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Leal-Bertioli SCM, de Blas FJ, Carolina Chavarro M, Simpson CE, Valls JFM, Tallury SP, Moretzsohn MC, Custodio AR, Thomas Stalker H, Seijo G, Bertioli DJ. Relationships of the wild peanut species, section Arachis: A resource for botanical classification, crop improvement, and germplasm management. AMERICAN JOURNAL OF BOTANY 2024; 111:e16357. [PMID: 38898619 DOI: 10.1002/ajb2.16357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 06/21/2024]
Abstract
PREMISE Wild species are strategic sources of valuable traits to be introduced into crops through hybridization. For peanut, the 33 currently described wild species in the section Arachis are particularly important because of their sexual compatibility with the domesticated species, Arachis hypogaea. Although numerous wild accessions are carefully preserved in seed banks, their morphological similarities pose challenges to routine classification. METHODS Using a high-density array, we genotyped 272 accessions encompassing all diploid species in section Arachis. Detailed relationships between accessions and species were revealed through phylogenetic analyses and interpreted using the expertise of germplasm collectors and curators. RESULTS Two main groups were identified: one with A genome species and the other with B, D, F, G, and K genomes. Species groupings generally showed clear boundaries. Structure within groups was informative, for instance, revealing the history of the proto-domesticate A. stenosperma. However, some groupings suggested multiple sibling species. Others were polyphyletic, indicating the need for taxonomic revision. Annual species were better defined than perennial ones, revealing limitations in applying classical and phylogenetic species concepts to the genus. We suggest new species assignments for several accessions. CONCLUSIONS Curated by germplasm collectors and curators, this analysis of species relationships lays the foundation for future species descriptions, classification of unknown accessions, and germplasm use for peanut improvement. It supports the conservation and curation of current germplasm, both critical tasks considering the threats to the genus posed by habitat loss and the current restrictions on new collections and germplasm transfer.
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Affiliation(s)
- Soraya C M Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
- Department of Plant Pathology, University of Georgia, Athens, 30602, GA, USA
| | - Francisco J de Blas
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
- Botanical Institute of the Northeast (IBONE), CC 209, Corrientes, W3402, Argentina
| | - M Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
| | - Charles E Simpson
- Texas AgriLife Research, Texas A&M University, Stephenville, 76401, TX, USA
| | - José F M Valls
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, Brasília, DF 70.770-917, Brazil
| | - Shyam P Tallury
- USDA-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, 30223, GA, USA
| | - Márcio C Moretzsohn
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, Brasília, DF 70.770-917, Brazil
| | - Adriana R Custodio
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, Brasília, DF 70.770-917, Brazil
| | - H Thomas Stalker
- Department of Crop and Soil Sciences North Carolina State University, Raleigh, 27695, NC, USA
| | - Guillermo Seijo
- Botanical Institute of the Northeast (IBONE), CC 209, Corrientes, W3402, Argentina
- Faculty of Exact and Natural Sciences, National University of Northeast, Libertad 5470, Corrientes, W3402, Argentina
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
- Department of Crop and Soil Science, University of Georgia, Athens, 30602, GA, USA
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2
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Lu Q, Huang L, Liu H, Garg V, Gangurde SS, Li H, Chitikineni A, Guo D, Pandey MK, Li S, Liu H, Wang R, Deng Q, Du P, Varshney RK, Liang X, Hong Y, Chen X. A genomic variation map provides insights into peanut diversity in China and associations with 28 agronomic traits. Nat Genet 2024; 56:530-540. [PMID: 38378864 DOI: 10.1038/s41588-024-01660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 01/09/2024] [Indexed: 02/22/2024]
Abstract
Peanut (Arachis hypogaea L.) is an important allotetraploid oil and food legume crop. China is one of the world's largest peanut producers and consumers. However, genomic variations underlying the migration and divergence of peanuts in China remain unclear. Here we reported a genome-wide variation map based on the resequencing of 390 peanut accessions, suggesting that peanuts might have been introduced into southern and northern China separately, forming two cultivation centers. Selective sweep analysis highlights asymmetric selection between the two subgenomes during peanut improvement. A classical pedigree from South China offers a context for the examination of the impact of artificial selection on peanut genome. Genome-wide association studies identified 22,309 significant associations with 28 agronomic traits, including candidate genes for plant architecture and oil biosynthesis. Our findings shed light on peanut migration and diversity in China and provide valuable genomic resources for peanut improvement.
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Affiliation(s)
- Qing Lu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
| | - Lu Huang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Vanika Garg
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Annapurna Chitikineni
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Dandan Guo
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shaoxiong Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Haiyan Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Runfeng Wang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Quanqing Deng
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Puxuan Du
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
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3
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Sithole TR, Ma YX, Qin Z, Liu HM, Wang XD. Influence of Peanut Varieties on the Sensory Quality of Peanut Butter. Foods 2022; 11:3499. [PMID: 36360111 PMCID: PMC9656606 DOI: 10.3390/foods11213499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 10/20/2023] Open
Abstract
Over the years, concentrated efforts have been directed toward the improvement of desirable characteristics and attributes in peanut cultivars. Most of these breed improvement programs have been targeting attributes that involve peanut growth, productivity, drought and disease tolerance, and oil quality and content, with only a few articles focusing directly on improvements in peanut butter organoleptic qualities. There are numerous peanut cultivars on the market today, with widely differing chemical compositions and metabolite profiles, about which little is known concerning their suitability for making peanut butter. In this review, we detail how the numerous peanut varieties on the market today, with their genetically conferred physiochemical attributes, can significantly affect the sensory quality attributes of peanut butter, even in peanut butter processing lines with optimized processes. If other peanut butter processing parameters are held constant, variations in the chemical composition and metabolite profiles of peanuts have a significant impact on peanut butter color, flavor, texture, storage stability, shelf life, and overall product acceptance by consumers. Further research on breeding programs for peanut varieties that are specifically tailored for peanut butter production, and even more comprehensive research on the synergetic relationship between peanut chemical composition and peanut butter organoleptic quality, are still required.
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Affiliation(s)
| | | | | | | | - Xue-De Wang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
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4
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Hsu YM, Wang SS, Tseng YC, Lee SR, Fang H, Hung WC, Kuo HI, Dai HY. Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq. Sci Rep 2022; 12:14495. [PMID: 36008445 PMCID: PMC9411510 DOI: 10.1038/s41598-022-18737-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/18/2022] [Indexed: 11/09/2022] Open
Abstract
The cultivated peanut (Arachis hypogaea L.) is an important oil crop but has a narrow genetic diversity. Molecular markers can be used to probe the genetic diversity of various germplasm. In this study, the restriction site associated DNA (RAD) approach was utilized to sequence 31 accessions of Taiwanese peanut germplasm, leading to the identification of a total of 17,610 single nucleotide polymorphisms (SNPs). When we grouped these 31 accessions into two subsets according to origin, we found that the "global" subset (n = 17) was more genetically diverse than the "local" subset (n = 14). Concerning botanical varieties, the var. fastigiata subset had greater genetic diversity than the other two subsets of var. vulgaris and var. hypogaea, suggesting that novel genetic resources should be introduced into breeding programs to enhance genetic diversity. Principal component analysis (PCA) of genotyping data separated the 31 accessions into three clusters largely according to the botanical varieties, consistent with the PCA result for 282 accessions genotyped by 14 kompetitive allele-specific PCR (KASP) markers developed in this study. The SNP markers identified in this work not only revealed the genetic relationship and population structure of current germplasm in Taiwan, but also offer an efficient tool for breeding and further genetic applications.
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Affiliation(s)
- Yu-Ming Hsu
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.,Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.,Crop Science Division, Taiwan Agricultural Research Institute, Taichung, 413008, Taiwan, ROC
| | - Sheng-Shan Wang
- Crop Improvement Division, Tainan District Agricultural Research and Extension Station, Tainan, 71246, Taiwan, ROC
| | - Yu-Chien Tseng
- Agronomy Department, National Chiayi University, Chiayi, 60004, Taiwan, ROC
| | - Shin-Ruei Lee
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, 413008, Taiwan, ROC
| | - Hsiang Fang
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, 413008, Taiwan, ROC
| | - Wei-Chia Hung
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, 413008, Taiwan, ROC
| | - Hsin-I Kuo
- Agronomy Department, National Chiayi University, Chiayi, 60004, Taiwan, ROC
| | - Hung-Yu Dai
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, 413008, Taiwan, ROC.
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5
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Samoluk SS, Vaio M, Ortíz AM, Chalup LMI, Robledo G, Bertioli DJ, Seijo G. Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species. PLANTA 2022; 256:50. [PMID: 35895167 DOI: 10.1007/s00425-022-03961-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids. The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
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Affiliation(s)
- Sergio S Samoluk
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina.
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Alejandra M Ortíz
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
| | - Laura M I Chalup
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
| | - Germán Robledo
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
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6
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Tian X, Shi L, Guo J, Fu L, Du P, Huang B, Wu Y, Zhang X, Wang Z. Chloroplast Phylogenomic Analyses Reveal a Maternal Hybridization Event Leading to the Formation of Cultivated Peanuts. FRONTIERS IN PLANT SCIENCE 2021; 12:804568. [PMID: 34975994 PMCID: PMC8718879 DOI: 10.3389/fpls.2021.804568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Peanuts (Arachis hypogaea L.) offer numerous healthy benefits, and the production of peanuts has a prominent role in global food security. As a result, it is in the interest of society to improve the productivity and quality of peanuts with transgenic means. However, the lack of a robust phylogeny of cultivated and wild peanut species has limited the utilization of genetic resources in peanut molecular breeding. In this study, a total of 33 complete peanut plastomes were sequenced, analyzed and used for phylogenetic analyses. Our results suggest that sect. Arachis can be subdivided into two lineages. All the cultivated species are contained in Lineage I with AABB and AA are the two predominant genome types present, while species in Lineage II possess diverse genome types, including BB, KK, GG, etc. Phylogenetic studies also indicate that all allotetraploid cultivated peanut species have been derived from a possible maternal hybridization event with one of the diploid Arachis duranensis accessions being a potential AA sub-genome ancestor. In addition, Arachis monticola, a tetraploid wild species, is placed in the same group with all the cultivated peanuts, and it may represent a transitional species, which has been through the recent hybridization event. This research could facilitate a better understanding of the taxonomic status of various Arachis species/accessions and the evolutionary relationship among them, and assists in the correct and efficient use of germplasm resources in breeding efforts to improve peanuts for the benefit of human beings.
