumina TruSeq, and the Oxford Nanopore sequencing could solve the problem of genome assembly. On the applications side, next generation sequencing (NGS) technologies played a major role in the discovery of single nucleotide polymorphism (SNP) and the development of low to high throughput genotyping platforms. The two mainstream high throughput genotyping platforms are the SNP microarray and genotyping by sequencing (GBS). This paper reviews the NGS in sugarcane genomics, genotyping methodologies, and the choice of these methods. Array-based SNP genotyping is robust, provides consistent SNPs, and relatively easier downstream data analysis. The GBS method identifies large scale SNPs across the germplasm. A combination of targeted GBS and array-based genotyping methods should be used to increase the accuracy of genomic selection and marker-assisted breeding.
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Affiliation(s)
- Ramaswamy Manimekalai
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Gayathri Suresh
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Hemaprabha Govinda Kurup
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Selvi Athiappan
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Mallikarjuna Kandalam
- Business Development, Asia Pacific Japan region, Thermo Fisher Scientific, Waltham, MA, USA
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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 C, Balsalobre TWA, Carneiro MS. Molecular diversity and genetic structure of Saccharum complex accessions. PLoS One 2020; 15:e0233211. [PMID: 32442233 PMCID: PMC7244124 DOI: 10.1371/journal.pone.0233211] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
Sugarcane is an important crop for food and energy security, providing sucrose and bioethanol from sugar content and bioelectricity from lignocellulosic bagasse. In order to evaluate the diversity and genetic structure of the Brazilian Panel of Sugarcane Genotypes (BPSG), a core collection composed by 254 accessions of the Saccharum complex, eight TRAP markers anchored in sucrose and lignin metabolism genes were evaluated. A total of 584 polymorphic fragments were identified and used to investigate the genetic structure of BPSG through analysis of molecular variance (AMOVA), principal components analysis (PCA), a Bayesian method using STRUCTURE software, genetic dissimilarity and phylogenetic tree. AMOVA showed a moderate genetic differentiation between ancestors and improved accessions, 0.14, and the molecular variance was higher within populations than among populations, with values of 86%, 95% and 97% when constrasting improved with ancestors, foreign with ancestors and improved with foreign, respectively. The PCA approach suggests clustering in according with evolutionary and Brazilian breeding sugarcane history, since improved accessions from older generations were positioned closer to ancestors than improved accessions from recent generations. This result was also confirmed by STRUCTURE analysis and phylogenetic tree. The Bayesian method was able to separate ancestors of the improved accessions while the phylogenetic tree showed clusters considering the family relatedness within three major clades; the first being composed mainly by ancestors and the other two mainly by improved accessions. This work can contribute to better management of the crosses considering functional regions of the sugarcane genome.
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Affiliation(s)
- Carolina Medeiros
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Araras, São Paulo, Brasil
| | - Thiago Willian Almeida Balsalobre
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Araras, São Paulo, Brasil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Araras, São Paulo, Brasil
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Sforça DA, Vautrin S, Cardoso-Silva CB, Mancini MC, Romero-da Cruz MV, Pereira GDS, Conte M, Bellec A, Dahmer N, Fourment J, Rodde N, Van Sluys MA, Vicentini R, Garcia AAF, Forni-Martins ER, Carneiro MS, Hoffmann HP, Pinto LR, Landell MGDA, Vincentz M, Berges H, de Souza AP. Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions. FRONTIERS IN PLANT SCIENCE 2019; 10:553. [PMID: 31134109 PMCID: PMC6514446 DOI: 10.3389/fpls.2019.00553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/11/2019] [Indexed: 05/25/2023]
Abstract
Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (~10 Gb) and a high content of repetitive regions. An approach using genomic, transcriptomic, and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane. The hypothetical HP600 and Centromere Protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behaviors of this complex polyploid. The physically linked side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog region with all haplotypes of HP600 and CENP-C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing partial duplications of HP600 and CENP-C (paralogs). This duplication resulted in a non-expressed HP600 pseudogene and a recombined fusion version of CENP-C and the orthologous gene Sobic.003G299500 with at least two chimeric gene haplotypes expressed. It was also determined that it occurred before Saccharum genus formation and after the separation of sorghum and sugarcane. A linkage map was constructed using markers from nonduplicated Region01 and for the duplication (Region01 and Region02). We compare the physical and linkage maps, demonstrating the possibility of mapping markers located in duplicated regions with markers in nonduplicated region. Our results contribute directly to the improvement of linkage mapping in complex polyploids and improve the integration of physical and genetic data for sugarcane breeding programs. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding complex polyploid genomes.
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Affiliation(s)
| | - Sonia Vautrin
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | - Mônica Conte
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Arnaud Bellec
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nair Dahmer
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Joelle Fourment
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nathalie Rodde
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | | | - Hermann Paulo Hoffmann
- Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCAR), Araras, Brazil
| | | | | | - Michel Vincentz
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Helene Berges
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
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12
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Böhme K, Calo-Mata P, Barros-Velázquez J, Ortea I. Review of Recent DNA-Based Methods for Main Food-Authentication Topics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3854-3864. [PMID: 30901215 DOI: 10.1021/acs.jafc.8b07016] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Adulteration and mislabeling of food products and the commercial fraud derived, either intentionally or not, is a global source of economic fraud to consumers but also to all stakeholders involved in food production and distribution. Legislation has been enforced all over the world aimed at guaranteeing the authenticity of the food products all along the distribution chain, thereby avoiding food fraud and adulteration. Accordingly, there is a growing need for new analytical methods able to verify that all the ingredients included in a foodstuff match the qualities claimed by the manufacturer or distributor. In this sense, the improved performance of most recent DNA-based tools in term of sensitivity, multiplexing ability, high-throughput, and relatively low-cost give them a game-changing role in food-authenticity-related topics. Here, we provide a thorough and updated vision on the recently reported approaches that are applying these DNA-based tools to assess the authenticity of food components and products.
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Affiliation(s)
- Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science , University of Santiago de Compostela , E-27002 Lugo , Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science , University of Santiago de Compostela , E-27002 Lugo , Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science , University of Santiago de Compostela , E-27002 Lugo , Spain
| | - Ignacio Ortea
- Proteomics Unit , Maimonides Institute for Biomedical Research (IMIBIC) , E-14004 Córdoba , Spain
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