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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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Ocampo J, Ovalle T, Labarta R, Le DP, de Haan S, Vu NA, Kha LQ, Becerra Lopez-Lavalle LA. DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers' field and genebank collections. PLANT MOLECULAR BIOLOGY 2022; 109:215-232. [PMID: 33630231 PMCID: PMC9162981 DOI: 10.1007/s11103-021-01124-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 01/29/2021] [Indexed: 05/24/2023]
Abstract
A molecular analysis using informative SNP markers in 1570 clones of cassava from Vietnam reveals varietal composition from farmers' field and genebank collections Cassava is the most important smallholder cash crops in Southeast Asia and is especially used in industrial products. Yet, systematic genetic studies on molecular markers from Vietnamese germplasm have not been considered for breeding and conservation programs. We conducted a molecular analysis of 1570 clones of cassava germplasm from farms across six agro-ecological zones using informative SNP markers. We unraveled the genetic diversity and population structure and provided insights into the value of breeding and conservation programs. Duplicated genotypes comprised 98% of the total sample of the Central Highlands region. Ninety-six SNPs were amplified Central Highlands and South East provinces had the highest allelic richness, covering up to 83% of alleles. The average observed heterozygosity (Ho = 0.43) was slightly higher than expected (He = 0.40) across SNP markers, suggesting an excess of heterozygotes plants. Diversity indexes indicated that cassava populations from North West and Eastern Vietnam are genetically diverse (mean He = 0.40). Genetic parentage tests identified 85 unique genetic groups within the varieties KM94, KM419, BRA1305, KM101, KM140, PER262, KM60, KM57 and two unidentified varieties, which accounted for 82% of the frequency distribution. KM94 is the most dominant variety in Vietnamese farms surveyed (38%), reflecting its superior quality and productivity. Discriminant analysis of principal components (DAPC) revealed four main subgroups, which were partially corroborated by neighbor joining (NJ) analyses. After removing duplicates, 31 unique genotypes were distributed across five of the agro-ecological zones. These were well distributed in the subgroups revealed via DAPC and NJ analyses. The genetic groups identified herein could be used to select unique accessions that should ideally conform with ex situ germplasm collections and identify areas where on-farm conservation programs should be targeted. Newly identified genotypes may also contribute as genetic breeding resources that could be used to adapt cassava to future changes and farmers' needs.
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Affiliation(s)
- John Ocampo
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
- National University of Colombia (UNAL), Palmira, Colombia
| | - Tatiana Ovalle
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Ricardo Labarta
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Dung Phuong Le
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Stefan de Haan
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Nguyen Anh Vu
- Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Le Quy Kha
- Institute of Agricultural Sciences for Southern Vietnam (IAS), Ho Chi Minh, Vietnam
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Alves-Pereira A, Zucchi MI, Clement CR, Viana JPG, Pinheiro JB, Veasey EA, de Souza AP. Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties. Sci Rep 2022; 12:1268. [PMID: 35075210 PMCID: PMC8786832 DOI: 10.1038/s41598-022-05160-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/05/2022] [Indexed: 11/09/2022] Open
Abstract
Knowledge about genetic diversity is essential to promote effective use and conservation of crops, because it enables farmers to adapt their crops to specific needs and is the raw material for breeding. Manioc (Manihot esculenta ssp. esculenta) is one of the world's major food crops and has the potential to help achieve food security in the context of on-going climate changes. We evaluated single nucleotide polymorphisms in traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of São Paulo. We assessed genome-wide diversity and identified selective signatures contrasting varieties from different biomes with samples of manioc's wild ancestor M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses that might have been important for the crop's domestication and diversification resulting from cultivation in different environments. Additionally, high neutral genetic diversity within groups of varieties from different biomes and low genetic divergence among biomes reflect the complexity of manioc's evolutionary dynamics under traditional cultivation. Our results exemplify how smallholder practices contribute to conserve manioc's genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.
