1
|
Liu D, Ye Y, Tang R, Gong Y, Chen S, Zhang C, Mei P, Chen J, Chen L, Ma C. High-density genetic map construction and QTL mapping of a zigzag-shaped stem trait in tea plant (Camellia sinensis). BMC PLANT BIOLOGY 2024; 24:382. [PMID: 38724900 PMCID: PMC11080114 DOI: 10.1186/s12870-024-05082-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
The highly unique zigzag-shaped stem phenotype in tea plants boasts significant ornamental value and is exceptionally rare. To investigate the genetic mechanism behind this trait, we developed BC1 artificial hybrid populations. Our genetic analysis revealed the zigzag-shaped trait as a qualitative trait. Utilizing whole-genome resequencing, we constructed a high-density genetic map from the BC1 population, incorporating 5,250 SNP markers across 15 linkage groups, covering 3,328.51 cM with an average marker interval distance of 0.68 cM. A quantitative trait locus (QTL) for the zigzag-shaped trait was identified on chromosome 4, within a 61.2 to 97.2 Mb range, accounting for a phenotypic variation explained (PVE) value of 13.62%. Within this QTL, six candidate genes were pinpointed. To better understand their roles, we analyzed gene expression in various tissues and individuals with erect and zigzag-shaped stems. The results implicated CsXTH (CSS0035625) and CsCIPK14 (CSS0044366) as potential key contributors to the zigzag-shaped stem formation. These discoveries lay a robust foundation for future functional genetic mapping and tea plant genetic enhancement.
Collapse
Affiliation(s)
- Dingding Liu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Yuanyuan Ye
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Rongjin Tang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Yang Gong
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Si Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Chenyu Zhang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Piao Mei
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Jiedan Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
| | - Liang Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
| | - Chunlei Ma
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
| |
Collapse
|
2
|
Li JW, Li H, Liu ZW, Wang YX, Chen Y, Yang N, Hu ZH, Li T, Zhuang J. Molecular markers in tea plant (Camellia sinensis): Applications to evolution, genetic identification, and molecular breeding. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107704. [PMID: 37086694 DOI: 10.1016/j.plaphy.2023.107704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Tea plants have a long cultivation history in the world, and the beverage (tea) made from its leaves is well known in the world. Due to the characteristics of self-incompatibility, long-term natural and artificial hybridization, tea plants have a very complex genetic background, which make the classification of tea plants unclear. Molecular marker, one type of genetic markers, has the advantages of stable inheritance, large amount of information, and high reliability. The development of molecular marker has facilitated the understanding of complex tea germplasm resources. So far, molecular markers had played important roles in the study of the origin and evolution, the preservation and identification of tea germplasms, and the excellent cultivars breeding of tea plants. However, the information is scattered, making it difficult to understand the advance of molecular markers in tea plants. In this paper, we summarized the development process and types of molecular markers in tea plants. In addition, the application advance of these molecular markers in tea plants was reviewed. Perspectives of molecular markers in tea plants were also systematically provided and discussed. The elaboration of molecular markers in this paper should help us to renew understanding of its application in tea plants.
Collapse
Affiliation(s)
- Jing-Wen Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Wei Liu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yi Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ni Yang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Hang Hu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tong Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| |
Collapse
|
3
|
Muoki CR, Maritim TK, Oluoch WA, Kamunya SM, Bore JK. Combating Climate Change in the Kenyan Tea Industry. FRONTIERS IN PLANT SCIENCE 2020; 11:339. [PMID: 32269583 PMCID: PMC7109314 DOI: 10.3389/fpls.2020.00339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/06/2020] [Indexed: 05/23/2023]
Abstract
Climate change triggered by global warming poses a major threat to agricultural systems globally. This phenomenon is characterized by emergence of pests and diseases, extreme weather events, such as prolonged drought, high intensity rains, hailstones and frosts, which are becoming more frequent ultimately impacting negatively to agricultural production including rain-fed tea cultivation. Kenya is predominantly an agricultural based economy, with the tea sector generating about 26% of the total export earnings and about 4% gross domestic product (GDP). In the recent years, however, the country has witnessed unstable trends in tea production associated with climate driven stresses. Toward mitigation and adaptation of climate change, multiple approaches for impact assessment, intensity prediction and adaptation have been advanced in the Kenyan tea sub-sector. Further, pressure on tea breeders to release improved climate-compatible cultivars for the rapidly deteriorating environment has resulted in the adoption of a multi-targeted approach seeking to understand the complex molecular regulatory networks associated with biotic and abiotic stresses adaptation and tolerance in tea. Genetic modeling, a powerful tool that assists in breeding process, has also been adopted for selection of tea cultivars for optimal performance under varying climatic conditions. A range of physiological and biochemical responses known to counteract the effects of environmental stresses in most plants that include lowering the rates of cellular growth and net photosynthesis, stomatal closure, and the accumulation of organic solutes such as sugar alcohols, or osmolytes have been used to support breeding programs through screening of new tea cultivars suitable for changing environment. This review describes simulation models combined with high resolution climate change scenarios required to quantify the relative importance of climate change on tea production. In addition, both biodiversity and ecosystem based approaches are described as a part of an overall adaptation strategy to mitigate adverse effects of climate change on tea in Kenya and gaps highlighted for urgent investigations.
