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Li G, Che J, Gong J, Duan L, Zhang Z, Jiang X, Xu P, Fan S, Gong W, Shi Y, Liu A, Li J, Li P, Pan J, Deng X, Yuan Y, Shang H. Quantitative Trait Locus Mapping for Plant Height and Branch Number in CCRI70 Recombinant Inbred Line Population of Upland Cotton (Gossypium hirsutum). PLANTS (BASEL, SWITZERLAND) 2024; 13:1509. [PMID: 38891318 PMCID: PMC11174691 DOI: 10.3390/plants13111509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/08/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Upland cotton accounts for a high percentage (95%) of the world's cotton production. Plant height (PH) and branch number (BN) are two important agronomic traits that have an impact on improving the level of cotton mechanical harvesting and cotton yield. In this research, a recombinant inbred line (RIL) population with 250 lines developed from the variety CCRI70 was used for constructing a high-density genetic map and identification of quantitative trait locus (QTL). The results showed that the map harbored 8298 single nucleotide polymorphism (SNP) markers, spanning a total distance of 4876.70 centimorgans (cMs). A total of 69 QTLs for PH (9 stable) and 63 for BN (11 stable) were identified and only one for PH was reported in previous studies. The QTLs for PH and BN harbored 495 and 446 genes, respectively. Combining the annotation information, expression patterns and previous studies of these genes, six genes could be considered as potential candidate genes for PH and BN. The results could be helpful for cotton researchers to better understand the genetic mechanism of PH and BN development, as well as provide valuable genetic resources for cotton breeders to manipulate cotton plant architecture to meet future demands.
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Affiliation(s)
- Gangling Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (G.L.); (J.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Jincan Che
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (G.L.); (J.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Juwu Gong
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Li Duan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng 475001, China
| | - Zhen Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Xiao Jiang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Peng Xu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Senmiao Fan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Wankui Gong
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Yuzhen Shi
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Aiying Liu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Junwen Li
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Pengtao Li
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Jingtao Pan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Xiaoying Deng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Youlu Yuan
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (G.L.); (J.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
| | - Haihong Shang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (G.L.); (J.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (J.G.); (L.D.); (X.J.); (P.X.); (S.F.); (W.G.); (A.L.); (J.L.); (P.L.); (J.P.); (X.D.)
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Xiahou ZY, Wambulwa MC, Xu ZC, Ye LJ, Fan PZ, Magige EA, Luo YH, Liu J. A Multiplex PCR System of Novel Microsatellite Loci for Population Genetic Application in Walnuts. PLANTS (BASEL, SWITZERLAND) 2023; 12:4101. [PMID: 38140428 PMCID: PMC10747719 DOI: 10.3390/plants12244101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
Multiplex polymerase chain reaction (PCR) of microsatellite loci allows for simultaneous amplification of two or more pairs of primers in a single PCR reaction; hence, it is cost and time effective. However, very few attempts have been reported in non-model species. In this study, by combining a genome-based de novo development and cross-species application approach, a multiplex PCR system comprising 5 PCR reactions of 33 microsatellites consisting of 26 novel genomic and 7 literature-sourced loci was tested for polymorphisms, cross-species transferability, and the ability to assess genetic diversity and population structure of three walnut species (Juglans spp.). We found that the genome-based approach is more efficient than other methods. An allelic ladder was developed for each locus to enhance consistent genotyping among laboratories. The population genetic analysis results showed that all 33 loci were successfully transferred across the three species, showing high polymorphism and a strong genetic structure. Hence, the multiplex PCR system is highly applicable in walnut species. Furthermore, we propose an efficient pipeline to characterize and genotype polymorphic microsatellite loci. The novel toolbox developed here will aid future ecology and evolution studies in walnut and could serve as a model for other plant species.
