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Gomes RS, Machado Júnior R, de Almeida CF, de Oliveira RL, Nascimento M, Nardino M, do Nascimento WF, da Silva DJH. Artificial neural networks optimize the establishment of a Brazilian germplasm core collection of winter squash (Cucurbita moschata D.). Sci Rep 2024; 14:5930. [PMID: 38467669 PMCID: PMC10928206 DOI: 10.1038/s41598-024-54818-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 02/16/2024] [Indexed: 03/13/2024] Open
Abstract
With widespread cultivation, Cucurbita moschata stands out for the carotenoid content of its fruits such as β and α-carotene, components with pronounced provitamin A function and antioxidant activity. C. moschata seed oil has a high monounsaturated fatty acid content and vitamin E, constituting a lipid source of high chemical-nutritional quality. The present study evaluates the agronomic and chemical-nutritional aspects of 91 accessions of C. moschata kept at the BGH-UFV and propose the establishment of a core collection based on multivariate approaches and on the implementation of Artificial Neural Networks (ANNs). ANNs was more efficient in identifying similarity patterns and in organizing the distance between the genotypes in the groups. The averages and variances of traits in the CC formed using a 15% sampling of accessions, were closer to those of the complete collection, particularly for accumulated degree days for flowering, the mass of seeds per fruit, and seed and oil productivity. Establishing the 15% CC, based on the broad characterization of this germplasm, will be crucial to optimize the evaluation and use of promising accessions from this collection in C. moschata breeding programs, especially for traits of high chemical-nutritional importance such as the carotenoid content and the fatty acid profile.
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Affiliation(s)
- Ronaldo Silva Gomes
- Agronomy Department, Federal University of Viçosa-UFV, PH Rolfs Avenue, Viçosa, MG, 36570-000, Brazil.
| | - Ronaldo Machado Júnior
- Agronomy Department, Federal University of Viçosa-UFV, PH Rolfs Avenue, Viçosa, MG, 36570-000, Brazil
| | | | | | - Moysés Nascimento
- Statistics Departament, Federal University of Viçosa-UFV, PH Rolfs Avenue, Viçosa, MG, 36570-000, Brazil
| | - Maicon Nardino
- Agronomy Department, Federal University of Viçosa-UFV, PH Rolfs Avenue, Viçosa, MG, 36570-000, Brazil
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Lv YW, He ZH, Xiao Y, Ouyang KX, Wang X, Hu XS. Population Structure and Genetic Diversity in the Natural Distribution of Neolamarckia cadamba in China. Genes (Basel) 2023; 14:genes14040855. [PMID: 37107613 PMCID: PMC10137889 DOI: 10.3390/genes14040855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/23/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Neolamarckia cadamba (Roxb.) Bosser is a fast-growing deciduous tree species and belongs to the Neolamarckia genus of the Rubiaceae family. This species has great economic and medical values in addition to being an important timber species for multiple industrial purposes. However, few studies have examined the genetic diversity and population structure in the natural distribution of this species in China. Here, we applied both the haploid nrDNA ITS (619 bp for aligned sequences) and mtDNA (2 polymorphic loci) markers to investigate 10 natural populations (239 individuals in total) that covered most of the distribution of the species in China. The results showed that the nucleotide diversity was π = 0.1185 ± 0.0242 for the nrDNA ITS markers and π = 0.00038 ± 0.00052 for the mtDNA markers. The haplotype diversity for the mtDNA markers was h = 0.1952 ± 0.2532. The population genetic differentiation was small (Fstn = 0.0294) for the nrDNA ITS markers but large (Fstm = 0.6765) for the mtDNA markers. There were no significant effects of isolation by distance (IBD), by elevation, and by two climatic factors (annual average precipitation and tem perature). A geographic structure among populations (Nst<Gst) was absent. Phylogenetic analysis showed a highly genetic mixture among individuals of the ten populations. Pollen flow was substantially greater than seed flow (mp/ms ≫ 1.0) and played a dominant role in shaping population genetic structure. The nrDNA ITS sequences were neutral and all local populations did not undergo demographic expansion. The overall results provide fundamental information for the genetic conservation and breeding of this miraculous tree.