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Affiliation(s)
- Xiangyu Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Luye Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Jia Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Liuyang Fu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Pei Du
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Bingyan Huang
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xinyou Zhang
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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7
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Abady S, Shimelis H, Janila P, Yaduru S, Shayanowako AIT, Deshmukh D, Chaudhari S, Manohar SS. Assessment of the genetic diversity and population structure of groundnut germplasm collections using phenotypic traits and SNP markers: Implications for drought tolerance breeding. PLoS One 2021; 16:e0259883. [PMID: 34788339 PMCID: PMC8598071 DOI: 10.1371/journal.pone.0259883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/28/2021] [Indexed: 01/15/2023] Open
Abstract
Profiling the genetic composition and relationships among groundnut germplasm collections is essential for the breeding of new cultivars. The objectives of this study were to assess the genetic diversity and population structure among 100 improved groundnut genotypes using agronomic traits and high-density single nucleotide polymorphism (SNP) markers. The genotypes were evaluated for agronomic traits and drought tolerance at the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT)/India across two seasons. Ninety-nine of the test genotypes were profiled with 16363 SNP markers. Pod yield per plant (PY), seed yield per plant (SY), and harvest index (HI) were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes ICGV 07222, ICGV 06040, ICGV 01260, ICGV 15083, ICGV 10143, ICGV 03042, ICGV 06039, ICGV 14001, ICGV 11380, and ICGV 13200 ranked top in terms of pod yield under both drought-stressed and optimum conditions. PY exhibited a significant (p ≤ 0.05) correlation with SY, HI, and total biomass (TBM) under both test conditions. Based on the principal component (PC) analysis, PY, SY, HSW, shelling percentage (SHP), and HI were allocated in PC 1 and contributed to the maximum variability for yield under the two water regimes. Hence, selecting these traits could be successful for screening groundnut genotypes under drought-stressed and optimum conditions. The model-based population structure analysis grouped the studied genotypes into three sub-populations. Dendrogram for phenotypic and genotypic also grouped the studied 99 genotypes into three heterogeneous clusters. Analysis of molecular variance revealed that 98% of the total genetic variation was attributed to individuals, while only 2% of the total variance was due to variation among the subspecies. The genetic distance between the Spanish bunch and Virginia bunch types ranged from 0.11 to 0.52. The genotypes ICGV 13189, ICGV 95111, ICGV 14421, and ICGV 171007 were selected for further breeding based on their wide genetic divergence. Data presented in this study will guide groundnut cultivar development emphasizing economic traits and adaptation to water-limited agro-ecologies, including in Ethiopia.
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Affiliation(s)
- Seltene Abady
- African Centre for Crop Improvement (ACCI), School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, South Africa
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Hussein Shimelis
- African Centre for Crop Improvement (ACCI), School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Telangana, India
| | - Shasidhar Yaduru
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Telangana, India
| | - Admire I. T. Shayanowako
- African Centre for Crop Improvement (ACCI), School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | - Dnyaneshwar Deshmukh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Telangana, India
| | - Sunil Chaudhari
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Telangana, India
| | - Surendra S. Manohar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Telangana, India
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8
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Brown N, Branch WD, Johnson M, Wallace J. Genetic diversity assessment of Georgia peanut cultivars developed during ninety years of breeding. THE PLANT GENOME 2021; 14:e20141. [PMID: 34482640 DOI: 10.1002/tpg2.20141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
The cultivated peanut(Arachis hypogaea L.) has experienced severe genetic bottlenecks over the course of its evolution and domestication. Most genetic diversity studies in peanut have focused on global genetic stocks, wild accessions, and related species, but few have focused on elite cultivars. The objective of this project was to assess the genetic diversity of 32 peanut cultivars developed by the University of Georgia breeding program since its inception in 1931. Quantifying genetic similarity (GSIM) among these cultivars will provide a better understanding of their relationships and aid in breeding for cultivar development. Genotyping-by-sequencing (GBS), in concert with the recently published A. hypogaea genome sequence, was used to identify a total of 27,142 single nucleotide polymorphisms (SNPs) among these cultivars. Coefficients of parentage (CoP) were calculated based on publicly available pedigree information and compared with SNP-based GSIM estimates; the resulting correlations were low, ranging from R2 = 0.212-0.279. Although genetic diversity is generally low in cultivated peanut, our data indicate that the genetic diversity of Georgia cultivars has actually increased since the early days of the breeding program, likely a result of the incorporation of diverse germplasm and breeding lines into the program. The results reported here provide a valuable understanding of genetic variation among elite Georgia peanut cultivars that have had a significant impact on the peanut industry within the United States.
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Affiliation(s)
- Nino Brown
- Institute of Plant Breeding, Genetics and Genomics, Dept. of Crop and Soil Sciences, University of Georgia, 2360 Rainwater Rd., Tifton, GA, 31793-5766, USA
| | - William D Branch
- Institute of Plant Breeding, Genetics and Genomics, Dept. of Crop and Soil Sciences, University of Georgia, 2360 Rainwater Rd., Tifton, GA, 31793-5766, USA
| | - Matthew Johnson
- Institute of Plant Breeding, Genetics and Genomics, Dept. of Crop and Soil Sciences, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA
| | - Jason Wallace
- Institute of Plant Breeding, Genetics and Genomics, Dept. of Crop and Soil Sciences, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA
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9
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Chu Y, Bertioli D, Levinson CM, Stalker HT, Holbrook CC, Ozias-Akins P. Homoeologous recombination is recurrent in the nascent synthetic allotetraploid Arachis ipaënsis × Arachis correntina4x and its derivatives. G3-GENES GENOMES GENETICS 2021; 11:6162164. [PMID: 33693764 PMCID: PMC8759810 DOI: 10.1093/g3journal/jkab066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/21/2021] [Indexed: 11/13/2022]
Abstract
Genome instability in newly synthesized allotetraploids of peanut has breeding implications that have not been fully appreciated. Synthesis of wild species-derived neo-tetraploids offers the opportunity to broaden the gene pool of peanut; however, the dynamics among the newly merged genomes creates predictable and unpredictable variation. Selfed progenies from the neo-tetraploid Arachis ipaënsis × Arachis correntina (A. ipaënsis × A. correntina)4x and F1 hybrids and F2 progenies from crosses between A. hypogaea × [A. ipaënsis × A. correntina]4x were genotyped by the Axiom Arachis 48 K SNP array. Homoeologous recombination between the A. ipaënsis and A. correntina derived subgenomes was observed in the S0 generation. Among the S1 progenies, these recombined segments segregated and new events of homoeologous recombination emerged. The genomic regions undergoing homoeologous recombination segregated mostly disomically in the F2 progenies from A. hypogaea × [A. ipaënsis × A. correntina]4x crosses. New homoeologous recombination events also occurred in the F2 population, mostly found on chromosomes 03, 04, 05, and 06. From the breeding perspective, these phenomena offer both possibilities and perils; recombination between genomes increases genetic diversity, but genome instability could lead to instability of traits or even loss of viability within lineages.
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Affiliation(s)
- Ye Chu
- Horticulture Department, University of Georgia, Tifton, GA 31793, USA
| | - David Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA.,Department of Crop and Soil Science, University of Georgia, Athens, GA 30602, USA
| | - Chandler M Levinson
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
| | - H Thomas Stalker
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - C Corley Holbrook
- USDA- Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA 31793, USA
| | - Peggy Ozias-Akins
- Horticulture Department, University of Georgia, Tifton, GA 31793, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
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Nascimento EFDMBD, Leal-Bertioli SCDM, Bertioli DJ, Chavarro C, Freitas FO, Moretzsohn MDC, Guimarães PM, Valls JFM, Araujo ACGD. Brazilian Kayabi Indian accessions of peanut, Arachis hypogaea (Fabales, Fabaceae): origin, diversity and evolution. Genet Mol Biol 2020; 43:e20190418. [PMID: 33174976 PMCID: PMC7644258 DOI: 10.1590/1678-4685-gmb-2019-0418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/26/2020] [Indexed: 11/22/2022] Open
Abstract
Peanut is a crop of the Kayabi tribe, inhabiting the Xingu Indigenous Park, Brazil. Morphological analysis of Xingu accessions showed variation exceeding that described for cultivated peanuts. This raised questions as to the origin of the Xingu accessions: are they derived from different species, or is their diversity a result of different evolutionary and selection processes? To answer these questions, cytogenetic and genotyping analyses were conducted. The karyotypes of Xingu accessions analyzed are very similar to each other, to an A. hypogaea subsp. fastigiata accession and to the wild allotetraploid A. monticola. The accessions share the number and general morphology of the chromosomes; DAPI+ bands; 5S and 45S rDNA loci distribution and a high genomic affinity with A. duranensis and A. ipaënsis genomic probes. However, the number of CMA3+ bands differs from those determined for A. hypogaea and A. monticola, which are also different from each other. SNP genotyping grouped all Arachis allotetraploids into four taxonomic groups: Xingu accessions were closer to A. monticola and A. hypogaea subsp. hypogaea. Our data suggests that the morphological diversity within these accessions is not associated with a different origin and can be attributed to morphological plasticity and different selection by the Indian tribes.
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Affiliation(s)
| | | | - David John Bertioli
- University of Georgia, Center for Applied Genetic Technologies, Athens, GA, USA
| | - Carolina Chavarro
- University of Georgia, Center for Applied Genetic Technologies, Athens, GA, USA
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11
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Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes. Genes (Basel) 2020; 11:genes11101220. [PMID: 33080972 PMCID: PMC7650781 DOI: 10.3390/genes11101220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 11/18/2022] Open
Abstract
The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.
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Khedikar Y, Clarke WE, Chen L, Higgins EE, Kagale S, Koh CS, Bennett R, Parkin IAP. Narrow genetic base shapes population structure and linkage disequilibrium in an industrial oilseed crop, Brassica carinata A. Braun. Sci Rep 2020; 10:12629. [PMID: 32724070 PMCID: PMC7387349 DOI: 10.1038/s41598-020-69255-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/09/2020] [Indexed: 12/16/2022] Open
Abstract
Ethiopian mustard (Brassica carinata A. Braun) is an emerging sustainable source of vegetable oil, in particular for the biofuel industry. The present study exploited genome assemblies of the Brassica diploids, Brassica nigra and Brassica oleracea, to discover over 10,000 genome-wide SNPs using genotype by sequencing of 620 B. carinata lines. The analyses revealed a SNP frequency of one every 91.7 kb, a heterozygosity level of 0.30, nucleotide diversity levels of 1.31 × 10-05, and the first five principal components captured only 13% molecular variation, indicating low levels of genetic diversity among the B. carinata collection. Genome bias was observed, with greater SNP density found on the B subgenome. The 620 lines clustered into two distinct sub-populations (SP1 and SP2) with the majority of accessions (88%) clustered in SP1 with those from Ethiopia, the presumed centre of origin. SP2 was distinguished by a collection of breeding lines, implicating targeted selection in creating population structure. Two selective sweep regions on B3 and B8 were detected, which harbour genes involved in fatty acid and aliphatic glucosinolate biosynthesis, respectively. The assessment of genetic diversity, population structure, and LD in the global B. carinata collection provides critical information to assist future crop improvement.
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Affiliation(s)
- Yogendra Khedikar
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Wayne E Clarke
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Lifeng Chen
- Agrisoma Biosciences Inc., 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Erin E Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Sateesh Kagale
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Chu Shin Koh
- Global Institute of Food Security, Saskatoon, SK, Canada
| | - Rick Bennett
- Agrisoma Biosciences Inc., 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada.
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13
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Muralidharan S, Poon YY, Wright GC, Haynes PA, Lee NA. Quantitative proteomics analysis of high and low polyphenol expressing recombinant inbred lines (RILs) of peanut (Arachis hypogaea L.). Food Chem 2020; 334:127517. [PMID: 32711266 DOI: 10.1016/j.foodchem.2020.127517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 06/22/2020] [Accepted: 07/05/2020] [Indexed: 11/28/2022]
Abstract
To facilitate selective breeding of polyphenol-rich peanuts, we looked for mass spectrometry-based proteomic evidence, investigating a subset of recombinant inbred lines (RILs) developed by the Australian peanut breeding program. To do this, we used label-free shotgun proteomics for protein and peptide quantitation, statistically analyzed normalized spectral abundance factors using R-package, as well as assayed important antioxidants. Results revealed statistically significant protein expression changes in 82 proteins classified between high or low polyphenols expressing RILs. Metabolic changes in polyphenol-rich RIL p27-362 point towards increased enzymatic breakdown of sugars and phenylalanine biosynthesis. The study revealed phenylpropanoid pathway overexpression resulting in increased polyphenols biosynthesis. Overexpression of antioxidant enzymes such as catalase, by 73.4 fold was also observed. A strong metabolic correlation exists with the observed phenotypic traits. Peanut RIL p27-362 presents a superior nutritional composition with antioxidant-rich peanut phenotype and could yield commercial profits. Data are available via ProteomeXchange with identifierPXD015493.
