Edson Perito Amorim

Genetic diversity and population structure of Musa accessions in ex situ conservation

BackgroundBanana cultivars are mostly derived from hybridization between wild diploid subspecies of Musa acuminata (A genome) and M. balbisiana (B genome), and they exhibit various levels of ploidy and genomic constitution. The Embrapa ex situ Musa collection contains over 220 accessions, of which only a few have been genetically characterized. Knowledge regarding the genetic relationships and diversity between modern cultivars and wild relatives would assist in conservation and breeding strategies. Our objectives were to determine the genomic constitution based on Internal Transcribed Spacer (ITS) regions polymorphism and the ploidy of all accessions by flow cytometry and to investigate the population structure of the collection using Simple Sequence Repeat (SSR) loci as co-dominant markers based on Structure software, not previously performed in Musa.ResultsFrom the 221 accessions analyzed by flow cytometry, the correct ploidy was confirmed or established for 212 (95.9%), whereas digestion of the ITS region confirmed the genomic constitution of 209 (94.6%). Neighbor-joining clustering analysis derived from SSR binary data allowed the detection of two major groups, essentially distinguished by the presence or absence of the B genome, while subgroups were formed according to the genomic composition and commercial classification. The co-dominant nature of SSR was explored to analyze the structure of the population based on a Bayesian approach, detecting 21 subpopulations. Most of the subpopulations were in agreement with the clustering analysis.ConclusionsThe data generated by flow cytometry, ITS and SSR supported the hypothesis about the occurrence of homeologue recombination between A and B genomes, leading to discrepancies in the number of sets or portions from each parental genome. These phenomenons have been largely disregarded in the evolution of banana, as the “single-step domestication” hypothesis had long predominated. These findings will have an impact in future breeding approaches. Structure analysis enabled the efficient detection of ancestry of recently developed tetraploid hybrids by breeding programs, and for some triploids. However, for the main commercial subgroups, Structure appeared to be less efficient to detect the ancestry in diploid groups, possibly due to sampling restrictions. The possibility of inferring the membership among accessions to correct the effects of genetic structure opens possibilities for its use in marker-assisted selection by association mapping.

Correlações e análise de trilha em girassol

Possible correlations among grain yield and thirteen agronomic characteristics were investigated in fourteen sunflower germplasm in a field experiment in Campinas, Brazil. In order to better understand the interrelationships among the studied variables path coefficient analysis was used for partitioning correlation in direct and indirect effects. Significant positive correlations were observed between grain yield and head diameter (r=0.63), and weight of 1000 grains (r=0.55). Head diameter, percentage of normal grains and weight of 1000 grains can be easily measured and showed positive direct effects on grain yield which led them suitable for indirect selection.

Genetic diversity of carotenoid-rich bananas evaluated by Diversity Arrays Technology (DArT)

The aim of this work was to evaluate the carotenoid content and genetic variability of banana accessions from the Musa germplasm collection held at Embrapa Cassava and Tropical Fruits, Brazil. Forty-two samples were analyzed, including 21 diploids, 19 triploids and two tetraploids. The carotenoid content was analyzed spectrophotometrically and genetic variability was estimated using 653 DArT markers. The average carotenoid content was 4.73 μg.g -1 , and ranged from 1.06 μg.g -1 for the triploid Nanica (Cavendish group) to 19.24 μg.g -1 for the triploid Saney. The diploids Modok Gier and NBA-14 and the triploid Saney had a carotenoid content that was, respectively, 7-fold, 6-fold and 9-fold greater than that of cultivars from the Cavendish group (2.19 μg.g -1). The mean similarity among the 42 accessions was 0.63 (range: 0.24 to 1.00). DArT analysis revealed extensive genetic variability in accessions from the Embrapa Musa germplasm bank.

Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development.