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Affiliation(s)
- Yan-Wen Lv
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Zi-Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Kun-Xi Ouyang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
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Xiao Y, Zhang XX, Hu Y, Wang X, Li P, He ZH, Lv YW, Chen XY, Hu XS. Phylogeography of Toona ciliata (Meliaceae) Complex in China Inferred from Cytonuclear Markers. Genes (Basel) 2022; 14:116. [PMID: 36672857 PMCID: PMC9858616 DOI: 10.3390/genes14010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Toona ciliata is an important timber species but is recognized as an endangered species at level II in China. Its genetic conservation is of increasing concern. Provenance trials and other breeding programs were conducted to develop seed transfer rules and multiplications. Here, we investigated twenty-nine populations sampled across the natural distribution of the T. ciliata complex using mtDNA and nrDNA ITS (ribosomal internal transcribed spacer) markers. Haplotype diversity was h = 0.190 ± 0.202 and nucleotide diversity was π = 0.000383 ± 0.000536 for mtDNA marker. Nucleotide diversity for ITS sequences was 0.00837 ± 0.000783. Haplotypes exhibited phylogeographic structure in spatial distribution. The extent of genetic differentiation was significant (Fst = 0.6994 ± 0.0079 for ITS and 0.8870 ± 0.0077 for mtDNA marker). Isolation by distance (IBD) and by elevation (IBE) occurred among populations. Phylogenetic relationships from mtDNA marker indicated three genetically distinct regions, each without IBD effects. Compared with pollen flow, seed flow was strongly impeded in the western region, but extensive in the central region, and less impeded in the eastern region. Most populations did not exhibit expansion, with only a few populations showing expansion after bottleneck effects. We discussed a strategy of region-based genetic conservation and proposed to conserve multiple populations in the western and eastern regions and a few populations in the central region.
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Affiliation(s)
- Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Xin Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Ying Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Pei Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Zi-Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Yan-Wen Lv
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Yang Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
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Martínez-González C, Castellanos-Morales G, Barrera-Redondo J, Sánchez-de la Vega G, Hernández-Rosales HS, Gasca-Pineda J, Aguirre-Planter E, Moreno-Letelier A, Escalante AE, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Recent and Historical Gene Flow in Cultivars, Landraces, and a Wild Taxon of Cucurbita pepo in Mexico. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.656051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gene flow among crops and their wild relatives is an active study area in evolutionary biology and horticulture, because genetic exchange between them may impact their evolutionary trajectories and increase the genetic variation of the cultivated lineages. Mexico is a center of diversity for the genus Cucurbita that includes pumpkins, squash and gourds. Gene flow between domesticated and wild species has been reported as common in Cucurbita; but gene flow among populations of C. pepo ssp. pepo from Mexico and its wild relative has not been studied. We used 2,061 SNPs, derived from tunable genotyping by sequencing (tGBS) to estimate gene flow among 14 Mexican traditional landraces of C. pepo ssp. pepo, also including individuals from five improved cultivars of C. pepo ssp. pepo and C. pepo ssp. ovifera var. ovifera, and individuals of their wild relative C. pepo ssp. fraterna. We found moderate to high levels of genetic diversity, and low to moderate genetic differentiation. In the test of introgression between lineages, we found that all possible arrangements for ancestral and derived sites between the lineages showed similar frequencies; thus, incomplete lineage sorting, but also gene flow, might be taking place in C. pepo. Overall, our results suggest that gene flow between these subspecies and cultigens, incomplete lineage sorting and the retention of ancestral characters shaped the evolutionary trajectory of C. pepo in its area of origin and diversification. In addition, we found evidence of the use of Mexican landraces as genetic material for the improvement of commercial cultivars. The landraces of Mexico are an important source of genetic diversity for C. pepo, which has been preserved both by management practices of small farmers and by the natural gene flow that exists between the different crop fields of the region.