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Affiliation(s)
- Zuo-Ying Xiahou
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Moses C. Wambulwa
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui 170-90200, Kenya
| | - Zu-Chang Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Lin-Jiang Ye
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Key Laboratory of Plant Resources and Biodiversity of Jiangxi Province, Jingdezhen University, Jingdezhen 333400, China
| | - Peng-Zhen Fan
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ephie A. Magige
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
| | - Jie Liu
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Zhang C, Jia C, Liu X, Zhao H, Hou L, Li M, Cui B, Li Y. Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:903674. [PMID: 35646027 PMCID: PMC9134938 DOI: 10.3389/fpls.2022.903674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Elsholtzia stauntonii Benth. (Lamiaceae) is an economically important ornamental, medicinal and aromatic plant species. To meet the increasing market demand for E. stauntonii, it is necessary to assess genetic diversity within the species to accelerate the process of genetic improvement. Analysis of the transferability of simple sequence repeat (SSR) markers from related species or genera is a fast and economical method to evaluate diversity, and can ensure the availability of molecular markers in crops with limited genomic resources. In this study, the cross-genera transferability of 497 SSR markers selected from other members of the Lamiaceae (Salvia L., Perilla L., Mentha L., Hyptis Jacq., Leonurus L., Pogostemon Desf., Rosmarinus L., and Scutella L.) to E. stauntonii was 9.05% (45 primers). Among the 45 transferable markers, 10 markers revealed relatively high polymorphism in E. stauntonii. The genetic variation among 825 individuals from 18 natural populations of E. stauntonii in Hebei Province of China was analyzed using the 10 polymorphic SSR markers. On the basis of the SSR data, the average number of alleles (N A), expected heterozygosity (H E), and Shannon's information index (I) of the 10 primers pairs were 7.000, 0.478, and 0.688, respectively. Lower gene flow (N m = 1.252) and high genetic differentiation (F st = 0.181) were detected in the populations. Analysis of molecular variance (AMOVA) revealed that most of the variation (81.47%) was within the populations. Integrating the results of STRUCTURE, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and principal coordinate analysis, the 825 samples were grouped into two clusters associated with geographical provenance (southwestern and northeastern regions), which was consistent with the results of a Mantel test (r = 0.56, p < 0.001). Overall, SSR markers developed in related genera were effective to study the genetic structure and genetic diversity in geographical populations of E. stauntonii. The results provide a theoretical basis for conservation of genetic resources, genetic improvement, and construction of a core collection for E. stauntonii.
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Affiliation(s)
- Chenxing Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Chunfeng Jia
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Xinru Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Hanqing Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Lu Hou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Meng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Binbin Cui
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Yingyue Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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Kpatènon MJ, Salako KV, Santoni S, Zekraoui L, Latreille M, Tollon-Cordet C, Mariac C, Jaligot E, Beulé T, Adéoti K. Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin. BMC Genet 2020; 21:145. [PMID: 33272218 PMCID: PMC7713368 DOI: 10.1186/s12863-020-00955-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023] Open
Abstract
Background In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. Results During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. The global correlation between genetic and geographic distances is weak; however, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the North than to samples from other Central sites. Conclusions In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species, and suggest future applications for our molecular resources. We propose that, while prominent short-range pollen and seed dispersal in Benin explain most of our results, gene flux between the Central and Northern regions, as a result of animal and/or human migrations, might underlie the Savè discrepancy. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00955-y.
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Affiliation(s)
- Mariano Joly Kpatènon
- Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,DIADE, Univ Montpellier, IRD, Montpellier, France
| | - Kolawolé Valère Salako
- Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,Laboratoire de Biomathématiques et d'Estimations Forestières (LABEF), Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Sylvain Santoni
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Muriel Latreille
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | | | - Estelle Jaligot
- DIADE, Univ Montpellier, IRD, Montpellier, France.,CIRAD, UMR DIADE, Montpellier, France
| | - Thierry Beulé
- DIADE, Univ Montpellier, IRD, Montpellier, France.,CIRAD, UMR DIADE, Montpellier, France
| | - Kifouli Adéoti
- Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin. .,Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.