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Affiliation(s)
- Sridevi Muralidharan
- ARC Training Centre for Advanced Technologies in Food Manufacture, School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Yan Yee Poon
- ARC Training Centre for Advanced Technologies in Food Manufacture, School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Graeme C Wright
- Peanut Company of Australia, Kingaroy, Queensland, Australia
| | - Paul A Haynes
- ARC Training Centre for Molecular Technology in the Food Industry, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Nanju A Lee
- ARC Training Centre for Advanced Technologies in Food Manufacture, School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia.
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14
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High-resolution mass spectrometry-based selection of peanut peptide biomarkers considering food processing and market type variation. Food Chem 2020; 304:125428. [DOI: 10.1016/j.foodchem.2019.125428] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/14/2019] [Accepted: 08/24/2019] [Indexed: 12/17/2022]
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15
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Samaha GM, Ahmed MA, Abd El-Hameid AR. Assessment of growth and productivity of five peanut cultivars and genetic diversity using RAPD markers. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2019; 43:168. [DOI: 10.1186/s42269-019-0201-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/24/2019] [Indexed: 09/02/2023]
Abstract
AbstractBackgroundThis study was conducted to evaluate the genetic diversity of five peanut cultivars grown under field conditions. A field experiment was conducted using five peanut cultivars (Giza-5, Giza-6, Ismailia-1, Gregory, and R92) in a randomized complete block design with five replications during two following seasons to estimate the performance of five peanut cultivars for vegetative growth, yield, and yield component traits as well as seed quality traits. Twenty RAPD primers were used to identify a unique fingerprint for each of five cultivars.ResultsGiza-6 cultivar surpassed all the tested peanut cultivars in the most vegetative growth traits and yield and its components traits, while the lowest values were observed in Giza-5 cultivar. The dendrogram constructed from RAPD analysis showed that Gregory and Giza-5 were the most distant among five peanut cultivars.ConclusionsRAPD markers are useful in the detection of genetic diversity of peanut. The availability of genetic diversity is important for the genetic improvement of peanut.
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16
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Wang J, Li Y, Li C, Yan C, Zhao X, Yuan C, Sun Q, Shi C, Shan S. Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny. BMC PLANT BIOLOGY 2019; 19:504. [PMID: 31744457 PMCID: PMC6862822 DOI: 10.1186/s12870-019-2121-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 11/05/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. RESULTS Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. CONCLUSION In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.
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Affiliation(s)
- Juan Wang
- Shandong Peanut Research Institute, Qingdao, China
| | - Yuan Li
- Computational Biology and Biological Physics, Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao, China
| | - Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao, China
| | - Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao, China
| | - Chengren Shi
- Shandong Peanut Research Institute, Qingdao, China
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, China
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17
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Iqdiam BM, Abuagela MO, Boz Z, Marshall SM, Goodrich‐Schneider R, Sims CA, Marshall MR, MacIntosh AJ, Welt BA. Effects of atmospheric pressure plasma jet treatment on aflatoxin level, physiochemical quality, and sensory attributes of peanuts. J FOOD PROCESS PRES 2019. [DOI: 10.1111/jfpp.14305] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Basheer M. Iqdiam
- Food Science and Human Nutrition Department Institute of Food and Agricultural Sciences University of Florida Gainesville Florida
- Agricultural and Biological Engineering Department University of Florida Gainesville Florida
| | - Manal O. Abuagela
- Food Science and Human Nutrition Department Institute of Food and Agricultural Sciences University of Florida Gainesville Florida
| | - Ziynet Boz
- Agricultural and Biological Engineering Department University of Florida Gainesville Florida
| | - Sara M. Marshall
- Food Science and Human Nutrition Department Institute of Food and Agricultural Sciences University of Florida Gainesville Florida
| | - Renee Goodrich‐Schneider
- Food Science and Human Nutrition Department Institute of Food and Agricultural Sciences University of Florida Gainesville Florida
| | - Charles A. Sims
- Food Science and Human Nutrition Department Institute of Food and Agricultural Sciences University of Florida Gainesville Florida
| | - Maurice R. Marshall
- Food Science and Human Nutrition Department Institute of Food and Agricultural Sciences University of Florida Gainesville Florida
| | - Andrew J. MacIntosh
- Food Science and Human Nutrition Department Institute of Food and Agricultural Sciences University of Florida Gainesville Florida
| | - Bruce A. Welt
- Agricultural and Biological Engineering Department University of Florida Gainesville Florida
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18
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Maia RA, da Cruz Saraiva KD, Roque ALM, Thiers KLL, Dos Santos CP, da Silva JHM, Feijó DF, Arnholdt-Schmitt B, Costa JH. Differential expression of recently duplicated PTOX genes in Glycine max during plant development and stress conditions. J Bioenerg Biomembr 2019; 51:355-370. [PMID: 31506801 DOI: 10.1007/s10863-019-09810-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/29/2019] [Indexed: 12/13/2022]
Abstract
Plastid terminal oxidase (PTOX) is a chloroplast enzyme that catalyzes oxidation of plastoquinol (PQH2) and reduction of molecular oxygen to water. Its function has been associated with carotenoid biosynthesis, chlororespiration and environmental stress responses in plants. In the majority of plant species, a single gene encodes the protein and little is known about events of PTOX gene duplication and their implication to plant metabolism. Previously, two putative PTOX (PTOX1 and 2) genes were identified in Glycine max, but the evolutionary origin and the specific function of each gene was not explored. Phylogenetic analyses revealed that this gene duplication occurred apparently during speciation involving the Glycine genus ancestor, an event absent in all other available plant leguminous genomes. Gene expression evaluated by RT-qPCR and RNA-seq data revealed that both PTOX genes are ubiquitously expressed in G. max tissues, but their mRNA levels varied during development and stress conditions. In development, PTOX1 was predominant in young tissues, while PTOX2 was more expressed in aged tissues. Under stress conditions, the PTOX transcripts varied according to stress severity, i.e., PTOX1 mRNA was prevalent under mild or moderate stresses while PTOX2 was predominant in drastic stresses. Despite the high identity between proteins (97%), molecular docking revealed that PTOX1 has higher affinity to substrate plastoquinol than PTOX2. Overall, our results indicate a functional relevance of this gene duplication in G. max metabolism, whereas PTOX1 could be associated with chloroplast effectiveness and PTOX2 to senescence and/or apoptosis.
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Affiliation(s)
- Rachel Alves Maia
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Kátia Daniella da Cruz Saraiva
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
- Federal Institute of Education, Science and Technology of Paraíba - IFPB, Campus Princesa Isabel, 58755-000, BR-426, S/N - Rural Zone, Princesa Isabel, Paraíba, Brazil
| | - André Luiz Maia Roque
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Karine Leitão Lima Thiers
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Clesivan Pereira Dos Santos
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | | | - Daniel Ferreira Feijó
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Birgit Arnholdt-Schmitt
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
- Functional Cell Reprogramming and Organism Plasticity (FunCrop - virtual network), EU Marie Curie Chair, ICAAM, University of Évora, Apartado 94, 7002-554, Évora, Portugal
- Science and Technology Park Alentejo (PACT), 7005-841, Évora, Portugal
| | - José Hélio Costa
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil.
- Functional Cell Reprogramming and Organism Plasticity (FunCrop - virtual network), EU Marie Curie Chair, ICAAM, University of Évora, Apartado 94, 7002-554, Évora, Portugal.
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19
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Desmae H, Janila P, Okori P, Pandey MK, Motagi BN, Monyo E, Mponda O, Okello D, Sako D, Echeckwu C, Oteng‐Frimpong R, Miningou A, Ojiewo C, Varshney RK. Genetics, genomics and breeding of groundnut ( Arachis hypogaea L.). PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:425-444. [PMID: 31598026 PMCID: PMC6774334 DOI: 10.1111/pbr.12645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 04/10/2018] [Accepted: 07/13/2018] [Indexed: 05/04/2023]
Abstract
Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.
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Affiliation(s)
- Haile Desmae
- International Crop Research Institute for the Semi‐Arid Tropics (ICRISAT)BamakoMali
| | | | | | | | | | | | - Omari Mponda
- Division of Research and Development (DRD)Tanzania Agricultural Research Institute (TARI) ‐ NaliendeleMtwaraTanzania
| | - David Okello
- National Agricultural Research Organization (NARO)EntebbeUganda
| | | | | | | | - Amos Miningou
- Institut National d'Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
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Introgression of peanut smut resistance from landraces to elite peanut cultivars (Arachis hypogaea L.). PLoS One 2019; 14:e0211920. [PMID: 30735547 PMCID: PMC6368304 DOI: 10.1371/journal.pone.0211920] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/22/2019] [Indexed: 11/19/2022] Open
Abstract
Smut disease caused by the fungal pathogen Thecaphora frezii Carranza & Lindquist is threatening the peanut production in Argentina. Fungicides commonly used in the peanut crop have shown little or no effect controlling the disease, making it a priority to obtain peanut varieties resistant to smut. In this study, recombinant inbred lines (RILs) were developed from three crosses between three susceptible peanut elite cultivars (Arachis hypogaea L. subsp. hypogaea) and two resistant landraces (Arachis hypogaea L. subsp. fastigiata Waldron). Parents and RILs were evaluated under high inoculum pressure (12000 teliospores g-1 of soil) over three years. Disease resistance parameters showed a broad range of variation with incidence mean values ranging from 1.0 to 35.0% and disease severity index ranging from 0.01 to 0.30. Average heritability (h2) estimates of 0.61 to 0.73 indicated that resistance in the RILs was heritable, with several lines (4 to 7 from each cross) showing a high degree of resistance and stability over three years. Evidence of genetic transfer between genetically distinguishable germplasm (introgression in a broad sense) was further supported by simple-sequence repeats (SSRs) and Insertion/Deletion (InDel) marker genotyping. This is the first report of smut genetic resistance identified in peanut landraces and its introgression into elite peanut cultivars.
