The Brazilian palm fruits and hearts-of-palm of
Euterpe edulis
,
E
.
oleracea and E
.
precatoria
are an important source for agro-industrial production, due to overexploitation, conservation ...strategies are required to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three
Euterpe
species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these
Euterpe
species. The
Euterpe
chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between
E
.
edulis
/
E
.
oleracea
and
E
.
edulis
/
E
.
precatoria
when compared to
E
.
oleracea
/
E
.
precatoria
(58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between
E
.
oleracea
/
E
.
precatoria
. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (F
ST
= 0.77), especially between
E
.
edulis
and
E
.
precatoria
(F
ST
= 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these
Euterpe
palms, a differentiation between
E
.
edulis
and the other
Euterpe
species can be identified by point mutations. This study not only brings new knowledge about the evolution of
Euterpe
chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Copernicia prunifera (Miller) H. E. Moore is a palm tree native to Brazil. The products obtained from its leaf extracts are a source of income for local families and the agroindustry. Owing to the ...reduction of natural habitats and the absence of a sustainable management plan, the maintenance of the natural populations of this palm tree has been compromised. Therefore, this study aimed to evaluate the diversity and genetic structure of 14 C. prunifera populations using single nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing (GBS) to provide information that contributes to the conservation of this species. A total of 1,013 SNP markers were identified, of which 84 loci showed outlier behavior and may reflect responses to natural selection. Overall, the level of genomic diversity was compatible with the biological aspects of this species. The inbreeding coefficient (f) was negative for all populations, indicating excess heterozygotes. Most genetic variations occurred within populations (77.26%), and a positive correlation existed between genetic and geographic distances. The population structure evaluated through discriminant analysis of principal components (DAPC) revealed low genetic differentiation between populations. The results highlight the need for efforts to conserve C. prunifera as well as its distribution range to preserve its global genetic diversity and evolutionary potential.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food ...and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.
ABSTRACT The knowledge of genetic diversity in plant population is essential to the success of plant breeding programs. Thus, previous characterization of landraces is one of the first steps before ...the indication of genotypes to these plant breeding programs. This study aimed to characterize, through morphological traits, and estimate the genetic diversity in landraces of lima bean (Phaseolus lunatus L.). Genetic diversity was estimated by using multivariate methods that selected individual landraces to be indicated for farmers and consumers. According to morphological traits proposed by Biodiversity International, the genotypes UFPI-667 and UFPI- 682 showed higher dissimilarity and high potential to be used in crosses since they are genetically distant and complementary. The principal component analysis identified positive and significant phenotypic associations between variables: pod length, pod width, and grain production. According to the multivariate methods used, the landraces UFPI-666, UFPI-650, UFPI-651, UFPI-687, UFPI-658, UFPI-673, UFPI-667, and UFPI-674 are potential candidates for selection since they have relevant features for lima bean breeding, such as shorter cycles and higher grain production. This study showed that multivariate analysis can be used as an effective tool to find potential traits in lima bean and can assist the lima bean breeders in the selection of potential landraces. Accessions UFPI-667 and UFPI-682 can be indicated as genitors for breeding programs, as they are genetically distant and complementary in their characteristics.
RESUMO O desenvolvimento de programas de melhoramento genético requer o conhecimento dos níveis de diversidade presente nas populações, desse modo o objetivo desse estudo foi caracterizar com base em descritores morfológicos a diversidade genética de variedades crioulas de feijão-fava (Phaseolus lunatus L.). A diversidade genética foi estimada a partir dos métodos multivariados que selecionaram variedades crioulas atendendo tanto os agricultores como o mercado consumidor. De acordo com as características morfológicas propostas pelo Biodiversity International, os genótipos UFPI-667 e UFPI-682 são os mais divergentes e apresentam alto potencial para serem utilizados em cruzamentos por serem geneticamente distantes e complementares. A análise de componentes principais detectou associações fenotípicas positivas e significativas entre as variáveis: comprimento da vagem, largura da vagem e produção de grãos. Ao usar métodos multivariados, as variedades crioulas UFPI-666, UFPI-650, UFPI-651, UFPI-687, UFPI-658, UFPI- 673, UFPI-667 e UFPI-674 são candidatos à seleção por apresentarem ciclos mais curtos e maiores produções de grãos, características importantes para o melhoramento do feijão-fava. Este estudo mostrou que as análises multivariadas podem ser usadas como uma ferramenta eficaz para encontrar características potenciais em feijão-fava e pode auxiliar os melhoristas de feijão-fava na seleção de variedades locais superiores. Os acessos UFPI- 667 e UFPI-682 podem ser indicados como genitores em programas de melhoramento genético, pois são distantes geneticamente e complementares em suas características.
