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Genetic Structure and Geographical Differentiation of Traditional Rice ( Oryza sativa L.) from Northern Vietnam. PLANTS 2021; 10:plants10102094. [PMID: 34685903 PMCID: PMC8540186 DOI: 10.3390/plants10102094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/24/2022]
Abstract
Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.
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Gan ST, Teo CJ, Manirasa S, Wong WC, Wong CK. Assessment of genetic diversity and population structure of oil palm (Elaeis guineensis Jacq.) field genebank: A step towards molecular-assisted germplasm conservation. PLoS One 2021; 16:e0255418. [PMID: 34324602 PMCID: PMC8320974 DOI: 10.1371/journal.pone.0255418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/15/2021] [Indexed: 11/19/2022] Open
Abstract
Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright's fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei's genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.
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Affiliation(s)
- Siou Ting Gan
- Biotechnology Section, Advanced Agriecological Research Sdn. Bhd. (AAR), AAR-UNMC Biotechnology Research Centre, Semenyih, Selangor, Malaysia
- * E-mail:
| | - Chin Jit Teo
- Plant Breeding Section, Advanced Agriecological Research Sdn. Bhd. (AAR), Paloh, Johor, Malaysia
| | - Shobana Manirasa
- Biotechnology Section, Advanced Agriecological Research Sdn. Bhd. (AAR), AAR-UNMC Biotechnology Research Centre, Semenyih, Selangor, Malaysia
| | - Wei Chee Wong
- Biotechnology Section, Advanced Agriecological Research Sdn. Bhd. (AAR), AAR-UNMC Biotechnology Research Centre, Semenyih, Selangor, Malaysia
| | - Choo Kien Wong
- Plant Breeding Section, Advanced Agriecological Research Sdn. Bhd. (AAR), Paloh, Johor, Malaysia
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Cortés AJ, López-Hernández F. Harnessing Crop Wild Diversity for Climate Change Adaptation. Genes (Basel) 2021; 12:783. [PMID: 34065368 PMCID: PMC8161384 DOI: 10.3390/genes12050783] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 12/20/2022] Open
Abstract
Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer concrete opportunities to increase yield and crop adaptability. However, the rate at which the threat is happening requires powering new strategies in order to meet the global food demand. In this review, we highlight major recent 'big data' developments from both empirical and theoretical genomics that may speed up the identification, conservation, and breeding of exotic and elite crop varieties with the potential to feed humans. We first emphasize the major bottlenecks to capture and utilize novel sources of variation in abiotic stress (i.e., heat and drought) tolerance. We argue that adaptation of crop wild relatives to dry environments could be informative on how plant phenotypes may react to a drier climate because natural selection has already tested more options than humans ever will. Because isolated pockets of cryptic diversity may still persist in remote semi-arid regions, we encourage new habitat-based population-guided collections for genebanks. We continue discussing how to systematically study abiotic stress tolerance in these crop collections of wild and landraces using geo-referencing and extensive environmental data. By uncovering the genes that underlie the tolerance adaptive trait, natural variation has the potential to be introgressed into elite cultivars. However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated by many low-effect genes). Therefore, we finish prospecting modern analytical approaches that will serve to overcome this issue. Concretely, genomic prediction, machine learning, and multi-trait gene editing, all offer innovative alternatives to speed up more accurate pre- and breeding efforts toward the increase in crop adaptability and yield, while matching future global food demands in the face of increased heat and drought. In order for these 'big data' approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding. The recent developments and perspectives discussed throughout this review ultimately aim to contribute to increased crop adaptability and yield in the face of heat waves and drought events.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia
| | - Felipe López-Hernández
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
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Juma I, Geleta M, Hovmalm HP, Nyomora A, Saripella GV, Carlsson AS, Fatih M, Ortiz R. Comparison of Morphological and Genetic Characteristics of Avocados Grown in Tanzania. Genes (Basel) 2021; 12:genes12010063. [PMID: 33406797 PMCID: PMC7824774 DOI: 10.3390/genes12010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/26/2020] [Accepted: 12/30/2020] [Indexed: 11/24/2022] Open
Abstract
Tanzania has been growing avocado for decades. A wide variability of the avocado germplasm has been found, and the crop is largely contributing to the earnings of the farmers, traders, and the government, but its genetic diversity is scantly investigated. With the purpose of comparing morphological and genetic characteristics of this germplasm and uncovering the correlation between them and the geographical location, 226 adult seedling avocado trees were sampled in southwestern Tanzania. Their morphological characters were recorded, and their genetic diversity was evaluated based on 10 microsatellite loci. Discriminant analysis of principal components showed that the germplasm studied consisted of four genetic clusters that had an overall average gene diversity of 0.59 and 15.9% molecular variation among them. Most of the phenotypes were common in at least two clusters. The genetic clusters were also portrayed by multivariate analysis and hierarchical clustering for the molecular data but not for the morphology data. Using the Mantel test, a weak significant correlation was found between the genetic, morphological, and geographical distances, which indicates that the genetic variation present in the material is weakly reflected by the observed phenotypic variation and that both measures of variation varied slightly with the geographical sampling locations.
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Affiliation(s)
- Ibrahim Juma
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (M.G.); (H.P.H.); (G.V.S.); (A.S.C.); (M.F.); (R.O.)
