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Kallow S, Panis B, Vu DT, Vu TD, Paofa J, Mertens A, Swennen R, Janssens SB. Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives. BMC PLANT BIOLOGY 2021; 21:415. [PMID: 34503446 PMCID: PMC8431884 DOI: 10.1186/s12870-021-03142-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/06/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Conservation of plant genetic resources, including the wild relatives of crops, plays an important and well recognised role in addressing some of the key challenges faced by humanity and the planet including ending hunger and biodiversity loss. However, the genetic diversity and representativeness of ex situ collections, especially that contained in seed collections, is often unknown. This limits meaningful assessments against conservation targets, impairs targeting of future collecting and limits their use. We assessed genetic representation of seed collections compared to source populations for three wild relatives of bananas and plantains. Focal species and sampling regions were M. acuminata subsp. banksii (Papua New Guinea), M. balbisiana (Viet Nam) and M. maclayi s.l. (Bougainville, Papua New Guinea). We sequenced 445 samples using suites of 16-20 existing and newly developed taxon-specific polymorphic microsatellite markers. Samples of each species were from five populations in a region; 15 leaf samples from different individuals and 16 seed samples from one infructescence ('bunch') were analysed for each population. RESULTS Allelic richness of seeds compared to populations was 51, 81 and 93% (M. acuminata, M. balbisiana and M. maclayi respectively). Seed samples represented all common alleles in populations but omitted some rarer alleles. The number of collections required to achieve the 70% target of the Global Strategy for Plant Conservation was species dependent, relating to mating systems. Musa acuminata populations had low heterozygosity and diversity, indicating self-fertilization; many bunches were needed (> 15) to represent regional alleles to 70%; over 90% of the alleles from a bunch are included in only two seeds. Musa maclayi was characteristically cross-fertilizing; only three bunches were needed to represent regional alleles; within a bunch, 16 seeds represent alleles. Musa balbisiana, considered cross-fertilized, had low genetic diversity; seeds of four bunches are needed to represent regional alleles; only two seeds represent alleles in a bunch. CONCLUSIONS We demonstrate empirical measurement of representation of genetic material in seeds collections in ex situ conservation towards conservation targets. Species mating systems profoundly affected genetic representation in seed collections and therefore should be a primary consideration to maximize genetic representation. Results are applicable to sampling strategies for other wild species.
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Affiliation(s)
- Simon Kallow
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium.
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium.
- Royal Botanic Gardens Kew, Millennium Seed Bank, Wakehurst, Ardingly, Sussex, RH17 6TN, UK.
| | - Bart Panis
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- Bioversity International, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Dang Toan Vu
- Plant Resources Center, Ankhanh, Hoaiduc, Hà Noi, Viet Nam
| | - Tuong Dang Vu
- Plant Resources Center, Ankhanh, Hoaiduc, Hà Noi, Viet Nam
| | - Janet Paofa
- National Agricultural Research Institute, Laloki, Port Moresby, 121, Papua New Guinea
| | - Arne Mertens
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
- Department of Biology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
| | - Rony Swennen
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- International Institute of Tropical Agriculture, Plot 15B Naguru East Road, Upper Naguru, 7878, Kampala, Uganda
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
- Department of Biology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
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Kumar M, Kim SR, Sharma PC, Pareek A. Simple and efficient way to detect small polymorphic bands in plants. GENOMICS DATA 2015; 5:218-22. [PMID: 26484259 PMCID: PMC4583843 DOI: 10.1016/j.gdata.2015.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/02/2015] [Accepted: 06/03/2015] [Indexed: 11/24/2022]
Abstract
There are many ways to detect polymorphism. In this study we use the microsatellite markers to detect the polymorphism for the salt tolerance. This method has been successfully conducted in Oryza sativa and Brassica juncea. The results are reproducible. In contrast to previous methods, our method is simple and quite accurate for detecting the polymorphic bands. In this study instead of using agarose gel and ethidium bromide staining, we used non-denaturing polyacrylamide gel and a low-cost improved method for silver staining when we compare it to 11 other methods for their ability to detect simple sequence repeat polymorphisms as small as 50 bp in denaturing polyacrylamide gels. All methods detected the same alleles and banding pattern. However, important differences in sensitivity, contrast, time consumption and background were observed.
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Affiliation(s)
- Manu Kumar
- Department of Life Science, Sogang University, Seoul 121-742, South Korea
| | - Seong Ryong Kim
- Department of Life Science, Sogang University, Seoul 121-742, South Korea
| | - Prabodh Chander Sharma
- Crop Improvement Division, Central Soil Salinity Research Institute, Karnal 132 001 (Haryana) India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Science, Jawaharlal Nehru University, New Delhi 110067, India
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Dambier D, Benyahia H, Pensabene-Bellavia G, Aka Kaçar Y, Froelicher Y, Belfalah Z, Lhou B, Handaji N, Printz B, Morillon R, Yesiloglu T, Navarro L, Ollitrault P. Somatic hybridization for citrus rootstock breeding: an effective tool to solve some important issues of the Mediterranean citrus industry. PLANT CELL REPORTS 2011; 30:883-900. [PMID: 21225429 DOI: 10.1007/s00299-010-1000-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 12/29/2010] [Accepted: 12/30/2010] [Indexed: 05/18/2023]
Abstract
The prevalence of sour orange rootstock in the southern and eastern part of the Mediterranean Basin is presently threatened by the spread of Citrus Tristeza Virus (CTV) and its main vector Toxoptera citricida, combined with abiotic constraints such as drought, salinity and alkalinity. The search for alternative CTV-resistant rootstocks that also withstand the other constraints is now considered an urgent priority for a sustainable citrus industry in the area. Complementary progenitors can be found in citrus germplasm to combine the desired traits, particularly between Poncirus and Citrus genera. The production of somatic hybrids allows cumulating all dominant traits irrespective of their heterozygosity level, and would appear to be an effective way to solve the rootstock challenge facing the Mediterranean citrus industry. This paper presents the results obtained during a regional collaborative effort between five countries, to develop new rootstocks by somatic hybridization. New embryogenic callus lines to be used for somatic hybridization have been created. Protoplast fusions have been performed at CIRAD and IVIA laboratories, focusing on intergeneric combinations. Analysis of ploidy level by flow cytometry and molecular markers confirmed the acquisition of new interesting tetraploid somatic hybrids for six combinations. Diploid cybrids with intergeneric (Citrus × Poncirus) nucleus and C. reticulata or C. aurantifolia mitochondria were also identified for four combinations. The agronomical performance of a pre-existing somatic hybrid between Poncirus trifoliata and Citrus reticulata was validated in calcareous soils in Morocco. Somatic hybridization is now integrated into the breeding programs of the five Mediterranean countries.
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Affiliation(s)
- Dominique Dambier
- UPR 75, Département BIOS, CIRAD, Av. Agropolis, TA A-75/02, 34398, Montpellier Cedex 5, France
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Grapin A, Noyer JL, Carreel F, Dambier D, Baurens FC, Lanaud C, Lagoda PJ. Diploid Musa acuminata genetic diversity assayed with sequence-tagged microsatellite sites. Electrophoresis 1998; 19:1374-80. [PMID: 9694284 DOI: 10.1002/elps.1150190829] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.
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Affiliation(s)
- A Grapin
- FLHOR/CATIE, Turrialba, Costa-Rica
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