Collapse
Affiliation(s)
- Chalo Richard Muoki
- Crop Improvement and Management Programme, Kenya Agricultural and Livestock Research Organization, Tea Research Institute, Kericho, Kenya
| | - Tony Kipkoech Maritim
- Crop Improvement and Management Programme, Kenya Agricultural and Livestock Research Organization, Tea Research Institute, Kericho, Kenya
| | - Wyclife Agumba Oluoch
- Sustainable Ecosystem Management and Conservation Programme, Kenya Agricultural and Livestock Research Organization, Tea Research Institute, Kericho, Kenya
| | - Samson Machohi Kamunya
- Crop Improvement and Management Programme, Kenya Agricultural and Livestock Research Organization, Tea Research Institute, Kericho, Kenya
| | - John Kipkoech Bore
- Sustainable Ecosystem Management and Conservation Programme, Kenya Agricultural and Livestock Research Organization, Tea Research Institute, Kericho, Kenya
| |
Collapse
|
4
|
Xia EH, Tong W, Wu Q, Wei S, Zhao J, Zhang ZZ, Wei CL, Wan XC. Tea plant genomics: achievements, challenges and perspectives. HORTICULTURE RESEARCH 2020; 7:7. [PMID: 31908810 PMCID: PMC6938499 DOI: 10.1038/s41438-019-0225-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/17/2019] [Accepted: 11/03/2019] [Indexed: 05/18/2023]
Abstract
Tea is among the world's most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.
Collapse
Affiliation(s)
- En-Hua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Xiao-Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| |
Collapse
|
5
|
Unraveling the Roles of Regulatory Genes during Domestication of Cultivated Camellia: Evidence and Insights from Comparative and Evolutionary Genomics. Genes (Basel) 2018; 9:genes9100488. [PMID: 30308953 PMCID: PMC6211025 DOI: 10.3390/genes9100488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 09/29/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023] Open
Abstract
With the increasing power of DNA sequencing, the genomics-based approach is becoming a promising resolution to dissect the molecular mechanism of domestication of complex traits in trees. Genus Camellia possesses rich resources with a substantial value for producing beverage, ornaments, edible oil and more. Currently, a vast number of genetic and genomic research studies in Camellia plants have emerged and provided an unprecedented opportunity to expedite the molecular breeding program. In this paper, we summarize the recent advances of gene expression and genomic resources in Camellia species and focus on identifying genes related to key economic traits such as flower and fruit development and stress tolerances. We investigate the genetic alterations and genomic impacts under different selection programs in closely related species. We discuss future directions of integrating large-scale population and quantitative genetics and multiple omics to identify key candidates to accelerate the breeding process. We propose that future work of exploiting the genomic data can provide insights related to the targets of domestication during breeding and the evolution of natural trait adaptations in genus Camellia.
Collapse
|
6
|
Tony M, Samson K, Charles M, Paul M, Richard M, Mark W, Stomeo F, Sarah S, Martina K, Francis W. Transcriptome-based identification of water-deficit stress responsive genes in the tea plant,Camellia sinensis. ACTA ACUST UNITED AC 2016. [DOI: 10.5010/jpb.2016.43.3.302] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Maritim Tony
- Tea Breeding and Genetics Improvement, Kenya Agriculture and Livestock Research Organization-Tea Research Institute, P. O Box 820-20200, Kericho, Kenya
| | - Kamunya Samson
- Tea Breeding and Genetics Improvement, Kenya Agriculture and Livestock Research Organization-Tea Research Institute, P. O Box 820-20200, Kericho, Kenya
| | - Mwendia Charles
- Department of Biochemistry and Molecular Biology, Egerton University, P.O Box 536, Njoro-Nakuru, Kenya
| | - Mireji Paul
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St., New Haven, CT 06510, USA
| | - Muoki Richard
- Tea Breeding and Genetics Improvement, Kenya Agriculture and Livestock Research Organization-Tea Research Institute, P. O Box 820-20200, Kericho, Kenya
| | - Wamalwa Mark
- International Livestock Research Institute- Bioscience East and Central Africa, P.O Box 30709, Nairobi, Kenya
| | - Francesca Stomeo
- International Livestock Research Institute- Bioscience East and Central Africa, P.O Box 30709, Nairobi, Kenya
| | - Schaack Sarah
- International Livestock Research Institute- Bioscience East and Central Africa, P.O Box 30709, Nairobi, Kenya
| | - Kyalo Martina
- International Livestock Research Institute- Bioscience East and Central Africa, P.O Box 30709, Nairobi, Kenya
| | - Wachira Francis
- Association for Strengthening Agricultural Research in Eastern and Central Africa, P.O Box 765, Entebbe, Uganda
| |
Collapse
|
7
|
Mukhopadhyay M, Mondal TK, Chand PK. Biotechnological advances in tea (Camellia sinensis [L.] O. Kuntze): a review. PLANT CELL REPORTS 2016; 35:255-87. [PMID: 26563347 DOI: 10.1007/s00299-015-1884-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 05/28/2023]
Abstract