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Genome survey and development of 18 microsatellite markers to assess genetic diversity in Spondias tuberosa Arruda Câmara (Anacardiaceae) and cross-amplification in congeneric species. Mol Biol Rep 2019; 46:3511-3517. [PMID: 30915689 DOI: 10.1007/s11033-019-04768-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
Abstract
Spondias tuberosa Arr. Cam belongs to the Anacardiaceae family, an economically important family of plants whose fruits are consumed by humans and animals. The aim of this study was to develop microsatellite markers using sequences from high-throughput sequencing and a magnetic bead enrichment method. The sequences were used to obtain contigs with a minimum of 500 nucleotides using Ray software and the mining of the simple sequence repeats (SSR) was performed with Phobos software, while the primers were designed by Primer3. We developed 18 polymorphic nuclear microsatellite markers and successfully cross-amplified them to three Spondias species. In S. tuberosa, the alleles ranged from 2 to 5 for each locus and Hardy-Weinberg equilibrium was found for 16 loci, with an expected and observed heterozygosity at 0.095-0.755 and 0.1-0.75, respectively. Cross-transferability was obtained for all loci in S. bahiensis, S. dulcis and S. purpurea. We concluded that the microsatellite markers developed in this study are useful in genetic population and conservation studies, as well as for investigating the hybrid origins of Spondias species.
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Bombonato JR, Bonatelli IAS, Silva GAR, Moraes EM, Zappi DC, Taylor NP, Franco FF. Cross-genera SSR transferability in cacti revealed by a case study using Cereus (Cereeae, Cactaceae). Genet Mol Biol 2019; 42:87-94. [PMID: 30794719 PMCID: PMC6428128 DOI: 10.1590/1678-4685-gmb-2017-0293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 06/13/2018] [Indexed: 11/22/2022] Open
Abstract
The study of transferability of simple sequence repeats (SSR) among closely
related species is a well-known strategy in population genetics, however
transferability among distinct genera is less common. We tested cross-genera SSR
amplification in the family Cactaceae using a total of 20 heterologous primers
previously developed for the genera Ariocarpus, Echinocactus,
Polaskia and Pilosocereus, in four taxa of the
genus Cereus: C. fernambucensis subsp.
fernambucensis, C. fernambucensis subsp.
sericifer, C. jamacaru and C.
insularis. Nine microsatellite loci were amplified in
Cereus resulting in 35.2% of success in transferability,
which is higher than the average rate of 10% reported in the literature for
cross-genera transferability in eudicots. The genetic variation in the
transferred markers was sufficient to perform standard clustering analysis,
indicating each population as a cohesive genetic cluster. Overall, the amount of
genetic variation found indicates that the transferred SSR markers might be
useful in large-scale population studies within the genus
Cereus.
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Affiliation(s)
- Juliana Rodrigues Bombonato
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil.,Programa de Pós-graduação em Biologia Comparada, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | - Evandro Marsola Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
| | - Daniela Cristina Zappi
- Instituto Tecnológico Vale, Museu Paraense Emilio Goeldi, Coord. Botânica, Belém, PA, Brazil
| | - Nigel P Taylor
- Singapore Botanic Gardens (National Parks Board), Singapore, Republic of Singapore
| | - Fernando Faria Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
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Yang Z, Dai Z, Xie D, Chen J, Tang Q, Cheng C, Xu Y, Wang T, Su J. Development of an InDel polymorphism database for jute via comparative transcriptome analysis. Genome 2018; 61:323-327. [PMID: 29420906 DOI: 10.1139/gen-2017-0191] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Jute (Corchorus spp.) is one of the most commercially important bast fiber crops in the world. However, molecular markers and high-density genetic maps are still lacking on jute compared with other crops. Insertion/deletion (InDel) markers, one of the most abundant sources of DNA/RNA variations in plant genomes, can easily be distinguished among different accessions using high-throughput sequencing. Using three transcriptome datasets, we identified and developed InDel markers. Altogether, 51 172 InDel sites in 18 800 unigenes were discovered, and the number of InDel loci per unigene varied from 1 to 31. Further, we found 94 InDel types, varying from 1 to 159 bp; the most common were single-nucleotide (23 028), binucleotide (9824), and trinucleotide (9182). In total, 49 563 InDels in 18 445 transcripts were discovered in the comparison between TC and YG, followed by 48 934 InDels in 18 408 transcripts between NY and YG, and 3570 InDels in 2701 unigenes between NY and TC. Additionally, there were 1273 InDel sites in 1129 unigenes with polymorphisms between any two of the three accessions. Twenty-nine (58%) primer pairs represented polymorphisms when compared to the jute accessions, and PIC varied from 0.340 to 0.680, with an average of 0.491.
