|
1
|
Pan R, Zhu Q, Jia X, Li B, Li Z, Xiao Y, Luo S, Wang S, Shan N, Sun J, Zhou Q, Huang Y. Genome-Wide Development of InDel-SSRs and Association Analysis of Important Agronomic Traits of Taro ( Colocasia esculenta) in China. Curr Issues Mol Biol 2024; 46:13347-13363. [PMID: 39727924 PMCID: PMC11727045 DOI: 10.3390/cimb46120796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Revised: 11/04/2024] [Accepted: 11/19/2024] [Indexed: 12/28/2024] Open
Abstract
Taro (Colocasia esculenta (L.) Schott) is a tropical tuber crop whose underground corms are used as an important staple food. However, due to a lack of molecular markers, the genetic diversity, germplasm identification, and molecular breeding of taro are greatly limited. In this study, high-density InDel-SSR molecular markers covering the whole genome were developed based on the resequencing data of taro core germplasm. A total of 1,805,634 InDel-SSR loci were identified, and 219 highly polymorphic markers with an average polymorphism information content PIC value of 0.428 were screened. Furthermore, a genetic diversity analysis of 121 taro germplasm resources was conducted based on 219 markers, dividing the resources into three groups. In addition, an association analysis showed that, of the multiple InDel-SSR markers, g13.52 and g12.82 were significantly associated with leaf area and average cormel weight, respectively; the candidate genes CeARF17 (EVM0014444) and CeGA20ox (EVM0001890) were related to cormel expansion; and we excavated the candidate genes CeXXT2 (EVM0016820) and CeLOG1 (EVM0017064), which regulate leaf development. The InDel-SSRs and candidate genes identified in this study are expected to provide important support for genetically improving and breeding new varieties of taro.
Collapse
Affiliation(s)
- Rao Pan
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qianglong Zhu
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xinbi Jia
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bicong Li
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zihao Li
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yao Xiao
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Sha Luo
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shenglin Wang
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Nan Shan
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jingyu Sun
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qinghong Zhou
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yingjin Huang
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| |
Collapse
|
|
2
|
Oladimeji JJ, Abe A, Kumar PL, Agre PA, Ilesanmi OJ, Vetukuri RR, Bhattacharjee R. Extent and patterns of morphological and molecular genetic diversity and population structure of Nigerian Taro cultivars. BMC PLANT BIOLOGY 2024; 24:1077. [PMID: 39538118 PMCID: PMC11562719 DOI: 10.1186/s12870-024-05791-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 11/06/2024] [Indexed: 11/16/2024]
Abstract
BACKGROUND Genetic diversity is crucial for conservation efforts as well as breeding programs targeted at the development of improved varieties. Taro, a climate-resilient crop, plays a vital role in the nutritional and economic livelihoods of many households in Nigeria, but its yield is very low due to inadequate genetic improvement efforts. A diversity assessment of Nigerian taro is therefore required to create a premise for its improvement in yield, quality and disease tolerance. In this study, the genetic diversity and population structure of 490 taro cultivars comprising two main gene pools: Dasheen (215) and Eddoe (275), collected from farmers and marketers across seven states in Nigeria was assessed using 3047 Diversity Array Technology single nucleotide polymorphism (DArT-SNP) markers. A subset of 114 taro cultivars, comprising 30 Dasheens and 84 Eddoes were further phenotyped using 24 agro-morphological descriptors. RESULTS Both phenotypic and molecular characterization revealed higher genetic diversity among the Eddoes than Dasheens. Estimates of gene flow (Nm = 0.353) revealed intermixing of cultivars among the States of collection, with the highest gene flow occurring between cultivars from Anambra and Ondo states and the lowest between Anambra and Kwara states. Population structure and Ward's minimum variance hierarchical cluster based on DArT-SNPs identified four groups, one comprising Dasheen and three comprising Eddoe cultivars. Hierarchical clustering based on phenotypic traits delineated three clusters. Variation between gene pools (49%) was higher than within gene pools (32%). Variation among States of collection was high (41%), while variation among individuals within gene pools (18%) and States of collection (19%) was relatively low. Correlation between phenotypic and genotypic diversity assessments was low (r = 0.01), indicating that both approaches were necessary for assessing genetic diversity in taro. However, genotypic assessment provided better information about genetic diversity of the taro cultivars. CONCLUSION This is the first study that represented germplasm collection across the major taro growing regions of Nigeria. The findings from this study based on agro-morphological characterization and DArT-SNP genotyping are critical for genetic characterization, conservation and breeding of taro in Nigeria, mainly initiating hybridization between the two genepools after careful assessment of ploidy levels of the accessions collected in this study. This will facilitate in developing improved taro varieties with desirable traits, such as higher yield, better disease resistance, and improved nutritional quality.