This article presents a comprehensive review on the success and limitations of biotechnological approaches aimed at genetic improvement of tea with a purpose to explore possibilities to address challenging areas. Tea is a woody perennial tree with a life span of more than 100 years. Conventional breeding of tea is slow and limited primarily to selection which leads to narrowing down of its genetic base. Harnessing the benefits of wild relatives has been negligible due to low cross-compatibility, genetic drag and undesirable alleles for low yield. Additionally, being a recalcitrant species, in vitro propagation of tea is constrained too. Nevertheless, maneuvering with tissue/cell culture techniques, a considerable success has been achieved in the area of micropropagation, somatic embryogenesis as well as genetic transformation. Besides, use of molecular markers, "expressomics" (transcriptomics, proteomics, metabolomics), map-based cloning towards construction of physical maps, generation of expressed sequenced tags (ESTs) have facilitated the identification of QTLs and discovery of genes associated with abiotic or biotic stress tolerance and agronomic traits. Furthermore, the complete genome (or at least gene space) sequence of tea is expected to be accessible in the near future which will strengthen combinational approaches for improvement of tea. This review presents a comprehensive account of the success and limitations of the biotechnological tools and techniques hitherto applied to tea and its wild relatives. Expectedly, this will form a basis for making further advances aimed at genetic improvement of tea in particular and of economically important woody perennials in general.
Collapse
Affiliation(s)
- Mainaak Mukhopadhyay
- Department of Botany, University of Kalyani, Kalyani, 741235, Nadia, West Bengal, India.
| | - Tapan K Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India.
| | - Pradeep K Chand
- Plant Cell and Tissue Culture Facility, Post-Graduate Department of Botany, Utkal University, Vani Vihar, Bhubaneswar, 751004, Odisha, India.
| |
Collapse
|
8
|
Large-Scale SNP Discovery and Genotyping for Constructing a High-Density Genetic Map of Tea Plant Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). PLoS One 2015; 10:e0128798. [PMID: 26035838 PMCID: PMC4452719 DOI: 10.1371/journal.pone.0128798] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/30/2015] [Indexed: 11/19/2022] Open
Abstract
Genetic maps are important tools in plant genomics and breeding. The present study reports the large-scale discovery of single nucleotide polymorphisms (SNPs) for genetic map construction in tea plant. We developed a total of 6,042 valid SNP markers using specific-locus amplified fragment sequencing (SLAF-seq), and subsequently mapped them into the previous framework map. The final map contained 6,448 molecular markers, distributing on fifteen linkage groups corresponding to the number of tea plant chromosomes. The total map length was 3,965 cM, with an average inter-locus distance of 1.0 cM. This map is the first SNP-based reference map of tea plant, as well as the most saturated one developed to date. The SNP markers and map resources generated in this study provide a wealth of genetic information that can serve as a foundation for downstream genetic analyses, such as the fine mapping of quantitative trait loci (QTL), map-based cloning, marker-assisted selection, and anchoring of scaffolds to facilitate the process of whole genome sequencing projects for tea plant.
Collapse
|
9
|
Ma JQ, Yao MZ, Ma CL, Wang XC, Jin JQ, Wang XM, Chen L. Construction of a SSR-based genetic map and identification of QTLs for catechins content in tea plant (Camellia sinensis). PLoS One 2014; 9:e93131. [PMID: 24676054 PMCID: PMC3968092 DOI: 10.1371/journal.pone.0093131] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 03/03/2014] [Indexed: 02/04/2023] Open
Abstract
Catechins are the most important bioactive compounds in tea, and have been demonstrated to possess a wide variety of pharmacological activities. To characterize quantitative trait loci (QTLs) for catechins content in the tender shoots of tea plant, we constructed a moderately saturated genetic map using 406 simple sequence repeat (SSR) markers, based on a pseudo-testcross population of 183 individuals derived from an intraspecific cross of two Camellia sinensis varieties with diverse catechins composition. The map consisted of fifteen linkage groups (LGs), corresponding to the haploid chromosome number of tea plant (2n = 2x = 30). The total map length was 1,143.5 cM, with an average locus spacing of 2.9 cM. A total of 25 QTLs associated with catechins content were identified over two measurement years. Of these, nine stable QTLs were validated across years, and clustered into four main chromosome regions on LG03, LG11, LG12 and LG15. The population variability explained by each QTL was predominantly at moderate-to-high levels and ranged from 2.4% to 71.0%, with an average of 17.7%. The total number of QTL for each trait varied from four to eight, while the total population variability explained by all QTLs for a trait ranged between 38.4% and 79.7%. This is the first report on the identification of QTL for catechins content in tea plant. The results of this study provide a foundation for further cloning and functional characterization of catechin QTLs for utilization in improvement of tea plant.