BackgroundAlthough banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in this genus. 454 GS-FLX Titanium technology was employed to determine the sequence of gene transcripts in genotypes of Musa acuminata ssp. burmannicoides Calcutta 4 and M. acuminata subgroup Cavendish cv. Grande Naine, contrasting in resistance to the fungal pathogen Mycosphaerella musicola, causal organism of Sigatoka leaf spot disease. To enrich for transcripts under biotic stress responses, full length-enriched cDNA libraries were prepared from whole plant leaf materials, both uninfected and artificially challenged with pathogen conidiospores.ResultsThe study generated 846,762 high quality sequence reads, with an average length of 334 bp and totalling 283 Mbp. De novo assembly generated 36,384 and 35,269 unigene sequences for M. acuminata Calcutta 4 and Cavendish Grande Naine, respectively. A total of 64.4% of the unigenes were annotated through Basic Local Alignment Search Tool (BLAST) similarity analyses against public databases.Assembled sequences were functionally mapped to Gene Ontology (GO) terms, with unigene functions covering a diverse range of molecular functions, biological processes and cellular components. Genes from a number of defense-related pathways were observed in transcripts from each cDNA library. Over 99% of contig unigenes mapped to exon regions in the reference M. acuminata DH Pahang whole genome sequence. A total of 4068 genic-SSR loci were identified in Calcutta 4 and 4095 in Cavendish Grande Naine. A subset of 95 potential defense-related gene-derived simple sequence repeat (SSR) loci were validated for specific amplification and polymorphism across M. acuminata accessions. Fourteen loci were polymorphic, with alleles per polymorphic locus ranging from 3 to 8 and polymorphism information content ranging from 0.34 to 0.82.ConclusionsA large set of unigenes were characterized in this study for both M. acuminata Calcutta 4 and Cavendish Grande Naine, increasing the number of public domain Musa ESTs. This transcriptome is an invaluable resource for furthering our understanding of biological processes elicited during biotic stresses in Musa. Gene-based markers will facilitate molecular breeding strategies, forming the basis of genetic linkage mapping and analysis of quantitative trait loci.

Diversidade genética entre acessos de açaizeiro baseada em marcadores RAPD

One characterized the genetic diversity among accessions of assai palm using RAPD markers. One hundred and sixteen accessions conserved in the Embrapa Eastern Amazon germplasm collection, in Belem, PA, were analyzed using 28 primers. The data of the binary matrix were used to estimate the genetic dissimilarities using the arithmetical complement of Dice similarity coefficient and also for the bootstrap analysis. The genetic dissimilarities were represented in a dendrogram generated by the UPGMA method. The primers revealed 263 polymorphic RAPD loci presented wide genetic diversity among the accessions, varying from 0,06 to 0,67, being two accessions of the Chaves, PA the most divergent. But, some accessions of the same origin presented low dissimilarities. The dendrogram allowed the formation of eight groups delimited by the genetic mean dissimilarity (dgm: 0,40): two formed by a single accession; two constituted by two accessions and the others for several sub-groups with accessions of different origin. The ideal number of bands for estimating the genetic diversity among 116 accessions was 180. Therefore, the number of bands used in this study was efficient to characterize with precision the genetic relationship among the accessions of assai palm. The accessions divergent should be useful in the formation of nuclear collections and genetic breeding.

Agronomic and molecular characterization of diploid improved banana genotypes.

An investigation about the genetical diversity among eleven banana diploid genotypes using nine agronomical characteristics and sixteen microsatellite markers was implanted at Embrapa Cassava and Tropical Fruits, Cruz das Almas (BA), Brazil. The generalized distance of Mahalanobis indicated the presence of genetic diversity. The genotypes were grouped into tree clusters. Among the investigated characteristics, the plant height, number of bunchs, number of fruits per bunch and pseudostem exhibited high contribution towards genetic divergence. The average number of alleles per primer was 7.51, with a total of 120 alleles identified. The average similarity among the all diploid was 0.44, range from 0.29 up to 0.60. New parental combinations can be identified with base of the divergence between these diploids, contributing for development of new improved diploids preventing the narrow genetic base and creating new genetic variability for selection.

Agronomic and molecular characterization of gamma ray induced banana (Musa sp.) mutants using a multivariate statistical algorithm

Bananas are tropical fruits grown worldwide playing a key role in market trade and especially used as main food source for low income populations. In Brazil, bananas are mainly consumed in natura, occupying the second largest internal market. Nevertheless, this crop presents low availability of productive commercial varieties with good agronomic characteristics. A strategy undertaken to solve this problem is the development of new cultivars through conventional genetic breeding methods. However, this strategy presents some obstacles such as female sterility and low number of seeds. In order to overcome these shortcomings, use of mutation induction aiming the selection of mutants with desirable agronomic characteristics seems to have great potential for developing new cultivars. The objective of the present work was to evaluate the genetic variability in putative banana ‘Pacovan’ (AAB genome, subgroup Prata Type) mutants submitted to gamma ray irradiation, using a set of agronomical and molecular data (ISSR markers). The distance between the putative ‘Pacovan’ mutants varied from 0.26 to 0.64 with cophenetic correlation coefficient of 0.7669. Four mutants were selected based on best agronomical characteristics and height. This data also shows that there is variability that can be explored after the irradiation of ‘Pacovan’ banana mutants, which can be used in the genetic breeding program of banana aiming to develop short new varieties that also present good agronomic characteristics. This is the first attempt to use combined data in order to evaluate the genetic variability in putative banana mutants.