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Affiliation(s)
- Alessandro Alves-Pereira
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia Dos Agronegócios (APTA), Pólo Centro-Sul. Rodovia SP 127, km 30, Piracicaba, SP, 13400-970, Brazil
| | - Charles R Clement
- Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM, 69067-375, Brazil
| | - João Paulo Gomes Viana
- Department of Crop Sciences, University of Illinois at Urbana-Champaign (UIUC), AW-101 Turner Hall, 1102 South Goodwin Avenue, Urbana, IL, 61801-4798, USA
| | - José Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil. .,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.
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Yao D, Cheng L, Du L, Li M, Daroch M, Tang J. Genome-Wide Investigation and Analysis of Microsatellites and Compound Microsatellites in Leptolyngbya-like Species, Cyanobacteria. Life (Basel) 2021; 11:life11111258. [PMID: 34833134 PMCID: PMC8619395 DOI: 10.3390/life11111258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/03/2021] [Accepted: 11/16/2021] [Indexed: 01/12/2023] Open
Abstract
Microsatellites (simple sequence repeats, SSRs) are ubiquitously distributed in almost all known genomes. Here, the first investigation was designed to examine the SSRs and compound microsatellites (CSSRs) in genomes of Leptolyngbya-like strains. The results disclosed diversified patterns of distribution, abundance, density, and diversity of SSRs and CSSRs in genomes, indicating that they may be subject to rapid evolutionary change. The numbers of SSRs and CSSRs were extremely unevenly distributed among genomes, ranging from 11,086 to 24,000 and from 580 to 1865, respectively. Dinucleotide SSRs were the most abundant category in 31 genomes, while the other 15 genomes followed the pattern: mono- > di- > trinucleotide SSRs. The patterns related to SSRs and CSSRs showed differences among phylogenetic groups. Both SSRs and CSSRs were overwhelmingly distributed in coding regions. The numbers of SSRs and CSSRs were significantly positively correlated with genome size (p < 0.01) and negatively correlated with GC content (p < 0.05). Moreover, the motif (A/C)n and (AG)n was predominant in mononucleotide and dinucleotide SSRs, and unique motifs of CSSRs were identified in 39 genomes. This study provides the first insight into SSRs and CSSRs in genomes of Leptolyngbya-like strains and will be useful to understanding their distribution, predicting their function, and tracking their evolution. Additionally, the identified SSRs may provide an evolutionary advantage of fast adaptation to environmental changes and may play an important role in the cosmopolitan distribution of Leptolyngbya strains to globally diverse niches.
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Affiliation(s)
- Dan Yao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610106, China; (D.Y.); (L.D.)
| | - Lei Cheng
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing 100048, China;
| | - Lianming Du
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610106, China; (D.Y.); (L.D.)
| | - Meijin Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; (M.L.); (M.D.)
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; (M.L.); (M.D.)
| | - Jie Tang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610106, China; (D.Y.); (L.D.)