Collapse
Affiliation(s)
- Joy Jesumeda Oladimeji
- Plant Breeding Program, Pan African University Life and Earth Sciences Institute (Including Health and Agriculture), Ibadan, Oyo State, 200284, Nigeria.
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan, Oyo State, 200001, Nigeria.
| | - Ayodeji Abe
- Department of Crop and Horticultural Sciences, University of Ibadan, Ibadan, Oyo State, 200284, Nigeria
| | - Pullikanti Lava Kumar
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan, Oyo State, 200001, Nigeria
| | - Paterne A Agre
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan, Oyo State, 200001, Nigeria
| | - Oluyinka Johnson Ilesanmi
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan, Oyo State, 200001, Nigeria
| | - Ramesh Raju Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Lomma, SE-23422, Sweden.
| | - Ranjana Bhattacharjee
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan, Oyo State, 200001, Nigeria.
| |
Collapse
|
|
3
|
Attikora AJP, Yao SDM, Dago DN, Silué S, De Clerck C, Kwibuka Y, Diarrassouba N, Alabi T, Achigan-Dako EG, Lassois L. Genetic diversity and population structure of superior shea trees (Vitellaria paradoxa subsp. paradoxa) using SNP markers for the establishment of a core collection in Côte d'Ivoire. BMC PLANT BIOLOGY 2024; 24:913. [PMID: 39350060 PMCID: PMC11443911 DOI: 10.1186/s12870-024-05617-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 09/23/2024] [Indexed: 10/04/2024]
Abstract
BACKGROUND The shea tree is a well-known carbon sink in Africa that requires a sustainable conservation of its gene pool. However, the genetic structure of its population is not well studied, especially in Côte d'Ivoire. In this study, 333 superior shea tree genotypes conserved in situ in Côte d'Ivoire were collected and genotyped with the aim of investigating its genetic diversity and population structure to facilitate suitable conservation and support future breeding efforts to adapt to climate change effects. RESULTS A total of 7,559 filtered high-quality single nucleotide polymorphisms (SNPs) were identified using the genotyping by sequencing technology. The gene diversity (HE) ranged between 0.1 to 0.5 with an average of 0.26, while the polymorphism information content (PIC) value ranged between 0.1 to 0.5 with an average of 0.24, indicating a moderate genetic diversity among the studied genotypes. The population structure model classified the 333 genotypes into three genetic groups (GP1, GP2, and GP3). GP1 contained shea trees that mainly originated from the Poro, Tchologo, and Hambol districts, while GP2 and GP3 contained shea trees collected from the Bagoué district. Analysis of molecular variance (AMOVA) identified 55% variance within populations and 45% variance within individuals, indicating a very low genetic differentiation (or very high gene exchange) between these three groups (FST = 0.004, gene flow Nm = 59.02). Morphologically, GP1 displayed spreading tree growth habit, oval nut shape, higher mean nut weight (10.62 g), wide leaf (limb width = 4.63 cm), and small trunk size (trunk circumference = 133.4 cm). Meanwhile, GP2 and GP3 showed similar morphological characteristics: erect and spreading tree growth habit, ovoid nut shape, lower mean nut weight (GP2: 8.89 g; GP3: 8.36 g), thin leaf (limb width = 4.45 cm), and large trunk size ( GP2: 160.5 cm, GP3: 149.1 cm). A core set of 100 superior shea trees, representing 30% of the original population size and including individuals from all four study districts, was proposed using the "maximum length sub-tree function" in DARwin v. 6.0.21. CONCLUSION These findings provide new knowledge of the genetic diversity and population structure of Ivorian shea tree genetic resources for the design of effective collection and conservation strategies for the efficient use of inbreeding.