Collapse
Affiliation(s)
- Jian-Qiang Ma
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Ming-Zhe Yao
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Chun-Lei Ma
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Xin-Chao Wang
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Ji-Qiang Jin
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Xue-Min Wang
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Liang Chen
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
- * E-mail:
| |
Collapse
|
10
|
Tan LQ, Wang LY, Wei K, Zhang CC, Wu LY, Qi GN, Cheng H, Zhang Q, Cui QM, Liang JB. Floral transcriptome sequencing for SSR marker development and linkage map construction in the tea plant (Camellia sinensis). PLoS One 2013; 8:e81611. [PMID: 24303059 PMCID: PMC3841144 DOI: 10.1371/journal.pone.0081611] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/14/2013] [Indexed: 11/18/2022] Open
Abstract
Despite the worldwide consumption and high economic importance of tea, the plant (Camellia sinensis) is not well studied in molecular biology. Under the few circumstances in which the plant is studied, C. sinensis flowers, which are important for reproduction and cross-breeding, receive less emphasis than investigation of its leaves or roots. Using high-throughput Illumina RNA sequencing, we analyzed a C. sinensis floral transcriptome, and 26.9 million clean reads were assembled into 75,531 unigenes averaging 402 bp. Among them, 50,792 (67.2%) unigenes were annotated with a BLAST search against the NCBI Non-Redundant (NR) database and 10,290 (16.67%) were detected that contained one or more simple sequence repeats (SSRs). From these SSR-containing sequences, 2,439 candidate SSR markers were developed and 720 were experimentally tested, validating 431 (59.9%) novel polymorphic SSR markers for C. sinensis. Then, a consensus SSR-based linkage map was constructed that covered 1,156.9 cM with 237 SSR markers distributed in 15 linkage groups. Both transcriptome information and the genetic map of C. sinensis presented here offer a valuable foundation for molecular biology investigations such as functional gene isolation, quantitative trait loci mapping, and marker-assisted selection breeding in this important species.
Collapse
Affiliation(s)
- Li-Qiang Tan
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
- College of Horticulture, Sichuan Agricultural University, Yaan, P. R. China
| | - Li-Yuan Wang
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
- * E-mail: (HC); (LYW); (GNQ)
| | - Kang Wei
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
| | - Cheng-Cai Zhang
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
| | - Li-Yun Wu
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
| | - Gui-Nian Qi
- College of Horticulture, Sichuan Agricultural University, Yaan, P. R. China
- * E-mail: (HC); (LYW); (GNQ)
| | - Hao Cheng
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
- * E-mail: (HC); (LYW); (GNQ)
| | - Qiang Zhang
- Tea Research Institute, Enshi Academy of Agricultural Sciences, Enshi, P. R. China
| | - Qing-Mei Cui
- Tea Research Institute, Enshi Academy of Agricultural Sciences, Enshi, P. R. China
| | - Jin-Bo Liang
- Tea Research Institute, Enshi Academy of Agricultural Sciences, Enshi, P. R. China
| |
Collapse
|
11
|
Castro P, Stafne ET, Clark JR, Lewers KS. Genetic map of the primocane-fruiting and thornless traits of tetraploid blackberry. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2521-32. [PMID: 23856741 DOI: 10.1007/s00122-013-2152-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 07/01/2013] [Indexed: 05/23/2023]
Abstract
Blackberry primocane fruiting, fruiting on first-year canes, has the potential to expand blackberry production both seasonally and geographically. The incorporation of the primocane-fruiting trait into cultivars with desirable horticultural attributes is challenging due to its recessive nature and tetrasomic inheritance. Molecular marker-assisted selection has high potential to facilitate incorporation, because breeders already use morphological marker-assisted selection of seedlings without marginal cotyledonary hairs to identify progeny that will be thornless when mature. The development of a genetic linkage map with these two traits is the first step to utilizing molecular markers in breeding for thornless primocane-fruiting blackberry cultivars. A full-sib family segregating for thornlessness and primocane fruiting, from a cross between 'APF-12' and 'Arapaho', was used to construct the first genetic map of tetraploid blackberry. Segregation patterns of several dominant markers and the two phenotypic traits fit those expected uniquely with tetrasomic inheritance (e.g., 5:1, 11:1 and 35:1). Some loci showed significant double reduction frequencies, but genotypes that could have originated only from double reduction were not found. The map consists of seven linkage groups (LG) in each parent, consistent with the basic number of chromosomes (2n = 4x = 28). Naming of LG1-LG6 followed that of the recently revised system for raspberry using SSR markers in common between blackberry and raspberry, and LG7 was tentatively defined by default. The loci controlling primocane fruiting and thornlessness were not linked to each other; thornless/thorny, the S Locus, was mapped on LG4, and the primocane-/floricane-fruiting locus, named in this work the F Locus, on LG7.