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21
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Arias RS, Sobolev VS, Massa AN, Orner VA, Walk TE, Ballard LL, Simpson SA, Puppala N, Scheffler BE, de Blas F, Seijo GJ. New tools to screen wild peanut species for aflatoxin accumulation and genetic fingerprinting. BMC PLANT BIOLOGY 2018; 18:170. [PMID: 30111278 PMCID: PMC6094572 DOI: 10.1186/s12870-018-1355-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 06/19/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Aflatoxin contamination in peanut seeds is still a serious problem for the industry and human health. No stable aflatoxin resistant cultivars have yet been produced, and given the narrow genetic background of cultivated peanuts, wild species became an important source of genetic diversity. Wild peanut seeds, however, are not abundant, thus, an effective method of screening for aflatoxin accumulation using minimal seeds is highly desirable. In addition, keeping record of genetic fingerprinting of each accession would be very useful for breeding programs and for the identification of accessions within germplasm collections. RESULTS In this study, we report a method of screening for aflatoxin accumulation that is applicable to the small-size seeds of wild peanuts, increases the reliability by testing seed viability, and records the genetic fingerprinting of the samples. Aflatoxin levels observed among 20 wild peanut species varied from zero to 19000 ng.g-1 and 155 ng.g-1 of aflatoxin B1 and B2, respectively. We report the screening of 373 molecular markers, including 288 novel SSRs, tested on 20 wild peanut species. Multivariate analysis by Neighbor-Joining, Principal Component Analysis and 3D-Principal Coordinate Analysis using 134 (36 %) transferable markers, in general grouped the samples according to their reported genomes. The best 88 markers, those with high fluorescence, good scorability and transferability, are reported with BLAST results. High quality markers (total 98) that discriminated genomes are reported. A high quality marker with UPIC score 16 (16 out of 20 species discriminated) had significant hits on BLAST2GO to a pentatricopeptide-repeat protein, another marker with score 5 had hits on UDP-D-apiose synthase, and a third one with score 12 had BLASTn hits on La-RP 1B protein. Together, these three markers discriminated all 20 species tested. CONCLUSIONS This study provides a reliable method to screen wild species of peanut for aflatoxin resistance using minimal seeds. In addition we report 288 new SSRs for peanut, and a cost-effective combination of markers sufficient to discriminate all 20 species tested. These tools can be used for the systematic search of aflatoxin resistant germplasm keeping record of the genetic fingerprinting of the accessions tested for breeding purpose.
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Affiliation(s)
- Renee S. Arias
- USDA-ARS-NPRL, National Peanut Research Laboratory (NPRL), 1011 Forrester Dr. S.E, Dawson, GA 39842 USA
| | - Victor S. Sobolev
- USDA-ARS-NPRL, National Peanut Research Laboratory (NPRL), 1011 Forrester Dr. S.E, Dawson, GA 39842 USA
| | - Alicia N. Massa
- USDA-ARS-NPRL, National Peanut Research Laboratory (NPRL), 1011 Forrester Dr. S.E, Dawson, GA 39842 USA
| | - Valerie A. Orner
- USDA-ARS-NPRL, National Peanut Research Laboratory (NPRL), 1011 Forrester Dr. S.E, Dawson, GA 39842 USA
| | - Travis E. Walk
- USDA-ARS-NPRL, National Peanut Research Laboratory (NPRL), 1011 Forrester Dr. S.E, Dawson, GA 39842 USA
| | - Linda L. Ballard
- USDA-ARS-GBRU, Genomics and Bioinformatics Research Unit, 141 Experiment Station rd, Stoneville, MS 38776 USA
| | - Sheron A. Simpson
- USDA-ARS-GBRU, Genomics and Bioinformatics Research Unit, 141 Experiment Station rd, Stoneville, MS 38776 USA
| | - Naveen Puppala
- New Mexico State University, Agricultural Science Center at Clovis, 2346 SR 288, Clovis, NM 88101 USA
| | - Brian E. Scheffler
- USDA-ARS-GBRU, Genomics and Bioinformatics Research Unit, 141 Experiment Station rd, Stoneville, MS 38776 USA
| | - Francisco de Blas
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Av. Libertad 5470, C.P, 3400 Corrientes, Argentina
| | - Guillermo J. Seijo
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Av. Libertad 5470, C.P, 3400 Corrientes, Argentina
- Instituto de Botánica del Nordeste, (UNNE-CONICET), Casilla de Correo 209, 3400 Corrientes, Argentina
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Mondal S, Badigannavar AM. Mapping of a dominant rust resistance gene revealed two R genes around the major Rust_QTL in cultivated peanut (Arachis hypogaea L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1671-1681. [PMID: 29744525 DOI: 10.1007/s00122-018-3106-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/02/2018] [Indexed: 05/16/2023]
Abstract
A consensus rust QTL was identified within a 1.25 cM map interval of A03 chromosome in cultivated peanut. This map interval contains a TIR-NB-LRR R gene and four pathogenesis-related genes. Disease resistance in plants is manifested due to the specific interaction between the R gene product and its cognate avirulence gene product (AVR) in the pathogen. Puccinia arachidis Speg. causes rust disease and inflicts economic damages to peanut. Till now, no experimental evidence is known for the action of R gene in peanut for rust resistance. A fine mapping approach towards the development of closely linked markers for rust resistance gene was undertaken in this study. Phenotyping of an RIL population at five environments for field rust score and subsequent QTL analysis has identified a 1.25 cM map interval that harbored a consensus major Rust_QTL in A03 chromosome. This Rust_QTL is flanked by two SSR markers: FRS72 and SSR_GO340445. Both the markers clearly identified strong association of the mapped region with rust reaction in both resistant and susceptible genotypes from a collection of 95 cultivated peanut germplasm. This 1.25 cM map interval contained 331.7 kb in the physical map of A. duranensis and had a TIR-NB-LRR category R gene (Aradu.Z87JB) and four glucan endo-1,3 β glucosidase genes (Aradu.RKA6 M, Aradu.T44NR, Aradu.IWV86 and Aradu.VG51Q). Another resistance gene analog was also found in the vicinity of mapped Rust_QTL. The sequence between SSR markers, FRS72 and FRS49, contains an LRR-PK (Aradu.JG217) which is equivalent to RHG4 in soybean. Probably, the protein kinase domain in AhRHG4 acts as an integrated decoy for the cognate AVR from Puccinia arachidis and helps the TIR-NB-LRR R-protein to initiate a controlled program cell death in resistant peanut plants.
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Affiliation(s)
- Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India.
| | - Anand M Badigannavar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
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Abuagela MO, Iqdiam BM, Mostafa H, Gu L, Smith ME, Sarnoski PJ. Assessing pulsed light treatment on the reduction of aflatoxins in peanuts with and without skin. Int J Food Sci Technol 2018. [DOI: 10.1111/ijfs.13851] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Manal O. Abuagela
- Food Science and Human Nutrition Department; Institute of Food and Agricultural Sciences; University of Florida; Gainesville FL 32611 USA
| | - Basheer M. Iqdiam
- Food Science and Human Nutrition Department; Institute of Food and Agricultural Sciences; University of Florida; Gainesville FL 32611 USA
| | - Hussein Mostafa
- Food Science and Human Nutrition Department; Institute of Food and Agricultural Sciences; University of Florida; Gainesville FL 32611 USA
| | - Liwei Gu
- Food Science and Human Nutrition Department; Institute of Food and Agricultural Sciences; University of Florida; Gainesville FL 32611 USA
| | - Matthew E. Smith
- Plant Pathology Department; Institute of Food and Agricultural Sciences; University of Florida; Gainesville FL 32611 USA
| | - Paul J. Sarnoski
- Food Science and Human Nutrition Department; Institute of Food and Agricultural Sciences; University of Florida; Gainesville FL 32611 USA
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Singh A, Raina SN, Rajpal VR, Singh AK. Seed protein fraction electrophoresis in peanut ( Arachis hypogaea L.) accessions and wild species. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:465-481. [PMID: 29692554 PMCID: PMC5911266 DOI: 10.1007/s12298-018-0521-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 01/12/2018] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Abstract
Total seed storage proteins were studied in 50 accessions of A. hypogaea (11 A. hypogaea ssp. hypogaea var hypogaea, 13 A. hypogaea ssp. hypogaea var hirsuta, 11 A. hypogaea ssp. fastigiata var fastigiata and 15 A. hypogaea ssp. fastigiata var. vulgaris accessions) in SDS PAGE. These accessions were also analysed for albumin and globulin seed protein fractions. Among the six seed protein markers presently used, it was found that globulin fraction showed maximum diversity (77.2%) in A. hypogaea accessions followed by albumin (52.3%), denatured total soluble protein fraction in embryo (33.3%) and cotyledon (28.5%). The cluster analysis based on combined data of cotyledons, embryos, albumins and globulins seed protein fractions demarcated the accessions of two subspecies hypogaea and fastigiata into two separate clusters supported by 51% bootstrap value, with few exceptions, suggesting the genotypes to be moderately diverse. Native and denatured total soluble seed storage proteins were also electrophoretically analysed in 27 wild Arachis species belonging to six sections of the genus. Cluster analysis using different methods were performed for different seed proteins data alone and also in combination. Section Caulorrhizae (C genome) and Triseminatae (T genome) formed one, distantly related group to A. hypogaea and other section Arachis species in the dendrogram based on denatured seed storage proteins data. The present analysis has maintained that the section Arachis species belong to primary and secondary genepools and, sections Procumbenetes and Erectoides belong to tertiary gene pools.
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Affiliation(s)
- Apekshita Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh 201313 India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh 201313 India
| | - Vijay Rani Rajpal
- Department of Botany, Hans Raj College, University of Delhi, Delhi, 110007 India
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25
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Jeyaramraja P, Meenakshi SN, Woldesenbet F. Relationship between drought and preharvest aflatoxin contamination in groundnut (Arachis hypogaea L.). WORLD MYCOTOXIN J 2018. [DOI: 10.3920/wmj2017.2248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Groundnut is a commercial oilseed crop that is prone to infection by Aspergillus flavus or Aspergillus parasiticus. Drought impairs the defence mechanism of the plant and favours the production of aflatoxin by the fungus. Aflatoxin is a carcinogen and its presence in food and feed causes significant economic loss. The answer to the question, ‘how drought tolerance and aflatoxin resistance are related?’ is not clear. In this review paper, the relationship of drought and preharvest aflatoxin contamination (AC), the relationship of drought tolerance traits and AC, and the approaches to enhance resistance to AC are discussed using up-to-date literature. Factors leading to AC are drought, high geocarposphere temperature, kernel/pod damage, and reduced phytoalexin synthesis by the plant. If the fungus colonises a kernel with reduced water activity, the plant cannot synthesise phytoalexin and then, the fungus synthesises aflatoxin. Breeding for resistance to AC is complicated because aflatoxin concentration is costly to measure, highly variable, and influenced by the environment. Since drought tolerant cultivars have resistance to AC, traits of drought tolerance have been used as indirect selection tools for reduced AC. The genetics of aflatoxin resistance mechanisms have not been made clear as the environment influences the host-pathogen relationship. Host-pathogen interactions under the influence of environment should be studied at molecular level to identify plant resistant factors using the tools of genomics, proteomics, and metabolomics in order to develop cultivars with durable resistance. Many candidate genes involved in host-pathogen interactions have been identified due to improvements in fungal expressed sequence tags, microarrays, and genome sequencing techniques. Moreover, research projects are underway on identifying genes coding for antifungal compounds, resistance associated proteins and quantitative trait loci associated with aflatoxin resistance. This review is expected to help those who wish to work on reducing AC in groundnuts.