Collapse
Affiliation(s)
- Affi Jean Paul Attikora
- Plant Genetics and Rhizosphere Processes Lab, University of Liege, Gembloux Agro Bio-Tech, Terra Research Center, Passage Des Déportés 2, Gembloux, 5030, Belgium.
| | - Saraka Didier Martial Yao
- Faculty of Biological Sciences, Department of Biochemistry-Genetics, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), Korhogo, BP 1328, Côte d'Ivoire
- African Center for Shea Research and Application (CRAK), Korhogo, Côte d'Ivoire
| | - Dougba Noel Dago
- Faculty of Biological Sciences, Department of Biochemistry-Genetics, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), Korhogo, BP 1328, Côte d'Ivoire
| | - Souleymane Silué
- Faculty of Biological Sciences, Department of Biochemistry-Genetics, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), Korhogo, BP 1328, Côte d'Ivoire
| | - Caroline De Clerck
- AgricultureIsLife, University of Liege, Gembloux Agro Bio-Tech, Passage Des Déportés 2, Gembloux, 5030, Belgium
| | - Yves Kwibuka
- Faculté Des Sciences Agronomiques, Département de Production Végétale, Université Catholique de Bukavu (UCB), Bukavu, Democratic Republic of the Congo
| | - Nafan Diarrassouba
- Faculty of Biological Sciences, Department of Biochemistry-Genetics, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), Korhogo, BP 1328, Côte d'Ivoire
- African Center for Shea Research and Application (CRAK), Korhogo, Côte d'Ivoire
| | - Taofic Alabi
- Faculty of Biological Sciences, Department of Biochemistry-Genetics, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), Korhogo, BP 1328, Côte d'Ivoire
- Functional and Evolutive Entomology, University of Liege, Gembloux Agro Bio-Tech, Passage Des Déportés 2, 5030, Gembloux, Belgium
| | - Enoch G Achigan-Dako
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526, Abomey‑Calavi, Benin
| | - Ludivine Lassois
- Plant Genetics and Rhizosphere Processes Lab, University of Liege, Gembloux Agro Bio-Tech, Terra Research Center, Passage Des Déportés 2, Gembloux, 5030, Belgium
| |
Collapse
|
|
4
|
Puglisi D, Pasquariello M, Martinelli T, Paris R, De Vita P, Pecchioni N, Esposito S, Bassolino L. Genetic diversity of a Silybum marianum (L.) Gaertn. germplasm collection revealed by DNA Diversity Array Technology (DArTseq). PLoS One 2024; 19:e0308368. [PMID: 39110685 PMCID: PMC11305583 DOI: 10.1371/journal.pone.0308368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
Silybum marianum (L.) Gaertn. is a multipurpose crop native to the Mediterranean and middle east regions and mainly known for the hepatoprotective properties of fruit-derived silymarin. Despite growing interest in milk thistle as a versatile crop with medicinal value, its potential in agroindustry is hindered by incomplete domestication and limited genomic knowledge, impeding the development of competitive breeding programs. The present study aimed to evaluate genetic diversity in a panel of S. marianum accessions (n = 31), previously characterized for morphological and phytochemical traits, using 5,178 polymorphic DArTseq SNP markers. The genetic structure investigated using both parametric and non-parametric approaches (e.g. PCA, AWclust, Admixture), revealed three distinctive groups reflecting geographical origins. Indeed, Pop1 grouped accessions from Central Europe and UK, Pop3 consisted mainly of accessions of Italian origin, and Pop2 included accessions from different geographical areas. Interestingly, Italian genotypes showed a divergent phenotypic distribution, particularly in fruit oleic and linoleic acid content, compared to the other two groups. Genetic differentiation among the three groups, investigated by computing pairwise fixation index (FST), confirmed a greater differentiation of Pop3 compared to other subpopulations, also based on other diversity indices (e.g. private alleles, heterozygosity). Finally, 22 markers were declared as putatively under natural selection, of which seven significantly affected some important phenotypic traits such as oleic, arachidonic, behenic and linoleic acid content. These findings suggest that these markers, and overall, the seven SNP markers identified within Pop3, could be exploited in specific breeding programs, potentially aimed at diversifying the use of milk thistle. Indeed, incorporating genetic material from Pop3 haplotypes carrying the selected loci into milk thistle breeding populations might be the basis for developing milk thistle lines with higher levels of oleic, arachidonic, and behenic acids, and lower levels of linoleic acid, paving new avenues for enhancing the nutritional and agronomic characteristics of milk thistle.