- Correspondence: ; Tel.: +86-028-84616063
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Sobukola OP, Ajayi FF, Faloye OR, Henshaw FO, Sanni SA, Bodunde G, Agbonlahor M. Characterization of some quality attributes of vacuum fried yellow fleshed cassava chips from different varieties using designed experiment. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olajide P. Sobukola
- Department of Food Science and Technology Federal University of Agriculture Abeokuta Nigeria
| | | | - Opeyemi R. Faloye
- Department of Food Science and Technology Federal University of Agriculture Abeokuta Nigeria
| | - Folake O. Henshaw
- Department of Food Science and Technology Federal University of Agriculture Abeokuta Nigeria
| | - Silifat A. Sanni
- Department of Nutrition and Dietetics Federal University of Agriculture Abeokuta Nigeria
| | - Goke Bodunde
- Department of Horticulture Federal University of Agriculture Abeokuta Nigeria
| | - Mure Agbonlahor
- Department of Agricultural Economics and Farm Management National Open University of Nigeria Lagos Nigeria
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Karim KY, Ifie B, Dzidzienyo D, Danquah EY, Blay ET, Whyte JBA, Kulakow P, Rabbi I, Parkes E, Omoigui L, Norman PE, Iluebbey P. Genetic characterization of cassava ( Manihot esculenta Crantz) genotypes using agro-morphological and single nucleotide polymorphism markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:317-330. [PMID: 32158137 PMCID: PMC7036393 DOI: 10.1007/s12298-019-00740-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/15/2019] [Accepted: 11/24/2019] [Indexed: 06/01/2023]
Abstract
Dearth of information on extent of genetic variability in cassava limits the genetic improvement of cassava genotypes in Sierra Leone. The aim of this study was to assess the genetic diversity and relationships within 102 cassava genotypes using agro-morphological and single nucleotide polymorphism markers. Morphological classification based on qualitative traits categorized the germplasm into five different groups, whereas the quantitative trait set had four groups. The SNP markers classified the germplasm into three main cluster groups. A total of seven principal components (PCs) in the qualitative and four PCs in the quantitative trait sets accounted for 79.03% and 72.30% of the total genetic variation, respectively. Significant and positive correlations were observed between average yield per plant and harvest index (r = 0.76***), number of storage roots per plant and harvest index (r = 0.33*), height at first branching and harvest index (0.26*), number of storage roots per plant and average yield per plant (r = 0.58*), height at first branching and average yield per plant (r = 0.24*), length of leaf lobe and petiole length (r = 0.38*), number of leaf lobe and petiole length (r = 0.31*), width of leaf lobe and length of leaf lobe (r = 0.36*), number of leaf lobe and length of leaf lobe (r = 0.43*), starch content and dry matter content (r = 0.99***), number of leaf lobe and root dry matter (r = 0.30*), number of leaf lobe and starch content (r = 0.28*), and height at first branching and plant height (r = 0.45**). Findings are useful for conservation, management, short term recommendation for release and genetic improvement of the crop.
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Affiliation(s)
- Kumba Y. Karim
- Sierra Leone Agricultural Research Institute, Tower Hill, Freetown, PMB 1313 Sierra Leone
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Beatrice Ifie
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Daniel Dzidzienyo
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Eric Y. Danquah
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Essie T. Blay
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Jim B. A. Whyte
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Lucky Omoigui
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Prince E. Norman
- Sierra Leone Agricultural Research Institute, Tower Hill, Freetown, PMB 1313 Sierra Leone
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Peter Iluebbey
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
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Adjebeng-Danquah J, Manu-Aduening J, Asante IK, Agyare RY, Gracen V, Offei SK. Genetic diversity and population structure analysis of Ghanaian and exotic cassava accessions using simple sequence repeat (SSR) markers. Heliyon 2020; 6:e03154. [PMID: 32042951 PMCID: PMC7002781 DOI: 10.1016/j.heliyon.2019.e03154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/23/2019] [Accepted: 12/20/2019] [Indexed: 11/28/2022] Open
Abstract
Genetic diversity is fundamentally important in crop improvement and provides plants with the capacity to meet the demands of changing environments. This work was carried out to assess the diversity and the extent of genetic relatedness among a number of assembled cassava (Manihot esculenta Crantz) accessions. We conducted a microsatellite marker analysis of 89 cassava accessions collected from Ghanaian and exotic sources. These accessions were assayed using 35 simple sequence repeat (SSR) markers. A total of 167 alleles were detected from 35 polymorphic markers with an average of 4.77 alleles per locus. High allelic frequency was detected across the accessions, ranging from 0.32 to 0.99 with an average of 0.62 per marker. Observed heterozygosity ranged from 0.03 - 0.97 across the accessions. Polymorphism information content (PIC) ranged from 0.03 to 0.78 with a mean of 0.45, indicating high level of polymorphism across the accessions. Comparatively, higher number of alleles, gene diversity and observed heterozygosity were detected among the local accessions compared with the exotic accessions indicating rich genetic diversity among them. Population structure analysis based on STRUCTURE identified two subpopulations and a large number of admixtures. Cluster analysis based on the neighbour joining algorithim further separated the collection into seven sub-groupings irrespective of geographical origin. This indicates the possible sharing of common genomic regions occurring across the accessions. High allelic frequency differences and levels of heterozygosity were observed among the germplasm. These findings indicated significant genetic variability in the germplasm to warrant selection.