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Affiliation(s)
- P.R. Jeyaramraja
- Department of Biology, College of Natural Sciences, Arba Minch University, P.O. Box 21, Arba Minch, Gamo Gofa Zone, Ethiopia
| | - S. Nithya Meenakshi
- Department of Botany, PSGR Krishnammal College for Women, Peelamedu, Coimbatore 641 004, Tamilnadu, India
| | - F. Woldesenbet
- Department of Biology, College of Natural Sciences, Arba Minch University, P.O. Box 21, Arba Minch, Gamo Gofa Zone, Ethiopia
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Luo H, Guo J, Ren X, Chen W, Huang L, Zhou X, Chen Y, Liu N, Xiong F, Lei Y, Liao B, Jiang H. Chromosomes A07 and A05 associated with stable and major QTLs for pod weight and size in cultivated peanut (Arachis hypogaea L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:267-282. [PMID: 29058050 DOI: 10.1007/s00122-017-3000-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/07/2017] [Indexed: 05/22/2023]
Abstract
Co-localized intervals and candidate genes were identified for major and stable QTLs controlling pod weight and size on chromosomes A07 and A05 in an RIL population across four environments. Cultivated peanut (Arachis hypogaea L.) is an important legume crops grown in > 100 countries. Hundred-pod weight (HPW) is an important yield trait in peanut, but its underlying genetic mechanism was not well studied. In this study, a mapping population (Xuhua 13 × Zhonghua 6) with 187 recombinant inbred lines (RILs) was developed to map quantitative trait loci (QTLs) for HPW together with pod length (PL) and pod width (PW) by both unconditional and conditional QTL analyses. A genetic map covering 1756.48 cM was constructed with 817 markers. Additive effects, epistatic interactions, and genotype-by-environment interactions were analyzed using the phenotyping data generated across four environments. Twelve additive QTLs were identified on chromosomes A05, A07, and A08 by unconditional analysis, and five of them (qPLA07, qPLA05.1, qPWA07, qHPWA07.1, and qHPWA05.2) showed major and stable expressions in all environments. Conditional QTL mapping found that PL had stronger influences on HPW than PW. Notably, qHPWA07.1, qPLA07, and qPWA07 that explained 17.93-43.63% of the phenotypic variations of the three traits were co-localized in a 5 cM interval (1.48 Mb in physical map) on chromosome A07 with 147 candidate genes related to catalytic activity and metabolic process. In addition, qHPWA05.2 and qPLA05.1 were co-localized with minor QTL qPWA05.2 to a 1.3 cM genetic interval (280 kb in physical map) on chromosome A05 with 12 candidate genes. This study provides a comprehensive characterization of the genetic components controlling pod weight and size as well as candidate QTLs and genes for improving pod yield in future peanut breeding.
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Affiliation(s)
- Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Fei Xiong
- Huanggang Academy of Agricultural Sciences, Huanggang, 463000, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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27
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Luo H, Xu Z, Li Z, Li X, Lv J, Ren X, Huang L, Zhou X, Chen Y, Yu J, Chen W, Lei Y, Liao B, Jiang H. Development of SSR markers and identification of major quantitative trait loci controlling shelling percentage in cultivated peanut (Arachis hypogaea L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1635-1648. [PMID: 28508097 PMCID: PMC5511596 DOI: 10.1007/s00122-017-2915-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/27/2017] [Indexed: 05/04/2023]
Abstract
A total of 204,439 SSR markers were developed in diploid genomes, and 25 QTLs for shelling percentage were identified in a RIL population across 4 years including five consistent QTLs. Cultivated peanut (Arachis hypogaea L.) is an important grain legume providing edible oil and protein for human nutrition. Genome sequences of its diploid ancestors, Arachis duranensis and A. ipaensis, were reported, but their SSRs have not been well exploited and utilized hitherto. Shelling percentage is an important economic trait and its improvement has been one of the major objectives in peanut breeding programs. In this study, the genome sequences of A. duranensis and A. ipaensis were used to develop SSR markers, and a mapping population (Yuanza 9102 × Xuzhou 68-4) with 195 recombinant inbred lines was used to map QTLs controlling shelling percentage. The numbers of newly developed SSR markers were 84,383 and 120,056 in the A. duranensis and A. ipaensis genomes, respectively. Genotyping of the mapping population was conducted with both newly developed and previously reported markers. QTL analysis using the phenotyping data generated in Wuhan across four consecutive years and genotyping data of 830 mapped loci identified 25 QTLs with 4.46-17.01% of phenotypic variance explained in the four environments. Meta-analysis revealed five consistent QTLs that could be detected in at least two environments. Notably, the consistent QTL cqSPA09 was detected in all four environments and explained 10.47-17.01% of the phenotypic variance. The segregation in the progeny of a residual heterozygous line confirmed that the cpSPA09 locus had additive effect in increasing shelling percentage. These consistent and major QTL regions provide opportunity not only for further gene discovery, but also for the development of functional markers for breeding.
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Affiliation(s)
- Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Zhijun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Zhendong Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xinping Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jianwei Lv
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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28
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de Paula AF, Dinato NB, Vigna BBZ, Fávero AP. Recombinants from the crosses between amphidiploid and cultivated peanut (Arachis hypogaea) for pest-resistance breeding programs. PLoS One 2017; 12:e0175940. [PMID: 28423007 PMCID: PMC5396913 DOI: 10.1371/journal.pone.0175940] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 04/03/2017] [Indexed: 11/19/2022] Open
Abstract
Peanut is a major oilseed crop worldwide. In the Brazilian peanut production, silvering thrips and red necked peanut worm are the most threatening pests. Resistant varieties are considered an alternative to pest control. Many wild diploid Arachis species have shown resistance to these pests, and these can be used in peanut breeding by obtaining hybrid of A and B genomes and subsequent polyploidization with colchicine, resulting in an AABB amphidiploid. This amphidiploid can be crossed with cultivated peanut (AABB) to provide genes of interest to the cultivar. In this study, the sterile diploid hybrids from A. magna V 13751 and A. kempff-mercadoi V 13250 were treated with colchicine for polyploidization, and the amphidiploids were crossed with A. hypogaea cv. IAC OL 4 to initiate the introgression of the wild genes into the cultivated peanut. The confirmation of the hybridity of the progenies was obtained by: (1) reproductive characterization through viability of pollen, (2) molecular characterization using microsatellite markers and (3) morphological characterization using 61 morphological traits with principal component analysis. The diploid hybrid individual was polyploidized, generating the amphidiploid An 13 (A. magna V 13751 x A. kempff-mercadoi V 13250)4x. Four F1 hybrid plants were obtained from IAC OL 4 × An 13, and 51 F2 seeds were obtained from these F1 plants. Using reproductive, molecular and morphological characterizations, it was possible to distinguish hybrid plants from selfed plants. In the cross between A. hypogaea and the amphidiploid, as the two parents are polyploid, the hybrid progeny and selves had the viability of the pollen grains as high as the parents. This fact turns the use of reproductive characteristics impossible for discriminating, in this case, the hybrid individuals from selfing. The hybrids between A. hypogaea and An 13 will be used in breeding programs seeking pest resistance, being subjected to successive backcrosses until recovering all traits of interest of A. hypogaea, keeping the pest resistance.
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Affiliation(s)
- Ailton Ferreira de Paula
- Departamendo de Morfologia e Patologia, Universidade Federal de São Carlos, São Carlos, São Paulo, Brasil
- * E-mail:
| | - Naiana Barbosa Dinato
- Departamendo de Morfologia e Patologia, Universidade Federal de São Carlos, São Carlos, São Paulo, Brasil
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Zhao H, Sun H, Li L, Lou Y, Li R, Qi L, Gao Z. Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan (Daemonorops jenkinsiana). Sci Rep 2017; 7:46107. [PMID: 28383053 PMCID: PMC5382692 DOI: 10.1038/srep46107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/08/2017] [Indexed: 11/09/2022] Open
Abstract
Rattan is an important group of regenerating non-wood climbing palm in tropical forests. The cirrus is an essential climbing organ and provides morphological evidence for evolutionary and taxonomic studies. However, limited data are available on the molecular mechanisms underlying the development of the cirrus. Thus, we performed in-depth transcriptomic sequencing analyses to characterize the cirrus development at different developmental stages of Daemonorops jenkinsiana. The result showed 404,875 transcripts were assembled, including 61,569 high-quality unigenes were identified, of which approximately 76.16% were annotated and classified by seven authorized databases. Moreover, a comprehensive analysis of the gene expression profiles identified differentially expressed genes (DEGs) concentrated in developmental pathways, cell wall metabolism, and hook formation between the different stages of the cirri. Among them, 37 DEGs were validated by qRT-PCR. Furthermore, 14,693 transcriptome-based microsatellites were identified. Of the 168 designed SSR primer pairs, 153 were validated and 16 pairs were utilized for the polymorphic analysis of 25 rattan accessions. These findings can be used to interpret the molecular mechanisms of cirrus development, and the developed microsatellites markers provide valuable data for assisting rattan taxonomy and expanding the understanding of genomic study in rattan.
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Affiliation(s)
- Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Huayu Sun
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Lichao Li
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yongfeng Lou
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Rongsheng Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510000, China
| | - Lianghua Qi
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Zhimin Gao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
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30
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Mondal S, Petwal VC, Badigannavar AM, Bhad PG, Verma VP, Goswami SG, Dwivedi J. Electron beam irradiation revealed genetic differences in radio-sensitivity and generated mutants in groundnut ( Arachis hypogaea L.). Appl Radiat Isot 2017; 122:78-83. [DOI: 10.1016/j.apradiso.2017.01.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 01/06/2017] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
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31
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Vishwakarma MK, Kale SM, Sriswathi M, Naresh T, Shasidhar Y, Garg V, Pandey MK, Varshney RK. Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis. FRONTIERS IN PLANT SCIENCE 2017; 8:2064. [PMID: 29312366 PMCID: PMC5742254 DOI: 10.3389/fpls.2017.02064] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/17/2017] [Indexed: 05/04/2023]
Abstract
Small insertions and deletions (InDels) are the second most prevalent and the most abundant structural variations in plant genomes. In order to deploy these genetic variations for genetic analysis in genus Arachis, we conducted comparative analysis of the draft genome assemblies of both the diploid progenitor species of cultivated tetraploid groundnut (Arachis hypogaea L.) i.e., Arachis duranensis (A subgenome) and Arachis ipaënsis (B subgenome) and identified 515,223 InDels. These InDels include 269,973 insertions identified in A. ipaënsis against A. duranensis while 245,250 deletions in A. duranensis against A. ipaënsis. The majority of the InDels were of single bp (43.7%) and 2-10 bp (39.9%) while the remaining were >10 bp (16.4%). Phylogenetic analysis using genotyping data for 86 (40.19%) polymorphic markers grouped 96 diverse Arachis accessions into eight clusters mostly by the affinity of their genome. This study also provided evidence for the existence of "K" genome, although distinct from both the "A" and "B" genomes, but more similar to "B" genome. The complete homology between A. monticola and A. hypogaea tetraploid taxa showed a very similar genome composition. The above analysis has provided greater insights into the phylogenetic relationship among accessions, genomes, sub species and sections. These InDel markers are very useful resource for groundnut research community for genetic analysis and breeding applications.
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Affiliation(s)
| | - Sandip M. Kale
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manda Sriswathi
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Talari Naresh
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- *Correspondence: Manish K. Pandey
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- The University of Western Australia, Crawley, WA, Australia
- Rajeev K. Varshney
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32
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Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability. G3-GENES GENOMES GENETICS 2016; 6:3825-3836. [PMID: 27729436 PMCID: PMC5144954 DOI: 10.1534/g3.115.026898] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.