Collapse
Affiliation(s)
- P Castro
- IFAPA, Centro 'Alameda del Obispo', Mejora y Biotecnologia, Avenida Menendez Pidal, s/n, 14080, Córdoba, Spain
| | | | | | | |
Collapse
|
12
|
Screening of Tea (Camellia sinensis) for Trait-Associated Molecular Markers. Appl Biochem Biotechnol 2013; 171:437-49. [DOI: 10.1007/s12010-013-0370-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 06/23/2013] [Indexed: 10/26/2022]
|
13
|
Taniguchi F, Furukawa K, Ota-Metoku S, Yamaguchi N, Ujihara T, Kono I, Fukuoka H, Tanaka J. Construction of a high-density reference linkage map of tea (Camellia sinensis). BREEDING SCIENCE 2012; 62:263-73. [PMID: 23226087 PMCID: PMC3501944 DOI: 10.1270/jsbbs.62.263] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 05/14/2012] [Indexed: 05/19/2023]
Abstract
A few linkage maps of tea have been constructed using pseudo-testcross theory based on dominant marker systems. However, dominant markers are not suitable as landmark markers across a wide range of materials. Therefore, we developed co-dominant SSR markers from genomic DNA and ESTs and constructed a reference map using these co-dominant markers as landmarks. A population of 54 F(1) clones derived from reciprocal crosses between 'Sayamakaori' and 'Kana-Ck17' was used for the linkage analysis. Maps of both parents were constructed from the F(1) population that was taken for BC(1) population. The order of most of the dominant markers in the parental maps was consistent. We constructed a core map by merging the linkage data for markers that detected polymorphisms in both parents. The core map contains 15 linkage groups, which corresponds to the basic chromosome number of tea. The total length of the core map is 1218 cM. Here, we present the reference map as a central core map sandwiched between the parental maps for each linkage group; the combined maps contain 441 SSRs, 7 CAPS, 2 STS and 674 RAPDs. This newly constructed linkage map can be used as a basic reference linkage map of tea.
Collapse
Affiliation(s)
- Fumiya Taniguchi
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87 Seto, Makurazaki, Kagoshima 898-0032, Japan
- Graduate School of Life and Environmental Science, University of Tsukuba, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazumi Furukawa
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87 Seto, Makurazaki, Kagoshima 898-0032, Japan
- Present address: Numazu National College of Technology, 3600 Ooka, Numazu, Shizuoka 410-8501, Japan
| | - Sakura Ota-Metoku
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87 Seto, Makurazaki, Kagoshima 898-0032, Japan
| | - Nobuo Yamaguchi
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87 Seto, Makurazaki, Kagoshima 898-0032, Japan
- Present address: Marine Biological Laboratory, Graduate School of Science, Hiroshima University, 2445 Mukaishima, Onomichi, Hiroshima 722-0073, Japan
| | - Tomomi Ujihara
- Kanaya Tea Research Station, NARO Institute of Vegetable and Tea Science, 2769 Kanaya, Shimada, Shizuoka 428-8501, Japan
| | - Izumi Kono
- STAFF-Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
- Present address: Laboratory of Synaptic Plasticity and Connectivity, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Fukuoka
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Junichi Tanaka
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87 Seto, Makurazaki, Kagoshima 898-0032, Japan
- Graduate School of Life and Environmental Science, University of Tsukuba, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Present address: NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Corresponding author (e-mail: )
| |
Collapse
|
14
|
Rabbi IY, Kulembeka HP, Masumba E, Marri PR, Ferguson M. An EST-derived SNP and SSR genetic linkage map of cassava (Manihot esculenta Crantz). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:329-42. [PMID: 22419105 DOI: 10.1007/s00122-012-1836-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 02/24/2012] [Indexed: 05/05/2023]
Abstract
Cassava (Manihot esculenta Crantz) is one of the most important food security crops in the tropics and increasingly being adopted for agro-industrial processing. Genetic improvement of cassava can be enhanced through marker-assisted breeding. For this, appropriate genomic tools are required to dissect the genetic architecture of economically important traits. Here, a genome-wide SNP-based genetic map of cassava anchored in SSRs is presented. An outbreeder full-sib (F1) family was genotyped on two independent SNP assay platforms: an array of 1,536 SNPs on Illumina's GoldenGate platform was used to genotype a first batch of 60 F1. Of the 1,358 successfully converted SNPs, 600 which were polymorphic in at least one of the parents and was subsequently converted to KBiosciences' KASPar assay platform for genotyping 70 additional F1. High-precision genotyping of 163 informative SSRs using capillary electrophoresis was also carried out. Linkage analysis resulted in a final linkage map of 1,837 centi-Morgans (cM) containing 568 markers (434 SNPs and 134 SSRs) distributed across 19 linkage groups. The average distance between adjacent markers was 3.4 cM. About 94.2% of the mapped SNPs and SSRs have also been localized on scaffolds of version 4.1 assembly of the cassava draft genome sequence. This more saturated genetic linkage map of cassava that combines SSR and SNP markers should find several applications in the improvement of cassava including aligning scaffolds of the cassava genome sequence, genetic analyses of important agro-morphological traits, studying the linkage disequilibrium landscape and comparative genomics.