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Affiliation(s)
| | | | - Isaac Kwadwo Asante
- West Africa Centre Crop Improvement (WACCI), University of Ghana, Legon, Accra, Ghana
| | - Richard Yaw Agyare
- CSIR-Savanna Agricultural Research Institute, P. O. Box TL 52, Tamale, Ghana
| | - Vernon Gracen
- West Africa Centre Crop Improvement (WACCI), University of Ghana, Legon, Accra, Ghana
| | - Samuel Kwame Offei
- West Africa Centre Crop Improvement (WACCI), University of Ghana, Legon, Accra, Ghana
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Alves-Pereira A, Clement CR, Picanço-Rodrigues D, Veasey EA, Dequigiovanni G, Ramos SLF, Pinheiro JB, Zucchi MI. Patterns of nuclear and chloroplast genetic diversity and structure of manioc along major Brazilian Amazonian rivers. ANNALS OF BOTANY 2018; 121:625-639. [PMID: 29309531 PMCID: PMC5853005 DOI: 10.1093/aob/mcx190] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/23/2017] [Indexed: 05/20/2023]
Abstract
Background and Aims Amazonia is a major world centre of plant domestication, but little is known about how the crops were dispersed across the region. Manioc (Manihot esculenta) was domesticated in the south-western Amazon basin, and is the most important staple food crop that originated in Amazonia. Current contrasting distributions may reflect distinct histories of dispersal of bitter and sweet manioc landraces. To produce new insights into the evolutionary history of the crop, we investigated the contemporary genetic diversity and structure of bitter and sweet manioc along major Amazonian rivers. Methods The patterns of genetic structure and diversity of wild and cultivated sweet and bitter manioc with four chloroplast and 14 nuclear microsatellite markers were evaluated. Results were interpreted in terms of the crop's dispersal. Key results No phylogeographic patterns among rivers were detected, and genetic structure among rivers was confounded by the bitter-sweet divergence. However, differences in the distribution of nuclear diversity and somewhat distinctive patterns of genetic structure across rivers were observed within bitter and sweet manioc. Conclusions Various pre-Columbian and post-European conquest events in the history of Amazonian occupation may explain the absence of clearer patterns of genetic structure. However, the wide distribution of the most common chloroplast haplotype agrees with an early dispersal of manioc across Brazilian Amazonia. Furthermore, differences in genetic structure and in the spatial distribution of genetic diversity suggest that bitter and sweet manioc had distinct dispersal histories. Knowledge about how prehistoric and contemporary Amazonian peoples manage their crops is valuable for the maintenance and conservation of the impressive diversity of their native crops.
