Paulo Eduardo de Melo

Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the World's Third Most Important Food Crop

Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potato.ResumenLa papa es un miembro de las Solanaceae, una familia de plantas que incluye varias otras especies económicamente importantes, tales como tomate, berenjena, petunia, tabaco y ají o chili. El consorcio de secuenciación del genoma de la papa (PGSC) tiene por objeto dilucidar la secuencia completa del genoma de la papa, el tercer cultivo alimentario más importante del mundo. El PGSC es una colaboración entre 13 grupos de investigación procedentes de China, India, Polonia, Rusia, los Países Bajos, Irlanda, Argentina, Brasil, Chile, Perú, EE.UU., Nueva Zelanda y el Reino Unido. El genoma de la papa consiste de 12 cromosomas y tiene una longitud (haploide) de aproximadamente 840 millones de pares de bases, por lo que es una planta con un genoma de tamaño mediano. El proyecto de secuenciación se basa en una biblioteca de 78000 clones de cromosoma artificial bacteriano genomico de papa diploide (BAC), del que se ha obtenido la huella genética y alineado en 7000 ~ contigs de mapa físico. Además, los extremos terminales BAC se han secuenciado y están a disposición del público. Aproximadamente 30000 BACS están anclados al mapa genético de ultra alta densidad de la papa, compuesto de 10000 marcadores AFLPTM únicos. De esta mapa genético-físico integrado, entre 50 a 150 semillas BACs han sido identificadas para cada cromosoma. Experimentos de hibridación in situ fluorescente en clones BAC selectos confirman estos puntos de anclaje. La clones semilla proveen el punto de partida para la estrategia de secuenciación de BAC a BAC. Esta estrategia se complementa con los enfoques de secuenciación escopeta del genoma completo usando los instrumentos 454 GS FLX e Illumina GA2. El ensamblaje y anotación de los datos de la secuencia será realizados mediante herramientas publicas disponibles y hechas a la medida. La disponibilidad de los datos anotados ayudarán a caracterizar las colecciones de germoplasma basándose en variación alélica y ayudará a los fitomejoradores de papa a explotar más plenamente el potencial genético de la papa.

Ocorrência de vírus em batata em sete estados do Brasil

Viruses are responsible for the quick degeneration of potato seed-tubers. In the tropics, where aphid vectors are constantly present and the structure of virus populations is dynamic, the disease pressure is enormous. Therefore, the knowledge of such dynamics is definitely an extremely valuable tool towards the sustainability of the national potato production. In this study, we report a broad survey of virus occurrence in potato, in Brazil. In addition, we studied the distribution of the Potato virus Y (PVY) strains associated with mosaic symptoms on potatoes. In 2005 and 2006, we visited potato fields in seven Brazilian States. We collected leaves of symptomatic plants (1,256 samples) and also at random (360 samples). In addition, in several fields a visual assessment was carried out to estimate mosaic and leafroll incidence. From the 1,256 samples with symptoms, 840 tested serologically were positive to PVY (66.9%), 128 to PLRV (10.2%), 79 to PVS (6.3%), and none to PVX. Serology using DAS-ELISA and also biological and RT-PCR tests revealed an almost exclusive occurrence of the PVY necrotic strain, predominantly the necrotic subgroup PVYNTN. The analysis of a sub-sample representing all surveyed Counties indicated that the necrotic strain was universally present. Cultivars Asterix, Atlantic, Agata, Achat, Baronesa, Baraka, Bintje, Caesar, Cupido, Marijke, Monalisa, Panda, and Vivaldi, although displaying different susceptibility levels, were all infected by PVYNTN. The analysis of leaves collected at random showed similar results. PLRV was identified in four States (Minas Gerais, Bahia, Parana, and Santa Catarina), while PVS was present in the State of Sao Paulo as well. PVX was found in only one sample collected at random in Serra do Salitre, State of Minas Gerais. The contrast between visual evaluation and the results of the detection test by ELISA strongly indicated the presence of a relevant rate of PVY latent infection on cultivar Asterix.