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Lee HY, Jang S, Yu CR, Kang BC, Chin JH, Song K. Population Structure and Genetic Diversity of Cucurbita moschata Based on Genome-Wide High-Quality SNPs. PLANTS 2020; 10:plants10010056. [PMID: 33383787 PMCID: PMC7823833 DOI: 10.3390/plants10010056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 12/30/2022]
Abstract
Pumpkins (Cucurbita moschata) are one of the most important economic crops in genus Cucurbita worldwide. They are a popular food resource and an important rootstock resource for various Cucurbitaceae. Especially, C. moschata is widely used as a rootstock for the commercial production of bloomless cucumbers in East Asia. Since the genetic diversity of the commercial rootstock varieties is narrow, there has been an increasing demand for the trait development of abiotic and biotic stress tolerance breeding. In this study, 2071 high-quality SNPs that were distributed evenly across 20 chromosomes of pumpkins were discovered through the genotyping-by-sequencing (GBS) analysis of 610 accessions of C. moschata germplasm with a global origin. Using these SNPs, various analyses of the genetic diversity and the population structure were performed. Three subgroups were clustered from the germplasm collection, which included East Asia, Africa, and America, and these areas were included the most in each subgroup. Among those groups, accessions from Africa and South Asia showed the highest genetic diversity, which was followed by the Mexico accessions. This result reflected that large gene pools that consist of various native landraces have been conserved in those of countries. Based on the genetic diversity, we finally constructed the C. moschata core collection, which included 67 representative accessions from the 610 germplasms. Five morphological traits that are important in commercial grafting and rootstock seed production, which include the cotyledon length, the cotyledon width, the hypocotyl length, the internode length, and the number of female flowers, were investigated for three years and used to confirm the validity of the core collection selection. The results are expected to provide valuable information about the genetic structure of the worldwide C. moschata germplasm and help to create new gene pools to develop genetically diverse rootstock breeding materials.
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Affiliation(s)
- Hea-Young Lee
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea; (H.-Y.L.); (C.-R.Y.); (J.-H.C.)
| | - Siyoung Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea; (S.J.); (B.-C.K.)
| | - Chea-Rin Yu
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea; (H.-Y.L.); (C.-R.Y.); (J.-H.C.)
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea; (S.J.); (B.-C.K.)
| | - Joong-Hyoun Chin
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea; (H.-Y.L.); (C.-R.Y.); (J.-H.C.)
| | - Kihwan Song
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea; (H.-Y.L.); (C.-R.Y.); (J.-H.C.)
- Correspondence: ; Tel.: +82-2-3408-2905
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Gomes RS, Machado Júnior R, de Almeida CF, Chagas RR, de Oliveira RL, Delazari FT, da Silva DJH. Brazilian germplasm of winter squash (Cucurbita moschata D.) displays vast genetic variability, allowing identification of promising genotypes for agro-morphological traits. PLoS One 2020; 15:e0230546. [PMID: 32516347 PMCID: PMC7282630 DOI: 10.1371/journal.pone.0230546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/14/2020] [Indexed: 01/10/2023] Open
Abstract
Winter squash fruits (Cucurbita moschata D.) are among the best sources of vitamin A precursors and constitute sources of bioactive components such as phenolic compounds and flavonoids. Approximately 70% of C. moschata seed oil is made up of unsaturated fatty acids, with high levels of monounsaturated fatty acids and components such as vitamin E and carotenoids, which represent a promising nutritional aspect in the production of this vegetable. C. moschata germplasm expresses high genetic variability, especially in Brazil. We assessed 91 C. moschata accessions, from different regions of Brazil, and maintained at the Federal University of Viçosa (UFV) Vegetable Germplasm Bank, to identify early-flowering accessions with high levels of carotenoids in the fruit pulp and high yields of seed and seed oil. Results showed that the accessions have high variability in the number and mass of seeds per fruit, number of accumulated degree-days for flowering, total carotenoid content, and fruit productivity, which allowed selection for considerable gains in these characteristics. Analysis of the correlation between these characteristics provided information that will assist in selection to improve this crop. Cluster analysis resulted in the formation of 16 groups, confirming the variability of the accessions. Per se analysis identified accessions BGH-6749, BGH-5639, and BGH-219 as those with the earliest flowering. Accessions BGH-5455A and BGH-5598A had the highest carotenoid content, with averages greater than 170.00 μg g-1 of fresh mass. With a productivity of 0.13 t ha-1, accessions BGH-5485A, BGH-4610A, and BGH-5472A were the most promising for seed oil production. These last two accessions corresponded to those with higher seed productivity, averaging 0.58 and 0.54 t ha-1, respectively. This study confirms the high potential of this germplasm for use in breeding for promotion of earlier flowering and increase in total content of fruit pulp carotenoids and in seed and seed oil productivity.
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Affiliation(s)
- Ronaldo Silva Gomes
- Agronomy Department, Federal University of Viçosa-UFV, Viçosa, MG, Brazil
- * E-mail:
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