ABSTRACT Some germplasm collections have a high number of accessions, which makes it difficult to explore the genetic variability present in the germplasm bank due to the redundancy and the ...difficulty of detailed analysis of all conserved accessions. Therefore, our study aimed to analyze the genetic diversity of 153 lima bean (Phaseolus lunatus) accessions for the purpose of constructing a core collection. Eleven SSRs were used for this purpose. The 153 lima bean accessions can be represented by low redundancy using a minimum of 34 accessions, thus representing 22 % of the size of the entire germplasm bank. The core collection had a higher Shannon diversity index and expected heterozygosity (1.906 and 0.811, respectively) than those presented by the entire germplasm bank (1.605 and 0.713, respectively), indicating a higher polymorphism of the representative cultivars in relation to the entire collection. The accessions selected for the core collection may be used in future studies of genome association as well as in genetic crosses in breeding programs aimed at developing improved cultivars with high genetic diversity which can meet current and future market needs.
Molecular markers are important tools in the characterization of plant genetic diversity and can provide support for conservation strategies for endangered populations. The different molecular ...techniques involve the evaluation of many individuals; therefore, it is crucial to have fast, efficient, and inexpensive methods for DNA extraction. Given the importance of the Aroeira (Myracrodruon urundeuva Fr. All.) it is pertinent to optimize a protocol that allows the obtainment of intact and pure DNA, aiming to assist conservation strategies for this species that is threatened with extinction. Thus, this study aimed to compare five DNA extraction methods: Dellaporta et al. (1983), Doyle and Doyle (1987) modified, Ferreira and Grattapaglia (1995), Romano and Brasileiro (2015), and Khanuja et al. (1999) and optimize the most efficient protocol for M. urundeuva. The modified DNA extraction protocol proposed by Doyle and Doyle (1987), using 100 mg of leaf tissue and 6 µl of β-mercaptoethanol was the protocol that presented the sharpest bands after DNA electrophoresis and after the reactions of amplification employing Polymerase Chain Reaction (PCR). Therefore, it is suggested to use the protocol described by Doyle and Doyle (1987) modified for the extraction of DNA from young M. urundeuva leaves to carry out techniques involving molecular markers.
“Sucupira branca” is a plant found in the Brazilian Cerrado and is adapted to low fertility soils, and its fruit extract has anti-inflammatory, healing, antiulcerogenic, antimicrobial, cercaricidal, ...leishmanicidal and antioxidant activities. Furthermore, it provides protection against oxidative stress, is a natural biocontrol agent of Aedes aegypti, has very resistant wood, is a melliferous plant and has been used in reforestation programs. The development of conservation strategies is important for maintaining diversity in natural populations of “sucupira branca” since these populations are in the process of genetic erosion. Molecular biology techniques, which are important for characterizing the genetic diversity of plants to develop conservation strategies, require sufficient high-quality genomic deoxyribonucleic acid (DNA). This study aimed to compare five methods to extract DNA from “sucupira branca”. The quality and concentration of DNA were revealed by agarose gel electrophoresis, and only the protocols of Dellaporta, Wood and Hicks et al. (1983) and Khanuja et al. (1999) did not result in satisfactory quantities of DNA. When PCR (Polymerase Chain Reaction) was performed with three inter-simple sequence repeat (ISSR) primers, DNA was successfully amplified from extractions performed with the protocols proposed by Doyle and Doyle (1987), Romano and Brasileiro (1998) and Ferreira and Grattapaglia (1995), which are less expensive than commercial purification kits. These protocols resulted in DNA of sufficient quality and quantity after the amplification reactions were performed.