Seleção de clones de batata para microclimas de altitude no Planalto Central

A potato selection program was done in Anapolis, State of Goias, Brazil, beginning in 1986 with 15,000 genotypes, resulting from 200 crosses obtained by Embrapa Hortalicas in 1985 and 1986. In the first selection cycle, in 1986, 5,000 genotypes were selected, considering plant growth and development, disease incidence, tuber quality and yield potential. These criteria were also adopted in further generations, when 15 to 20% of the best genotypes were yearly selected. In 1990 52 of the selected genotypes were evaluated in comparison with the cultivars Achat and Bintje. The best 28 clones were then named BAT, cleaned by meristem tip culture and evaluated from 1995 to 1997 at Anapolis, Morrinhos, Pirenopolis, Urutai and Jaboticabal. All data were submitted to the analysis of variance. In addition, data from fourteen genotypes in seven environments were analyzed by the linear regression technique of Ebehart & Russell. Clones BAT 2, BAT 3, BAT 4, BAT 19, BAT 27 and BAT 28 ranked best among the highest yielding ones, in addition to good tuber quality. Genotypes had similar behavior regarding adaptability, responding in a proportional way to environment improvement. BAT 19 was the most stable clone.

Effect of Ogura male-sterile cytoplasm on the performance of cabbage hybrid variety. II. Commercial characteristics

SummaryThe main constraint of using Ogura male-sterile cytoplasm in Brassica is the induction of leaf yellowing at low temperature and the low seed set. But whether or not the cytoplasm can disturb the general commerical performance of the plants is not well-known. Therefore, this work was carried out with the purpose of evaluating Ogura cytoplasmic male-sterile cabbage hybrids and compare them to genomic similar male-fertile ones and to the most popular cabbage hybrid cultivated in Brazil. Harvest data showed an effect of the cytoplasm on reducing plant and head weight, core length and head length and width, although not altering heading index, shape and core indexes, nor head compactness. On the other hand, it was observed also that a careful selection of the parental lineages can produce male-sterile hybrids as good as their male-fertile analogues. All the evaluated hybrids were similar or better than the check for the characteristics under study.

Effect of Ogura male-sterile cytoplasm on the performance of cabbage hybrid variety

SummaryCabbage hybrid seeds are commercially produced by means of self-incompatibility. This system may show some instability mainly under tropical conditions, where cytoplasmic male sterility can be an alternative approach for hybrid seeds production. However, cabbage hybrids holding Ogura male-sterile cytoplasm show some irregularities during development. By assessing some characteristics during the growing cycle of male-sterile cabbage hybrids and comparing them to genomic similar male-fertile ones and to the most common cabbage hybrid cultivated in Brazil, it was observed that the male-sterile hybrids had the same vigour, uniformity, number of leaves, resistance to Xanthomonas campestris pv. campestris, and earliness as their male-fertile counterparts and performed better than the commercial check hybrid for some of these characteristics. Although male-sterile hybrids showed yellowing of leaves, some parental combinations succeeded in overcoming or strongly reducing this cytoplasmic effect.

BRS Ana: cultivar de batata de duplo propósito

The genotype BRS Ana is a new potato cultivar adequate for French fries, with potential for processing into frozen French fries and flakes, released in 2007. It was developed by the Embrapa Potato Breeding Program (Embrapa Temperate Agriculture, Pelotas-RS; Embrapa Transference of Technology, Office of Canoinhas-SC; and Embrapa Vegetables, Brasilia-DF), based on tuber appearance and yield, specific gravity and French fries quality. Tubers are red-skinned, lightly rough, oval shaped with shallow eyes. The pulp is white. Cultivar BRS Ana has high yield potential. In the subtropical ecosystem, cultivar BRS Ana showed higher yield (31.2 t ha-1) than the most used cultivars in Brazil when grown in autumn, and did not differ from them in the spring. In the tropical ecosystem, under irrigation, BRS Ana did not differ from both control cultivars. It produced higher percentage of marketable tubers (55.6%) and average tuber weight (108.4 g) than the controls in the fall crop of subtropical ecosystem. In both ecosystems, cultivar BRS Ana presented high specific gravity (1.086) and dry matter content (19.7%). The sensorial analysis showed that cultivar BRS Ana is adequate for home made French fries as well as for industrial processing. It is moderately susceptible to late blight (Phytophthora infestans) and presents good resistance to early blight (Alternaria solani). The reaction to the tuber soft rot (Pectobacterium sp.) is similar to the most used cultivars. It has low seed degeneration conferred by moderate resistance to PVY and low incidence of PLRV. Susceptibility to tuber physiological disorders has not been observed. It seems that BRS Ana has lower fertilizer and water requirements than the most planted cultivars, meaning reduction of crop cost and risk. In the subtropical ecosystem, tuberization starts later in spring, therefore BRS Ana should be planted earlier in the season.