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Affiliation(s)
- Zemao Yang
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Zhigang Dai
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Dongwei Xie
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Jiquan Chen
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Qing Tang
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Chaohua Cheng
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Ying Xu
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Tingzhang Wang
- b Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Jianguang Su
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
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Thakur AK, Singh KH, Singh L, Nanjundan J, Khan YJ, Singh D. SSR marker variations in Brassica species provide insight into the origin and evolution of Brassica amphidiploids. Hereditas 2017; 155:6. [PMID: 28729817 PMCID: PMC5516320 DOI: 10.1186/s41065-017-0041-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/11/2017] [Indexed: 11/10/2022] Open
Abstract
Background Oilseed Brassica represents an important group of oilseed crops with a long history of evolution and cultivation. To understand the origin and evolution of Brassica amphidiploids, simple sequence repeat (SSR) markers were used to unravel genetic variations in three diploids and three amphidiploid Brassica species of U’s triangle along with Eruca sativa as an outlier. Results Of 124 Brassica-derived SSR loci assayed, 100% cross-transferability was obtained for B. juncea and three subspecies of B. rapa, while lowest cross-transferability (91.93%) was obtained for Eruca sativa. The average % age of cross-transferability across all the seven species was 98.15%. The number of alleles detected at each locus ranged from one to six with an average of 3.41 alleles per primer pair. Neighbor-Joining-based dendrogram divided all the 40 accessions into two main groups composed of B. juncea/B. nigra/B. rapa and B. carinata/B. napus/B. oleracea. C-genome of oilseed Brassica species remained relatively more conserved than A- and B-genome. A- genome present in B. juncea and B. napus seems distinct from each other and hence provides great opportunity for generating diversity through synthesizing amphidiploids from different sources of A- genome. B. juncea had least intra-specific distance indicating narrow genetic base. B. rapa appears to be more primitive species from which other two diploid species might have evolved. Conclusion The SSR marker set developed in this study will assist in DNA fingerprinting of various Brassica species cultivars, evaluating the genetic diversity in Brassica germplasm, genome mapping and construction of linkage maps, gene tagging and various other genomics-related studies in Brassica species. Further, the evolutionary relationship established among various Brassica species would assist in formulating suitable breeding strategies for widening the genetic base of Brassica amphidiploids by exploiting the genetic diversity present in diploid progenitor gene pools. Electronic supplementary material The online version of this article (doi:10.1186/s41065-017-0041-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ajay Kumar Thakur
- ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, Rajasthan 321 303 India
| | | | - Lal Singh
- ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, Rajasthan 321 303 India
| | - Joghee Nanjundan
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, The Nilgiris, Tamilnadu 643 231 India
| | - Yasin Jeshima Khan
- Division of Genomic Resources, ICAR-NBPGR, PUSA Campus, New Delhi, 110 012 India
| | - Dhiraj Singh
- ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, Rajasthan 321 303 India
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