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Tseng YC, Tillman BL, Peng Z, Wang J. Identification of major QTLs underlying tomato spotted wilt virus resistance in peanut cultivar Florida-EP(TM) '113'. BMC Genet 2016; 17:128. [PMID: 27600750 PMCID: PMC5012072 DOI: 10.1186/s12863-016-0435-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/25/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Spotted wilt caused by tomato spotted wilt virus (TSWV) is one of the major peanut (Arachis hypogaea L.) diseases in the southeastern United States. Occurrence, severity, and symptoms of spotted wilt disease are highly variable from season to season, making it difficult to efficiently evaluate breeding populations for resistance. Molecular markers linked to spotted wilt resistance could overcome this problem and allow selection of resistant lines regardless of environmental conditions. Florida-EP(TM) '113' is a spotted wilt resistant cultivar with a significantly lower infection frequency. However, the genetic basis is still unknown. The objective of this study is to map the major quantitative trait loci (QTLs) linked to spotted wilt resistance in Florida-EP(TM) '113'. RESULTS Among 2,431 SSR markers located across the whole peanut genome screened between the two parental lines, 329 were polymorphic. Those polymorphic markers were used to further genotype a representative set of individuals in a segregating population. Only polymorphic markers on chromosome A01 showed co-segregation between genotype and phenotype. Genotyping by sequencing (GBS) of the representative set of individuals in the segregating population also depicted a strong association between several SNPs on chromosome A01 and the trait, indicating a major QTL on chromosome A01. Therefore marker density was enriched on the A01 chromosome. A linkage map with 23 makers on chromosome A01 was constructed, showing collinearity with the physical map. Combined with phenotypic data, a major QTL flanked by marker AHGS4584 and GM672 was identified on chromosome A01, with up to 22.7 % PVE and 9.0 LOD value. CONCLUSION A major QTL controlling the spotted wilt resistance in Florida-EP(TM) '113' was identified. The resistance is most likely contributed by PI 576638, a hirsuta botanical-type line, introduced from Mexico with spotted wilt resistance. The flanking markers of this QTL can be used for further fine mapping and marker assisted selection in peanut breeding programs.
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Affiliation(s)
- Yu-Chien Tseng
- Agronomy Department, University of Florida, 2033 Mowry Road, Room 337 Cancer/Genetics Research Complex, Gainesville, FL 32610 USA
- North Florida Research and Education Center, University of Florida, Marianna, FL 32446 USA
| | - Barry L. Tillman
- Agronomy Department, University of Florida, 2033 Mowry Road, Room 337 Cancer/Genetics Research Complex, Gainesville, FL 32610 USA
- North Florida Research and Education Center, University of Florida, Marianna, FL 32446 USA
| | - Ze Peng
- Agronomy Department, University of Florida, 2033 Mowry Road, Room 337 Cancer/Genetics Research Complex, Gainesville, FL 32610 USA
| | - Jianping Wang
- Agronomy Department, University of Florida, 2033 Mowry Road, Room 337 Cancer/Genetics Research Complex, Gainesville, FL 32610 USA
- Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610 USA
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Chaintreuil C, Gully D, Hervouet C, Tittabutr P, Randriambanona H, Brown SC, Lewis GP, Bourge M, Cartieaux F, Boursot M, Ramanankierana H, D'Hont A, Teaumroong N, Giraud E, Arrighi JF. The evolutionary dynamics of ancient and recent polyploidy in the African semiaquatic species of the legume genus Aeschynomene. THE NEW PHYTOLOGIST 2016; 211:1077-1091. [PMID: 27061605 DOI: 10.1111/nph.13956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/04/2016] [Indexed: 06/05/2023]
Abstract
The legume genus Aeschynomene is notable in the ability of certain semiaquatic species to develop nitrogen-fixing stem nodules. These species are distributed in two clades. In the first clade, all the species are characterized by the use of a unique Nod-independent symbiotic process. In the second clade, the species use a Nod-dependent symbiotic process and some of them display a profuse stem nodulation as exemplified in the African Aeschynomene afraspera. To facilitate the molecular analysis of the symbiotic characteristics of such legumes, we took an integrated molecular and cytogenetic approach to track occurrences of polyploidy events and to analyze their impact on the evolution of the African species of Aeschynomene. Our results revealed two rounds of polyploidy: a paleopolyploid event predating the African group and two neopolyploid speciations, along with significant chromosomal variations. Hence, we found that A. afraspera (8x) has inherited the contrasted genomic properties and the stem-nodulation habit of its parental lineages (4x). This study reveals a comprehensive picture of African Aeschynomene diversification. It notably evidences a history that is distinct from the diploid Nod-independent clade, providing clues for the identification of the specific determinants of the Nod-dependent and Nod-independent symbiotic processes, and for comparative analysis of stem nodulation.
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Affiliation(s)
- Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, 34398, Montpellier, France
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l'Environnement/Centre National de Recherche sur l'Environnement, Antananarivo, 101, Madagascar
| | - Spencer C Brown
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91 198, Gif-sur-Yvette, France
| | - Gwilym P Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK
| | - Mickaël Bourge
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91 198, Gif-sur-Yvette, France
| | - Fabienne Cartieaux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Marc Boursot
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l'Environnement/Centre National de Recherche sur l'Environnement, Antananarivo, 101, Madagascar
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, 34398, Montpellier, France
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Jean-François Arrighi
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
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Zhou X, Dong Y, Zhao J, Huang L, Ren X, Chen Y, Huang S, Liao B, Lei Y, Yan L, Jiang H. Genomic survey sequencing for development and validation of single-locus SSR markers in peanut (Arachis hypogaea L.). BMC Genomics 2016; 17:420. [PMID: 27251557 PMCID: PMC4888616 DOI: 10.1186/s12864-016-2743-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/14/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single-locus markers have many advantages compared with multi-locus markers in genetic and breeding studies because their alleles can be assigned to particular genomic loci in diversity analyses. However, there is little research on single-locus SSR markers in peanut. Through the de novo assembly of DNA sequencing reads of A. hypogaea, we developed single-locus SSR markers in a genomic survey for better application in genetic and breeding studies of peanut. RESULTS In this study, DNA libraries with four different insert sizes were used for sequencing with 150 bp paired-end reads. Approximately 237 gigabases of clean data containing 1,675,631,984 reads were obtained after filtering. These reads were assembled into 2,102,446 contigs with an N50 length of 1,782 bp, and the contigs were further assembled into 1,176,527 scaffolds with an N50 of 3,920 bp. The total length of the assembled scaffold sequences was 2.0 Gbp, and 134,652 single-locus SSRs were identified from 375,180 SSRs. Among these developed single-locus SSRs, trinucleotide motifs were the most abundant, followed by tetra-, di-, mono-, penta- and hexanucleotide motifs. The most common motif repeats for the various types of single-locus SSRs have a tendency to be A/T rich. A total of 1,790 developed in silico single-locus SSR markers were chosen and used in PCR experiments to confirm amplification patterns. Of them, 1,637 markers that produced single amplicons in twelve inbred lines were considered putative single-locus markers, and 290 (17.7 %) showed polymorphisms. A further F2 population study showed that the segregation ratios of the 97 developed SSR markers, which showed polymorphisms between the parents, were consistent with the Mendelian inheritance law for single loci (1:2:1). Finally, 89 markers were assigned to an A. hypogaea linkage map. A subset of 100 single-locus SSR markers was shown to be highly stable and universal in a collection of 96 peanut accessions. A neighbor-joining tree of this natural population showed that genotypes have obviously correlation with botanical varieties. CONCLUSIONS We have shown that the detection of single-locus SSR markers from a de novo genomic assembly of a combination of different-insert-size libraries is highly efficient. This is the first report of the development of genome-wide single-locus markers for A. hypogaea, and the markers developed in this study will be useful for gene tagging, sequence scaffold assignment, linkage map construction, diversity analysis, variety identification and association mapping in peanut.
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Affiliation(s)
- Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yang Dong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Jiaojiao Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Shunmou Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.,Databridge Technologies Corporation, Wuhan, 430062, Hubei, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.
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Fu PC, Zhang YZ, Ya HY, Gao QB. Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.). PeerJ 2016; 4:e1735. [PMID: 26925343 PMCID: PMC4768703 DOI: 10.7717/peerj.1735] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 02/03/2016] [Indexed: 01/10/2023] Open
Abstract
Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1–6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+ T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop.
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Affiliation(s)
- Peng-Cheng Fu
- College of Life Science, Luoyang Normal University , Luoyang , China
| | - Yan-Zhao Zhang
- College of Life Science, Luoyang Normal University , Luoyang , China
| | - Hui-Yuan Ya
- College of Life Science, Luoyang Normal University , Luoyang , China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining , China
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Chen W, Jiao Y, Cheng L, Huang L, Liao B, Tang M, Ren X, Zhou X, Chen Y, Jiang H. Quantitative trait locus analysis for pod- and kernel-related traits in the cultivated peanut (Arachis hypogaea L.). BMC Genet 2016; 17:25. [PMID: 26810040 PMCID: PMC4727316 DOI: 10.1186/s12863-016-0337-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 01/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cultivated peanut (Arachis hypogaea L.) is an important oil and food crop in the world. Pod- and kernel-related traits are direct factors involved in determining the yield of the peanut. However, the genetic basis underlying pod- and kernel-related traits in the peanut remained largely unknown, which hampered the improvement of peanut through marker-assisted selection. To understand the genetic basis underlying pod- and kernel-related traits in the peanut and provide more useful information for marker-assisted breeding, we conducted quantitative trait locus (QTL) analysis for pod length and width and seed length and width by use of two F2:3 populations derived from cultivar Fuchuan Dahuasheng × ICG 6375 (FI population) and cultivar Xuhua 13 × cultivar Zhonghua 6 (XZ population) in this study. RESULTS Two genetic maps containing 347 and 228 polymorphic markers were constructed for FI and XZ populations respectively. In total, 39 QTLs explaining 1.25-26.11% of the phenotypic variations were detected in two populations. For the FI population, 26 QTLs were detected between the two environments, among which twelve were not mapped before. For the XZ population, thirteen QTLs were detected, among which eight were not reported before. One QTL for pod width was repeatedly mapped between the two populations. CONCLUSION The QTL analyses for pod length and width and seed length and width were conducted in this study using two mapping populations. Novel QTLs were identified, which included two for pod length, four for pod width, five for seed length and one for seed width in the FI population, and three for pod length, three for pod width and two for seed width in the XZ population. Our results will be helpful for improving pod- and seed-related traits in peanuts through marker-assisted selection.
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Affiliation(s)
- Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Yongqing Jiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Liangqiang Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Mei Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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Leal-Bertioli SCM, Santos SP, Dantas KM, Inglis PW, Nielen S, Araujo ACG, Silva JP, Cavalcante U, Guimarães PM, Brasileiro ACM, Carrasquilla-Garcia N, Penmetsa RV, Cook D, Moretzsohn MC, Bertioli DJ. Arachis batizocoi: a study of its relationship to cultivated peanut (A. hypogaea) and its potential for introgression of wild genes into the peanut crop using induced allotetraploids. ANNALS OF BOTANY 2015; 115:237-49. [PMID: 25538110 PMCID: PMC4551086 DOI: 10.1093/aob/mcu237] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/30/2014] [Accepted: 10/17/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Arachis batizocoi is a wild relative of cultivated peanut (A. hypogaea), an allotetraploid with an AABB genome. Arachis batizocoi was once considered the ancestral donor of the peanut B genome, but cytogenetics and DNA phylogenies have indicated a new genome classification, 'K'. These observations seem inconsistent with genetic studies and breeding that have shown that A. batizocoi can behave as a B genome. METHODS The genetic behaviour, genome composition and phylogenetic position of A. batizocoi were studied using controlled hybridizations, induced tetraploidy, whole-genome in situ fluorescent hybridization (GISH) and molecular phylogenetics. KEY RESULTS Sterile diploid hybrids containing AK genomes were obtained using A. batizocoi and the A genome species A. duranensis, A. stenosperma, A. correntina or A. villosa. From these, three types of AAKK allotetraploids were obtained, each in multiple independent polyploidy events. Induced allotetraploids were vigorous and fertile, and were hybridized to A. hypogaea to produce F1 hybrids. Even with the same parental combination, fertility of these F1 hybrids varied greatly, suggesting the influence of stochastic genetic or epigenetic events. Interestingly, hybrids with A. hypogaea ssp. hypogaea were significantly more fertile than those with the subspecies fastigiata. GISH in cultivated × induced allotetraploids hybrids (harbouring AABK genomes) and a molecular phylogeny using 16 intron sequences showed that the K genome is distinct, but more closely related to the B than to the A genome. CONCLUSIONS The K genome of A. batizocoi is more related to B than to the A genome, but is distinct. As such, when incorporated in an induced allotetraploid (AAKK) it can behave as a B genome in crosses with peanut. However, the fertility of hybrids and their progeny depends upon the compatibility of the A genome interactions. The genetic distinctness of A. batizocoi makes it an important source of allelic diversity in itself, especially in crosses involving A. hypogaea ssp. hypogaea.