Resistance of genetically modified potatoes to Potato virus Y under field conditions.

The objective of this work was to evaluate the resistance of genetically modified clones of potato to Potato virus Y (PVY) under field conditions. Genetically modified plants were compared with nontransformed plants of the same cultivar. The plots were flanked with potato plants infected with both PVYo and PVYN strains (spread lines), in order to provide the experimental area with the source of virus, which was naturally spread by the native aphid population. The experiment was weekly monitored by visual inspections and by DAS-Elisa in the plants produced from the harvested tubers, in order to evaluate the resistance of transgenic plants throughout the plant growth cycle. By the end of the third year, no infection symptoms were observed in the 1P clone; clone 63P showed 1% of infection, in contrast to about 90% of nontransformed plants infected. The stable expression of resistance to PVY provided by the coat protein gene was obtained in genetically modified clones of potato plants cultivar Achat under field conditions, during three consecutive years.

Breeding potatoes for resistance to bacterial blight in Brazil: a quick review in face of a more effective screening protocol.

Abstract Bacterial wilt (BW), caused by Ralstonia solanacearum , is one of the most important diseases of potato ( Solanum tuberosum subsp. tuberosum ) in Brazil and the main cause of rejection of fields for tuber seed certification. Genetic resistance is not a feasible control currently since no commercially-appealing BW resistant cultivars are available. The development of resistant cultivars is challenging due to the genetic complexity of resistance, pathogen variability, lack of resistance sources in the species, and the tetraploid background of the crop. In addition, to date, only field selection has been effective in identifying stable resistance in progenies derived from crosses involving resistant wild relatives. Field selection is laborious and demands uniformly infested fields. After many years of germplasm breeding, we succeeded in developing two resistant clones, MB-03 and MB9846-01, both producing tubers with rather reasonable characteristics. These clones are being crossed with elite genotypes. To speed up progeny evaluation, we developed a straightforward screening protocol in greenhouse conditions, based on selection at the seedling stage. The methodology is presented and discussed here. Briefly, the early selection was very effective to screen a large number of seedlings in a rather short period of time. It considerably increased the rates of selection of resistant clones in the field when compared to selection directly in the field, without the prior greenhouse seedling stage. Nevertheless, field selection remains crucial for confirming resistance, testing for genotype-environment interaction and evaluating agronomic and tuber characteristics. Among the resistant clones previously identified in our program, progenies of clone MB9846-01 resulted in higher selection indexes in the field (BW resistance + tuber characteristics) than those of clone MB-03 when both clones were crossed with the susceptible cultivar Baraka. We adjusted the protocol to allow screening around 5,000 seedlings per year, counting with eight part-time workers, four in the laboratory/screenhouse and four in the field in critical periods. Keywords: Ralstonia solanacearum , Solanum tuberosum ssp. tuberosum , greenhouse screening, early selection, selection rates, germplasm breeding