Collapse
Affiliation(s)
- Damiano Puglisi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina, Palermo, Italy
| | - Marianna Pasquariello
- NBFC, National Biodiversity Future Center, Piazza Marina, Palermo, Italy
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), Bologna, Italy
| | - Tommaso Martinelli
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification (CREA-DC), Firenze, Italy
| | - Roberta Paris
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), Bologna, Italy
| | - Pasquale De Vita
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Salvatore Esposito
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Laura Bassolino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), Bologna, Italy
| |
Collapse
|
|
5
|
Wang C, Lan J, Wang J, He W, Lu W, Lin Y, Luo J. Population structure and genetic diversity in Eucalyptus pellita based on SNP markers. FRONTIERS IN PLANT SCIENCE 2023; 14:1278427. [PMID: 38162312 PMCID: PMC10757378 DOI: 10.3389/fpls.2023.1278427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/25/2023] [Indexed: 01/03/2024]
Abstract
Eucalyptus pellita has the characteristics of rapid growth and high resistance. However, there is little research on molecular breeding of E. pellita, which is essential to shortening breeding life and selecting quality varieties. Therefore, a crucial step before selective breeding can be carried out to increase the wood quality of E. pellita is identifying genetic diversity and population structure using single nucleotide polymorphism (SNP) markers. In this study, the genetic diversity of 1st generation 196 E. pellita families from 23 geographically defined was assessed using 1,677,732 SNP markers identified by whole genome resequencing. SNP annotation showed that the ratio of non-synonymous to synonymous coding mutations was 0.83. Principal component analysis (PCA), phylogenetic tree, and population structure analysis permitted the families to be categorized into three groups, one of which (G2) contains most of the Indonesian (IDN) and Papua New Guinea (PNG) families. Genetic relationship analysis showed that IDN was closely related to PNG. Genetic diversity analysis showed that He, PIC, I, and H mean values were 0.2502, 0.2027, 0.3815, and 0.2680, respectively. PCA analysis classified various provenances in QLD into two categories (G1 and G3). The genetic diversity of G3 was higher than that of G2. The results of genetic differentiation (Fst) showed that PNG region was divided into two groups (PNG1 and PNG2), the Fst (0.172) between QLD and PNG2 region was higher than QLD and PNG1, and the Fst (0.024) between IDN and PNG1 is smaller than IDN and PNG2. A Mantel test revealed a positive correlation between the genetic and geographic distance of E. pellita. This study has a certain reference value for genetic identification, germplasm preservation, and breeding of E. pellita. Also, it provides a basis for subsequent association analysis to explore excellent alleles and introduction.
Collapse
Affiliation(s)
- Chubiao Wang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, China
| | - Jun Lan
- Forestry Science Research Institute, Guangxi Dongmen Forest Farm, Fusui, China
| | - Jianzhong Wang
- Forestry Science Research Institute, Guangxi Dongmen Forest Farm, Fusui, China
| | - Wenliang He
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, China
| | - Wanhong Lu
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, China
| | - Yan Lin
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, China
| | - Jianzhong Luo
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, China
| |
Collapse
|