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Affiliation(s)
- Soraya C M Leal-Bertioli
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Silvio P Santos
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Karinne M Dantas
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Peter W Inglis
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Stephan Nielen
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ana C G Araujo
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Joseane P Silva
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Uiara Cavalcante
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Patricia M Guimarães
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ana Cristina M Brasileiro
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Noelia Carrasquilla-Garcia
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - R Varma Penmetsa
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Douglas Cook
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Márcio C Moretzsohn
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - David J Bertioli
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil, University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil, Catholic University of Brasilia, Biotechnology and Genomic Sciences, SGAN 916 Avenida W5, CEP 70.790-160, Brasilia, DF, Brazil, Plant Breeding and Genetics Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, Vienna A-1400, Austria and Department of Plant Pathology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
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Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys. Sci Rep 2015; 5:8018. [PMID: 25620112 PMCID: PMC4306134 DOI: 10.1038/srep08018] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/29/2014] [Indexed: 01/02/2023] Open
Abstract
Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species.
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Martínez-Castillo J, Camacho-Pérez L, Villanueva-Viramontes S, Andueza-Noh RH, Chacón-Sánchez MI. Genetic structure within the Mesoamerican gene pool of wild Phaseolus lunatus (Fabaceae) from Mexico as revealed by microsatellite markers: Implications for conservation and the domestication of the species. AMERICAN JOURNAL OF BOTANY 2014; 101:851-64. [PMID: 24778203 DOI: 10.3732/ajb.1300412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 04/04/2014] [Indexed: 05/19/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Understanding genetic structure in wild relatives of a crop is important for crop improvement and conservation. Recently, two gene pools (MI and MII) were reported in wild Lima bean (Phaseolus lunatus) from Mexico, a domestication center of Mesoamerican landraces. However, the evidence was based on limited genomic sampling. Here we sought to confirm the existence of these two gene pools by increased genome and population sampling.• METHODS We characterized 67 wild populations of P. lunatus from Mexico with 10 microsatellite loci and studied the genetic structure by means of AMOVA, cluster analyses, assignment tests, and a georeferenced map.• KEY RESULTS AMOVA indicated that most of the variation is found among populations (77%) rather than within populations (23%). Assignment tests were key to confirm not only the presence of the two gene pools (MI and MII) in Mexico, but also to propose the possible existence of two subgroups within MI (MIa and MIb). While MI and MII are mainly divergent geographically, MIa and MIb overlap in their distribution. Admixed individuals, which may represent cases of gene flow among gene pools, were detected.• CONCLUSIONS Our results show that the genetic structure of wild Lima bean in Mexico is more complex than previously thought and propose the presence of three gene pools (MIa, MIb, and MII), each one possessing relatively high levels of genetic diversity. We still need additional evidence, however, to confirm without doubt the split of the gene pool MI into subgroups MIa and MIb.
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Affiliation(s)
- Jaime Martínez-Castillo
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México, C. P. 97200
| | - Luciana Camacho-Pérez
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México, C. P. 97200
| | - Sara Villanueva-Viramontes
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México, C. P. 97200
| | - Rubén H Andueza-Noh
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México, C. P. 97200
| | - María I Chacón-Sánchez
- Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Edificio 500, Bogotá, D.C., Colombia
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Arrighi JF, Chaintreuil C, Cartieaux F, Cardi C, Rodier-Goud M, Brown SC, Boursot M, D'Hont A, Dreyfus B, Giraud E. Radiation of the Nod-independent Aeschynomene relies on multiple allopolyploid speciation events. THE NEW PHYTOLOGIST 2014; 201:1457-1468. [PMID: 24237245 DOI: 10.1111/nph.12594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/08/2013] [Indexed: 06/02/2023]
Abstract
• The semi-aquatic legumes belonging to the genus Aeschynomene constitute a premium system for investigating the origin and evolution of unusual symbiotic features such as stem nodulation and the presence of a Nod-independent infection process. This latter apparently arose in a single Aeschynomene lineage. But how this unique Nod-independent group then radiated is not yet known. • We have investigated the role of polyploidy in Aeschynomene speciation via a case study of the pantropical A. indica and then extended the analysis to the other Nod-independent species. For this, we combined SSR genotyping, genome characterization through flow cytometry, chromosome counting, FISH and GISH experiments, molecular phylogenies using ITS and single nuclear gene sequences, and artificial hybridizations. • These analyses demonstrate the existence of an A. indica polyploid species complex comprising A. evenia (C. Wright) (2n = 2x = 20), A. indica L. s.s. (2n = 4x = 40) and a new hexaploid form (2n = 6x = 60). This latter contains the two genomes present in the tetraploid (A. evenia and A. scabra) and another unidentified genome. Two other species, A. pratensis and A. virginica, are also shown to be of allopolyploid origin. • This work reveals multiple hybridization/polyploidization events, thus highlighting a prominent role of allopolyploidy in the radiation of the Nod-independent Aeschynomene.
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Affiliation(s)
- Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Fabienne Cartieaux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - C Cardi
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, TA-A 108/03, 34398, Montpellier Cedex 5, France
| | - M Rodier-Goud
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, TA-A 108/03, 34398, Montpellier Cedex 5, France
| | - Spencer C Brown
- CNRS, IBiSA Imagerie Gif et Imagif BioCell, Institut des Sciences du Végétal, UPR 2355, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Marc Boursot
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, TA-A 108/03, 34398, Montpellier Cedex 5, France
| | - Bernard Dreyfus
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
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Ren X, Jiang H, Yan Z, Chen Y, Zhou X, Huang L, Lei Y, Huang J, Yan L, Qi Y, Wei W, Liao B. Genetic diversity and population structure of the major peanut (Arachis hypogaea L.) cultivars grown in China by SSR markers. PLoS One 2014; 9:e88091. [PMID: 24520347 PMCID: PMC3919752 DOI: 10.1371/journal.pone.0088091] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 01/05/2014] [Indexed: 11/18/2022] Open
Abstract
One hundred and forty-six highly polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 196 peanut (Arachis Hypogaea L.) cultivars which had been extensively planted in different regions in China. These SSR markers amplified 440 polymorphic bands with an average of 2.99, and the average gene diversity index was 0.11. Eighty-six rare alleles with a frequency of less than 1% were identified in these cultivars. The largest Fst or genetic distance was found between the cultivars that adapted to the south regions and those to the north regions in China. A neighbor-joining tree of cultivars adapted to different ecological regions was constructed based on pairwise Nei's genetic distances, which showed a significant difference between cultivars from the south and the north regions. A model-based population structure analysis divided these peanut cultivars into five subpopulations (P1a, P1b, P2, P3a and P3b). P1a and P1b included most the cultivars from the southern provinces including Guangdong, Guangxi and Fujian. P2 population consisted of the cultivars from Hubei province and parts from Shandong and Henan. P3a and P3b had cultivars from the northern provinces including Shandong, Anhui, Henan, Hebei, Jiangsu and the Yangtze River region including Sichuan province. The cluster analysis, PCoA and PCA based on the marker genotypes, revealed five distinct clusters for the entire population that were related to their germplasm regions. The results indicated that there were obvious genetic variations between cultivars from the south and the north, and there were distinct genetic differentiation among individual cultivars from the south and the north. Taken together, these results provided a molecular basis for understanding genetic diversity of Chinese peanut cultivars.
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Affiliation(s)
- Xiaoping Ren
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Huifang Jiang
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- * E-mail: (HJ); (BL)
| | - Zhongyuan Yan
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yuning Chen
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Xiaojing Zhou
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Li Huang
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yong Lei
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Jiaquan Huang
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Liying Yan
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yue Qi
- National Facility for Training Personnel in Life Sciences and Biotechnology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Wenhui Wei
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Boshou Liao
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- * E-mail: (HJ); (BL)
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Custódio AR, Seijo G, Valls JFM. Characterization of Brazilian accessions of wild Arachis species of section Arachis (Fabaceae) using heterochromatin detection and fluorescence in situ hybridization (FISH). Genet Mol Biol 2013; 36:364-70. [PMID: 24130444 PMCID: PMC3795162 DOI: 10.1590/s1415-47572013000300011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 04/18/2013] [Indexed: 12/03/2022] Open
Abstract
The cytogenetic characterization of Arachis species is useful for assessing the genomes present in this genus, for establishing the relationship among their representatives and for understanding the variability in the available germplasm. In this study, we used fluorescence in situ hybridization (FISH) to examine the distribution patterns of heterochromatin and rDNA genes in 12 Brazilian accessions of five species of the taxonomic section Arachis. The heterochromatic pattern varied considerably among the species: complements with centromeric bands in all of the chromosomes (A. hoehnei) and complements completely devoid of heterochromatin (A. gregoryi, A. magna) were observed. The number of 45S rDNA loci ranged from two (A. gregoryi) to eight (A. glandulifera), while the number of 5S rDNA loci was more conserved and varied from two (in most species) to four (A. hoehnei). In some species one pair of 5S rDNA loci was observed adjacent to 45S rDNA loci. The chromosomal markers revealed polymorphism in the three species with more than one accession (A. gregoryi, A. magna and A. valida) that were tested. The previous genome assignment for each of the species studied was confirmed, except for A. hoehnei. The intraspecific variability observed here suggests that an exhaustive cytogenetic and taxonomic analysis is still needed for some Arachis species.
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Affiliation(s)
- Adriana Regina Custódio
- Programa de Pós-Graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil . ; Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
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Stalker HT, Tallury SP, Ozias-Akins P, Bertioli D, Bertioli SCL. The Value of Diploid Peanut Relatives for Breeding and Genomics. ACTA ACUST UNITED AC 2013. [DOI: 10.3146/ps13-6.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
ABSTRACT
Collection, evaluation, and introgression research has been conducted with Arachis species for more than 60 years. Eighty species in the genus have been described and additional species will be named in the future. Extremely high levels of disease and insect resistances to immunity have been observed in many species of the genus as compared to the cultivated peanut, which makes them extremely important for crop improvement. Many thousands of interspecific hybrids have been produced in the genus, but introgression has been slow because of genomic incompatibilities and sterility of hybrids. Genomics research was initiated during the late 1980s to characterize species relationships and investigate more efficient methods to introgress genes from wild species to A. hypogaea. Relatively low density genetic maps have been created from inter- and intra-specific crosses, several of which have placed disease resistance genes into limited linkage groups. Of particular interest is associating molecular markers with traits of interest to enhance breeding for disease and insect resistances. Only recently have sufficiently large numbers of markers become available to effectively conduct marker assisted breeding in peanut. Future analyses of the diploid ancestors of the cultivated peanut, A. duranensis and A. ipaensis, will allow more detailed characterization of peanut genetics and the effects of Arachis species alleles on agronomic traits. Extensive efforts are being made to create populations for genomic analyses of peanut, and introgression of genes from wild to cultivated genotypes should become more efficient in the near future.