Collapse
Affiliation(s)
- Ismail Yusuf Rabbi
- International Institute of Tropical Agriculture, PMB 5320 Oyo Road, Ibadan, Nigeria.
| | | | | | | | | |
Collapse
|
15
|
Sarwat M, Nabi G, Das S, Srivastava PS. Molecular markers in medicinal plant biotechnology: past and present. Crit Rev Biotechnol 2011; 32:74-92. [DOI: 10.3109/07388551.2011.551872] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
16
|
Sraphet S, Boonchanawiwat A, Thanyasiriwat T, Boonseng O, Tabata S, Sasamoto S, Shirasawa K, Isobe S, Lightfoot DA, Tangphatsornruang S, Triwitayakorn K. SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1161-1170. [PMID: 21222095 DOI: 10.1007/s00122-010-1520-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 12/13/2010] [Indexed: 05/30/2023]
Abstract
Simple sequence repeat (SSR) markers provide a powerful tool for genetic linkage map construction that can be applied for identification of quantitative trait loci (QTL). In this study, a total of 640 new SSR markers were developed from an enriched genomic DNA library of the cassava variety 'Huay Bong 60' and 1,500 novel expressed sequence tag-simple sequence repeat (EST-SSR) loci were developed from the Genbank database. To construct a genetic linkage map of cassava, a 100 F(1) line mapping population was developed from the cross Huay Bong 60 by 'Hanatee'. Polymorphism screening between the parental lines revealed that 199 SSRs and 168 EST-SSRs were identified as novel polymorphic markers. Combining with previously developed SSRs, we report a linkage map consisted of 510 markers encompassing 1,420.3 cM, distributed on 23 linkage groups with a mean distance between markers of 4.54 cM. Comparison analysis of the SSR order on the cassava linkage map and the cassava genome sequences allowed us to locate 284 scaffolds on the genetic map. Although the number of linkage groups reported here revealed that this F(1) genetic linkage map is not yet a saturated map, it encompassed around 88% of the cassava genome indicating that the map was almost complete. Therefore, sufficient markers now exist to encompass most of the genomes and efficiently map traits in cassava.
Collapse
Affiliation(s)
- Supajit Sraphet
- Institute of Molecular Biosciences, Mahidol University, Nakhonpathom, Thailand
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Lin J, Kudrna D, Wing RA. Construction, characterization, and preliminary BAC-end sequence analysis of a bacterial artificial chromosome library of the tea plant (Camellia sinensis). J Biomed Biotechnol 2010; 2011:476723. [PMID: 21234344 PMCID: PMC3017946 DOI: 10.1155/2011/476723] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/28/2010] [Indexed: 12/17/2022] Open
Abstract
We describe the construction and characterization of a publicly available BAC library for the tea plant, Camellia sinensis. Using modified methods, the library was constructed with the aim of developing public molecular resources to advance tea plant genomics research. The library consists of a total of 401,280 clones with an average insert size of 135 kb, providing an approximate coverage of 13.5 haploid genome equivalents. No empty vector clones were observed in a random sampling of 576 BAC clones. Further analysis of 182 BAC-end sequences from randomly selected clones revealed a GC content of 40.35% and low chloroplast and mitochondrial contamination. Repetitive sequence analyses indicated that LTR retrotransposons were the most predominant sequence class (86.93%-87.24%), followed by DNA retrotransposons (11.16%-11.69%). Additionally, we found 25 simple sequence repeats (SSRs) that could potentially be used as genetic markers.