ABSTRACT The aim of this study was to characterize and estimate genetic divergence among twelve specimens of the Sansevieria genus from the collection of the Universidade Federal do Piauí (UFPI). A ...completely randomized experimental design was used with three replicates, and the plot consisted of four plants. In morphological characterization, qualitative and quantitative descriptors of leaves were evaluated. Genetic divergence among the specimens was determined by the Tocher clustering method and the hierarchical UPGMA. There is genetic variation among specimens evaluated, which was also expressed by the variability of colors, shapes, and sizes of the leaves. The Tocher clustering method and the hierarchical UPGMA were effective in differentiation of the specimens from multi-categorical qualitative descriptors, as the Tocher method grouped the accessions in two groups and the UPGMA in seven different groups. We highlight the accessions SSV 09 and SSV 10 as exhibiting the highest mean values in weekly leaf growth and in leaf height, important characteristics for local sale and for export.
RESUMO Este estudo teve como objetivo caracterizar e estimar a divergência genética entre doze espécimes do gênero Sansevieria da Coleção da Universidade Federal do Piauí (UFPI). Utilizou-se o delineamento experimental inteiramente ao acaso, com três repetições, sendo a parcela constituída por quatro plantas. Para caracterização morfológica foram avaliados descritores foliares de natureza qualitativa e quantitativa. A divergência genética entre os espécimes foi determinada pelos métodos de agrupamento de Tocher e o hierárquico UPGMA. Foi possível verificar que existe variação genética entre os indivíduos avaliados, em relação às cores, formatos e tamanhos das folhas. O método de agrupamento de Tocher e o método hierárquico UPGMA foram eficientes na diferenciação dos espécimes, a partir de descritores qualitativos multicategóricos, de modo que o método de Tocher reuniu os acessos em dois grupos e o UPGMA em sete grupos distintos. Destacamos os acessos SSV 09 e SSV 10 por apresentarem as maiores médias em crescimento foliar semanal e na altura da folha, características importantes para comercialização local e exportação.
RESUMO Casearia grandiflora (Salicaceae) é uma espécie típica do cerrado piauiense, o conhecimento da diversidade genética dessa espécie é de grande importância para estabelecimento de práticas e ...estratégias de conservação biológica. O presente estudo teve como objetivo caracterizar a diversidade de C. grandiflora em duas áreas de cerrado do Piauí. Foram analisados 15 descritores de natureza quantitativa, através da medição do caule, folha, fruto e semente, seguida de posterior análise multivariada (componentes principais e agrupamento). Tanto a análise de componentes principais quanto os métodos de agrupamento apresentaram semelhanças na associação das plantas, o que contribuiu para o conhecimento dos padrões de variação fenotípica e divergência da espécie, sendo que a maior variação da diversidade genética foi encontrada dentro das populações. Os resultados fornecem informações importantes, visto que na literatura descrições sobre caracterização morfológica e diversidade genética dessa espécie ainda são limitadas.
Copernicia prunifera (Miller) H. E. Moore is a palm tree native to Brazil. The products obtained from its leaf extracts are a source of income for local families and the agroindustry. Owing to the ...reduction of natural habitats and the absence of a sustainable management plan, the maintenance of the natural populations of this palm tree has been compromised. Therefore, this study aimed to evaluate the diversity and genetic structure of 14 C. prunifera populations using single nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing (GBS) to provide information that contributes to the conservation of this species. A total of 1,013 SNP markers were identified, of which 84 loci showed outlier behavior and may reflect responses to natural selection. Overall, the level of genomic diversity was compatible with the biological aspects of this species. The inbreeding coefficient (f) was negative for all populations, indicating excess heterozygotes. Most genetic variations occurred within populations (77.26%), and a positive correlation existed between genetic and geographic distances. The population structure evaluated through discriminant analysis of principal components (DAPC) revealed low genetic differentiation between populations. The results highlight the need for efforts to conserve C. prunifera as well as its distribution range to preserve its global genetic diversity and evolutionary potential.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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