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Affiliation(s)
- H. T. Stalker
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695
| | - S. P. Tallury
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695
| | - P. Ozias-Akins
- Department of Horticulture, The University of Georgia, Tifton, GA, 31973
| | - D. Bertioli
- Department of Gentics and Morphology, University of Brasilia, Campus Darcy Ribeiro, Brasília, DF. Brazil
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Guo B, Pandey MK, He G, Zhang X, Liao B, Culbreath A, Varshney RK, Nwosu V, Wilson RF, Stalker HT. Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut. ACTA ACUST UNITED AC 2013. [DOI: 10.3146/ps13-03.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
ABSTRACT
The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.
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Affiliation(s)
- Baozhu Guo
- USDA- Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA 31793
| | - Manish K. Pandey
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Guohao He
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36088
| | - Xinyou Zhang
- Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Boshou Liao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Albert Culbreath
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Victor Nwosu
- Plant Science Program, Global Chocolate Science & Technology, Mars Chocolate North America, Hackettstown, NJ 07840
| | - Richard F. Wilson
- Oilseeds & Bioscience Consulting, 5517 Hickory Leaf Drive, Raleigh, NC 27606
| | - H. Thomas Stalker
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695
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Moretzsohn MC, Gouvea EG, Inglis PW, Leal-Bertioli SCM, Valls JFM, Bertioli DJ. A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers. ANNALS OF BOTANY 2013; 111:113-26. [PMID: 23131301 PMCID: PMC3523650 DOI: 10.1093/aob/mcs237] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 10/02/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS The genus Arachis contains 80 described species. Section Arachis is of particular interest because it includes cultivated peanut, an allotetraploid, and closely related wild species, most of which are diploids. This study aimed to analyse the genetic relationships of multiple accessions of section Arachis species using two complementary methods. Microsatellites allowed the analysis of inter- and intraspecific variability. Intron sequences from single-copy genes allowed phylogenetic analysis including the separation of the allotetraploid genome components. METHODS Intron sequences and microsatellite markers were used to reconstruct phylogenetic relationships in section Arachis through maximum parsimony and genetic distance analyses. KEY RESULTS Although high intraspecific variability was evident, there was good support for most species. However, some problems were revealed, notably a probable polyphyletic origin for A. kuhlmannii. The validity of the genome groups was well supported. The F, K and D genomes grouped close to the A genome group. The 2n = 18 species grouped closer to the B genome group. The phylogenetic tree based on the intron data strongly indicated that A. duranensis and A. ipaënsis are the ancestors of A. hypogaea and A. monticola. Intron nucleotide substitutions allowed the ages of divergences of the main genome groups to be estimated at a relatively recent 2·3-2·9 million years ago. This age and the number of species described indicate a much higher speciation rate for section Arachis than for legumes in general. CONCLUSIONS The analyses revealed relationships between the species and genome groups and showed a generally high level of intraspecific genetic diversity. The improved knowledge of species relationships should facilitate the utilization of wild species for peanut improvement. The estimates of speciation rates in section Arachis are high, but not unprecedented. We suggest these high rates may be linked to the peculiar reproductive biology of Arachis.
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Affiliation(s)
- Márcio C Moretzsohn
- Embrapa Recursos Genéticos e Biotecnologia, C.P. 02372, CEP 70·770-917, Brasília, DF, Brazil.
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Huang L, Jiang H, Ren X, Chen Y, Xiao Y, Zhao X, Tang M, Huang J, Upadhyaya HD, Liao B. Abundant microsatellite diversity and oil content in wild Arachis species. PLoS One 2012; 7:e50002. [PMID: 23185514 PMCID: PMC3502184 DOI: 10.1371/journal.pone.0050002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 10/15/2012] [Indexed: 01/05/2023] Open
Abstract
The peanut (Arachis hypogaea) is an important oil crop. Breeding for high oil content is becoming increasingly important. Wild Arachis species have been reported to harbor genes for many valuable traits that may enable the improvement of cultivated Arachis hypogaea, such as resistance to pests and disease. However, only limited information is available on variation in oil content. In the present study, a collection of 72 wild Arachis accessions representing 19 species and 3 cultivated peanut accessions were genotyped using 136 genome-wide SSR markers and phenotyped for oil content over three growing seasons. The wild Arachis accessions showed abundant diversity across the 19 species. A. duranensis exhibited the highest diversity, with a Shannon-Weaver diversity index of 0.35. A total of 129 unique alleles were detected in the species studied. A. rigonii exhibited the largest number of unique alleles (75), indicating that this species is highly differentiated. AMOVA and genetic distance analyses confirmed the genetic differentiation between the wild Arachis species. The majority of SSR alleles were detected exclusively in the wild species and not in A. hypogaea, indicating that directional selection or the hitchhiking effect has played an important role in the domestication of the cultivated peanut. The 75 accessions were grouped into three clusters based on population structure and phylogenic analysis, consistent with their taxonomic sections, species and genome types. A. villosa and A. batizocoi were grouped with A. hypogaea, suggesting the close relationship between these two diploid wild species and the cultivated peanut. Considerable phenotypic variation in oil content was observed among different sections and species. Nine alleles were identified as associated with oil content based on association analysis, of these, three alleles were associated with higher oil content but were absent in the cultivated peanut. The results demonstrated that there is great potential to increase the oil content in A. hypogaea by using the wild Arachis germplasm.
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Affiliation(s)
- Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xinyan Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Mei Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jiaquan Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh, India
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Guo Y, Khanal S, Tang S, Bowers JE, Heesacker AF, Khalilian N, Nagy ED, Zhang D, Taylor CA, Stalker HT, Ozias-Akins P, Knapp SJ. Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut. BMC Genomics 2012; 13:608. [PMID: 23140574 PMCID: PMC3532320 DOI: 10.1186/1471-2164-13-608] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/31/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Cultivated peanut or groundnut (Arachis hypogaea L.) is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20), which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. RESULTS A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat) markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons) derived from 70,771 long-read (Sanger) and 270,957 short-read (454) sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639) and GKBSPSc 30081 (PI 468327) in the B-genome species A. batizocoi. A high degree of macrosynteny was observed when comparing the homoeologous linkage groups between A (A. duranensis) and B (A. batizocoi) genomes. Comparison of the A- and B-genome genetic linkage maps also showed a total of five inversions and one major reciprocal translocation between two pairs of chromosomes under our current mapping resolution. CONCLUSIONS Our findings will contribute to understanding tetraploid peanut genome origin and evolution and eventually promote its genetic improvement. The newly developed EST-SSR markers will enrich current molecular marker resources in peanut.
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Affiliation(s)
- Yufang Guo
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
- Department of Horticulture, The University of Georgia, Tifton, GA, 31973, USA
| | - Sameer Khanal
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Shunxue Tang
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - John E Bowers
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Adam F Heesacker
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Nelly Khalilian
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Ervin D Nagy
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Dong Zhang
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Christopher A Taylor
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - H Thomas Stalker
- Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Peggy Ozias-Akins
- Department of Horticulture, The University of Georgia, Tifton, GA, 31973, USA
| | - Steven J Knapp
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
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49
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Nagy ED, Guo Y, Tang S, Bowers JE, Okashah RA, Taylor CA, Zhang D, Khanal S, Heesacker AF, Khalilian N, Farmer AD, Carrasquilla-Garcia N, Penmetsa RV, Cook D, Stalker HT, Nielsen N, Ozias-Akins P, Knapp SJ. A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut. BMC Genomics 2012; 13:469. [PMID: 22967170 PMCID: PMC3542255 DOI: 10.1186/1471-2164-13-469] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 08/30/2012] [Indexed: 01/06/2023] Open
Abstract
Background Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea. Results More than one million expressed sequence tag (EST) sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC) and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago and Glycine revealed significant stretches of conserved gene clusters spread across the peanut genome. A higher level of colinearity was detected between A. duranensis and Glycine than with Medicago. Conclusions The first high-density, gene-based linkage map for A. duranensis was generated that can serve as a reference map for both wild and cultivated Arachis species. The markers developed here are valuable resources for the peanut, and more broadly, to the legume research community. The A-genome map will have utility for fine mapping in other peanut species and has already had application for mapping a nematode resistance gene that was introgressed into A. hypogaea from A. cardenasii.
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Affiliation(s)
- Ervin D Nagy
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia,111 Riverbend Rd, Athens, GA 30605, USA
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50
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Sujay V, Gowda MVC, Pandey MK, Bhat RS, Khedikar YP, Nadaf HL, Gautami B, Sarvamangala C, Lingaraju S, Radhakrishan T, Knapp SJ, Varshney RK. Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2012; 30:773-788. [PMID: 22924018 PMCID: PMC3410029 DOI: 10.1007/s11032-011-9661-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/17/2011] [Indexed: 05/20/2023]
Abstract
Late leaf spot (LLS) and rust have the greatest impact on yield losses worldwide in groundnut (Arachis hypogaea L.). With the objective of identifying tightly linked markers to these diseases, a total of 3,097 simple sequence repeats (SSRs) were screened on the parents of two recombinant inbred line (RIL) populations, namely TAG 24 × GPBD 4 (RIL-4) and TG 26 × GPBD 4 (RIL-5), and segregation data were obtained for 209 marker loci for each of the mapping populations. Linkage map analysis of the 209 loci resulted in the mapping of 188 and 181 loci in RIL-4 and RIL-5 respectively. Using 143 markers common to the two maps, a consensus map with 225 SSR loci and total map distance of 1,152.9 cM was developed. Comprehensive quantitative trait locus (QTL) analysis detected a total of 28 QTL for LLS and 15 QTL for rust. A major QTL for LLS, namely QTL(LLS)01 (GM1573/GM1009-pPGPseq8D09), with 10.27-62.34% phenotypic variance explained (PVE) was detected in all the six environments in the RIL-4 population. In the case of rust resistance, in addition to marker IPAHM103 identified earlier, four new markers (GM2009, GM1536, GM2301 and GM2079) showed significant association with the major QTL (82.96% PVE). Localization of 42 QTL for LLS and rust on the consensus map identified two candidate genomic regions conferring resistance to LLS and rust. One region present on linkage group AhXV contained three QTL each for LLS (up to 67.98% PVE) and rust (up to 82.96% PVE). The second candidate genomic region contained the major QTL with up to 62.34% PVE for LLS. Molecular markers associated with the major QTL for resistance to LLS and rust can be deployed in molecular breeding for developing groundnut varieties with enhanced resistance to foliar diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9661-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- V. Sujay
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580 005 India
| | - M. V. C. Gowda
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580 005 India
| | - M. K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
| | - R. S. Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, 580 005 India
| | - Y. P. Khedikar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580 005 India
| | - H. L. Nadaf
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580 005 India
| | - B. Gautami
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
| | - C. Sarvamangala
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580 005 India
| | - S. Lingaraju
- Department of Plant Pathology, University of Agricultural Sciences, Dharwad, 580 005 India
| | - T. Radhakrishan
- Directorate of Groundnut Research (DGR), Junagadh, 362 001 India
| | - S. J. Knapp
- The University of Georgia, Athens, GA 30602 USA
| | - R. K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
- CGIAR-Generation Challenge Programme (GCP), c/o CIMMYT, Mexico, DF 06600 Mexico
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