Collapse
Affiliation(s)
- Jinke Lin
- School of Plant Sciences, Arizona Genomics Institute, The University of Arizona, Tucson AZ 85721, USA
- Department of Tea Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Dave Kudrna
- School of Plant Sciences, Arizona Genomics Institute, The University of Arizona, Tucson AZ 85721, USA
| | - Rod A. Wing
- School of Plant Sciences, Arizona Genomics Institute, The University of Arizona, Tucson AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson AZ 85721, USA
| |
Collapse
|
18
|
|
19
|
|
20
|
Wu SB, Collins G, Sedgley M. A molecular linkage map of olive (Olea europaea L) based on RAPD, microsatellite, and SCAR markers. Genome 2004; 47:26-35. [PMID: 15060599 DOI: 10.1139/g03-091] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An integrated molecular linkage map of olive (Olea europaea L.) was constructed based on randomly amplified polymorphic DNA (RAPD), sequence characterized amplified region (SCAR), and microsatellite markers using the pseudo-testcross strategy. A mapping population of 104 individuals was generated from an F1 full-sib family of a cross between 'Frantoio' and 'Kalamata'. The hybridity of the mapping population was confirmed by genetic similarity and nonmetric multidimensional scaling. Twenty-three linkage groups were mapped for 'Kalamata', covering 759 cM of the genome with 89 loci and an average distance between loci of 11.5 cM. Twenty-seven linkage groups were mapped for 'Frantoio', covering 798 cM of the genome with 92 loci and an average distance between loci of 12.3 cM. For the integrated map, 15 linkage groups covered 879 cM of the genome with 101 loci and an average distance between loci of 10.2 cM. The size of the genomic DNA was estimated to be around 3000 cM. A sequence characterized amplified region marker linked to olive peacock disease resistance was mapped to linkage group 2 of the integrated map. These maps will be the starting point for studies on the structure, evolution, and function of the olive genome. When the mapping progeny pass through their juvenile phase and assume their adult characters, mapping morphological markers and identification of quantitative trait loci for adaptive traits will be the primary targets.
Collapse
Affiliation(s)
- Shu-Biao Wu
- Department of Horticulture, University of Adelaide, South Australia, Australia
| | | | | |
Collapse
|
21
|
Julier B, Flajoulot S, Barre P, Cardinet G, Santoni S, Huguet T, Huyghe C. Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers. BMC PLANT BIOLOGY 2003; 3:9. [PMID: 14683527 PMCID: PMC324403 DOI: 10.1186/1471-2229-3-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Accepted: 12/19/2003] [Indexed: 05/18/2023]
Abstract
BACKGROUND Alfalfa (Medicago sativa) is a major forage crop. The genetic progress is slow in this legume species because of its autotetraploidy and allogamy. The genetic structure of this species makes the construction of genetic maps difficult. To reach this objective, and to be able to detect QTLs in segregating populations, we used the available codominant microsatellite markers (SSRs), most of them identified in the model legume Medicago truncatula from EST database. A genetic map was constructed with AFLP and SSR markers using specific mapping procedures for autotetraploids. The tetrasomic inheritance was analysed in an alfalfa mapping population. RESULTS We have demonstrated that 80% of primer pairs defined on each side of SSR motifs in M. truncatula EST database amplify with the alfalfa DNA. Using a F1 mapping population of 168 individuals produced from the cross of 2 heterozygous parental plants from Magali and Mercedes cultivars, we obtained 599 AFLP markers and 107 SSR loci. All but 3 SSR loci showed a clear tetrasomic inheritance. For most of the SSR loci, the double-reduction was not significant. For the other loci no specific genotypes were produced, so the significant double-reduction could arise from segregation distortion. For each parent, the genetic map contained 8 groups of four homologous chromosomes. The lengths of the maps were 2649 and 3045 cM, with an average distance of 7.6 and 9.0 cM between markers, for Magali and Mercedes parents, respectively. Using only the SSR markers, we built a composite map covering 709 cM. CONCLUSIONS Compared to diploid alfalfa genetic maps, our maps cover about 88-100% of the genome and are close to saturation. The inheritance of the codominant markers (SSR) and the pattern of linkage repulsions between markers within each homology group are consistent with the hypothesis of a tetrasomic meiosis in alfalfa. Except for 2 out of 107 SSR markers, we found a similar order of markers on the chromosomes between the tetraploid alfalfa and M. truncatula genomes indicating a high level of colinearity between these two species. These maps will be a valuable tool for alfalfa breeding and are being used to locate QTLs.