Yield and marketable characteristics of tubers of clones and cultivars of potato

A batata ( Solanum tuberosum L.) e uma importante fonte de alimento por possuir uma elevada eficiencia na conversao de luz solar, agua e nutrientes em um alimento de alta qualidade. Ha necessidade de se realizar em pesquisas que contribuam para o desenvolvimento ou aprimoramento de novos genotipos de batata para atender as exigencias de consumidores e produtores. Assim, pesquisas que caracterizem a variacao genetica existente sao importantes para aumentar a eficiencia dos programas de melhoramento. O presente trabalho avaliou caracteres da morfologia, desempenho produtivo e resistencia pos-colheita ao esverdeamento dos tuberculos de cultivares e clones de batata. O experimento em campo foi conduzido na Embrapa Hortalicas, em Brasilia, DF. Com elevada produtividade total (83,5 t ha-1) e comercial (49,0 t ha-1) de tuberculos, o clone 085 destacou-se dentre os clones avaliados. Este clone alia alta produtividade comercial de tuberculos a tuberculos com baixa susceptibilidade ao esverdeamento, otima uniformidade, bom formato e olhos de profundidade rasa. Assim, o clone 085 torna-se forte candidato a ser lancado como uma nova cultivar ou para ser utilizado em cruzamentos para a selecao de novos clones, combinando qualidade e produtividade. Abstract The potato ( Solanum tuberosum L.) is an important source of food because its high efficiency to convert sunlight, water and nutrients into high quality food. It is necessary to do researches that contribute to the development or improvement of new potato genotypes to meet demands of consumers and producers. Thus, researches that characterize the existent genetic variation are important for increase the efficiency in breeding programs. This study evaluated morphological characters, yield performance and postharvest resistance to tuber greening in potato cultivars and clones. The field experiment was conducted at Embrapa Hortalicas, Brasilia, DF. With high total (83.5 t ha-1) and marketable (49.0 t ha-1) tuber yield, clone 085 stood out among the evaluated clones. This clone associates high commercial tuber yield with tubers with low susceptibility to greening, good uniformity, good format and shallow depth of eyes. Thus, clone 085 becomes strong candidate to be released as a new cultivar or to be used in crosses for selection of new clones, combining quality and yield.

Osmar Alves Carrijo: parte um grande nome do mundo das hortaliças

No último domingo, 12 de dezembro, nosso grande amigo, Osmar Alves Carrijo, aos 61 anos, sofreu um infarto fulminante, do qual não conseguiu se recuperar. Osmar era agrônomo, formado pela Universidade de Brasília (1976), com mestrado em Irrigação e Drenagem (ESALQ, 1980), doutorado em Solos e Irrigação, (Oregon State University, 1988) e pos-doc em Manejo e Tratos Culturais (Florida State University, 1998). Pesquisador da Embrapa Hortaliças desde 1976 até 2007, quando se aposentou; Osmar era ainda professor associado na Universidade de Brasília, onde atuava junto à pós-graduação. Como pesquisador, até mesmo pela sua origem e vínculos com o setor rural, que não só fez questão de manter, mas pelos quais sempre nutriu profundo orgulho, Osmar sempre optou pelas linhas de pesquisa e formas de atuação mais aplicadas, mais próximas aos agricultores e à transferência de tecnologia. Ainda assim, participou ativamente da vida científica da olericultura, tomando parte em congressos, reuniões e eventos e publicando livros e trabalhos. Cabe muito justamente ressaltar que seus trabalhos “Fibra da casca do coco verde como substrato agrícola” (Horticultura Brasileira 20: 533-535, 2002) e “Produtividade do tomateiro em diferentes substratos e modelos de casas de vegetação (Horticultura Brasileira 22: 5-9, 2004) são, entre os artigos publicados em Horticultura Brasileira, respectivamente o segundo e nono mais requisitados na base SciELO (www.scielo.br/hb, visitado em 14 de dezembro de 2010). Além da competência científica, Osmar sempre demonstrou habilidade no trato com as pessoas, fruto da sua conduta ética e franca, que sempre inspirou confiança, mas também conciliadora e avessa ao confronto. Assim, com grande habilidade e livre trânsito entre os colegas, Osmar exerceu, por diversas vezes, funções de gestão na Embrapa Hortaliças, tanto como Chefe Administrativo (de 1989 a 1990 e de 2003 a 2007), quanto como Chefe de Pesquisa e Desenvolvimento (de 1990 a 1991) e, também, Chefe Geral (1991-1993). Na ABH, além de associado com ativa participação, Osmar pertenceu à diretoria nas duas gestões da Profa Rumy Goto.