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Affiliation(s)
- Alessandro Alves-Pereira
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Charles R Clement
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
| | | | - Elizabeth A Veasey
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Gabriel Dequigiovanni
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Santiago L F Ramos
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - José B Pinheiro
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Maria I Zucchi
- Agência Paulista de Tecnologia dos Agronegócios, Pólo Centro-Sul (APTA), Piracicaba, SP, Brazil
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Wang B, Guo X, Zhao P, Ruan M, Yu X, Zou L, Yang Y, Li X, Deng D, Xiao J, Xiao Y, Hu C, Wang X, Wang X, Wang W, Peng M. Molecular diversity analysis, drought related marker-traits association mapping and discovery of excellent alleles for 100-day old plants by EST-SSRs in cassava germplasms (Manihot esculenta Cranz). PLoS One 2017; 12:e0177456. [PMID: 28493955 PMCID: PMC5426748 DOI: 10.1371/journal.pone.0177456] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/27/2017] [Indexed: 11/19/2022] Open
Abstract
Cassava is the third largest food crop of the world and has strong ability of drought tolerance. In order to evaluate the molecular diversity and to discover novel alleles for drought tolerance in cassava germplasms, we examined a total of 107 abiotic stress related expressed sequence tags-simple sequence repeat (EST-SSR) markers in 134 cassava genotypes coming from planting regions worldwide and performed drought related marker-traits association mapping. As results, we successfully amplified 98 of 107 markers in 97 polymorphic loci and 279 alleles, with 2.87 alleles per locus, gene diversity of 0.48 and polymorphic information content (PIC) of 0.41 on average. The genetic coefficient between every two lines was 0.37 on average, ranging from 0.21 to 0.82. According to our population structure analysis, these samples could be divided into three sub-populations showing obvious gene flow between them. We also performed water stress experiments using 100-day old cassava plants in two years and calculated the drought tolerance coefficients (DTCs) and used them as phenotypes for marker-trait association mapping. We found that 53 markers were significantly associated with these drought-related traits, with a contribution rate for trait variation of 8.60% on average, ranging between 2.66 and 28.09%. Twenty-four of these 53 associated genes showed differential transcription or protein levels which were confirmed by qRT-PCR under drought stress when compared to the control conditions in cassava. Twelve of twenty-four genes were the same differential expression patterns in omics data and results of qRT-PCR. Out of 33 marker-traits combinations on 24 loci, 34 were positive and 53 negative alleles according to their phenotypic effects and we also obtained the typical materials which carried these elite alleles. We also found 23 positive average allele effects while 10 loci were negative according to their allele effects (AAEs). Our results on molecular diversity, locus association and differential expression under drought can prove beneficial to select excellent materials through marker assisted selection and for functional genes research in the future.
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Affiliation(s)
- Bin Wang
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xin Guo
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Pingjuan Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Mengbin Ruan
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiaoling Yu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Liangping Zou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Yiling Yang
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiao Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Deli Deng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Jixiang Xiao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Yiwei Xiao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Chunji Hu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xue Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiaolin Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Wenquan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
- * E-mail:
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Iulianelli GC, Tavares MIB. Application of solid-state NMR spectroscopy to evaluate cassava genotypes. J Food Compost Anal 2016. [DOI: 10.1016/j.jfca.2016.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Thai elite cassava genetic diversity was fortuitously conserved through farming with different sets of varieties. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0631-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Siqueira MVBM, Pinheiro TT, Borges A, Valle TL, Zatarim M, Veasey EA. Microsatellite polymorphisms in cassava landraces from the Cerrado biome, Mato Grosso do sul, Brazil. Biochem Genet 2010; 48:879-95. [PMID: 20668929 DOI: 10.1007/s10528-010-9369-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 06/07/2010] [Indexed: 11/29/2022]
Abstract
Using nine microsatellite loci, we investigated genetic structure and diversity in 83 Brazilian cassava accessions, including several landraces, in the Cerrado biome in Mato Grosso do Sul, Brazil. All nine loci were polymorphic, averaging 6.00 alleles per locus. Treating each of seven municipalities as a cassava group or population, they averaged 3.5 alleles per locus, with 97% polymorphic loci, high values for observed heterozygosity (0.32) and gene diversity (0.56). Total genetic variability was high (0.668), and most of this genetic variability was concentrated within municipalities (0.577). Cluster and structure analyses divided accessions into two major clusters or populations (K = 2). Also, a significant genetic versus geographic correlation was found (r = 0.4567; P < 0.0260). Migratory routes in the Cerrado are considered main contributors to the region's high cassava diversity and spatial genetic structure, amplifying interactions between traditional farmers and the evolutionary dynamics of this crop.
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Affiliation(s)
- M V B M Siqueira
- Department of Genetics, College of Agriculture "Luiz de Queiroz," ESALQ, University of São Paulo, C.P. 83, 13400-970, Piracicaba, São Paulo, Brazil
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