Collapse
Affiliation(s)
- Bernadette Julier
- INRA, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France
| | | | - Philippe Barre
- INRA, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France
| | - Gaëlle Cardinet
- Laboratoire des Interactions Plantes-Microorganismes, UMR CNRS-INRA 2594/441, BP27, 31326 Castanet Tolosan cedex, France
| | - Sylvain Santoni
- INRA, Station de Génétique et d'Amélioration des Plantes, Domaine de Melgueil, 34130 Mauguio, France
| | - Thierry Huguet
- Laboratoire des Interactions Plantes-Microorganismes, UMR CNRS-INRA 2594/441, BP27, 31326 Castanet Tolosan cedex, France
| | - Christian Huyghe
- INRA, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France
| |
Collapse
|
22
|
Kaundun SS, Matsumoto S. Heterologous nuclear and chloroplast microsatellite amplification and variation in tea, Camellia sinensis. Genome 2002; 45:1041-8. [PMID: 12502248 DOI: 10.1139/g02-070] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The advantage of the cross transferability of heterologous chloroplast and nuclear microsatellite primers was taken to detect polymorphism among 24 tea (Camellia sinensis (L.) O. Kuntze) genotypes, including both the assamica and the sinensis varieties. Primer information was obtained from the closely related Camellia japonica species for four nuclear microsatellites, and from Nicotiana tabaccum for seven universal chloroplast microsatellites. All of the nuclear microsatellite loci tested generated an expected DNA fragment in tea, revealing between three and five alleles per locus. Four out of the seven chloroplast microsatellites primers amplified positively, and of these only one was polymorphic with three alleles, which is in agreement with the conserved nature of chloroplast microsatellites at the intraspecific level. A factorial correspondence analysis carried out on all genotypes and nuclear microsatellite alleles separated the assamica and sinensis genotypes into two groups, thus demonstrating the value of these markers in establishing the genetic relationship between tea varieties. Genetic diversity measured with nuclear microsatellites was higher than that measured with other types of molecular markers, offering prospects for their use in fingerprinting, mapping, and population genetic studies, whereas polymorphisms detected at a cpSSR locus will allow the determination of plastid inheritance in the species.
Collapse
Affiliation(s)
- Shiv Shankhar Kaundun
- National Institute of Vegetable and Tea Science, 2769 Kanaya, Kanaya-cho, 428-8501 Shizuoka, Japan.
| | | |
Collapse
|
23
|
Knox MR, Ellis THN. Excess heterozygosity contributes to genetic map expansion in pea recombinant inbred populations. Genetics 2002; 162:861-73. [PMID: 12399396 PMCID: PMC1462271 DOI: 10.1093/genetics/162.2.861] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several plant genetic maps presented in the literature are longer than expected from cytogenetic data. Here we compare F(2) and RI maps derived from a cross between the same two parental lines and show that excess heterozygosity contributes to map inflation. These maps have been constructed using a common set of dominant markers. Although not generally regarded as informative for F(2) mapping, these allowed rapid map construction, and the resulting data analysis has provided information not otherwise obvious when examining a population from only one generation. Segregation distortion, a common feature of most populations and marker systems, found in the F(2) but not the RI, has identified excess heterozygosity. A few markers with a deficiency of heterozygotes were found to map to linkage group V (chromosome 3), which is known to form rod bivalents in this cross. Although the final map length was longer for the F(2) population, the mapped order of markers was generally the same in the F(2) and RI maps. The data presented in this analysis reconcile much of the inconsistency between map length estimates from chiasma counts and genetic data.
Collapse
Affiliation(s)
- M R Knox
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, United Kingdom.
| | | |
Collapse
|
24
|
Chiappero MB, Gardenal CN. Inheritance of random amplified polymorphic DNA (RAPD-PCR) markers and their use in population genetic studies of Calomys musculinus (Rodentia, Muridae), the reservoir of Argentine hemorrhagic fever. Hereditas 2002; 135:85-93. [PMID: 12035619 DOI: 10.1111/j.1601-5223.2001.t01-1-00085.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In order to assess the reliability of RAPD markers in the estimation of the genetic structure of natural populations of the murid rodent Calomys musculinus (reservoir of Junin virus, ethiological agent of Argentine Hemorrhagic Fever), we have analyzed the heritability of RAPD bands in 10 parents and their offspring (33 individuals). Fourteen out of a total of 119 bands obtained were absent in the parental patterns, but consistently amplified in offspring from some families. These bands can be eliminated from analyses. Overall degree of band sharing between individuals, including non-parental bands, correctly grouped members of a family in the same cluster in a UPGMA tree, with a high bootstrap percentage. Results support the usefulness of RAPDs as hereditable markers. One hundred polymorphic RAPD loci were identified in three natural populations of C. musculinus. Mean expected heterozygosity in three natural populations ranged from 0.206 to 0.220. Allele frequency based and phenotype based measures of genetic differentiation among natural populations of C. musculinus gave similar results (Weir and Cockerham's theta = 0.133; Excoffier et al.'s phi = 0.127). These values were considerably higher than those found previously using allozymes as genetic markers, and are compatible with moderate to low levels of gene flow among populations.
Collapse
Affiliation(s)
- M B Chiappero
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | | |
Collapse
|