- Department of Botany, University of Dar es Salaam, P.O. Box 35060, Dar es Salaam, Tanzania;
- Correspondence: ; Tel.: +255-713-830-360
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (M.G.); (H.P.H.); (G.V.S.); (A.S.C.); (M.F.); (R.O.)
| | - Helena Persson Hovmalm
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (M.G.); (H.P.H.); (G.V.S.); (A.S.C.); (M.F.); (R.O.)
| | - Agnes Nyomora
- Department of Botany, University of Dar es Salaam, P.O. Box 35060, Dar es Salaam, Tanzania;
| | - Ganapathi Varma Saripella
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (M.G.); (H.P.H.); (G.V.S.); (A.S.C.); (M.F.); (R.O.)
| | - Anders S. Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (M.G.); (H.P.H.); (G.V.S.); (A.S.C.); (M.F.); (R.O.)
| | - Moneim Fatih
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (M.G.); (H.P.H.); (G.V.S.); (A.S.C.); (M.F.); (R.O.)
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (M.G.); (H.P.H.); (G.V.S.); (A.S.C.); (M.F.); (R.O.)
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Chen C, Chu Y, Ding C, Su X, Huang Q. Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers. BMC Genet 2020; 21:2. [PMID: 31906843 PMCID: PMC6945526 DOI: 10.1186/s12863-019-0805-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 12/19/2019] [Indexed: 11/30/2022] Open
Abstract
Background Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. Results In the present study, five loci containing null alleles were excluded and 15 pairs of SSR (simple sequence repeat) primers were used to analyze the genetic diversity and population structure of 384 individuals from six provenances (Missouri, Iowa, Washington, Louisiana, and Tennessee (USA), and Quebec in Canada) of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) per locus ranged from 0.070 to 0.905, and the average polymorphic information content (PIC) was 0.535. The provenance ‘Was’ had a relatively low genetic diversity, while ‘Que’, ‘Lou’, and ‘Ten’ provenances had high genetic diversity, with Shannon’s information index (I) above 1.0. The mean coefficient of genetic differentiation (Fst) and gene flow (Nm) were 0.129 and 1.931, respectively. Analysis of molecular variance (AMOVA) showed that 84.88% of the genetic variation originated from individuals. Based on principal coordinate analysis (PCoA) and STRUCTURE cluster analysis, individuals distributed in the Mississippi River Basin were roughly classified as one group, while those distributed in the St. Lawrence River Basin and Columbia River Basin were classified as another group. The cluster analysis based on the population level showed that provenance ‘Iow’ had a small gene flow and high degree of genetic differentiation compared with the other provenances, and was classified into one group. There was a significant relationship between genetic distance and geographical distance. Conclusions P. deltoides resources have high genetic diversity and there is a moderate level of genetic differentiation among provenances. Geographical isolation and natural conditions may be the main factors causing genetic differences among individuals. Individuals reflecting population genetic information can be selected to build a core germplasm bank. Meanwhile, the results could provide theoretical support for the scientific management and efficient utilization of P. deltoides genetic resources, and promote the development of molecular marker-assisted breeding of poplar.
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Affiliation(s)
- Cun Chen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Yanguang Chu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China. .,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu Province, China.
| | - Qinjun Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China. .,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China.
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Franco-Duran J, Crossa J, Chen J, Hearne SJ. The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections. BMC PLANT BIOLOGY 2019; 19:520. [PMID: 31775638 PMCID: PMC6882233 DOI: 10.1186/s12870-019-2142-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 11/15/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Germplasm banks maintain collections representing the most comprehensive catalogue of native genetic diversity available for crop improvement. Users of germplasm banks are interested in a fixed number of samples representing as broadly as possible the diversity present in the wider collection. A relevant question is whether it is necessary to develop completely independent germplasm samples or it is possible to select nested sets from a pre-defined core set panel not from the whole collection. We used data from 15,384, maize landraces stored in the CIMMYT germplasm bank to study the impact on 8 diversity criteria and the sample representativeness of: (1) two core selection strategies, a statistical sampling (DM), or a numerical maximization method (CH); (2) selecting samples of varying sizes; and (3) selecting samples of different sizes independently of each other or in a nested manner. RESULTS Sample sizes greater than 10% of the whole population size retained more than 75% of the polymorphic markers for all selection strategies and types of sample; lower sample sizes showed more variability (instability) among repetitions; the strongest effect of sample size was observed on the CH-independent combination. Independent and nested samples showed similar performance for all the criteria for the DM method, but there were differences between them for the CH method. The DM method achieved better approximations to the known values in the population than the CH method; 2-d multidimensional scaling plots of the collection and samples highlighted tendency of sample selection towards the extremes of diversity in the CH method, compared with sampling more representative of the overall genotypic distribution of diversity under the DM method. CONCLUSIONS The use of core subsets of size greater than or equal to 10% of the whole collection satisfied well the requirement of representativeness and diversity. Nested samples showed similar diversity and representativeness characteristics as independent samples offering a cost effective method of sample definition for germplasm banks. For most criteria assessed the DM method achieved better approximations to the known values in the whole population than the CH method, that is, it generated more statistically representative samples from collections.
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Affiliation(s)
- Jorge Franco-Duran
- Facultad de Agronomía, Universidad de la República and CIMMYT, Ruta 3, Km 363, 60000 Paysandú, Uruguay
| | - José Crossa
- CIMMYT, KM 45 Carretera Mexico-Veracruz, El Batan, 56237 Texcoco, Edo. De Mexico Mexico
| | - Jiafa Chen
- CIMMYT, KM 45 Carretera Mexico-Veracruz, El Batan, 56237 Texcoco, Edo. De Mexico Mexico
- Present Address: Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, 450002 Henan China
| | - Sarah Jane Hearne
- CIMMYT, KM 45 Carretera Mexico-Veracruz, El Batan, 56237 Texcoco, Edo. De Mexico Mexico
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