Divergência genética em genótipos de girassol

Uma investigacao sobre a diversidade genetica entre 15 genotipos de girassol, por meio de 12 caracteristicas agronomicas, foi implementada no Instituto Agronomico, Campinas, Brasil. Analises de variância univariada e multivariada revelaram diferencas entre os genotipos. A distância generalizada de Mahalanobis indicou um alto grau de divergencia genetica. Os genotipos foram agrupados em tres grupos. As caracteristicas inicio do florescimento, 50% do florescimento, numero de folhas e altura da insercao do capitulo contribuiram com grande parte da divergencia genetica observada. Por meio desses resultados, e possivel identificar materiais divergentes e com caracteristicas agronomicas complementares para o desenvolvimento de novos cultivares superiores.

Characterization of novel microsatellite markers in Musa acuminata subsp. burmannicoides , var. Calcutta 4

BackgroundBanana is a nutritionally important crop across tropical and sub-tropical countries in sub-Saharan Africa, Central and South America and Asia. Although cultivars have evolved from diploid, triploid and tetraploid wild Asian species of Musa acuminata (A genome) and Musa balbisiana (B genome), many of todays commercial cultivars are sterile triploids or diploids, with fruit developing via parthenocarpy. As a result of restricted genetic variation, improvement has been limited, resulting in a crop frequently lacking resistance to pests and disease. Considering the importance of molecular tools to facilitate development of disease resistant genotypes, the objectives of this study were to develop polymorphic microsatellite markers from BAC clone sequences for M. acuminata subsp. burmannicoides, var. Calcutta 4. This wild diploid species is used as a donor cultivar in breeding programs as a source of resistance to diverse biotic stresses.FindingsMicrosatellite sequences were identified from five Calcutta 4 BAC consensi datasets. Specific primers were designed for 41 loci. Isolated di-nucleotide repeat motifs were the most abundant, followed by tri-nucleotides. From 33 tested loci, 20 displayed polymorphism when screened across 21 diploid M. acuminata accessions, contrasting in resistance to Sigatoka diseases. The number of alleles per SSR locus ranged from two to four, with a total of 56. Six repeat classes were identified, with di-nucleotides the most abundant. Expected heterozygosity values for polymorphic markers ranged from 0.31 to 0.75.ConclusionsThis is the first report identifying polymorphic microsatellite markers from M. acuminata subsp. burmannicoides, var. Calcutta 4 across accessions contrasting in resistance to Sigatoka diseases. These BAC-derived polymorphic microsatellite markers are a useful resource for banana, applicable for genetic map development, germplasm characterization, evolutionary studies and marker assisted selection for traits.

Híbridos de milho inter e intrapopulacionais obtidosa partir de populações s0 de híbridossimples comerciais

O objetivo deste trabalho foi avaliar a viabilidade de se produzir hibridos inter e intrapopulacionais a partir de populacoes S0 de hibridos simples comerciais. Foram utilizadas tres populacoes S0 oriundas dos hibridos simples comerciais P30F45, Dow657 e DKB333B, sendo obtidos 163 hibridos (110 interpopulacionais e 53 intrapopulacionais). A avaliacao dos hibridos, em relacao a produtividade de graos, foi realizada no ano agricola 2003/2004, nos municipios de Lavras e Lambari (MG), em delineamento latice simples 13 x 13, utilizando-se como testemunhas os tres hibridos comerciais e suas populacoes S0. Os dados foram submetidos a analise de variância individual e conjunta. A partir das esperancas dos quadrados medios foram estimados alguns parâmetros geneticos e fenotipicos. A depressao por endogamia dos hibridos comerciais tambem foi estimada. Foram identificados hibridos S0 interpopulacionais superiores, tanto aos hibridos simples comerciais quanto a suas geracoes S0, em ambos os locais. Por outro lado, nao se identificou nenhum hibrido intrapopulacional superior a media dos hibridos comerciais, devido, em parte, ao numero de hibridos intrapopulacionais avaliados, 53 contra 110 hibridos S0 interpopulacionais. No entanto, foram identificados hibridos S0 intrapopulacionais com produtividade media de graos superior a 10 t ha-1. De acordo com os resultados e possivel obter hibridos, a partir de populacoes S0 de hibridos simples comerciais, com maior produtividade de graos. Verificou-se tambem, que hibridos simples comerciais sao excelente alternativa para a extracao de linhagens, ja que, em geracoes iniciais de endogamia, a obtencao de hibridos superiores ja e viavel.